Rosetta-Sapelo2: Difference between revisions
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=== Version === | === Version === | ||
2021.16.61629, 2022.46.334, 3.14-release371 | |||
=== Author / Distributor === | === Author / Distributor === | ||
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'''Version | '''Version 2022.46.334''' | ||
Compiled with GNU compilers v. | Compiled with GNU compilers v. 11.2.0 and Intel MPI libraries v. 2021.4.0. It is installed in /apps/eb/Rosetta/2022.46.334-intel-2021b, and the binaries (mpi) are available in /apps/eb/Rosetta/2022.46.334-intel-2021b/bin . | ||
To use this version of rosetta, first load the module with | To use this version of rosetta, first load the module with | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
module load Rosetta/ | module load Rosetta/2022.46.334-intel-2021b | ||
</pre> | </pre> | ||
This module also loads | This module also loads intel/2021b. | ||
'''Example of shell scripts to run Rosetta MPI on the batch partition:''' | '''Example of shell scripts to run Rosetta MPI version 2022.46.334 on the batch partition:''' | ||
To run minirosetta.mpi.linuxiccrelease as a parallel job, using e.g. | To run minirosetta.mpi.linuxiccrelease as a parallel job, using e.g. 2 nodes and 48 cores (24 cores per node) (sub.sh) | ||
<pre class="gscript"> | <pre class="gscript"> | ||
# | #!/bin/bash | ||
# | #SBATCH --job-name=j_rosetta # Job name | ||
# | #SBATCH --partition=batch # Partition (queue) name | ||
# | #SBATCH --constraint=EDR # node feature | ||
# | #SBATCH --nodes=2 # Number of nodes | ||
# | #SBATCH --ntasks=48 # Number of MPI ranks | ||
# | #SBATCH --ntasks-per-node=24 # How many tasks on each node | ||
# | #SBATCH --cpus-per-task=1 # Number of cores per MPI rank | ||
# | #SBATCH --mem-per-cpu=500mb # Memory per processor | ||
#SBATCH --time=48:00:00 # Time limit hrs:min:sec | |||
#SBATCH --output=log.%j.out # Standard output log | |||
#SBATCH --error=log.%j.err # Standard error log | |||
#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL) | |||
#SBATCH --mail-user=username@uga.edu # Where to send mail | |||
cd $SLURM_SUBMIT_DIR | |||
module load Rosetta/2022.46.334-intel-2021b | |||
srun minirosetta.mpi.linuxiccrelease [options] | |||
</pre> | </pre> | ||
| Line 84: | Line 82: | ||
=== Installation === | === Installation === | ||
*'''Version | *'''Version 2022.46.334''' - Compiled with intel/2021b. | ||
=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
Latest revision as of 13:29, 12 June 2024
Category
Chemistry
Program On
Sapelo2
Version
2021.16.61629, 2022.46.334, 3.14-release371
Author / Distributor
Please see https://www.rosettacommons.org/
Description
Rosetta is a software suite for macromolecular modeling. Please see https://www.rosettacommons.org/
Running Program
Also refer to Running Jobs on Sapelo2.
For more information on Environment Modules on Sapelo2 please see the Lmod page.
Version 2022.46.334
Compiled with GNU compilers v. 11.2.0 and Intel MPI libraries v. 2021.4.0. It is installed in /apps/eb/Rosetta/2022.46.334-intel-2021b, and the binaries (mpi) are available in /apps/eb/Rosetta/2022.46.334-intel-2021b/bin .
To use this version of rosetta, first load the module with
module load Rosetta/2022.46.334-intel-2021b
This module also loads intel/2021b.
Example of shell scripts to run Rosetta MPI version 2022.46.334 on the batch partition:
To run minirosetta.mpi.linuxiccrelease as a parallel job, using e.g. 2 nodes and 48 cores (24 cores per node) (sub.sh)
#!/bin/bash #SBATCH --job-name=j_rosetta # Job name #SBATCH --partition=batch # Partition (queue) name #SBATCH --constraint=EDR # node feature #SBATCH --nodes=2 # Number of nodes #SBATCH --ntasks=48 # Number of MPI ranks #SBATCH --ntasks-per-node=24 # How many tasks on each node #SBATCH --cpus-per-task=1 # Number of cores per MPI rank #SBATCH --mem-per-cpu=500mb # Memory per processor #SBATCH --time=48:00:00 # Time limit hrs:min:sec #SBATCH --output=log.%j.out # Standard output log #SBATCH --error=log.%j.err # Standard error log #SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL) #SBATCH --mail-user=username@uga.edu # Where to send mail cd $SLURM_SUBMIT_DIR module load Rosetta/2022.46.334-intel-2021b srun minirosetta.mpi.linuxiccrelease [options]
where [options] needs to be replaced by the options and input files that you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.
Sample job submission command:
sbatch sub.sh
Documentation
Please see https://www.rosettacommons.org/
Installation
- Version 2022.46.334 - Compiled with intel/2021b.
System
64-bit Linux