Both sides previous revision
Previous revision
Next revision
|
Previous revision
Next revision
Both sides next revision
|
cluster:119 [2013/09/20 15:13] hmeij [lava.mvampich2.wrapper] |
cluster:119 [2013/10/09 08:41] hmeij |
\\ | \\ |
**[[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 on host sharptail itself for now and will be dispatched to nodes n33-n37 in queue mwgpu. They can also be submitted from host greentail but remember any output will be in shraptail's /home. |
| --- //[[hmeij@wesleyan.edu|Meij, Henk]] 2013/09/25 08:33// |
| |
| **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 |
| |
| |
| |
#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) |
| |
# from greentail we need to recreate module env | # 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=/home/apps/bin:/cm/local/apps/cuda50/libs/304.54/bin:\ |
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 | /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 |
| |
#BSUB -o gromacs.out | #BSUB -o gromacs.out |
##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 |
#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 |
| |
</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:$PATH |
| export LD_LIBRARY_PATH=/cm/local/apps/cuda50/libs/304.54/lib64:\ |
| /cm/shared/apps/cuda50/toolkit/5.0.35/lib64:/cm/shared/apps/amber/amber12/lib:\ |
| /cm/shared/apps/amber/amber12/lib64:/cm/shared/apps/namd/ibverbs-smp-cuda/2013-06-02/:\ |
| /cm/shared/apps/cuda50/toolkit/5.0.35/lib64:/cm/shared/apps/cuda50/libs/current/lib64:\ |
| /cm/shared/apps/cuda50/toolkit/5.0.35/open64/lib:/cm/shared/apps/cuda50/toolkit/5.0.35/extras/CUPTI/lib:\ |
| /cm/shared/apps/mvapich2/gcc/64/1.6/lib |
| |
| #BSUB -o out |
| #BSUB -e err |
| #BSUB -N |
| #BSUB -J test |
| |
| # GPU RUN: (1-4), queue mwgpu, n (1-4, matches gpu count), must run on one node |
| #BSUB -q mwgpu |
| #BSUB -n 1 |
| #BSUB -R "rusage[gpu=1:mem=7000],span[hosts=1]" |
| # signal MATGPU is a gpu run |
| export MATGPU=1 |
| lava.mvapich2.wrapper matlab -nodisplay -r test |
| |
| |
| </code> |
| |
==== lava.mvampich2.wrapper ==== | ==== lava.mvampich2.wrapper ==== |
| |
fi | fi |
| |
| elif [ -n "$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} |