HPC commands

hpc.md

General

To check for avialable modules module avail
List the loaded modules module list

CHPC, WUSTL

Job status: qstat -t -u username

Comet, SDSC

http://www.sdsc.edu/support/user_guides/comet.html

Submit script

#!/bin/bash
#SBATCH --job-name="singularity_test"
#SBATCH --output="singularity_test.%j.out"
#SBATCH --error="singularity_test.%j.err"
#SBATCH --partition=gpu-shared
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --gres=gpu:1
#SBATCH --time=00:10:00
#SBATCH --export=all

module purge
module load gnu/4.9.2
module load mvapich2_ib/2.1
module load gnutools/2.69
module load singularity

CONTAINER=/home/rfarmer/img/chem-comet-oct-18.simg

ibrun singularity exec --nv ${CONTAINER} python /home/rfarmer/tests/test_conv_simple.py

Submitting Jobs Using sbatch sbatch jobscriptfile

Job Monitoring and Management
Job status: squeue -u user1
Can job: scancel <jobid>