Trinity-HpcGridRunner

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 command

#!/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.