ARSC HPC Users' Newsletter Issue 430 2014-03-19

ARSC HPC Users' Newsletter Issue 430 2014-03-19

A publication of the Arctic Region Supercomputing Center.

1 Open MPI Process Affinity

A recent tip from the ARSC Help Desk is to try utilizing Open MPI process affinity for improved performance. One of the Pacman users enabled this flag and saw a 3x speedup in his ROMS model. Recompiling is not necessary, one simply passes an MCA argument at runtime:

mpirun --mca mpi_paffinity_alone 1 ./a.out

Note, utilizing process affinity may be detrimental to hybrid codes (for example, codes running MPI and OpenMP together).1

2 Parallel Programming Resources

2.1 PHYS 693

ARSC users occasionally ask us what on-site resources are available for learning parallel programming. One helpful resource is the collection of Tom Logan's presentation PDF's from the UAF semester based course, "PHYS 693: Fundamental Skills for Computational Science", which runs during the Fall semester.

http://www.arsc.edu/arsc/support/training/coreskills/schedule/index.xml

(Watch for Logan's class listed in the UAF Fall 2014 classes, for those interested in taking the course.)

2.2 MPI Examples

On the pacman.arsc.edu system, there are MPI Hello World programs available in the ${SAMPLES_HOME}/parallelEnvironment/hello_world_mpi directory. These sample programs can be compiled and run on both pacman.arsc.edu and fish.arsc.edu using the example batch job submission scripts located in ${SAMPLES_HOME}/jobSubmission.

2.3 GPGPU Slides

As part of the ongoing ARSC 2014 Spring Training Series, ARSC HPC Systems Analyst Robert Torgerson has made presentation slides available from his recent class, "An Introduction to GPGPU Programming".

http://www.arsc.edu/files/arsc/GPGPU_Presentation.pptx

3 Upcoming Training

Four presentations remain in the ARSC 2014 Spring Training series. These classes are open to all who are interested. All sessions are held in the ARSC Mac lab located in the West Ridge Research Building, room 009. No registration is required.

The Basics of Compiling and Linking Chris Dawkins Mar 28 2-4pm
Intro. to Debugging Tools Kate Hedstrom Apr 11 2-4pm
Intro. to Using the GIT Repository Kate Hedstrom Apr 18 2-4pm
Intro. to the R Programming Language Katrina Bennett Apr 25 2-4pm

4 Attention Graduates!

4.1 Remember Your Data

As your studies wind down and your post-graduation plans pick up, please remember to make arrangements for your ARSC data. ARSC User Support can assist with moving data to your advisor's $ARCHIVE, or copying data to an external harddrive prior to inactivating your ARSC user account. The ARSC Data Retention Policy states data in an inactive account can be deleted at any time. Also, automatic file purging is currently enabled for the $CENTER file system, so please make sure all important data is migrated to an appropriate destination. If you plan to keep your ARSC account active post-graduation, please make special arrangements with ARSC User Support.

4.2 Acknowledging ARSC

As you prepare your written publications, if your research has benefited from the use of ARSC resources, remember to add ARSC to your acknowledgments page. We recommend a statement similar to the following:

This work was supported in part by a grant of HPC resources from the Arctic Region Supercomputing Center and the University of Alaska Fairbanks.

5 More Information

5.1 Editor

Christopher Howard mailto:cmhoward2@alaska.edu

5.2 Publication Schedule

The newsletter is usually released on the third Wednesday of each month.

5.4 Archived Newsletters

5.5 Questions or Comments

mailto:owner-hpc_users@arsc.edu

Need advice? Submit a question about HPC or ARSC software, and we will feature it in a Q&A section in the newsletter.

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