cluster:119
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| cluster:119 [2013/08/21 18:59] – hmeij | cluster:119 [2021/06/17 19:32] (current) – hmeij07 | ||
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| \\ | \\ | ||
| **[[cluster: | **[[cluster: | ||
| - | |||
| - | 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. | ||
| - | --- // | ||
| ==== Submitting GPU Jobs ==== | ==== Submitting GPU Jobs ==== | ||
| + | |||
| + | Please plenty of time between multiple GPU job submissions. | ||
| + | |||
| + | Jobs need to be submitted to the scheduler via cottontail to queues mwgpu, amber128, exx96. | ||
| + | |||
| + | This page is old, the gpu resource '' | ||
| + | --- // | ||
| + | |||
| + | **Articles** | ||
| + | |||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | |||
| Line 44: | Line 54: | ||
| </ | </ | ||
| - | With '' | + | With '' |
| < | < | ||
| Line 58: | Line 68: | ||
| 3 Tesla K20m 21 C 0 % | 3 Tesla K20m 21 C 0 % | ||
| ==================================================== | ==================================================== | ||
| + | |||
| + | [hmeij@sharptail sharptail]$ ssh n33 gpu-free | ||
| + | 1,3,0 | ||
| + | |||
| + | |||
| </ | </ | ||
| 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=/ | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | |||
| ## leave sufficient time between job submissions (30-60 secs) | ## leave sufficient time between job submissions (30-60 secs) | ||
| Line 171: | Line 202: | ||
| </ | </ | ||
| + | |||
| + | ==== gromacs.sub ==== | ||
| + | |||
| + | < | ||
| + | |||
| + | #!/bin/bash | ||
| + | |||
| + | rm -rf gromacs.out gromacs.err \#* *.log | ||
| + | |||
| + | # from greentail we need to recreate module env | ||
| + | export PATH=/ | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | |||
| + | #BSUB -o gromacs.out | ||
| + | #BSUB -e gromacs.err | ||
| + | #BSUB -N | ||
| + | #BSUB -J 325monolayer | ||
| + | |||
| + | # read / | ||
| + | . / | ||
| + | export VMDDIR=/ | ||
| + | |||
| + | ## CPU RUN: queue mw256, n<=28, must run on one node (thread_mpi) | ||
| + | ##BSUB -q mw256 | ||
| + | ##BSUB -n 2 | ||
| + | ##BSUB -R " | ||
| + | #export PATH=/ | ||
| + | #. / | ||
| + | #mdrun -nt 2 -s 325topol.tpr -c 325monolayer.gro -e 325ener.edr -o 325traj.trr -x 325traj.xtc | ||
| + | |||
| + | ## GPU RUN: gpu (1-4), queue mwgpu, n (1-4, matches gpu count), must run on one node | ||
| + | ##BSUB -q mwgpu | ||
| + | ##BSUB -n 1 | ||
| + | ##BSUB -R " | ||
| + | ## signal GMXRC is a gpu run with: 1=thread_mpi | ||
| + | #export GMXRC=1 | ||
| + | #export PATH=/ | ||
| + | #. / | ||
| + | # | ||
| + | # | ||
| + | |||
| + | # GPU RUN: gpu (1-4), queue mwgpu, n (1-4, matches gpu count), must run on one node | ||
| + | #BSUB -q mwgpu | ||
| + | #BSUB -n 1 | ||
| + | #BSUB -R " | ||
| + | # signal GMXRC is a gpu run with: 2=mvapich2 | ||
| + | export GMXRC=2 | ||
| + | export PATH=/ | ||
| + | . / | ||
| + | lava.mvapich2.wrapper mdrun_mpi \ | ||
| + | -testverlet -s 325topol.tpr -c 325monolayer.gro -e 325ener.edr -o 325traj.trr -x 325traj.xtc | ||
| + | |||
| + | |||
| + | </ | ||
| + | |||
| + | ==== matlab.sub ==== | ||
| + | |||
| + | < | ||
| + | |||
| + | #!/bin/bash | ||
| + | |||
| + | rm -rf out err *.out | ||
| + | |||
| + | # from greentail we need to recreate module env | ||
| + | export PATH=/ | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | |||
| + | #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 " | ||
| + | # signal MATGPU is a gpu run | ||
| + | export MATGPU=1 | ||
| + | lava.mvapich2.wrapper matlab -nodisplay | ||
| + | |||
| + | |||
| + | </ | ||
| ==== lava.mvampich2.wrapper ==== | ==== lava.mvampich2.wrapper ==== | ||
| Line 275: | Line 411: | ||
| #debug# echo " | #debug# echo " | ||
| - | if [ $CHARMRUN -eq 1 ]; then | + | |
| + | if [ -n " | ||
| + | # gromacs needs them from base 0, so gpu 2,3 is string 01 | ||
| + | if [ ${# | ||
| + | gmxrc_gpus=" | ||
| + | elif [ ${# | ||
| + | gmxrc_gpus=" | ||
| + | elif [ ${# | ||
| + | gmxrc_gpus=" | ||
| + | elif [ ${# | ||
| + | gmxrc_gpus=" | ||
| + | fi | ||
| + | |||
| + | if [ $GMXRC -eq 1 ]; then | ||
| + | newargs=`echo ${MYARGS} | sed " | ||
| + | echo " | ||
| + | $newargs | ||
| + | elif [ $GMXRC -eq 2 ]; then | ||
| + | newargs=`echo ${MYARGS} | sed " | ||
| + | echo " | ||
| + | ${MPIRUN} -ssh -hostfile ${MACHFILE} -np $gpunp $newargs | ||
| + | fi | ||
| + | |||
| + | elif [ -n " | ||
| + | echo " | ||
| + | ${MYARGS} | ||
| + | elif [ -n " | ||
| cat ${MACHFILE}.lst | tr '\/ ' ' | cat ${MACHFILE}.lst | tr '\/ ' ' | ||
| echo " | echo " | ||
| Line 283: | Line 445: | ||
| ${MPIRUN} -ssh -hostfile ${MACHFILE} -np $gpunp ${MYARGS} | ${MPIRUN} -ssh -hostfile ${MACHFILE} -np $gpunp ${MYARGS} | ||
| fi | fi | ||
| + | |||
| exit $? | exit $? | ||
| + | |||
| + | |||
| + | </ | ||
| + | |||
| + | |||
| + | ===== elim code ===== | ||
| + | |||
| + | < | ||
| + | |||
| + | # | ||
| + | |||
| + | while (1) { | ||
| + | |||
| + | $gpu = 0; | ||
| + | $log = ''; | ||
| + | if (-e "/ | ||
| + | $tmp = `/ | ||
| + | @tmp = split(/ | ||
| + | foreach $i (0..$#tmp) { | ||
| + | ($a, | ||
| + | if ( $f == 0 ) { $gpu = $gpu + 1; } | ||
| + | #print "$a $f $gpu\n"; | ||
| + | $log .= " | ||
| + | } | ||
| + | } | ||
| + | # nr_of_args name1 value1 | ||
| + | $string = "1 gpu $gpu"; | ||
| + | |||
| + | $h = `hostname`; chop($h); | ||
| + | $d = `date +%m/ | ||
| + | foreach $i (' | ||
| + | if ( " | ||
| + | `echo " | ||
| + | } | ||
| + | } | ||
| + | |||
| + | # you need the \n to flush -hmeij | ||
| + | # you also need the space before the line feed -hmeij | ||
| + | print " | ||
| + | # or use | ||
| + | # | ||
| + | |||
| + | # smaller than specified in lsf.shared | ||
| + | sleep 10; | ||
| + | |||
| + | } | ||
cluster/119.1377111557.txt.gz · Last modified: by hmeij