ARSC HPC Users' Newsletter Number 427 2013-11-13

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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ARSC's New Extranet

In September's newsletter (#425), principal investigators (PIs) on ARSC's projects were reminded to use the Extranet to submit project renewal information. Thanks to everyone who renewed!

All ARSC users are invited to take a look at the Extranet:

This is a front-end to view information about your ARSC projects, news items, and resource utilization. More features will be added in the future. PIs can use the Extranet to request additional project resources, see utilization, and submit adjustments to project membership.

Send feedback or questions to the ARSC helpdesk. Special thanks go to the ARSC student assistants who have worked on the Extranet.

Purging Policy in Effect

ARSC is implementing automated purging of files from the center-wide filesystem ($CENTER). Please review the "Temporary Storage and Purging" storage policy section of the ARSC Web pages:

Modules Command Output Tip

Thanks to Constantine Khroulev for this tip on capturing output from the "modules" command. Here is the message he sent:

I have noticed a while ago that module system scripts use stderr to print all reports. (I realize that this is not ARSC's design decision, though.)

There might be a good reason to use stderr (and I'm not asking you to do anything), but this has always been a source of irritation for me. Every time I want to look up what versions of FFTW are available (for example), I have to type

module avail 2>&1 | grep fftw

instead of

module avail | grep fftw

So, I thought I'd share a trick I came up with: add the following lines to ~/.bashrc

mod () { module $@ 2>&1 }

Now I can run

mod avail | grep fftw

and get the result I expect.

Maybe someone will find this useful.
 

Quick-Tip Q & A

Last time, we asked:

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?

A: We received an answer from the providers of the Intel compiler suite, which is now available on the Pacman and Fish systems (use "module load PrgEnv-intel"). The Intel Math Kernel Library (MKL) is part of the Intel compiler suite on ARSC systems, and provides BLAS, LAPACK and other performance libraries.

The Intel® Math Kernel Library Link Line Advisor is a tool that helps determine library link options for different platforms. Find it here:

ARSC will be developing some online Knowledge Base guides for the Intel compiler suite. Find all our guides at:
 

Here's a new question that was submitted:

Q: The program I'm using output UNIX time stamps, which is great for being able to compare one time to another, but occasionally I want to know the real date and time.

e.g.
 

1370000000

corresponds to
 

Fri May 31 03:33:20 AKDT 2013

Currently I use a script to use do a conversion, but I would rather not have to copy the script from machine to machine. Is there a standard command line tool that will do this?
 

[[ 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

Publication Schedule

Monthly, on approximately the third Wednesday.

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