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This will submit your code executable to the slurm partition using openmpi. See the slurm section of the wiki for further examples.
Is there a slurm partition for testing parallel programs that require a short run time?
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What mpi software is available?
OpenMPI is the default slurm supported mpi. Other types are available and requires a slurm option to override. Once the corresponding module is loaded, your environment will provide access to the various MPI compilers.
For example, OpenMPI provides the following:
mpic++ mpicxx mpicc mpiCC mpif77 mpif90
Likewise for mvapich and mvapich2.
How can I use Portland Compilers and MPI?
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>module load pgi
>module load mvapich2
>pgcc myname.c -o myname -Mmpi -I/opt/pgi/linux86-64/7.2-3/include/ >bsub -I -q parallel_public -a mvapich2 -n 8 mpirun.lsf ./myname
Where are all Where are the Portland executables and what are their names ?
When you load the module for Portland, all executables will be on your path.
> ls /opt/pgi/linux86-64/7.2-3/bin
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How does one find out gpu specific info?
> bsub -Ip -q short_gpu srun -p gpu /opt/shared/gpucomputingsdk/4.2.9/C/bin/linux/release/deviceQuery
Another option:
> bsub srun -q short_gpu -o gpu_info.txt p gpu nvidia-smi -a
To support GPU access new LSF GPU queues have been installed: short_gpu, normal_gpu and long_gpu.
For example to run one of the compiled cuda codes:
> cp /opt/shared/gpucomputingsdk/4.2.9/C/bin/linux/release/simpleStreams simpleStreams .
> module load cuda
> bsub srun -q short_gpu -Ip -R "rusage [n_gpu_jobs=1 ]" p gpu ./simpleStreams
To view a description of sample codes cuda codes from the command line:
> lynx file:///opt/shared/gpucomputingsdk/4.2.9/C/Samples.html
or
> firefox file:///opt/shared/gpucomputingsdk/4.0.17/C/Samples.html
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Matlab's Parallel Toolbox GPU demonstration applications is an excellent introduction. Additional applications such as Mathematica, Ansys, Maple and others offer various levels of support within their product. Bsub usage would be similar.
For example, to run Matlab and access GPU resources:
> module load matlab
> bsub -q short_gpu -Ip -R "rusage [n_gpu_jobs=1 ]" srun ...options... -p gpu matlab
Additional GPU resources
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Look around the web as there are many similar GPU resources.
Tufts Parallel Users group
A recently formed group with some common interests: link