ARSC HPC Users' Newsletter Number 426 2013-10-16

The Arctic Region Supercomputing Center Users' Newsletter provides a platform for discourse relevant to users of high performance computing systems. Topics include: programming, commands, tools, applications, and more.

Please send items, ideas, announcements, etc. to owner-hpc_users@arsc.edu.

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Intel Compilers On Pacman

ARSC's "pacman" supercomputer now has the Intel compiler collection available for general use. This provides an alternative to GNU and Portland Group compilers.

To make use of the Intel compilers, "module load PrgEnv-intel". You can then use mpicc, mpif90 and similar commands for parallel programs. Or, utilize ifort (Fortran), icc (C) and icpc (C++). The Intel Math Kernel Library is utilized automatically by these compilers. NetCDF and several other utilities are pre-compiled for your use.

Software Builds With Easybuild

Did you ever have trouble getting the best compiler options for building a high performance computing application from source code? Or, to figure out the needed dependencies?

Here is a project led by our colleagues at CERN that might help.

ScholarWorks@UA Launches

Bella Karr Gerlich, Dean of Libraries at UAF

ScholarWorks@UA (https://scholarworks.alaska.edu) is an institutional, state-wide institutional repository developed and implemented by a team comprised of at Rasmuson Library and ARSC. Using a free software package called DSpace, ARSC staff developed the underlying architecture, search and storage capabilities for ScholarWorks to the specification of Rasmuson Library staff, who were responsible for process, preservation, policies and interface design. An advisory board including representation from the three main UA campuses provided oversight, input and approval for the final product and policies.

Purposefully intuitive, ScholarWorks is designed to allow for self-publishing (within guidelines established) and encourages development of communities by users as needed, with the Library responsible for oversight, training, preservation and migration. ARSC provides storage and explores with Library staff ongoing improvements in search capabilities and potential integrations with other databases and data sets.

The ScholarWorks@UA team is committed to the continued accessibility and usability of our collections, and to preserve contributed materials using a variety of industry-standard techniques and best practices for digital preservation. Certain formats make this process easier, and to that end, we have a three-tiered support policy, which are detailed here:

Officially launched in September of 2013, ScholarWorks has experienced a 154.57% growth rate since its initial trial period began 11 months earlier, increasing it's cataloged items from 427 to 1087. Both ARSC and Library team members continue to work together to anticipate future growth rate, demands for training and promotion of the resource; in addition to encouraging scholarly communication amongst faculty, researchers and students, ScholarWorks provides the ability for meeting compliance for publishing research as required by funding agencies, while also enabling embargoes for time-senstitive materials and patent pending discoveries. With select publications and programs represented such as Honors, Theses & Dissertations, Undergraduate Research Posters, BOR Minutes, archives and all University Publications, an expectation of 75% - 100% growth rate increase each subsequent year may be realized. Using keyword searching and OCR capabilities, ScholarWorks will bring historical materials and cutting edge publications together to spark imaginations and new discoveries.

Training has occurred for UAF, UAA and UAS Library Staff for inputting data, creating metadata and scanning. Processes have been developed and implemented for scanning of materials, transferring of previously digitized items and born digital collections.

Quick-Tip Q & A

Last time, we asked:

Q: I noticed the ARSC Cray, called "fish," comes with NVIDIA general-purpose graphics processing units (GPUs). What has been the experience of ARSC users, in using GPUs?

A: No answers received. It seems the GPUs are not yet widely utilized on fish, other than for some small-scale testing.

Here's a new question to ponder, related to our new Intel compiler announcement:

Q: What techniques do you use with compilers, and what would you recommend for new users of high performance computing resources? Do you experiment with different compiler options, or do you prefer to make simple choices (such as -O2 for optimization)? Do you find that optimizations sometimes result in lower performance, or numerical instability, or other problems?

[[ Answers, Questions, and Tips Graciously Accepted. Email them to
owner-hpc_users@arsc.edu ]]


About ARSC

The Arctic Region Supercomputing Center (ARSC) provides research and high performance computing, large-scale storage, and related services to the students, faculty and staff of the University of Alaska.

Editor

Greg Newby, ARSC Director, gbnewby@alaska.edu, 907-450-8663

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Monthly, on approximately the third Wednesday.

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