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--- wiki:gpu_jobs [2012/10/18 13:01] – [How to submit a job] admin
+++ wiki:gpu_jobs [2013/12/11 11:21] (current) – removed admin
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-====== Running jobs on GPUs ======
-Keck II workstation ''w01''-''w10'' and ''w13''-''w15.keck2.ucsd.edu'' have NVidia GTX680 GPU installed each. These can be used to run computationally intensive jobs on.
-<color black/yellow>All jobs must be submitted through the SGE queue manager. All rogue jobs will be terminated and user accounts not adhering to this policy will be suspended.</color>
-===== How to submit a job =====
-  * Create all necessary input files for your job.
-  * Create an SGE script which is used to submit the job to the job queue manager.
-  * Submit your job suing this command: ''qsub script.sge'' Where ''script.sge'' is the filename of your SGE script.
-  * Check on progress of your job in the queue: ''qstat -f ''
-More information about SGE can be found [[https://ctbp.ucsd.edu/computing/wiki/introduction_to_sge_the_queuing_system_on_the_clusters|here]].
-===== Example SGE scripts =====
-These are example SGE script for running most common applications on the GPUs.
-==== Amber ====
-The optimal AMBER job configuration for KeckII is to use 1 CPU and 1 GPU per run.
-<code>
-#!/bin/bash
-#$ -cwd
-#$ -q all.q
-#$ -V
-#$ -N AMBER_job
-#$ -S /bin/bash
-#$ -e sge.err
-#$ -o sge.out
-myrun=my_simulation_name
-module load nvidia
-module load amber
-export CUDA_VISIBLE_DEVICES=1
-# create a scratch directory on the SDD and copy all runtime data there
-export scratch_dir=`mktemp -d /scratch/${USER}.XXXXXX`
-current_dir=`pwd`
-cp * $scratch_dir
-cd $scratch_dir
-$AMBERHOME/bin/pmemd.cuda -O -i $myrun.in -o $myrun.out -r $myrun.rst \
- -x $myrun.nc -p  $myrun.prmtop -c $myrun.rst
-# copy all data back from the scratch directory
-cp * $current_dir
-rm -rf $scratch_dir
-</code>
-==== NAMD ====
-Running NAMD on 2 CPUs and one GPU is the optimal number of CPUs/GPUs for a typical NAMD job on KeckII workstations.
-=== Running namd on 2 CPUs/1 GPU ===
-<code>
-#!/bin/bash
-#$ -cwd
-#$ -q all.q
-#$ -V
-#$ -N NAMD_job
-#$ -pe orte-host 2
-#$ -S /bin/bash
-#$ -e sge.err
-#$ -o sge.out
-module load nvidia
-module load namd-cuda
-# create a scratch directory and copy all runtime data there
-export scratch_dir=`mktemp -d /scratch/${USER}.XXXXXX`
-current_dir=`pwd`
-cp * $scratch_dir
-cd $scratch_dir
-# 2 CPUs/1 GPU
-namd2 +idlepoll +p2 +devices 1 apoa1.namd >& apoa1-2.1.out
-# copy all data back from the scratch directory
-cp * $current_dir
-rm -rf $scratch_dir
-</code>