High Performance Computing

August 28, 2008

This section introduces the methods used to run an HP MPI application. The examples below demonstrate three basic methods. Refer to the Command Line Options section of this document for all the mpirun command line options.

You should use the -j option to display the MPI job ID. The job ID is useful during troubleshooting to check for a hung job using mpijob or terminate a job using mpiclean.

There are four methods you can use to start your application. The first two are useful for short interactive (test) jobs, or in script files for jobs that only run on one node; the others are more general.

• Use mpirun with the -np # option and the name of your program. For example:
  
  
  mpirun -j -np 4 hello_world
  
  starts an executable file named hello_world with four processes.
  
  
• Start an executable file with the -np # option to specify the number of processes. For example:
  
  
  hello_world -j -np 4
  
  starts an executable file named hello_world with four processes. -j displays the MPI job ID. This method can be used for applications that run on a single host and have a single executable file.
  
  NOTE: Although this method can be used to run an MPI application, the method using mpirun described earlier is preferred.
  
  
• Submit an MPI job to be run via LSF on one node:
  
  
  bsub -q para -n 8 pam -mpi mpirun -np 8 mympi_program_exe
  
  pam is a program that allows LSF to control exactly which processors the program is run on. Actually, this method is largely the same as the next method, which is actually the preferred one for this situation.
  
  
• Submit an MPI job to be run via LSF on one or more nodes (hosts):
  
  bsub -q para128 -n 96 runpam mympi_program_exe
  
  submits a job that will run an executable file named mympi_program_exe under control of an LSF queue called para. runpam is a special script file that gets information from LSF to tell which machine(s) to run the program on, then runs the program using mpirun and the host information. The job will use up to 96 processors on two distinct machines. runpam actually uses the pam command, but is simpler to work with - it handles most of the details involved in using the command.
  
  NOTE: mympi_program_exe must be the full pathname to the executable.
  
  NOTE: Do NOT use runpam in conjunction with a script that includes an mpirun . This is redundant and will cause twice as many processes to run as you intended.

• Note: Use this for interactive jobs.
  
  mpirun [-np # ] [-help] [-version] [-djpvwW] [-ck] [-t spec ] [-i spec ] [-h host ] [-l user ] [-e var [= val ] [...]] [-sp paths ] program [ args ]
  
  
• Note: Use this version of the command only when submitting a job to run on a single host.
  
  bsub [ lsf_options ] pam -mpi mpirun [-np # ][-djvwW] [-t spec ] [-i spec ] [-h host ] [-l user ] [-e var [= val ] [...]] [-sp paths ] program [ args ]
  
  
• bsub [-n #] [ other_lsf_options ] runpam [-djvwW] [-t spec ] [-i spec ] [-h host ] [-l user ] [-e var [= val ] [...]] [-sp paths ] program [ args ]