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cluster:119 [2013/09/24 19:28] hmeij [lava.mvampich2.wrapper] |
cluster:119 [2013/10/09 12:41] hmeij |
\\ | \\ |
**[[cluster:0|Back]]** | **[[cluster:0|Back]]** |
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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// | |
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==== Submitting GPU Jobs ==== | ==== Submitting GPU Jobs ==== |
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| Please plenty of time between multiple GPU job submissions. Like minutes. |
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| 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// |
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| **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 |
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| |
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#BSUB -q mwgpu | #BSUB -q mwgpu |
#BSUB -J test | #BSUB -J test |
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| # 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 |
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## leave sufficient time between job submissions (30-60 secs) | ## leave sufficient time between job submissions (30-60 secs) |
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# NAMD | # NAMD |
# 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 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 | |
# signal that this is charmrun/namd job | # signal that this is charmrun/namd job |
export CHARMRUN=1 | export CHARMRUN=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: 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 |
/cm/shared/apps/cuda50/libs/current/bin:/cm/shared/apps/cuda50/toolkit/5.0.35/open64/bin:\ | /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 | /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:\ | 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/cuda50/toolkit/5.0.35/lib64:/cm/shared/apps/amber/amber12/lib:\ |
#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 MATGPU is a gpu run | # signal MATGPU is a gpu run |
export MATGPU=1 | export MATGPU=1 |