Research Computing Center Wiki - User contributions [en]

Bactopia-Sapelo2

2026-05-12T13:23:49Z

Chelsea: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==
3.2.0

== Author / Distributor ==

Please see https://bactopia.github.io/v3.1.0/

== Description ==
Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
This module can be loaded directly: module load Bactopia/3.2.0-conda
== Running Program ==

To load Bactopia, use <syntaxhighlight lang="bash">
ml Bactopia/3.2.0-conda
</syntaxhighlight>Please ensure you do not have any base conda environments active when running this program.

'''For errors such as "FileNotFoundError: [Errno 2] No such file or directory: '/home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config'"'''

Bactopia expects a snpEff.config file in /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/. If Bactopia installed a different version of snpeff (i.e. not 5.2-1), then you can create a symbolic link to your actual config file. First, check to see what version of snpeff you have installed with "ls /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/" and look for a directory named snpeff-<version>. There should be one with the version as 5.2-1 and another with a different version. Your snpEff.config file should exist inside the directory that is not version 5.2-1 (there should not be a snpEff.config file in the 5.2-1 directory, but we will fix that). You will create a symbolic link in the snpeff-5.2-1directory to the actual snpEff.config file in the other snpeff-<version> directory using this command (change MyID to your own MyID and <version> to the other snpeff version that is not 5.2-1): ln -s /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-<version>/snpEff.config /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config

'''For errors such as "ERROR Delly failed, skipping INFO Running snpEff ERROR Writing to /tmp/bcftools.gTh9nG "'''

Edit your snpEff.config file so that the 'data.dir' path points to your actual database directory that contains Mycobacterium_tuberculosis_h37rv (which may be something like /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/data/).

[02:10:40] ERROR Writing to /tmp/bcftools.gTh9nG utils.py:550"

'''For errors such as "ModuleNotFoundError: No module named 'pkg_resources' "'''

Ensure that the version of setuptools in your tbprofiler environment is less than or equal to 80.x. You check this by starting an interactive session, loading Bactopia, then activating your tbprofiler environment with "source activate ~/.bactopia/conda/bioconda--tb-profiler-6.6.3" and then "conda list". Then scroll to view the version of setuptools and change it if needed with "conda install setuptools=80.* "

== Documentation ==

<pre class="gcommand">
[cft07037@b1-24 ~]$ ml Bactopia/3.2.0-conda
[cft07037@b1-24 ~]$ bactopia --help
Nextflow 25.10.4 is available - Please consider updating your version to it
N E X T F L O W ~ version 23.10.1
Launching `/apps/eb/Bactopia/3.2.0-conda/share/bactopia-3.2.0/main.nf` [friendly_golick] DSL2 - revision: 0cd9f79ba7

---------------------------------------------
_ _ _
| |__ __ _ ___| |_ ___ _ __ (_) __ _
| '_ \ / _` |/ __| __/ _ \| '_ \| |/ _` |
| |_) | (_| | (__| || (_) | |_) | | (_| |
|_.__/ \__,_|\___|\__\___/| .__/|_|\__,_|
|_|
bactopia v3.2.0
Bactopia is a flexible pipeline for complete analysis of bacterial genomes
---------------------------------------------
Typical pipeline command:

bactopia --fastqs samples.txt --datasets datasets/ --species 'Staphylococcus aureus' -profile singularity

Required Parameters
Processing Multiple Samples
--samples [string] A FOFN (via bactopia prepare) with sample names and paths to FASTQ/FASTAs to process

Processing A Single Sample
--r1 [string] First set of compressed (gzip) Illumina paired-end FASTQ reads (requires --r2 and --sample)
--r2 [string] Second set of compressed (gzip) Illumina paired-end FASTQ reads (requires --r1 and --sample)
--se [string] Compressed (gzip) Illumina single-end FASTQ reads (requires --sample)
--ont [string] Compressed (gzip) Oxford Nanopore FASTQ reads (requires --sample)
--hybrid [boolean] Create hybrid assembly using Unicycler. (requires --r1, --r2, --ont and --sample)
--short_polish [boolean] Create hybrid assembly from long-read assembly and short read polishing. (requires --r1, --r2, --ont and
--sample)
--sample [string] Sample name to use for the input sequences

Downloading from SRA/ENA or NCBI Assembly
Note: Error free Illumina reads are simulated for assemblies
--accessions [string] A file containing ENA/SRA Experiment accessions or NCBI Assembly accessions to processed
--accession [string] Sample name to use for the input sequences

Processing an Assembly
Note: Error free Illumina reads are simulated for assemblies
--assembly [string] A assembled genome in compressed FASTA format. (requires --sample)
--check_samples [boolean] Validate the input FOFN provided by --samples

Dataset Parameters
--species [string] Name of species for species-specific dataset to use
--ask_merlin [boolean] Ask Merlin to execute species specific Bactopia tools based on Mash distances
--coverage [integer] Reduce samples to a given coverage, requires a genome size [default: 100]
--genome_size [string] Expected genome size (bp) for all samples, required for read error correction and read subsampling [default:
0]
--use_bakta [boolean] Use Bakta for annotation, instead of Prokka

QC Parameters
--use_bbmap [boolean] Illumina reads will be QC'd using BBMap
--use_porechop [boolean] Use Porechop to remove adapters from ONT reads

Assembler Parameters
--nanohq [boolean] For Flye, use '--nano-hq' instead of --nano-raw

AMRFinder+ Parameters
--organism [string] Taxonomy group to run additional screens against
--amrfinder_noplus [boolean] Disable running AMRFinder+ with the --plus option
--amrfinder_opts [string] Extra AMRFinder+ options in quotes.
--amrfinder_db [string] A custom AMRFinder+ database to use, either a tarball or a folder

MLST Parameters
--scheme [string] Don't autodetect, force this scheme on all inputs
--minid [integer] Minimum DNA percent identity of full allelle to consider 'similar' [default: 95]
--mincov [integer] Minimum DNA percent coverage to report partial allele at all [default: 10]
--minscore [integer] Minimum score out of 100 to match a scheme [default: 50]
--nopath [boolean] Strip filename paths from FILE column
--mlst_db [string] A custom MLST database to use, either a tarball or a directory

Prokka Parameters
--proteins [string] FASTA file of trusted proteins to first annotate from
--prodigal_tf [string] Training file to use for Prodigal
--prokka_coverage [integer] Minimum coverage on query protein [default: 80]

Optional Parameters
--outdir [string] Base directory to write results to [default: bactopia]

Nextflow Profile Parameters
--datasets_cache [string] Directory where downloaded datasets should be stored. [default: <BACTOPIA_DIR>/data/datasets]

Helpful Parameters
--wf [string] Specify which workflow or Bactopia Tool to execute [default: bactopia]
--list_wfs [boolean] List the available workflows and Bactopia Tools to use with '--wf'
--help_all [boolean] An alias for --help --show_hidden_params
--version [boolean] Display version text.

!! Hiding 110 params, use --show_hidden_params (or --help_all) to show them !!
--------------------------------------------------------------------
If you use bactopia for your analysis please cite:

* Bactopia
https://doi.org/10.1128/mSystems.00190-20

* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
https://bactopia.github.io/acknowledgements/
--------------------------------------------------------------------
</pre>

[[#top|Back to Top]]

== System ==
64-bit Linux

Bactopia-Sapelo2

2026-04-29T19:05:34Z

Chelsea: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==
3.2.0

== Author / Distributor ==

Please see https://bactopia.github.io/v3.1.0/

== Description ==
Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
This module can be loaded directly: module load Bactopia/3.2.0-conda
== Running Program ==

To load Bactopia, use <syntaxhighlight lang="bash">
ml Bactopia/3.2.0-conda
</syntaxhighlight>Please ensure you do not have any base conda environments active when running this program.

'''For errors such as "FileNotFoundError: [Errno 2] No such file or directory: '/home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config'"'''

Bactopia expects a snpEff.config file in /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/. If Bactopia installed a different version of snpeff (i.e. not 5.2-1), then you can create a symbolic link to your actual config file. First, check to see what version of snpeff you have installed with "ls /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/" and look for a directory named snpeff-<version>. There should be one with the version as 5.2-1 and another with a different version. Your snpEff.config file should exist inside the directory that is not version 5.2-1 (there should not be a snpEff.config file in the 5.2-1 directory, but we will fix that). You will create a symbolic link in the snpeff-5.2-1directory to the actual snpEff.config file in the other snpeff-<version> directory using this command (change MyID to your own MyID and <version> to the other snpeff version that is not 5.2-1): ln -s /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-<version>/snpEff.config /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config

'''For errors such as "ERROR Delly failed, skipping INFO Running snpEff ERROR Writing to /tmp/bcftools.gTh9nG "'''

Edit your snpEff.config file so that the 'data.dir' path points to your actual database directory that contains Mycobacterium_tuberculosis_h37rv (which may be something like /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/data/).

[02:10:40] ERROR Writing to /tmp/bcftools.gTh9nG utils.py:550"

== Documentation ==

<pre class="gcommand">
[cft07037@b1-24 ~]$ ml Bactopia/3.2.0-conda
[cft07037@b1-24 ~]$ bactopia --help
Nextflow 25.10.4 is available - Please consider updating your version to it
N E X T F L O W ~ version 23.10.1
Launching `/apps/eb/Bactopia/3.2.0-conda/share/bactopia-3.2.0/main.nf` [friendly_golick] DSL2 - revision: 0cd9f79ba7

---------------------------------------------
_ _ _
| |__ __ _ ___| |_ ___ _ __ (_) __ _
| '_ \ / _` |/ __| __/ _ \| '_ \| |/ _` |
| |_) | (_| | (__| || (_) | |_) | | (_| |
|_.__/ \__,_|\___|\__\___/| .__/|_|\__,_|
|_|
bactopia v3.2.0
Bactopia is a flexible pipeline for complete analysis of bacterial genomes
---------------------------------------------
Typical pipeline command:

bactopia --fastqs samples.txt --datasets datasets/ --species 'Staphylococcus aureus' -profile singularity

Required Parameters
Processing Multiple Samples
--samples [string] A FOFN (via bactopia prepare) with sample names and paths to FASTQ/FASTAs to process

Processing A Single Sample
--r1 [string] First set of compressed (gzip) Illumina paired-end FASTQ reads (requires --r2 and --sample)
--r2 [string] Second set of compressed (gzip) Illumina paired-end FASTQ reads (requires --r1 and --sample)
--se [string] Compressed (gzip) Illumina single-end FASTQ reads (requires --sample)
--ont [string] Compressed (gzip) Oxford Nanopore FASTQ reads (requires --sample)
--hybrid [boolean] Create hybrid assembly using Unicycler. (requires --r1, --r2, --ont and --sample)
--short_polish [boolean] Create hybrid assembly from long-read assembly and short read polishing. (requires --r1, --r2, --ont and
--sample)
--sample [string] Sample name to use for the input sequences

Downloading from SRA/ENA or NCBI Assembly
Note: Error free Illumina reads are simulated for assemblies
--accessions [string] A file containing ENA/SRA Experiment accessions or NCBI Assembly accessions to processed
--accession [string] Sample name to use for the input sequences

Processing an Assembly
Note: Error free Illumina reads are simulated for assemblies
--assembly [string] A assembled genome in compressed FASTA format. (requires --sample)
--check_samples [boolean] Validate the input FOFN provided by --samples

Dataset Parameters
--species [string] Name of species for species-specific dataset to use
--ask_merlin [boolean] Ask Merlin to execute species specific Bactopia tools based on Mash distances
--coverage [integer] Reduce samples to a given coverage, requires a genome size [default: 100]
--genome_size [string] Expected genome size (bp) for all samples, required for read error correction and read subsampling [default:
0]
--use_bakta [boolean] Use Bakta for annotation, instead of Prokka

QC Parameters
--use_bbmap [boolean] Illumina reads will be QC'd using BBMap
--use_porechop [boolean] Use Porechop to remove adapters from ONT reads

Assembler Parameters
--nanohq [boolean] For Flye, use '--nano-hq' instead of --nano-raw

AMRFinder+ Parameters
--organism [string] Taxonomy group to run additional screens against
--amrfinder_noplus [boolean] Disable running AMRFinder+ with the --plus option
--amrfinder_opts [string] Extra AMRFinder+ options in quotes.
--amrfinder_db [string] A custom AMRFinder+ database to use, either a tarball or a folder

MLST Parameters
--scheme [string] Don't autodetect, force this scheme on all inputs
--minid [integer] Minimum DNA percent identity of full allelle to consider 'similar' [default: 95]
--mincov [integer] Minimum DNA percent coverage to report partial allele at all [default: 10]
--minscore [integer] Minimum score out of 100 to match a scheme [default: 50]
--nopath [boolean] Strip filename paths from FILE column
--mlst_db [string] A custom MLST database to use, either a tarball or a directory

Prokka Parameters
--proteins [string] FASTA file of trusted proteins to first annotate from
--prodigal_tf [string] Training file to use for Prodigal
--prokka_coverage [integer] Minimum coverage on query protein [default: 80]

Optional Parameters
--outdir [string] Base directory to write results to [default: bactopia]

Nextflow Profile Parameters
--datasets_cache [string] Directory where downloaded datasets should be stored. [default: <BACTOPIA_DIR>/data/datasets]

Helpful Parameters
--wf [string] Specify which workflow or Bactopia Tool to execute [default: bactopia]
--list_wfs [boolean] List the available workflows and Bactopia Tools to use with '--wf'
--help_all [boolean] An alias for --help --show_hidden_params
--version [boolean] Display version text.

!! Hiding 110 params, use --show_hidden_params (or --help_all) to show them !!
--------------------------------------------------------------------
If you use bactopia for your analysis please cite:

* Bactopia
https://doi.org/10.1128/mSystems.00190-20

* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
https://bactopia.github.io/acknowledgements/
--------------------------------------------------------------------
</pre>

[[#top|Back to Top]]

== System ==
64-bit Linux

Bactopia-Sapelo2

2026-04-29T19:03:44Z

Chelsea: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==
3.2.0

== Author / Distributor ==

Please see https://bactopia.github.io/v3.1.0/

== Description ==
Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
This module can be loaded directly: module load Bactopia/3.2.0-conda
== Running Program ==

'''For errors such as "FileNotFoundError: [Errno 2] No such file or directory: '/home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config'"'''

Bactopia expects a snpEff.config file in /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/. If Bactopia installed a different version of snpeff (i.e. not 5.2-1), then you can create a symbolic link to your actual config file. First, check to see what version of snpeff you have installed with "ls /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/" and look for a directory named snpeff-<version>. There should be one with the version as 5.2-1 and another with a different version. Your snpEff.config file should exist inside the directory that is not version 5.2-1 (there should not be a snpEff.config file in the 5.2-1 directory, but we will fix that). You will create a symbolic link in the snpeff-5.2-1directory to the actual snpEff.config file in the other snpeff-<version> directory using this command (change MyID to your own MyID and <version> to the other snpeff version that is not 5.2-1): ln -s /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-<version>/snpEff.config /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config

'''For errors such as "ERROR Delly failed, skipping INFO Running snpEff ERROR Writing to /tmp/bcftools.gTh9nG "'''

Edit your snpEff.config file so that the 'data.dir' path points to your actual database directory that contains Mycobacterium_tuberculosis_h37rv (which may be something like /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/data/).

[02:10:40] ERROR Writing to /tmp/bcftools.gTh9nG utils.py:550"

== Documentation ==

<pre class="gcommand">
[cft07037@b1-24 ~]$ ml Bactopia/3.2.0-conda
[cft07037@b1-24 ~]$ bactopia --help
Nextflow 25.10.4 is available - Please consider updating your version to it
N E X T F L O W ~ version 23.10.1
Launching `/apps/eb/Bactopia/3.2.0-conda/share/bactopia-3.2.0/main.nf` [friendly_golick] DSL2 - revision: 0cd9f79ba7

---------------------------------------------
_ _ _
| |__ __ _ ___| |_ ___ _ __ (_) __ _
| '_ \ / _` |/ __| __/ _ \| '_ \| |/ _` |
| |_) | (_| | (__| || (_) | |_) | | (_| |
|_.__/ \__,_|\___|\__\___/| .__/|_|\__,_|
|_|
bactopia v3.2.0
Bactopia is a flexible pipeline for complete analysis of bacterial genomes
---------------------------------------------
Typical pipeline command:

bactopia --fastqs samples.txt --datasets datasets/ --species 'Staphylococcus aureus' -profile singularity

Required Parameters
Processing Multiple Samples
--samples [string] A FOFN (via bactopia prepare) with sample names and paths to FASTQ/FASTAs to process

Processing A Single Sample
--r1 [string] First set of compressed (gzip) Illumina paired-end FASTQ reads (requires --r2 and --sample)
--r2 [string] Second set of compressed (gzip) Illumina paired-end FASTQ reads (requires --r1 and --sample)
--se [string] Compressed (gzip) Illumina single-end FASTQ reads (requires --sample)
--ont [string] Compressed (gzip) Oxford Nanopore FASTQ reads (requires --sample)
--hybrid [boolean] Create hybrid assembly using Unicycler. (requires --r1, --r2, --ont and --sample)
--short_polish [boolean] Create hybrid assembly from long-read assembly and short read polishing. (requires --r1, --r2, --ont and
--sample)
--sample [string] Sample name to use for the input sequences

Downloading from SRA/ENA or NCBI Assembly
Note: Error free Illumina reads are simulated for assemblies
--accessions [string] A file containing ENA/SRA Experiment accessions or NCBI Assembly accessions to processed
--accession [string] Sample name to use for the input sequences

Processing an Assembly
Note: Error free Illumina reads are simulated for assemblies
--assembly [string] A assembled genome in compressed FASTA format. (requires --sample)
--check_samples [boolean] Validate the input FOFN provided by --samples

Dataset Parameters
--species [string] Name of species for species-specific dataset to use
--ask_merlin [boolean] Ask Merlin to execute species specific Bactopia tools based on Mash distances
--coverage [integer] Reduce samples to a given coverage, requires a genome size [default: 100]
--genome_size [string] Expected genome size (bp) for all samples, required for read error correction and read subsampling [default:
0]
--use_bakta [boolean] Use Bakta for annotation, instead of Prokka

QC Parameters
--use_bbmap [boolean] Illumina reads will be QC'd using BBMap
--use_porechop [boolean] Use Porechop to remove adapters from ONT reads

Assembler Parameters
--nanohq [boolean] For Flye, use '--nano-hq' instead of --nano-raw

AMRFinder+ Parameters
--organism [string] Taxonomy group to run additional screens against
--amrfinder_noplus [boolean] Disable running AMRFinder+ with the --plus option
--amrfinder_opts [string] Extra AMRFinder+ options in quotes.
--amrfinder_db [string] A custom AMRFinder+ database to use, either a tarball or a folder

MLST Parameters
--scheme [string] Don't autodetect, force this scheme on all inputs
--minid [integer] Minimum DNA percent identity of full allelle to consider 'similar' [default: 95]
--mincov [integer] Minimum DNA percent coverage to report partial allele at all [default: 10]
--minscore [integer] Minimum score out of 100 to match a scheme [default: 50]
--nopath [boolean] Strip filename paths from FILE column
--mlst_db [string] A custom MLST database to use, either a tarball or a directory

Prokka Parameters
--proteins [string] FASTA file of trusted proteins to first annotate from
--prodigal_tf [string] Training file to use for Prodigal
--prokka_coverage [integer] Minimum coverage on query protein [default: 80]

Optional Parameters
--outdir [string] Base directory to write results to [default: bactopia]

Nextflow Profile Parameters
--datasets_cache [string] Directory where downloaded datasets should be stored. [default: <BACTOPIA_DIR>/data/datasets]

Helpful Parameters
--wf [string] Specify which workflow or Bactopia Tool to execute [default: bactopia]
--list_wfs [boolean] List the available workflows and Bactopia Tools to use with '--wf'
--help_all [boolean] An alias for --help --show_hidden_params
--version [boolean] Display version text.

!! Hiding 110 params, use --show_hidden_params (or --help_all) to show them !!
--------------------------------------------------------------------
If you use bactopia for your analysis please cite:

* Bactopia
https://doi.org/10.1128/mSystems.00190-20

* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
https://bactopia.github.io/acknowledgements/
--------------------------------------------------------------------
</pre>

[[#top|Back to Top]]

== System ==
64-bit Linux

HpcGridRunner-Sapelo2

2026-04-29T18:43:58Z

Chelsea: /* HpcGridRunner submission script parameters: */

[[Category:Sapelo2]][[Category:Software]][[Category:Tools]]

== Category ==

Tools

== Program On ==

Sapelo2

== Version ==

1.0.2

== Author / Distributor ==

Please see https://github.com/HpcGridRunner/HpcGridRunner

== Description ==

This tool will help in executing a file full of commands in parallel using a compute cluster.

== Running Program ==

For instruction on running HpcGridRunner in conjunction with Trinity, please see [[Trinity-HpcGridRunner|here]].

Also refer to [[Running Jobs on Sapelo2]].

*HpcGridRunner/1.0.2-GCCcore-12.3.0
*HpcGridRunner/1.0.2-GCCcore-14.2.0

To use HpcGridRunner, please first load the module with
<pre class="gscript">
ml HpcGridRunner/1.0.2-GCCcore-14.2.0
</pre>

===Running a blast job in parallel by splitting the fasta file===

====HpcGridRunner submission script parameters:====

* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.
* --cmd_template: The cmd_template can be change to reflect your blast command. Leave the -query parameter set to __QUERY_FILE__ value and hpc_FASTA_Gridrunner will fill it dynamically. You can also change the values for outfmt, evalue, max_target_seqs and db.
** -num_threads: How many threads you want each blastp command to use. Be sure to request enough CPU cores in the .conf file (see conf file configuration instructions below)
* --seqs_per_bin:
* --query_fasta: You will need to change the YOUR_QUERY_FASTA.fasta to the name of your fasta file.
* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.

'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.

<pre class="gscript">
#!/bin/bash
#SBATCH --partition batch
#SBATCH --ntasks=1
#SBATCH --time=48:00:00
#SBATCH --mem=3gb

ml HpcGridRunner/1.0.2
ml BLAST+/2.13.0-gompi-2022a

hpc_FASTA_GridRunner.pl \
--grid_conf=$HPCGR_CONF_DIR/sapelo_1c_3g.conf \
--cmd_template "blastp -query __QUERY_FILE__ -db /db/uniprot/latest/uniprot_sprot -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 4" \
--seqs_per_bin 250 \
--query_fasta YOUR_QUERY_FASTA.fasta \
--out_dir blast_result

</pre>

To gather the blast output you can generally concatenate all the individual outputs. You can use the following command to find and concatenate all the output files.

<pre class="gcommand">
find OUTPUT_DIR -name '*.fa.OUT' | xargs cat > combined_blast_results.out
</pre>

====Configuration file contents:====

* cmd: This is the actual command that will be used to submit the HpcGridRunner command from the submission script specified in "--cmd_template". You will want to request enough resources for a single blastp command here.
** --mem: Request enough memory for a single blastp command based on how many seqs_per_bin you choose. This could be around 20-80gb.
** -n: Leave this at 1
** -c: This is how many CPU cores you want. '''Set this equal to whatever you put for "-num_threads"''' in the "--cmd_template" in your submission script.
* max_nodes: How many compute nodes you want running your blast commands. The more you request here, the faster it will go through all of your fasta file bins. It is suggested to request at least 80-100 nodes if not more, but this is up to your preference. The more nodes you have running jobs, the harder it can be to keep track of jobs if you are in the trouble-shooting phase.
* cmds_per_node: This is how many blast cmds you want to run on each node. It is suggested to leave this equal to 1 because these cmds run sequentially anyways (rather than concurrently) so it does not save time to increase this value in this case.

This specific sample configuration file can be found at /apps/eb/HpcGridRunner/1.0.2-GCCcore-12.3.0/hpc_conf/sapelo_1c_3g.conf, but you can copy it to your own directory to modify, or simply create a new text file and fill it in with this information<pre class="gscript">
# This was adapted for Slurm from:
# /usr/local/apps/hpcgridrunner/1.0.2/hpc_conf/sapelo_1c_3G_AMD.conf
# which was on the old (Torque/Moab) Sapelo2

# grid type:
grid=SLURM

# template for a grid submission:
cmd=sbatch -p batch --mem 16gb -n 1 -c 4 -t 6:00:00

##########################################################################################
# settings below configure the Trinity job submission system, not tied to the grid itself.
##########################################################################################

# number of grid submissions to be maintained at steady state by the Trinity submission system
max_nodes=10

# number of commands that are batched into a single grid submission job.
cmds_per_node=1
</pre>

== Documentation ==

Please see http://hpcgridrunner.github.io/

[[#top|Back to Top]]

== Installation ==

Installed in /apps/eb/HpcGridRunner/1.0.2

== System ==

64-bit Linux

HpcGridRunner-Sapelo2

2026-04-29T18:43:45Z

Chelsea: /* HpcGridRunner submission script parameters: */

HpcGridRunner-Sapelo2

2026-04-29T18:36:53Z

Chelsea: /* HpcGridRunner submission script parameters: */

HpcGridRunner-Sapelo2

2026-04-29T18:36:32Z

Chelsea: /* Running a blast job in parallel by splitting the fasta file: */

[[Category:Sapelo2]][[Category:Software]][[Category:Tools]]

== Category ==

Tools

== Program On ==

Sapelo2

== Version ==

1.0.2

== Author / Distributor ==

Please see https://github.com/HpcGridRunner/HpcGridRunner

== Description ==

This tool will help in executing a file full of commands in parallel using a compute cluster.

== Running Program ==

For instruction on running HpcGridRunner in conjunction with Trinity, please see [[Trinity-HpcGridRunner|here]].

Also refer to [[Running Jobs on Sapelo2]].

*HpcGridRunner/1.0.2-GCCcore-12.3.0
*HpcGridRunner/1.0.2-GCCcore-14.2.0

To use HpcGridRunner, please first load the module with
<pre class="gscript">
ml HpcGridRunner/1.0.2-GCCcore-14.2.0
</pre>

===Running a blast job in parallel by splitting the fasta file===

====HpcGridRunner submission script parameters:====

* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.
* --cmd_template: The cmd_template can be change to reflect your blast command. Leave the -query parameter set to __QUERY_FILE__ value and hpc_FASTA_Gridrunner will fill it dynamically. You can also change the values for outfmt, evalue, max_target_seqs and db.
** -num_threads: How many threads you want each blastp command to use. Be sure to request enough CPU cores in the .conf file (see conf file configuration instructions below)
* --seqs_per_bin:
* --query_fasta: You will need to change the YOUR_QUERY_FASTA.fasta to the name of your fasta file.
* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.

'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.

<pre class="gscript">
#!/bin/bash
#SBATCH --partition batch
#SBATCH --ntasks=1
#SBATCH --time=48:00:00
#SBATCH --mem=3gb

ml HpcGridRunner/1.0.2
ml BLAST+/2.13.0-gompi-2022a

hpc_FASTA_GridRunner.pl \
--grid_conf=$HPCGR_CONF_DIR/sapelo_1c_3g.conf \
--cmd_template "blastp -query __QUERY_FILE__ -db /db/uniprot/latest/uniprot_sprot -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 4" \
--seqs_per_bin 250 \
--query_fasta YOUR_QUERY_FASTA.fasta \
--out_dir blast_result

</pre>

To gather the blast output you can generally concatenate all the individual outputs. You can use the following command to find and concatenate all the output files.

<pre class="gcommand">
find OUTPUT_DIR -name '*.fa.OUT' | xargs cat > combined_blast_results.out
</pre>

====Configuration file contents:====

* cmd: This is the actual command that will be used to submit the HpcGridRunner command from the submission script specified in "--cmd_template". You will want to request enough resources for a single blastp command here.
** --mem: Request enough memory for a single blastp command based on how many seqs_per_bin you choose. This could be around 20-80gb.
** -n: Leave this at 1
** -c: This is how many CPU cores you want. '''Set this equal to whatever you put for "-num_threads"''' in the "--cmd_template" in your submission script.
* max_nodes: How many compute nodes you want running your blast commands. The more you request here, the faster it will go through all of your fasta file bins. It is suggested to request at least 80-100 nodes if not more, but this is up to your preference. The more nodes you have running jobs, the harder it can be to keep track of jobs if you are in the trouble-shooting phase.
* cmds_per_node: This is how many blast cmds you want to run on each node. It is suggested to leave this equal to 1 because these cmds run sequentially anyways (rather than concurrently) so it does not save time to increase this value in this case.

This specific sample configuration file can be found at /apps/eb/HpcGridRunner/1.0.2-GCCcore-12.3.0/hpc_conf/sapelo_1c_3g.conf, but you can copy it to your own directory to modify, or simply create a new text file and fill it in with this information<pre class="gscript">
# This was adapted for Slurm from:
# /usr/local/apps/hpcgridrunner/1.0.2/hpc_conf/sapelo_1c_3G_AMD.conf
# which was on the old (Torque/Moab) Sapelo2

# grid type:
grid=SLURM

# template for a grid submission:
cmd=sbatch -p batch --mem 16gb -n 1 -c 4 -t 6:00:00

##########################################################################################
# settings below configure the Trinity job submission system, not tied to the grid itself.
##########################################################################################

# number of grid submissions to be maintained at steady state by the Trinity submission system
max_nodes=10

# number of commands that are batched into a single grid submission job.
cmds_per_node=1
</pre>

== Documentation ==

Please see http://hpcgridrunner.github.io/

[[#top|Back to Top]]

== Installation ==

Installed in /apps/eb/HpcGridRunner/1.0.2

== System ==

64-bit Linux

HpcGridRunner-Sapelo2

2026-04-29T18:36:20Z

Chelsea: /* Running a blast job in parallel by splitting the fasta file: */

[[Category:Sapelo2]][[Category:Software]][[Category:Tools]]

== Category ==

Tools

== Program On ==

Sapelo2

== Version ==

1.0.2

== Author / Distributor ==

Please see https://github.com/HpcGridRunner/HpcGridRunner

== Description ==

This tool will help in executing a file full of commands in parallel using a compute cluster.

== Running Program ==

For instruction on running HpcGridRunner in conjunction with Trinity, please see [[Trinity-HpcGridRunner|here]].

Also refer to [[Running Jobs on Sapelo2]].

*HpcGridRunner/1.0.2-GCCcore-12.3.0
*HpcGridRunner/1.0.2-GCCcore-14.2.0

To use HpcGridRunner, please first load the module with
<pre class="gscript">
ml HpcGridRunner/1.0.2-GCCcore-14.2.0
</pre>

===Running a blast job in parallel by splitting the fasta file:===

====HpcGridRunner submission script parameters:====

* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.
* --cmd_template: The cmd_template can be change to reflect your blast command. Leave the -query parameter set to __QUERY_FILE__ value and hpc_FASTA_Gridrunner will fill it dynamically. You can also change the values for outfmt, evalue, max_target_seqs and db.
** -num_threads: How many threads you want each blastp command to use. Be sure to request enough CPU cores in the .conf file (see conf file configuration instructions below)
* --seqs_per_bin:
* --query_fasta: You will need to change the YOUR_QUERY_FASTA.fasta to the name of your fasta file.
* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.

'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.

<pre class="gscript">
#!/bin/bash
#SBATCH --partition batch
#SBATCH --ntasks=1
#SBATCH --time=48:00:00
#SBATCH --mem=3gb

ml HpcGridRunner/1.0.2
ml BLAST+/2.13.0-gompi-2022a

hpc_FASTA_GridRunner.pl \
--grid_conf=$HPCGR_CONF_DIR/sapelo_1c_3g.conf \
--cmd_template "blastp -query __QUERY_FILE__ -db /db/uniprot/latest/uniprot_sprot -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 4" \
--seqs_per_bin 250 \
--query_fasta YOUR_QUERY_FASTA.fasta \
--out_dir blast_result

</pre>

To gather the blast output you can generally concatenate all the individual outputs. You can use the following command to find and concatenate all the output files.

<pre class="gcommand">
find OUTPUT_DIR -name '*.fa.OUT' | xargs cat > combined_blast_results.out
</pre>

====Configuration file contents:====

* cmd: This is the actual command that will be used to submit the HpcGridRunner command from the submission script specified in "--cmd_template". You will want to request enough resources for a single blastp command here.
** --mem: Request enough memory for a single blastp command based on how many seqs_per_bin you choose. This could be around 20-80gb.
** -n: Leave this at 1
** -c: This is how many CPU cores you want. '''Set this equal to whatever you put for "-num_threads"''' in the "--cmd_template" in your submission script.
* max_nodes: How many compute nodes you want running your blast commands. The more you request here, the faster it will go through all of your fasta file bins. It is suggested to request at least 80-100 nodes if not more, but this is up to your preference. The more nodes you have running jobs, the harder it can be to keep track of jobs if you are in the trouble-shooting phase.
* cmds_per_node: This is how many blast cmds you want to run on each node. It is suggested to leave this equal to 1 because these cmds run sequentially anyways (rather than concurrently) so it does not save time to increase this value in this case.

This specific sample configuration file can be found at /apps/eb/HpcGridRunner/1.0.2-GCCcore-12.3.0/hpc_conf/sapelo_1c_3g.conf, but you can copy it to your own directory to modify, or simply create a new text file and fill it in with this information<pre class="gscript">
# This was adapted for Slurm from:
# /usr/local/apps/hpcgridrunner/1.0.2/hpc_conf/sapelo_1c_3G_AMD.conf
# which was on the old (Torque/Moab) Sapelo2

# grid type:
grid=SLURM

# template for a grid submission:
cmd=sbatch -p batch --mem 16gb -n 1 -c 4 -t 6:00:00

##########################################################################################
# settings below configure the Trinity job submission system, not tied to the grid itself.
##########################################################################################

# number of grid submissions to be maintained at steady state by the Trinity submission system
max_nodes=10

# number of commands that are batched into a single grid submission job.
cmds_per_node=1
</pre>

== Documentation ==

Please see http://hpcgridrunner.github.io/

[[#top|Back to Top]]

== Installation ==

Installed in /apps/eb/HpcGridRunner/1.0.2

== System ==

64-bit Linux

HpcGridRunner-Sapelo2

2026-04-29T18:35:17Z

Chelsea: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Tools]]

== Category ==

Tools

== Program On ==

Sapelo2

== Version ==

1.0.2

== Author / Distributor ==

Please see https://github.com/HpcGridRunner/HpcGridRunner

== Description ==

This tool will help in executing a file full of commands in parallel using a compute cluster.

== Running Program ==

For instruction on running HpcGridRunner in conjunction with Trinity, please see [[Trinity-HpcGridRunner|here]].

Also refer to [[Running Jobs on Sapelo2]].

*HpcGridRunner/1.0.2-GCCcore-12.3.0
*HpcGridRunner/1.0.2-GCCcore-14.2.0

To use HpcGridRunner, please first load the module with
<pre class="gscript">
ml HpcGridRunner/1.0.2-GCCcore-14.2.0
</pre>

=Running a blast job in parallel by splitting the fasta file:=

HpcGridRunner submission script parameters:

* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.
* --cmd_template: The cmd_template can be change to reflect your blast command. Leave the -query parameter set to __QUERY_FILE__ value and hpc_FASTA_Gridrunner will fill it dynamically. You can also change the values for outfmt, evalue, max_target_seqs and db.
** -num_threads: How many threads you want each blastp command to use. Be sure to request enough CPU cores in the .conf file (see conf file configuration instructions below)
* --seqs_per_bin:
* --query_fasta: You will need to change the YOUR_QUERY_FASTA.fasta to the name of your fasta file.
* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.

'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.

<pre class="gscript">
#!/bin/bash
#SBATCH --partition batch
#SBATCH --ntasks=1
#SBATCH --time=48:00:00
#SBATCH --mem=3gb

ml HpcGridRunner/1.0.2
ml BLAST+/2.13.0-gompi-2022a

hpc_FASTA_GridRunner.pl \
--grid_conf=$HPCGR_CONF_DIR/sapelo_1c_3g.conf \
--cmd_template "blastp -query __QUERY_FILE__ -db /db/uniprot/latest/uniprot_sprot -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 4" \
--seqs_per_bin 250 \
--query_fasta YOUR_QUERY_FASTA.fasta \
--out_dir blast_result

</pre>

To gather the blast output you can generally concatenate all the individual outputs. You can use the following command to find and concatenate all the output files.

<pre class="gcommand">
find OUTPUT_DIR -name '*.fa.OUT' | xargs cat > combined_blast_results.out
</pre>

Configuration file contents:

* cmd: This is the actual command that will be used to submit the HpcGridRunner command from the submission script specified in "--cmd_template". You will want to request enough resources for a single blastp command here.
** --mem: Request enough memory for a single blastp command based on how many seqs_per_bin you choose. This could be around 20-80gb.
** -n: Leave this at 1
** -c: This is how many CPU cores you want. '''Set this equal to whatever you put for "-num_threads"''' in the "--cmd_template" in your submission script.
* max_nodes: How many compute nodes you want running your blast commands. The more you request here, the faster it will go through all of your fasta file bins. It is suggested to request at least 80-100 nodes if not more, but this is up to your preference. The more nodes you have running jobs, the harder it can be to keep track of jobs if you are in the trouble-shooting phase.
* cmds_per_node: This is how many blast cmds you want to run on each node. It is suggested to leave this equal to 1 because these cmds run sequentially anyways (rather than concurrently) so it does not save time to increase this value in this case.

This specific sample configuration file can be found at /apps/eb/HpcGridRunner/1.0.2-GCCcore-12.3.0/hpc_conf/sapelo_1c_3g.conf, but you can copy it to your own directory to modify, or simply create a new text file and fill it in with this information<pre class="gscript">
# This was adapted for Slurm from:
# /usr/local/apps/hpcgridrunner/1.0.2/hpc_conf/sapelo_1c_3G_AMD.conf
# which was on the old (Torque/Moab) Sapelo2

# grid type:
grid=SLURM

# template for a grid submission:
cmd=sbatch -p batch --mem 16gb -n 1 -c 4 -t 6:00:00

##########################################################################################
# settings below configure the Trinity job submission system, not tied to the grid itself.
##########################################################################################

# number of grid submissions to be maintained at steady state by the Trinity submission system
max_nodes=10

# number of commands that are batched into a single grid submission job.
cmds_per_node=1
</pre>

== Documentation ==

Please see http://hpcgridrunner.github.io/

[[#top|Back to Top]]

== Installation ==

Installed in /apps/eb/HpcGridRunner/1.0.2

== System ==

64-bit Linux

HpcGridRunner-Sapelo2

2026-04-29T18:34:41Z

Chelsea: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Tools]]

== Category ==

Tools

== Program On ==

Sapelo2

== Version ==

1.0.2

== Author / Distributor ==

Please see https://github.com/HpcGridRunner/HpcGridRunner

== Description ==

This tool will help in executing a file full of commands in parallel using a compute cluster.

== Running Program ==

For instruction on running HpcGridRunner in conjunction with Trinity, please see [[Trinity-HpcGridRunner|here]].

Also refer to [[Running Jobs on Sapelo2]].

*HpcGridRunner/1.0.2-GCCcore-12.3.0
*HpcGridRunner/1.0.2-GCCcore-14.2.0

To use HpcGridRunner, please first load the module with
<pre class="gscript">
ml HpcGridRunner/1.0.2-GCCcore-14.2.0
</pre>

Running a blast job in parallel by splitting the fasta file:

HpcGridRunner submission script parameters:

* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.
* --cmd_template: The cmd_template can be change to reflect your blast command. Leave the -query parameter set to __QUERY_FILE__ value and hpc_FASTA_Gridrunner will fill it dynamically. You can also change the values for outfmt, evalue, max_target_seqs and db.
** -num_threads: How many threads you want each blastp command to use. Be sure to request enough CPU cores in the .conf file (see conf file configuration instructions below)
* --seqs_per_bin:
* --query_fasta: You will need to change the YOUR_QUERY_FASTA.fasta to the name of your fasta file.
* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.

'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.

<pre class="gscript">
#!/bin/bash
#SBATCH --partition batch
#SBATCH --ntasks=1
#SBATCH --time=48:00:00
#SBATCH --mem=3gb

ml HpcGridRunner/1.0.2
ml BLAST+/2.13.0-gompi-2022a

hpc_FASTA_GridRunner.pl \
--grid_conf=$HPCGR_CONF_DIR/sapelo_1c_3g.conf \
--cmd_template "blastp -query __QUERY_FILE__ -db /db/uniprot/latest/uniprot_sprot -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 4" \
--seqs_per_bin 250 \
--query_fasta YOUR_QUERY_FASTA.fasta \
--out_dir blast_result

</pre>

To gather the blast output you can generally concatenate all the individual outputs. You can use the following command to find and concatenate all the output files.

<pre class="gcommand">
find OUTPUT_DIR -name '*.fa.OUT' | xargs cat > combined_blast_results.out
</pre>

Configuration file contents:

* cmd: This is the actual command that will be used to submit the HpcGridRunner command from the submission script specified in "--cmd_template". You will want to request enough resources for a single blastp command here.
** --mem: Request enough memory for a single blastp command based on how many seqs_per_bin you choose. This could be around 20-80gb.
** -n: Leave this at 1
** -c: This is how many CPU cores you want. '''Set this equal to whatever you put for "-num_threads"''' in the "--cmd_template" in your submission script.
* max_nodes: How many compute nodes you want running your blast commands. The more you request here, the faster it will go through all of your fasta file bins. It is suggested to request at least 80-100 nodes if not more, but this is up to your preference. The more nodes you have running jobs, the harder it can be to keep track of jobs if you are in the trouble-shooting phase.
* cmds_per_node: This is how many blast cmds you want to run on each node. It is suggested to leave this equal to 1 because these cmds run sequentially anyways (rather than concurrently) so it does not save time to increase this value in this case.

This specific sample configuration file can be found at /apps/eb/HpcGridRunner/1.0.2-GCCcore-12.3.0/hpc_conf/sapelo_1c_3g.conf, but you can copy it to your own directory to modify, or simply create a new text file and fill it in with this information<pre class="gscript">
# This was adapted for Slurm from:
# /usr/local/apps/hpcgridrunner/1.0.2/hpc_conf/sapelo_1c_3G_AMD.conf
# which was on the old (Torque/Moab) Sapelo2

# grid type:
grid=SLURM

# template for a grid submission:
cmd=sbatch -p batch --mem 16gb -n 1 -c 4 -t 6:00:00

##########################################################################################
# settings below configure the Trinity job submission system, not tied to the grid itself.
##########################################################################################

# number of grid submissions to be maintained at steady state by the Trinity submission system
max_nodes=10

# number of commands that are batched into a single grid submission job.
cmds_per_node=1
</pre>

== Documentation ==

Please see http://hpcgridrunner.github.io/

[[#top|Back to Top]]

== Installation ==

Installed in /apps/eb/HpcGridRunner/1.0.2

== System ==

64-bit Linux

HpcGridRunner-Sapelo2

2026-04-29T14:51:29Z

Chelsea: /* Running Program */

HpcGridRunner-Sapelo2

2026-04-29T13:49:54Z

Chelsea: /* Running Program */

File:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf

2026-04-28T18:45:27Z

Chelsea: Chelsea uploaded a new version of File:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf

HpcGridRunner-Sapelo2

2026-04-23T16:29:07Z

Chelsea: /* Running Program */

HpcGridRunner-Sapelo2

2026-04-23T16:28:55Z

Chelsea: /* Running Program */

Trinity-HpcGridRunner

2026-04-23T16:25:55Z

Chelsea: /* Running Program */

===Description===
Instruction on how to modify a Trinity script to run in conjunction with HpcGridRunner
===Running Program===
Step 1: Create normal Trinity script

* Note: normal Trinity jobs should be run utilizing /lscratch, however, this method running with HpcGridRunner does not benefit from /lscratch so this example will not have any /lscratch components in it. For more information on running normal Trinity jobs with /lscratch, please see [[Trinity-Sapelo2#Utilizing /lscratch in Trinity Job Submission Script|here]].
* For more information on creating a Trinity job (without utilizing /lscratch) please see [[Trinity-Sapelo2#Trinity v2.15.1 Software Module on Sapelo2|here]].

Step 2: add a line to load HpcGridRunner module AND add the --grid_exec flag in your Trinity command (see how to format --grid exec below)

* Your grid_exec flag should look exactly like the one below, where the only part you'll change is the '''location to your config.conf''' file after --grid_conf. Note the location of the quotation marks as they are necessary.
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=Trinity_HpcGridRunner
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=200G
#SBATCH --time=48:00:00
#SBATCH --output=log.%j.out
#SBATCH --error=log.%j.err

cd $SLURM_SUBMIT_DIR

ml Trinity/2.15.1-foss-2022a
ml HpcGridRunner/1.0.2

Trinity --seqType <string> --max_memory 100G \
--CPU 8 \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--output /scratch/cft07037/trinity_tests/testing/${SLURM_JOB_ID}/outputs/trinity/ \
--full_cleanup \
--grid_exec "/apps/eb/HpcGridRunner/1.0.2/hpc_cmds_GridRunner.pl --grid_conf /scratch/path/to/your/configfile/config.conf -c"

</pre>
Step 3: create config.conf file<pre class="gscript">
# grid type:
grid=SLURM

# template for a grid submission:
cmd=sbatch -p batch --mem 80gb -n 1 --cpus-per-task 8 -t 01:00:00

##########################################################################################
# settings below configure the Trinity job submission system, not tied to the grid itself.
##########################################################################################

# number of grid submissions to be maintained at steady state by the Trinity submission system
max_nodes=5

# number of commands that are batched into a single grid submission job. These run sequentially, not concurrently, so you only need to request enough cpus-per-task for the threads of a single command
cmds_per_node=3
</pre>

* The main things to change in your config.conf file are the max_nodes (how many individual grid jobs will be allowed to run at the same time) and the cmds_per_node (number of commands per grid job), which together determine how the grid will run on the cluster. You can also alter the cmd, which is the command that will be used to submit the individual grid jobs.
* The number of grid jobs that will be submitted depends on how many recursive Trinity commands you have and what variables you choose for max_nodes and cmds_per_node.
** Increasing the number of cmds_per_node and max_nodes will lower the total time it takes for all of the recursive Trinity commands to finish running, however it is important to note that though you may put a large number for max_nodes, the amount actually used will be determined by SLURM and ultimately depends on what resources are currently available and how many jobs you already have running. Similarly, setting a large number for the variable cmds_per_node can make the overall job complete more quickly, but then those individual jobs (submitted by the cmd variable) may need more memory.

===Other Resources===

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity#optional-adapting-trinity-to-a-computing-grid-for-massively-parallel-processing-of-embarrassingly-parallel-steps

Bactopia-Sapelo2

2026-04-21T14:36:47Z

Chelsea: /* Documentation */

Bactopia-Sapelo2

2026-04-21T14:36:02Z

Chelsea: /* Running Program */

Bactopia-Sapelo2

2026-04-21T14:35:50Z

Chelsea: /* Description */

Bactopia-Sapelo2

2026-04-21T14:34:52Z

Chelsea: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics == Category == Bioinformatics == Program On == Sapelo2 == Version == 3.2.0 == Author / Distributor == Please see https://bactopia.github.io/v3.1.0/ == Description == tbd == Running Program == tbd == Documentation == <pre class="gcommand"> tbd </pre> Back to Top == System == 64-bit Linux"

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==
3.2.0

== Author / Distributor ==

Please see https://bactopia.github.io/v3.1.0/

== Description ==

tbd

== Running Program ==

tbd

== Documentation ==

<pre class="gcommand">
tbd
</pre>

[[#top|Back to Top]]

== System ==
64-bit Linux

Software

2026-04-21T14:31:40Z

Chelsea: /* Partial List of Installed Software */

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| [[Bactopia-Sapelo2|Bactopia]] || 3.2.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.5.1, 2.6.3, 2.7.3, 2.7.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 2.1.6, 3.0.3, 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 2.0, 4.0.5, 5.4.7, 5.5.0, 5.8.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.2||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || 0.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMarkET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.63-95.0, 5.64-96.0, 5.66-98.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 11.0.20, 17.0.6, 21.0.2, 21.0.5 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 23Jun2022 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023a, R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.4, 2.5.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

Trinity-HpcGridRunner

2026-04-21T13:47:35Z

Chelsea: /* Running Program */

===Description===
Instruction on how to modify a Trinity script to run in conjunction with HpcGridRunner
===Running Program===
Step 1: Create normal Trinity script

* Note: normal Trinity jobs should be run utilizing /lscratch, however, this method running with HpcGridRunner does not benefit from /lscratch so this example will not have any /lscratch components in it. For more information on running normal Trinity jobs with /lscratch, please see [[Trinity-Sapelo2#Utilizing /lscratch in Trinity Job Submission Script|here]].
* For more information on creating a Trinity job (without utilizing /lscratch) please see [[Trinity-Sapelo2#Trinity v2.15.1 Software Module on Sapelo2|here]].

Step 2: add a line to load HpcGridRunner module AND add the --grid_exec flag in your Trinity command (see how to format --grid exec below)

* Your grid_exec flag should look exactly like the one below, where the only part you'll change is the '''location to your config.conf''' file after --grid_conf. Note the location of the quotation marks as they are necessary.
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=Trinity_HpcGridRunner
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=200G
#SBATCH --time=48:00:00
#SBATCH --output=log.%j.out
#SBATCH --error=log.%j.err

cd $SLURM_SUBMIT_DIR

ml Trinity/2.15.1-foss-2022a
ml HpcGridRunner/1.0.2

Trinity --seqType <string> --max_memory 100G \
--CPU 8 \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--output /scratch/cft07037/trinity_tests/testing/${SLURM_JOB_ID}/outputs/trinity/ \
--full_cleanup \
--grid_exec "/apps/eb/HpcGridRunner/1.0.2/hpc_cmds_GridRunner.pl --grid_conf /scratch/path/to/your/configfile/config.conf -c"

</pre>
Step 3: create config.conf file<pre class="gscript">
# grid type:
grid=SLURM

# template for a grid submission:
cmd=sbatch -p batch --mem 80gb -n 1 --cpus-per-task 24 -t 01:00:00

##########################################################################################
# settings below configure the Trinity job submission system, not tied to the grid itself.
##########################################################################################

# number of grid submissions to be maintained at steady state by the Trinity submission system
max_nodes=5

# number of commands that are batched into a single grid submission job.
cmds_per_node=3
</pre>

* The main things to change in your config.conf file are the max_nodes (how many individual grid jobs will be allowed to run at the same time) and the cmds_per_node (number of commands per grid job), which together determine how the grid will run on the cluster. You can also alter the cmd, which is the command that will be used to submit the individual grid jobs.
* The number of grid jobs that will be submitted depends on how many recursive Trinity commands you have and what variables you choose for max_nodes and cmds_per_node.
** Increasing the number of cmds_per_node and max_nodes will lower the total time it takes for all of the recursive Trinity commands to finish running, however it is important to note that though you may put a large number for max_nodes, the amount actually used will be determined by SLURM and ultimately depends on what resources are currently available and how many jobs you already have running. Similarly, setting a large number for the variable cmds_per_node can make the overall job complete more quickly, but then those individual jobs (submitted by the cmd variable) may need more memory.

===Other Resources===

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity#optional-adapting-trinity-to-a-computing-grid-for-massively-parallel-processing-of-embarrassingly-parallel-steps

Training

2026-04-17T13:25:28Z

Chelsea:

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''April 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Sapelo2 Part II (1 session)

4. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

5. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

In '''May 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|April 17th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|April 22nd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|May 8th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|May 14th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|May 20th, Wednesday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|April 20th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|May 6th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|May 12th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|May 18th, Monday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|April 17th, Friday, 1:00 - 3:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|April 23rd, Thursday, 2:00 - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|April 30th, Thursday, 1:00 - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}


====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]

|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]] ; [[Media:Gacrc_handout2026_phys8601.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]

|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

File:GACRC Sapelo2 cluster new user training workshop v10.8.pdf

2026-04-02T19:41:41Z

Chelsea: Chelsea uploaded a new version of File:GACRC Sapelo2 cluster new user training workshop v10.8.pdf

Version 10.8 of Sapelo2 cluster training

Visual Studio Code SSH

2026-03-25T20:13:38Z

Chelsea: /* Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Code/Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand ([[OnDemand|https://wiki.gacrc.uga.edu/wiki/OnDemand]])

''Note'': Some VS Code extensions run in the background even if you are only editing code when you log in via your own VS Code installation on your computer (not through OnDemand). This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable these extensions for remote hosts using the instructions below.
=Disabling Heavy-Hitting Extensions=

Disabling extensions using "Disable (remote)" is simple and re-enabling them is also very quick and easy and does not require re-installation. "'''Disable (remote)" disables your VS Code extensions when on a remote host (like the Sapelo2 Cluster), but still allows you to use them locally.'''

If you log in to the Sapelo2 Cluster via VS Code (not through OnDemand), your enabled extensions may run in the background even if you are only editing code, which will still contribute to the load on the login node. High load on login nodes causes major disruptions in the performance of those nodes for all users logged in to those nodes.

The following VS Code extensions are some that commonly run in the background even when you are not running code. Please consider disabling them for remote hosts with "Disable (remote)" if you plan to log in to the Sapelo2 Cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code on the Sapelo2 Cluster within an interactive job in your VS Code session.

Extensions:
*C/C++ (ms-vscode.cpptools)
*Python (ms-python.python)
*Pylance (ms-python.vscode-pylance)
*Jupyter (ms-toolsai.jupyter)

* GitHub Copilot (github.copilot)

* GitHub Copilot Chat (github.copilot-chat)
* Codeium (codeium.codeium)
* Claude-related extensions
* Docker (ms-azuretools.vscode-docker)

Steps to disable extensions for remote hosts using "Disable (remote)":

#In VS Code, click on the extension panel to view your extensions
#Click on the gear icon next to the extension that you want to disable
#Click on 'Disable (remote)'

* You can then re-enable your extensions if you need to run tests on the Sapelo2 Cluster by starting an interactive job in your VS Code session and clicking "Enable" on your desired extension

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-25T16:20:44Z

Chelsea: /* Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Code/Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand ([[OnDemand|https://wiki.gacrc.uga.edu/wiki/OnDemand]])

''Note'': Some VS Code extensions run in the background even if you are only editing code when you log in via your own VS Code installation on your computer. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable these extensions for remote hosts using the instructions below.
=Disabling Heavy-Hitting Extensions=

Disabling extensions using "Disable (remote)" is simple and re-enabling them is also very quick and easy and does not require re-installation. "'''Disable (remote)" disables your VS Code extensions when on a remote host (like the Sapelo2 Cluster), but still allows you to use them locally.'''

If you log in to the Sapelo2 Cluster via VS Code (not through OnDemand), your enabled extensions may run in the background even if you are only editing code, which will still contribute to the load on the login node. High load on login nodes causes major disruptions in the performance of those nodes for all users logged in to those nodes.

The following VS Code extensions are some that commonly run in the background even when you are not running code. Please consider disabling them for remote hosts with "Disable (remote)" if you plan to log in to the Sapelo2 Cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code on the Sapelo2 Cluster within an interactive job in your VS Code session.

Extensions:
*C/C++ (ms-vscode.cpptools)
*Python (ms-python.python)
*Pylance (ms-python.vscode-pylance)
*Jupyter (ms-toolsai.jupyter)

* GitHub Copilot (github.copilot)

* GitHub Copilot Chat (github.copilot-chat)
* Codeium (codeium.codeium)
* Claude-related extensions
* Docker (ms-azuretools.vscode-docker)

Steps to disable extensions for remote hosts using "Disable (remote)":

#In VS Code, click on the extension panel to view your extensions
#Click on the gear icon next to the extension that you want to disable
#Click on 'Disable (remote)'

* You can then re-enable your extensions if you need to run tests on the Sapelo2 Cluster by starting an interactive job in your VS Code session and clicking "Enable" on your desired extension

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-25T16:20:11Z

Chelsea: /* Disabling Heavy-Hitting Extensions */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Code/Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand ([[OnDemand|https://wiki.gacrc.uga.edu/wiki/OnDemand]])

''Note'': Some VS Code extensions run in the background even if you are only editing code and not running anything. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable these extensions for remote hosts using the instructions below.
=Disabling Heavy-Hitting Extensions=

Disabling extensions using "Disable (remote)" is simple and re-enabling them is also very quick and easy and does not require re-installation. "'''Disable (remote)" disables your VS Code extensions when on a remote host (like the Sapelo2 Cluster), but still allows you to use them locally.'''

If you log in to the Sapelo2 Cluster via VS Code (not through OnDemand), your enabled extensions may run in the background even if you are only editing code, which will still contribute to the load on the login node. High load on login nodes causes major disruptions in the performance of those nodes for all users logged in to those nodes.

The following VS Code extensions are some that commonly run in the background even when you are not running code. Please consider disabling them for remote hosts with "Disable (remote)" if you plan to log in to the Sapelo2 Cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code on the Sapelo2 Cluster within an interactive job in your VS Code session.

Extensions:
*C/C++ (ms-vscode.cpptools)
*Python (ms-python.python)
*Pylance (ms-python.vscode-pylance)
*Jupyter (ms-toolsai.jupyter)

* GitHub Copilot (github.copilot)

* GitHub Copilot Chat (github.copilot-chat)
* Codeium (codeium.codeium)
* Claude-related extensions
* Docker (ms-azuretools.vscode-docker)

Steps to disable extensions for remote hosts using "Disable (remote)":

#In VS Code, click on the extension panel to view your extensions
#Click on the gear icon next to the extension that you want to disable
#Click on 'Disable (remote)'

* You can then re-enable your extensions if you need to run tests on the Sapelo2 Cluster by starting an interactive job in your VS Code session and clicking "Enable" on your desired extension

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-25T16:16:21Z

Chelsea: /* Disabling Heavy-Hitting Extensions */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Code/Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand ([[OnDemand|https://wiki.gacrc.uga.edu/wiki/OnDemand]])

''Note'': Some VS Code extensions run in the background even if you are only editing code and not running anything. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable these extensions for remote hosts using the instructions below.
=Disabling Heavy-Hitting Extensions=

Disabling extensions using "Disable (remote)" is simple and re-enabling them is also very quick and easy and does not require re-installation. "'''Disable (remote)" disables your VS Code extensions when on a remote host (like the Sapelo2 Cluster), but still allows you to use them locally.'''

If you log in to the Sapelo2 Cluster via VS Code, your enabled extensions may run in the background even if you are only editing code, which will still contribute to the load on the login node. High load on login nodes causes major disruptions in the performance of those nodes for all users logged in to those nodes.

The following VS Code extensions are some that commonly run in the background even when you are not running code. Please consider disabling them for remote hosts with "Disable (remote)" if you plan to log in to the Sapelo2 Cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code on the Sapelo2 Cluster within an interactive job in your VS Code session.

Extensions:
*C/C++ (ms-vscode.cpptools)
*Python (ms-python.python)
*Pylance (ms-python.vscode-pylance)
*Jupyter (ms-toolsai.jupyter)

* GitHub Copilot (github.copilot)

* GitHub Copilot Chat (github.copilot-chat)
* Codeium (codeium.codeium)
* Claude-related extensions
* Docker (ms-azuretools.vscode-docker)

Steps to disable extensions for remote hosts using "Disable (remote)":

#In VS Code, click on the extension panel to view your extensions
#Click on the gear icon next to the extension that you want to disable
#Click on 'Disable (remote)'

* You can then re-enable your extensions if you need to run tests on the Sapelo2 Cluster by starting an interactive job in your VS Code session and clicking "Enable" on your desired extension

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-25T16:15:34Z

Chelsea: /* Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Code/Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand ([[OnDemand|https://wiki.gacrc.uga.edu/wiki/OnDemand]])

''Note'': Some VS Code extensions run in the background even if you are only editing code and not running anything. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable these extensions for remote hosts using the instructions below.
=Disabling Heavy-Hitting Extensions=

Disabling extensions using "Disable (remote)" is simple and re-enabling them is also very quick and easy and does not require re-installation. "'''Disable (remote)" disables your VS Code extensions when on a remote host (like the Sapelo2 Cluster), but still allows you to use them locally.'''

If you log in to the Sapelo2 Cluster via VS Code, your enabled extensions may run in the background even if you are only editing code, which will still contribute to the load on the login node. High load on login nodes causes major disruptions in the performance of those nodes for all users logged in to those nodes.

The following VS Code extensions are some that commonly run in the background even when you are not running code. Please consider disabling them for remote hosts with "Disable (remote)" if you plan to log in to the Sapelo2 Cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code on the Sapelo2 Cluster within an interactive job in your VS Code session.
Extensions:
*C/C++ (ms-vscode.cpptools)
*Python (ms-python.python)
*Pylance (ms-python.vscode-pylance)
*Jupyter (ms-toolsai.jupyter)

* GitHub Copilot (github.copilot)

* GitHub Copilot Chat (github.copilot-chat)
* Codeium (codeium.codeium)
* Claude-related extensions
* Docker (ms-azuretools.vscode-docker)

Steps to disable extensions for remote hosts using "Disable (remote)":

#In VS Code, click on the extension panel to view your extensions
#Click on the gear icon next to the extension that you want to disable
#Click on 'Disable (remote)'

* You can then re-enable your extensions if you need to run tests on the Sapelo2 Cluster by starting an interactive job in your VS Code session and clicking "Enable" on your desired extension

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-25T16:14:37Z

Chelsea: /* Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Code/Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand ([[OnDemand|https://wiki.gacrc.uga.edu/wiki/OnDemand]])

''Note'': Some VS Code extensions run in the background even if you are only editing code and not running anything. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable these extensions for remote hosts using the instructions below.
=Disabling Heavy-Hitting Extensions=

Disabling extensions using "Disable (remote)" is simple and re-enabling them is also very quick and easy and does not require re-installation. "Disable (remote)" disables your VS Code extensions when on a remote host (like the Sapelo2 Cluster), but still allows you to use them locally.

If you log in to the Sapelo2 Cluster via VS Code, your enabled extensions may run in the background even if you are only editing code, which will still contribute to the load on the login node. High load on login nodes causes major disruptions in the performance of those nodes for all users logged in to those nodes.

The following VS Code extensions are some that commonly run in the background even when you are not running code. Please consider disabling them for remote hosts with "Disable (remote)" if you plan to log in to the Sapelo2 Cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code on the Sapelo2 Cluster within an interactive job in your VS Code session.
Extensions:
*C/C++ (ms-vscode.cpptools)
*Python (ms-python.python)
*Pylance (ms-python.vscode-pylance)
*Jupyter (ms-toolsai.jupyter)

* GitHub Copilot (github.copilot)

* GitHub Copilot Chat (github.copilot-chat)
* Codeium (codeium.codeium)
* Claude-related extensions
* Docker (ms-azuretools.vscode-docker)

Steps to disable extensions for remote hosts using "Disable (remote)":

#In VS Code, click on the extension panel to view your extensions
#Click on the gear icon next to the extension that you want to disable
#Click on 'Disable (remote)'

* You can then re-enable your extensions if you need to run tests on the Sapelo2 Cluster by starting an interactive job in your VS Code session and clicking "Enable" on your desired extension

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-25T16:14:04Z

Chelsea: /* Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Code/Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand ([[OnDemand|https://wiki.gacrc.uga.edu/wiki/OnDemand]])

Note:

Some VS Code extensions run in the background even if you are only editing code and not running anything. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable these extensions for remote hosts using the instructions below.
=Disabling Heavy-Hitting Extensions=

Disabling extensions using "Disable (remote)" is simple and re-enabling them is also very quick and easy and does not require re-installation. "Disable (remote)" disables your VS Code extensions when on a remote host (like the Sapelo2 Cluster), but still allows you to use them locally.

If you log in to the Sapelo2 Cluster via VS Code, your enabled extensions may run in the background even if you are only editing code, which will still contribute to the load on the login node. High load on login nodes causes major disruptions in the performance of those nodes for all users logged in to those nodes.

The following VS Code extensions are some that commonly run in the background even when you are not running code. Please consider disabling them for remote hosts with "Disable (remote)" if you plan to log in to the Sapelo2 Cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code on the Sapelo2 Cluster within an interactive job in your VS Code session.
Extensions:
*C/C++ (ms-vscode.cpptools)
*Python (ms-python.python)
*Pylance (ms-python.vscode-pylance)
*Jupyter (ms-toolsai.jupyter)

* GitHub Copilot (github.copilot)

* GitHub Copilot Chat (github.copilot-chat)
* Codeium (codeium.codeium)
* Claude-related extensions
* Docker (ms-azuretools.vscode-docker)

Steps to disable extensions for remote hosts using "Disable (remote)":

#In VS Code, click on the extension panel to view your extensions
#Click on the gear icon next to the extension that you want to disable
#Click on 'Disable (remote)'

* You can then re-enable your extensions if you need to run tests on the Sapelo2 Cluster by starting an interactive job in your VS Code session and clicking "Enable" on your desired extension

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-25T16:13:44Z

Chelsea: /* Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand ([[OnDemand|https://wiki.gacrc.uga.edu/wiki/OnDemand]])

Note:

Some VS Code extensions run in the background even if you are only editing code and not running anything. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable these extensions for remote hosts using the instructions below.
=Disabling Heavy-Hitting Extensions=

Disabling extensions using "Disable (remote)" is simple and re-enabling them is also very quick and easy and does not require re-installation. "Disable (remote)" disables your VS Code extensions when on a remote host (like the Sapelo2 Cluster), but still allows you to use them locally.

If you log in to the Sapelo2 Cluster via VS Code, your enabled extensions may run in the background even if you are only editing code, which will still contribute to the load on the login node. High load on login nodes causes major disruptions in the performance of those nodes for all users logged in to those nodes.

The following VS Code extensions are some that commonly run in the background even when you are not running code. Please consider disabling them for remote hosts with "Disable (remote)" if you plan to log in to the Sapelo2 Cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code on the Sapelo2 Cluster within an interactive job in your VS Code session.
Extensions:
*C/C++ (ms-vscode.cpptools)
*Python (ms-python.python)
*Pylance (ms-python.vscode-pylance)
*Jupyter (ms-toolsai.jupyter)

* GitHub Copilot (github.copilot)

* GitHub Copilot Chat (github.copilot-chat)
* Codeium (codeium.codeium)
* Claude-related extensions
* Docker (ms-azuretools.vscode-docker)

Steps to disable extensions for remote hosts using "Disable (remote)":

#In VS Code, click on the extension panel to view your extensions
#Click on the gear icon next to the extension that you want to disable
#Click on 'Disable (remote)'

* You can then re-enable your extensions if you need to run tests on the Sapelo2 Cluster by starting an interactive job in your VS Code session and clicking "Enable" on your desired extension

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-25T16:13:02Z

Chelsea: /* Disabling Heavy-Hitting Extensions */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand

Note:

Some VS Code extensions run in the background even if you are only editing code and not running anything. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable these extensions for remote hosts using the instructions below.
=Disabling Heavy-Hitting Extensions=

Disabling extensions using "Disable (remote)" is simple and re-enabling them is also very quick and easy and does not require re-installation. "Disable (remote)" disables your VS Code extensions when on a remote host (like the Sapelo2 Cluster), but still allows you to use them locally.

If you log in to the Sapelo2 Cluster via VS Code, your enabled extensions may run in the background even if you are only editing code, which will still contribute to the load on the login node. High load on login nodes causes major disruptions in the performance of those nodes for all users logged in to those nodes.

The following VS Code extensions are some that commonly run in the background even when you are not running code. Please consider disabling them for remote hosts with "Disable (remote)" if you plan to log in to the Sapelo2 Cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code on the Sapelo2 Cluster within an interactive job in your VS Code session.
Extensions:
*C/C++ (ms-vscode.cpptools)
*Python (ms-python.python)
*Pylance (ms-python.vscode-pylance)
*Jupyter (ms-toolsai.jupyter)

* GitHub Copilot (github.copilot)

* GitHub Copilot Chat (github.copilot-chat)
* Codeium (codeium.codeium)
* Claude-related extensions
* Docker (ms-azuretools.vscode-docker)

Steps to disable extensions for remote hosts using "Disable (remote)":

#In VS Code, click on the extension panel to view your extensions
#Click on the gear icon next to the extension that you want to disable
#Click on 'Disable (remote)'

* You can then re-enable your extensions if you need to run tests on the Sapelo2 Cluster by starting an interactive job in your VS Code session and clicking "Enable" on your desired extension

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-24T20:24:36Z

Chelsea: /* Disabling Heavy-Hitting Extensions */

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand

Note:

Some VS Code extensions run in the background, even if you are not actually running code. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable (remote) those heavy-hitting extensions.

=Disabling Heavy-Hitting Extensions=
If you use any of the following VS Code extensions, please disable them when logged in to the cluster via the VS Code IDE. You can easily and quickly enable the extension when you are ready to run your code. This can significantly help improve the performance on our login nodes when you are logged in via VS Code.

Extensions:

*

Steps to disable:

#

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-24T20:22:20Z

Chelsea:

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand

Note:

Some VS Code extensions run in the background, even if you are not actually running code. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable (remote) those heavy-hitting extensions.

=Disabling Heavy-Hitting Extensions=

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-24T20:21:45Z

Chelsea:

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

Please keep in mind that if you log in to the Sapelo2 Cluster via VS Code, you will be placed on a '''login node'''. This is acceptable only to edit code/files and other low-level tasks, but please do not run code there. It will likely overload our login nodes and cause disruptions to the performance of the login nodes. If you want to run tests in VS Code, please do one of the following first:

'''Running Tests in VS Code on the Cluster'''

# Start an interactive job within VS Code after logging in to the Sapelo2 Cluster
# Use VS Code through On Demand

Note:

Some VS Code extensions run in the background, even if you are not actually running code. This can still overload our login nodes and cause significant slowness for users logged in to the same login nodes. To remedy this, you can disable (remote) those heavy-hitting extensions.
=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Visual Studio Code SSH

2026-03-24T20:13:58Z

Chelsea:

=Introduction=

Visual Studio Code, or "VS Code", is a popular code editor. It is very customizable and allows the user to install many extensions.

=Correct Usage of VS Code and other IDEs on the Sapelo2 Cluster=

=Downloading VS Code=

If you haven't already, you can download VS Code [https://code.visualstudio.com/download here]. If you're using Windows, you'll almost certainly want to download the 64 bit User Installer.

=Installing the SSH extension=
Here we will go over how to set up its SSH extension. This will allow you to have VS Code connect to Sapelo2 so that you can edit files on the cluster with your local instance of VS Code.

====Open the Extensions Interface====

When you open VS Code, you'll see on the left the Activity Bar, with several buttons displayed vertically.

[[File:Vscode_activity_bar.png | frameless]]

----

====Search for the SSH Extension====

Clicking the button with the four squares opens up the extensions interface in the sidebar. Below you can see some of extensions I already have installed. Some of these are just simply color theme packages, to change syntax highlighting colors. Others provide features relevant to a particular programming language, such as the Python extension providing [https://code.visualstudio.com/docs/editor/intellisense#:~:text=IntelliSense%20is%20a%20general%20term,%2C%20and%20%22code%20hinting.%22 IntelliSense] for Python.

[[File:Vscode_extensions.png | 400px | frameless]]

----

At the top of the extensions interface is a search bar, where you can search for official or community-provided extensions. This is where you could search for the SSH extension, for example. Typically you'll want to install extensions provided by a known source, such as Microsoft in this case (the first option), and/or an extension that has many downloads and a high rating, as shown in this search output.

[[File:Vscode_ssh_extension.png | 600px | frameless]]

----

====Install the SSH Extension====

Once you find the extension you want, all you have to do is click the small "Install" button in the search output, and a tab will open in your editor with more information and instructions on how to use the extension that you have installed.

[[File:Vscode_installed.png | 800px | frameless]]

----

=Using the SSH Extension=

====Click the SSH Button====

You can hide the sidebar if you wish with cmd + b on Mac and ctrl + b on Windows. Once the SSH extension is installed you will see this small greater than & less than button in the bottom left corner of VS Code.

[[File:Vscode_sshbutton.png | frameless]]

----

====Add a new SSH Host Connection====

Upon clicking that small SSH button in the bottom left, a prompt window will appear in the top middle of VS Code, asking how you want to connect to whatever it is you're going to SSH. Select the first option, "Connect Current Window to Host...".

[[File:Vscode_connection_options.png | 600px | frameless]]

----

Next, click the "Add New SSH Host..." option, and type your MyID@sapelo2.gacrc.uga.edu in the prompt, and then press enter.

[[File:Vscode_add_new_ssh_host.png | 600px | frameless]]
[[File:Vscode_connection.png | 600px | frameless]]

----

If it asks you what SSH config file to update, you can just choose the first option.

[[File:Vscode_sshconfig.png | 600px | frameless]]

----

====Connect to Sapelo2====

The prompt will then disappear, but now you can click the small SSH button in the bottom left of VS Code and see that your connection has been saved, you don't have to type it every time. Click the Sapelo2 connection to then be presented with a password prompt. This just wants your MyID password, as if you were normally connecting to Sapelo2 via PuTTY or your terminal. Then you will get an ArchPass DUO prompt. You can respond to this with a 1 for a push notification to your phone, or however you normally authenticate with ArchPass DUO.

[[File:Vscode_chooseconnection.png | 600px | frameless]]
[[File:Vscode_password.png | 600px | frameless]]
[[File:Vscode_duo.png | 600px | frameless]]

----

====Open Directories on Sapelo2====

Once you approve the connection request via DUO, you're connected to Sapelo2! To open up a particular directory on Sapelo2, click the button on the side part that looks like two pieces of paper, which will open the explorer interface within the sidebar.

[[File:Vscode_explorer.png | 600px | frameless]]

----

Click the "Open Folder" button to then be presented with a prompt where you can enter any path on Sapelo2 to which you have permission to access.

[[File:Vscode_opendir.png | 800px | frameless]]

----

In this example, I've opened my home directory in the side bar. It presents it as a file tree that I can navigate graphically. Directories can be expanded by clicking them. Files can be opened in VS Code by double clicking them, as you can see here, with this file.txt in my home directory.

[[File:Vscode_homedir.png | 800px | frameless]]

----

You can open multiple directories on Sapelo2 in the sidebar of VS Code by clicking the "Add Folder to Workspace" option in the File menu.

[[File:Vscode_add_dir.png | 800px | frameless]]

----

====Open the Terminal in VS Code====

I highly recommend toggling the Terminal in VS Code, which will allow you to interact with Sapelo2 as you normally would from within VS Code. To do this, click "Terminal" under the View menu. This will open up a terminal in the bottom half of the editor. You can enter any command as you normally would on Sapelo2.

[[File:Vscode_terminal.png | 1000px | frameless ]]

----

Training

2026-03-13T14:09:56Z

Chelsea: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''March 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Sapelo2 Part II (1 session)

4. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

5. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

In '''April 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Sapelo2 Part II (1 session)

4. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

5. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|March 18th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|April 9th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|April 17th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|April 22nd, Wednesday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|March 16th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|April 7th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|April 15th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|April 20th, Monday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|March 20th, Friday, 1:00 - 3:00 PM
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|April 17th, Friday, 1:00 - 3:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|March 26th, Thursday, 2:00 - 3:00 PM
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|April 23rd, Thursday, 2:00 - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|March 23rd, Monday, 1:00 - 2:30 PM
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|April 30th, Thursday, 1:00 - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]] ; [[Media:Gacrc_handout2026_phys8601.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2026-02-11T16:39:31Z

Chelsea: /* Regular Training Announcement */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''February 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Sapelo2 Part II (1 session)

4. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

5. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

In '''March 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Sapelo2 Part II (1 session)

4. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

5. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|February 11th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|February 19th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|March 6th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|March 12th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|March 18th, Wednesday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|January 20th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 4th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 9th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 17th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|March 4th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|March 10th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|March 16th, Monday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|February 20th, Friday, 1:00 - 3:00 PM
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|March 20th, Friday, 1:00 - 3:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|February 27th, Friday, 2:00 - 3:00 PM
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|March 26th, Thursday, 2:00 - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|February 26th, Thursday, 1:00 - 2:30 PM
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|March 23rd, Monday, 1:00 - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]] ; [[Media:Gacrc_handout2026_phys8601.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2026-02-11T16:39:04Z

Chelsea: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''January 2025''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

In '''February 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Sapelo2 Part II (1 session)

4. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

5. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|February 11th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|February 19th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|March 6th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|March 12th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|March 18th, Wednesday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|January 20th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 4th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 9th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 17th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|March 4th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|March 10th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|March 16th, Monday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|February 20th, Friday, 1:00 - 3:00 PM
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|March 20th, Friday, 1:00 - 3:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|February 27th, Friday, 2:00 - 3:00 PM
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|March 26th, Thursday, 2:00 - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|February 26th, Thursday, 1:00 - 2:30 PM
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|March 23rd, Monday, 1:00 - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]] ; [[Media:Gacrc_handout2026_phys8601.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

File:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf

2026-01-23T18:04:47Z

Chelsea: Chelsea uploaded a new version of File:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf

Training

2026-01-13T18:27:19Z

Chelsea: /* Regular Training Announcement */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''January 2025''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

In '''February 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Sapelo2 Part II (1 session)

4. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

5. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|January 14th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 22nd, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|February 6th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|February 11th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|February 19th, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|January 20th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 4th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 9th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 17th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|February 20th, Friday, 1:00 - 3:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|February 27th, Friday, 2:00 - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|February 26th, Thursday, 1:00 - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]] ; [[Media:Gacrc_handout2026_phys8601.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2026-01-13T18:25:54Z

Chelsea: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''January 2025''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|January 14th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 22nd, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|February 6th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|February 11th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|February 19th, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|January 20th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 4th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 9th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 17th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|February 20th, Friday, 1:00 - 3:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|February 27th, Friday, 2:00 - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|February 26th, Thursday, 1:00 - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]] ; [[Media:Gacrc_handout2026_phys8601.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2025-12-15T21:10:06Z

Chelsea: /* Regular Training Announcement */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''January 2025''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|December 3rd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 11th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 19th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 9th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 14th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 22nd, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|December 1st, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 9th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 17th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|January 7th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|January 12th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|January 20th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Fall2025.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2025-12-15T21:08:57Z

Chelsea: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''November 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

In '''December 2025''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|December 3rd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 11th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 19th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 9th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 14th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 22nd, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|December 1st, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 9th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 17th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|January 7th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|January 12th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|January 20th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Fall2025.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2025-11-11T16:27:03Z

Chelsea: /* Regular Training Announcement */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''November 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

In '''December 2025''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|November 10th, Monday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|November 13th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|November 19th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 3rd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 11th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 19th, Friday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|November 11th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|November 17th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 1st, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 9th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 17th, Wednesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|November 14th, Friday, 2:00 PM - 4:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|November 20th, Thursday, 2:00 PM - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|November 24th, Monday, 1:00 PM - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Fall2025.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2025-11-11T16:26:23Z

Chelsea: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''October 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

In '''November 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|November 10th, Monday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|November 13th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|November 19th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 3rd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 11th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|December 19th, Friday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|November 11th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|November 17th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 1st, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 9th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|December 17th, Wednesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|November 14th, Friday, 2:00 PM - 4:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|November 20th, Thursday, 2:00 PM - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|November 24th, Monday, 1:00 PM - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Fall2025.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2025-11-10T18:51:28Z

Chelsea: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''October 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

In '''November 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|November 10th, Monday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|November 13th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|November 19th, Wednesday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|November 11th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|November 17th, Monday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|November 14th, Friday, 2:00 PM - 4:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|November 20th, Thursday, 2:00 PM - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|November 24th, Monday, 1:00 PM - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Fall2025.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2025-10-13T19:15:04Z

Chelsea: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''October 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

In '''November 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|October 16th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|October 24th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|October 28th, Tuesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|November 10th, Monday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|November 13th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|November 19th, Wednesday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|October 14th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|October 22nd, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|November 5th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|November 11th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|November 17th, Monday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|October 17th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|November 14th, Friday, 2:00 PM - 4:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|October 27th, Monday, 2:00 PM - 3:00 PM
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|November 20th, Thursday, 2:00 PM - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|October 30th, Thursday, 1:00 PM - 2:30 PM
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|November 24th, Monday, 1:00 PM - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Fall2025.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2025-09-22T16:42:06Z

Chelsea: /* Installing Software Packages in Virtual Environments on Sapelo2 */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''September 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

In '''October 2025''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|September 11th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|September 17th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|October 8th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|October 16th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|October 24th, Friday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|September 15th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|October 6th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|October 14th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|October 22nd, Wednesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|September 30th, Tuesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|October 17th, Friday, 2:00 PM - 4:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|September 22nd, Monday, 2:00 PM - 3:00 PM
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|October 27th, Monday, 2:00 PM - 3:00 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|September 25th, Thursday, 1:00 PM - 2:30 PM
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|October 30th, Thursday, 1:00 PM - 2:30 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

====Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Fall2025.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

====Installing Software Packages in Virtual Environments on Sapelo2====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC virtual environments training v1.2.pdf]]
|}

====Job Parallelization with GNU Parallel and Slurm Arrays====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}

====Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

====Out-Reach/In-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.