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cluster:119 [2013/09/20 15:16]
hmeij [gromacs.sub] 		cluster:119 [2021/06/17 15:32] (current)
hmeij07
Line 1: Line 1:
 \\ \\
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
- 
-Jobs need to be submitted to the scheduler on host sharptail itself for now and will be dispatched to nodes n33-n37 in queue mwgpu.  
- --- //[[hmeij@wesleyan.edu|Meij, Henk]] 2013/08/21 11:01// 
  
 ==== Submitting GPU Jobs ==== ==== Submitting GPU Jobs ====
 +
 +Please plenty of time between multiple GPU job submissions.  Like minutes.
 +
 +Jobs need to be submitted to the scheduler via cottontail to queues mwgpu, amber128, exx96.
 +
 +This page is old, the gpu resource ''gpu4'' should be used, a more recent page can be found [[cluster:173|K20 Redo Usage]]. Although there might some useful information on this page explaining gpu jobs.
 + --- //[[hmeij@wesleyan.edu|Henk]] 2021/06/17 15:29//
 +
 +**Articles**
 +
 +  * [[http://www.pgroup.com/lit/articles/insider/v5n2a1.htm]] Tesla vs. Xeon Phi vs. Radeon: A Compiler Writer's Perspective 
 +  * [[http://www.pgroup.com/lit/articles/insider/v5n2a5.htm]] Calling CUDA Fortran kernels from MATLAB 
 +
  
  
Line 44: Line 54:
 </code> </code>
  
-With ''gpu-info'' we can view our running job.  ''gpu-info'' and ''gpu-free'' are available [[http://ambermd.org/gpus/]] (I had to hard code my GPU string information as they came in at 02,03,82&83, you can use deviceQuery to find them).+With ''gpu-info'' we can view our running job.  ''gpu-info'' and ''gpu-free'' are available <del>[[http://ambermd.org/gpus/]]</del> [[http://ambermd.org/gpus12/#Running]](I had to hard code my GPU string information as they came in at 02,03,82&83, you can use deviceQuery to find them).
  
 <code> <code>
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 3       Tesla K20m      21 C            0 % 3       Tesla K20m      21 C            0 %
 ==================================================== ====================================================
 +
 +[hmeij@sharptail sharptail]$ ssh n33 gpu-free
 +1,3,0
 +
 +
  
 </code> </code>
Line 121: Line 136:
 #BSUB -q mwgpu #BSUB -q mwgpu
 #BSUB -J test #BSUB -J test
 +
 +# from greentail we need to set up the module env
 +export PATH=/home/apps/bin:/cm/local/apps/cuda50/libs/304.54/bin:\
 +/cm/shared/apps/cuda50/sdk/5.0.35/bin/linux/release:/cm/shared/apps/lammps/cuda/2013-01-27/:\
 +/cm/shared/apps/amber/amber12/bin:/cm/shared/apps/namd/ibverbs-smp-cuda/2013-06-02/:\
 +/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/sbin:\
 +/usr/sbin:/cm/shared/apps/cuda50/toolkit/5.0.35/bin:/cm/shared/apps/cuda50/sdk/5.0.35/bin/linux/release:\
 +/cm/shared/apps/cuda50/libs/current/bin:/cm/shared/apps/cuda50/toolkit/5.0.35/open64/bin:\
 +/cm/shared/apps/mvapich2/gcc/64/1.6/bin:/cm/shared/apps/mvapich2/gcc/64/1.6/sbin
 +export LD_LIBRARY_PATH=/cm/local/apps/cuda50/libs/304.54/lib64:\
 +/cm/shared/apps/cuda50/toolkit/5.0.35/lib64:/cm/shared/apps/amber/amber12/lib:\
 +/cm/shared/apps/amber/amber12/lib64:/cm/shared/apps/namd/ibverbs-smp-cuda/2013-06-02/:\
 +/cm/shared/apps/cuda50/toolkit/5.0.35/lib64:/cm/shared/apps/cuda50/libs/current/lib64:\
 +/cm/shared/apps/cuda50/toolkit/5.0.35/open64/lib:/cm/shared/apps/cuda50/toolkit/5.0.35/extras/CUPTI/lib:\
 +/cm/shared/apps/mvapich2/gcc/64/1.6/lib
 +
  
 ## leave sufficient time between job submissions (30-60 secs) ## leave sufficient time between job submissions (30-60 secs)
Line 215: Line 246:
 ##BSUB -q mwgpu ##BSUB -q mwgpu
 ##BSUB -n 1 ##BSUB -n 1
-##BSUB -R "rusage[gpu=1],span[hosts=1]"+##BSUB -R "rusage[gpu=1:mem=7000],span[hosts=1]"
 ## signal GMXRC is a gpu run with: 1=thread_mpi ## signal GMXRC is a gpu run with: 1=thread_mpi
 #export GMXRC=1 #export GMXRC=1
Line 226: Line 257:
 #BSUB -q mwgpu #BSUB -q mwgpu
 #BSUB -n 1 #BSUB -n 1
-#BSUB -R "rusage[gpu=1],span[hosts=1]"+#BSUB -R "rusage[gpu=1:mem=7000],span[hosts=1]"
 # signal GMXRC is a gpu run with: 2=mvapich2 # signal GMXRC is a gpu run with: 2=mvapich2
 export GMXRC=2 export GMXRC=2
Line 236: Line 267:
  
 </code> </code>
 +
 +==== matlab.sub ====
 +
 +<code>
 +
 +#!/bin/bash
 +
 +rm -rf out err *.out
 +
 +# from greentail we need to recreate module env
 +export PATH=/home/apps/bin:/cm/local/apps/cuda50/libs/304.54/bin:\
 +/cm/shared/apps/cuda50/sdk/5.0.35/bin/linux/release:/cm/shared/apps/lammps/cuda/2013-01-27/:\
 +/cm/shared/apps/amber/amber12/bin:/cm/shared/apps/namd/ibverbs-smp-cuda/2013-06-02/:\
 +/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/sbin:\
 +/usr/sbin:/cm/shared/apps/cuda50/toolkit/5.0.35/bin:/cm/shared/apps/cuda50/sdk/5.0.35/bin/linux/release:\
 +/cm/shared/apps/cuda50/libs/current/bin:/cm/shared/apps/cuda50/toolkit/5.0.35/open64/bin:\
 +/cm/shared/apps/mvapich2/gcc/64/1.6/bin:/cm/shared/apps/mvapich2/gcc/64/1.6/sbin
 +export PATH=/share/apps/matlab/2013a/bin:$PATH
 +export LD_LIBRARY_PATH=/cm/local/apps/cuda50/libs/304.54/lib64:\
 +/cm/shared/apps/cuda50/toolkit/5.0.35/lib64:/cm/shared/apps/amber/amber12/lib:\
 +/cm/shared/apps/amber/amber12/lib64:/cm/shared/apps/namd/ibverbs-smp-cuda/2013-06-02/:\
 +/cm/shared/apps/cuda50/toolkit/5.0.35/lib64:/cm/shared/apps/cuda50/libs/current/lib64:\
 +/cm/shared/apps/cuda50/toolkit/5.0.35/open64/lib:/cm/shared/apps/cuda50/toolkit/5.0.35/extras/CUPTI/lib:\
 +/cm/shared/apps/mvapich2/gcc/64/1.6/lib
 +
 +#BSUB -o out
 +#BSUB -e err
 +#BSUB -N
 +#BSUB -J test
 +
 +# GPU RUN: (1-4), queue mwgpu, n (1-4, matches gpu count), must run on one node
 +#BSUB -q mwgpu
 +#BSUB -n 1
 +#BSUB -R "rusage[gpu=1:mem=7000],span[hosts=1]"
 +# signal MATGPU is a gpu run
 +export MATGPU=1
 +lava.mvapich2.wrapper matlab -nodisplay  -r test
 +
 +
 +</code>
 +
 ==== lava.mvampich2.wrapper ==== ==== lava.mvampich2.wrapper ====
  
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         fi         fi
  
 +elif [ -n "$MATGPU" ] && [ $MATGPU -eq 1 ]; then
 +        echo "executing: ${MYARGS}
 +        ${MYARGS}
 elif [ -n "$CHARMRUN" ] && [ $CHARMRUN -eq 1 ]; then elif [ -n "$CHARMRUN" ] && [ $CHARMRUN -eq 1 ]; then
         cat ${MACHFILE}.lst | tr '\/ ' '\r\n' | sed 's/^/host /g' > ${MACHFILE}         cat ${MACHFILE}.lst | tr '\/ ' '\r\n' | sed 's/^/host /g' > ${MACHFILE}
Line 372: Line 447:
  
 exit $? exit $?
 +
 +
 +</code>
 +
 +
 +===== elim code =====
 +
 +<code>
 +
 +#!/usr/bin/perl
 +
 +while (1) {
 +
 +        $gpu = 0;
 +        $log = '';
 +        if (-e "/usr/local/bin/gpu-info" ) {
 +                $tmp = `/usr/local/bin/gpu-info | egrep "Tesla K20"`;
 +                @tmp = split(/\n/,$tmp);
 +                foreach $i (0..$#tmp) {
 +                        ($a,$b,$c,$d,$e,$f,$g) = split(/\s+/,$tmp[$i]);
 +                        if ( $f == 0 ) { $gpu = $gpu + 1; }
 +                        #print "$a $f $gpu\n";
 +                        $log .= "$f,";
 +                }
 +        }
 +        # nr_of_args name1 value1 
 +        $string = "1 gpu $gpu";
 +
 +        $h = `hostname`; chop($h);
 +        $d = `date +%m/%d/%y_%H:%M:%S`; chop($d);
 +        foreach $i ('n33','n34','n35','n36','n37') {
 +                if ( "$h" eq "$i" ) {
 +                        `echo "$d,$log" >> /share/apps/logs/$h.gpu.log`;
 +                }
 +        }
 +
 +        # you need the \n to flush -hmeij
 +        # you also need the space before the line feed -hmeij
 +        print "$string \n"; 
 +        # or use
 +        #syswrite(OUT,$string,1);
 +
 +        # smaller than specified in lsf.shared
 +        sleep 10;
 +
 +}
  
  
cluster/119.1379704572.txt.gz ยท Last modified: 2013/09/20 15:16 by hmeij

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