ARCHIVED: On AVIDD at IU, how do I run my MPI program as a parallel batch job using LAM?
Note: UITS began retiring the AVIDD system on May 1 as originally scheduled, but portions of the system will remain online until mid-August. UITS retired AVIDD-T, AVIDD-N, and AVIDD-I on May 1, but is delaying the retirement of AVIDD-B and AVIDD-O pending the installation of a replacement system based on Intel's X86-64 technology. If you use AVIDD-B or AVIDD-O, UITS encourages you to migrate to Big Red and/or the TeraGrid; for help, email High Performance Computing. If you cannot migrate, AVIDD-B and AVIDD-O will remain available to you until the new system is ready for use in mid-August.
For instructions on how to compile your program, see the Knowledge Base document ARCHIVED: On AVIDD at IU, how do I compile my program so I can run it as a parallel job using LAM? For instructions on running your job interactively, see the Knowledge Base document ARCHIVED: On AVIDD at IU, how do I run a parallel job interactively using LAM?
If you have code that works fine, you can write a short PBS
script and submit your jobs to the PBS job submission system on the
AVIDD cluster at Indiana University. You must have
+lam-gm-intel defined before the
@avidd line in your ~/.soft file; for more
information, see the Knowledge Base document ARCHIVED: On AVIDD at IU, how do I compile my program so I can run it as a parallel job using LAM?
For example, you could submit a run non-interactively using the following script:
#PBS -l nodes=2:ppn=2,walltime=10:00 #PBS -m ae #PBS -N hello_example #PBS -j oe #PBS -V lamboot $PBS_NODEFILE #### Comment out above lamboot line and uncomment out the next two lines if you wish to use Myrinet instead of Ethernet ## cat $PBS_NODEFILE | sed 's/-eth1//' | sed 's/$/-myri0 cpu=2/' > ${HOME}/my_machine_file ## lamboot ${HOME}/my_machine_file mpirun C ~/bin/helloworlds lamhalt
If the above script is called hello_example.sh, you would
submit a background job using qsub as follows:
To learn more about PBS, see the Knowledge Base document ARCHIVED: What is PBS, and how do I use it?
For more information on LAM, refer to the LAM FAQ at:
http://www.lam-mpi.org/faq/This document was developed with support from the National Science Foundation (NSF) under Grant No. 0503697 to the University of Chicago and subcontracted to Indiana University. Additional support was provided by IU through its participation in the TeraGrid, which is supported by the NSF under Grants No. 0833618, SCI451237, SCI535258, and SCI504075. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.
Last modified on December 18, 2007.
