Parallel programming related information
What are some reasons for using the cluster
- access to MPI based parallel programs
- access to larger amounts of memory than 32bit computers offer
- access to the large public domain of scientific computing programs
- access to compilers
- assess to large amounts of storage
- access to batch processing for running numerous independent serial jobs
- access to 64bit versions of programs you may already have on your 32bit desktop
What is MPI?
MPI stands for Message Passing Interface. The goal of MPI is to develop a widely used standard for writing message-passing programs.
What installed programs provide a parallel solution?
The following provide MPI based solutions: Abaqus, Ansys, Fluent, gridMathematica, StarP/matlab, StarP/python, paraview, MaterialStudio, Dacapo
The following provide thread based parallelism: comsol, matlab
The default setting is single thread.
When does 64bit computing matter?
When there is a need for memory and storage beyond the 32bit barriers.
Is it possible to run linux 32-bit executables on the cluster?
There is a good chance that it will succeed. But there might be other issues preventing it from running. Try it out...
Where can I find additional information about MPI?
http://www-unix.mcs.anl.gov/mpi/
http://www.nersc.gov/nusers/resources/software/libs/mpi/
http://www.faqs.org/faqs/mpi-faq/
http://www.redbooks.ibm.com/abstracts/sg245380.html
http://www.nccs.gov/user-support/training-education/hpcparallel-computing-links/
What are some good web based tutorials for MPI?
http://ci-tutor.ncsa.uiuc.edu/login.php
http://www.slac.stanford.edu/~alfw/Parallel.html
https://computing.llnl.gov/tutorials/parallel_comp/
How do I run a compiled mpi based program?
-bash-3.2$ bsub -I -q parallel_public -a mvapich2 -n 8 mpirun.lsf yourcode
This will submit your code executable to the parallel queue using mvapich2 and requesting 8 cpus.
Is there a queue for testing parallel programs that require a short run time?
There is queue called paralleltest_public just for this purpose. It has a run time limit of 10 minutes.
What mpi software is available?
Openmpi and Mvapich is offered and under module setup control.
Can you recommend a good text on MPI?
The Tisch Library has:
William Gropp, Ewing Lusk, Anthony Skjellum, Using MPI: Portable Parallel Programming with the Message-Passing Interface, Second Edition, MIT Press, 1999, ISBN: 0262571323.
Another resource, Designing and Building Parallel Programs may be useful.
*Some additional supporting info on a parallel computing course can be found on this Computer Science link.
Interesting thread parallelism links and codes
Threading Building Blocks
Tufts Parallel Users group
A recently formed group with some common interests: link