Trinity-HpcGridRunner: Difference between revisions
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* For more information on creating a Trinity job (without utilizing /lscratch) please see [[Trinity-Sapelo2#Trinity v2.15.1 Software Module on Sapelo2|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 | Step 2: add a line to load HpcGridRunner module AND add the --grid_exec flag in your Trinity comma<pre class="gscript"> | ||
#!/bin/bash | #!/bin/bash | ||
#SBATCH --job-name=Trinity_HpcGridRunner | #SBATCH --job-name=Trinity_HpcGridRunner |
Revision as of 13:08, 31 July 2024
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 here.
- For more information on creating a Trinity job (without utilizing /lscratch) please see here.
Step 2: add a line to load HpcGridRunner module AND add the --grid_exec flag in your Trinity comma
#!/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 $SLURM_SUBMIT_DIR ml Trinity/2.15.1-foss-2022a ml HpcGridRunner/1.0.2 Trinity --seqType <string> --max_memory 100G \ --CPU 1 \ --left reads.left.fq.gz \ --right reads.right.fq.gz \ --output /scratch/cft07037/trinity_tests/testing/${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"
- Your grid_exec flag should look exactly like the one above, 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.
Step 3: create config.conf file
**To be updated after maintenance**
- The main things to change in your config.conf file are the max_nodes and the number of jobs, which together determine how the grid will run on the cluster.