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Login first to pslogin
(from SLAC) or to psexport
(from anywhere). From there you can submit a job with the following command:
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bsub -q psnehq -o <output file name> <job_script_command>
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For example:
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bsub -q psnehq -o ~/output/job.out my_program
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This will submit a job (my_program) to the queue psnehq
and write its output to a file named ~/output/job.out. You may check on the status of your jobs using the bjobs
command.
The RedHat supplied OpenMPI packages are installed on pslogin, psexport and all of the psana batch servers.
The system default has been set to the current version as supplied by RedHat.
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$ mpi-selector --query
default:openmpi-1.4-gcc-x86_64
level:system
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Your environment should be set up to use this version (unless you have used RedHat's mpi-selector
script, or your login scripts, to override the default). You can check to see if your PATH
is correct by issuing the command which mpirun
. Currently, this should return /usr/lib64/openmpi/1.4-gcc/bin/mpirun
. Future updates to the MPI version may change the exact details of this path.
In addition, your LD_LIBRARY_PATH }}should include {{/usr/lib64/openmpi/1.4-gcc/lib
(or something similar).
For notes on compiling examples, please see:
http://www.slac.stanford.edu/comp/unix/farm/mpi.html
The following are examples of how to submit OpenMPI jobs to the PCDS psnehmpiq batch queue:
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bsub -q psnehmpiq -a mympi -n 32 -o ~/output/%J.out ~/bin/hello
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Will submit an OpenMPI job (-a mympi) requesting 32 processors (-n 32) to the psnehmpiq batch queue (-q psnehmpiq).
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bsub -q psfehmpiq -a mympi -n 16 -R "span[ptile=1]" -o ~/output/%J.out ~/bin/hello
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Will submit an OpenMPI job (-a mympi) requesting 16 processors (-n 16) spanned as one processor per host (-R "span\[ptile=1\]") to the psfehmpiq batch queue (-q psfehmpiq). |
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bsub -q psfehmpiq -a mympi -n 12 -R "span[hosts=1]" -o ~/output/%J.out ~/bin/hello
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