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User Mailing

ICHEC Mail #46


Posted: 2012-10-19

Dear ICHEC users,

Contents:
1. External Access Programmes
2. PRACE Winter School in Dublin (Jan/Feb 2013)
3. Default Compiler/Library Update
4. HPCWire Readers' Choice Awards
5. Stoney GPGPU Partition
6. ISC 2012
7. Software Carpentry in the Cloud Bootcamp in Association with AWS
8. Reporting Publications
9. Social Media

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1 External Access Programmes (PRACE 6th & DECI-10 Calls)
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Exploiting the possibilities of external access programmes such as PRACE (Tier-0)
and DECI (Tier-1) are an opportunity to get access to some of the world's largest
HPC systems. ICHEC has assisted numerous users in the preparation of applications
for such programmes and will be happy to help should you be interested. It is our
policy to offer assistance to users who secure time outside Ireland as we do on
our own systems in so far as is possible.

The European PRACE (http://prace-ri.eu) organisation has opened the 6th Call
for Proposals on the 18th September 2012. PRACE encourages researchers from
across Europe to apply for access to its world class resources for research
with potential high European and international impact. PRACE resources are
available through three forms of access:

* Multi-year Access,
* Project Access and
* Preparatory Access.

Multi-year Access is available to major European projects or infrastructures
that can benefit from PRACE resources and for which Project Access is not
appropriate. Project Access is intended for individual researchers and
research groups including multi-national research groups and has a one year
duration. Calls for Proposals for Project Access are issued twice yearly.
Preparatory Access is intended for resource use required to prepare proposals
for Project Access. Applications for Preparatory Access are accepted at any
time.

The Call for Proposals for 6th PRACE Project Access (Tier-0) is now open.
Dates for this call:

* Opening date: 18th September 2012
* Closing date: 23rd October 2012, 12:00 (noon) CET
* Response of applicants to reviews: January 11-18th, 2013
* Anticipated allocation decisions: 3rd week of February 2013
* Allocation start date of awarded proposals: 4th March 2013
* Allocation end date of award: 3rd March 2014

For Details see: http://www.prace-project.eu/Call-Announcements

The 10th DECI Call for proposals will open in early November. The description of
the available resources can be found here: http://www.prace-ri.eu/Tier-1-Resources

Dates for the call:
* Opening date: 2nd November 2012
* Closing date: 14th December 2012

We would invite PIs interested in these calls to notify our user support activity
leader, Dr. Martin Peters (martin.peters@ichec.ie) in good time.

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2 PRACE Winter School in Dublin (Jan/Feb 2013)
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ICHEC would like to announce that Dublin will be hosting the PRACE Winter school
in early 2013. The school will run over 4-5 days covering topics such as parallel
programming and scientific visualisation. We would invite users (students/post-docs/PIs)
interested in this school to notify our training coordinator Dr. Simon Wong
(training@ichec.ie).

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3 Default Compiler/Libraries Update
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On the 5th November the default Intel compilers, math and mpi libraries will be
updated by our systems teams on Stokes to ensure users are taking advantage of
the latest releases that include various bug fixes and performance improvements.

The following changes will be made:
* intel-cc/2011.1.107 -> intel-cc/2013.0.079
* intel-fc/2011.1.107 -> intel-fc/2013.0.079
* intel-mkl/10.2.6.038 -> intel-mkl/11.0.0.079
* intel-mpi/4.0.1.007 -> intel-mpi/4.1.0.024

Please recompile your code or update your environment or PBS submit scripts
where necessary to continue using the old default versions if desired.

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4 HPCWire Readers' Choice Awards
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ICHEC is delighted to announce that a project led by two of ICHEC's staff, Mr.
Gilles Civario and Mr. Renato Miceli, has been nominated among only five
organisations worldwide for the 'HPCwire Reader's Choice Awards 2012' under the
'Best use of HPC in financial services' category. HPCwire (http://www.HPCwire.com)
is the most widely recognised news and information portal covering the entire
spectrum of high performance computing. The winners of the Readers' and Editors'
Choice awards will be formally announced live during the SC12 Conference, taking
place November 12 - 19, 2012 in Salt Lake City, Utah.

The project, 'Real-Time Risk Simulation: The GPU Revolution In Profit Margin
Analysis', led by Gilles and Renato, generated huge interest from the Financial
Risk community at this year's GPU Technology Conference (GTC 2012) held in San
Jose, California, where both Gilles and Renato were invited to present their
work. More information plus slides and video of their presentation are
available on our web site:

* http://www.ichec.ie/news/1347977723
* http://www.ichec.ie/conferences/GTC12

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5 Stoney GPGPU Partition
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As you may be aware the Stoney (http://www.ichec.ie/infrastructure/stoney)
machine was upgraded earlier this year. 24 compute nodes are now reserved for
GPGPU computing. These nodes have two NVIDIA Tesla M2090 cards installed, with
each card providing 512 GPU cores, 6GB of local GDDR5 memory and a theoretical
peak double-precision performance of 665GFlops. The current list of accelerated
software packages installed include:

* VASP
* AMBER
* NAMD
* LAMMPS
* DL_POLY
* GROMACS
* ABAQUS

The benchmarking results of AMBER and DL_POLY and can be seen here:

* http://www.ichec.ie/infrastructure/software/Amber
* http://www.ichec.ie/infrastructure/software/DL_POLY

If there is an accelerated package that is not on our list please get in touch
with us.

To apply for time on this accelerated partition of Stoney will require users to
submit a GPGPU class B application:
* http://www.ichec.ie/services/full_national_service

The GPGPU Class B application form can be found here:
* https://www.ichec.ie/gpuproject/apply

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6 ISC 2012
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The 27th International Supercomputing Conference, ISC'12, was held from June
18th to June 21st in Hamburg, Germany (http://isc-events.com/isc12/). It
featured over 300 world-class speakers and 175 exhibitors discussing every aspect
of supercomputing, networking and storage.

This year ICHEC was again an exhibitor, promoting its work and the work of our
users to the international community. ICHEC in association with Prof. Gary
McGuire (UCD), Bastian Tugemann and SGI were one of the first groups to
present work on the latest Intel coprocessor (Intel Xeon Phi) based on the MIC
Architecture.

The aim of the demo was to showcase the Xeon Phi's capabilities for integer-based
computations. For this purpose, the code Gary McGuire's team developed for their
Sudoku 16 clues grand challenge was adapted for searching 17 clues grids, then
ported and hand tuned for both Intel Sandy Bridge and Xeon Phi architectures.

* http://www.nature.com/news/mathematician-claims-breakthrough-in-sudoku-puzzle-1.9751

Over the duration of the exhibition, both versions were run in parallel over
the same dataset, allowing for a direct performance comparison between the two
architectures. This was actually the only place in the world where performance
figures for Xeon Phi were publicly disclosed.

More information about this conference is available:
* http://www.ichec.ie/conferences/ISC12

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7 Software Carpentry in the Cloud Bootcamp in Association with AWS
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ICHEC is pleased the announce the successful running of the first Software
Carpentry in the Cloud Bootcamp in association with Amazon Web Services. 30
participants from across Ireland attended the three day (1st-3rd Sept, 2012)
bootcamp where presentations and hands-on sessions were held by ICHEC and
AWS staff. Topics including general software development best practices, cloud
computing, test-driven development, code management, and NoSQL. The following
AWS services EC2, S3, EBS, DynamoDB, SQS, SNS, and EMR were also introduced.
More details can be found here:
* http://www.ichec.ie/education_training/software_carpentry_cloud_bootcamp
* http://www.ichec.ie/news/1346777582

We would invite users interested in attending a similar bootcamp in the future
to notify our training coordinator Dr. Simon Wong (training@ichec.ie).

A full list of courses can be found on the ICHEC site:
* http://www.ichec.ie/education_training/

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8 Reporting Publications
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If you have acknowledged ICHEC in a publication as per our request in our AUP,
we ask that you please let us know. Following recent changes to the Science
Council review procedures, publications resulting from previous work which
used ICHEC resources will form part of the material taken into account.

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9 Social Media
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If you would like to stay up to date with all activities at ICHEC please follow
our twitter account:
* http://twitter.com/ichec

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Previous User Mailings can be found at http://www.ichec.ie/newsletters

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Dr. Martin Peters
User support Activity Leader

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