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, Mathematica, Matlab, Paraview
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/
http://software.intel.com/en-us/multi-core/
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 and a high priority.
Can parallel jobs be sent to any queue?
No... The Parallel_public queue and the test version is where most jobs should go. This queue has a limit of 64 cores/cpus. If you need access to more cores, we can add you to the Express_public queue which has a limit of 256 cores.
What mpi software is available?
OpenMPI, Mvapich and Mvapich2 are available on the cluster as a loadable module. Once the corresponding module is loaded, your environment will provide access to the various MPI compilers.
> module load openmpi
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?
Try the broadcast example found in the PGI directory tree:
/opt/pgi/linux86-64/7.2-3/EXAMPLES/MPI/mpihello/mynane.c
As an example that requests 8 cores:
>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 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
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 Tufts Computer Science link.
Interesting Intel thread parallelism links and codes
Threading Building Blocks
See attachment for Intel white paper introduction pdf document.
Tufts Parallel Users group
A recently formed group with some common interests: link