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User Mailing

ICHEC Mail #51


Posted: 2013-12-23

Dear ICHEC users,

Contents:
1. Christmas Holiday Arrangements
2. Accounting on Fionn
3. Fionn Class A/B Proposal Template
4. Benchmarking on Fionn
5. Access to data on Stokes
6. ICHEC @ BT Young Scientist & Technology Exhibition 2014
7. Fionn Launch Event
8. PRACE DECI-12 (Tier-1) Call announcement

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1 Christmas Holiday Arrangements
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Over the holiday period ICHEC staff will only be providing emergency cover
only, between the following two dates (inclusive):

Saturday, 21st December 2013 to Wednesday, 1st January 2014

If users encounter any problems during this period they can submit a Helpdesk
query by logging into http://helpdesk.ichec.ie or email support@ichec.ie.
It will be dealt with by a member of staff as soon as possible. We would advise
users to consult the updated documentation and migration guide as many of the
issues may have already been addressed:

http://www.ichec.ie/infrastructure/fionn
http://www.ichec.ie/support/documentation/
http://www.ichec.ie/support/ichec-fionn-migration-guide.pdf

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2 Accounting on Fionn
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Accounting on Fionn will be enabled on 1/1/2014. The remaining project balances
from Stokes will be transferred to Fionn. The balances of Class C & B
projects will be increased by a factor of 2x & 1.5x respectively.

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3 Fionn Class A/B Proposal Template
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We would encourage users to apply for resources as accounting is turned on in
the New Year. Users planning on submitting class A or B applications should be
advised that new Fionn templates are now available in a range of formats: docx,
tex, and pages. They can be download from the following links:

http://s.ichec.ie/classAB_proposaltemplate
http://s.ichec.ie/classAB_proposaltemplate_pages
http://s.ichec.ie/classAB_proposaltemplate_latex

To avoid delays we recommend that users follow these guidelines when writing
new proposals. The template provides examples of application scaling graphs,
a requested core hour breakdown table and workplan graphics that should be
used. It should be noted that the different partitions on Fionn are charged
to your project balances differently. Currently, a factor of 2.5 for the Fat or
Shared Memory partition and 1.25 for the Hybrid or Accelerator partition. Note,
access to these partitions is on a project basis and full justification should
be provided during the application process.

If you have any questions ahead of submitting a class A or B application
please contact our user support activity leader, Dr. Martin Peters
(martin.peters@ichec.ie) to discuss your proposal ahead of submission.

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4 Benchmarking on Fionn
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Along with many other applications NAMD, GROMACS, LAMMPS and OpenFoam have
recently been installed on Fionn.

Benchmarking graphs can be found on the following pages:
http://www.ichec.ie/infrastructure/software/NAMD
http://www.ichec.ie/infrastructure/software/LAMMPS
http://www.ichec.ie/infrastructure/software/GROMACS
http://www.ichec.ie/infrastructure/software/OpenFOAM

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5 Access to data on Stokes
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Access to Stokes will cease on Sunday, 12th January 2014. We strongly advise
users to move their data to Fionn and back it up locally. We remind you that as
with Stokes project (or work) directories on Fionn are NOT backed up by ICHEC.

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6 ICHEC @ BT Young Scientist & Technology Exhibition 2014
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ICHEC is proud to announce that we will again exhibit at the BT Young Scientist
& Technology Exhibition (BTYSTE - www.btyoungscientist.ie/), its 50th
anniversary. A preview of our stand can be found here:

http://s.ichec.ie/BTYSTE14

We will showcase the uses of supercomputing to primary and secondary level
students. Similar to our stand at last year's event, ICHEC will display a fully
configured live mini supercomputer built from the Raspberry Pi boards and
give presentations of 3D scientific visualisations of climate and weather
data. This year we will reveal a new game called PhiDoku where students will
complete against the Intel Ivy Bridge processor and Intel Xeon Phi co-processor
to solve Sudoku puzzles. The fastest students will be in with a chance to win
some great prizes.

Please stop by the stand (#5) in the World of Science & Technology Hall. We look
forward to seeing you there!

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7 Fionn Launch Event
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On the 13th November Minister Seán Sherlock TD, Minister for Research and
Innovation announced Ireland's latest supercomputer called Fionn at the Dunsink
Observatory. The name, chosen by Oscar O'Donoghue, a student from DCU CoderDojo,
stems from Fionnachtana (Irish for Discovery) and Fionn Mac Cumhaill. It aptly
reflects the size of the new machine and the new R&D that it will enable.

The inaugural ICHEC coding competition winner was also announced. The challenge
was set to take image processing code and make it run in parallel to take
advantage of modern multicore processors. The Minister presented the winning
prize to Maciej Goszczycki who met the challenge and showed great skill in
completing it. Maciej regularly attends the TCD Science Gallery CoderDojo in
Dublin. Images from the event can be seen here:

http://www.ichec.ie/outreach/nameourcomputer

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8 PRACE DECI-12 (Tier-1) Call announcement
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The DECI-12 call for PRACE Tier-1 resources is now open:

http://www.prace-ri.eu/DECI-12-Call

This Call invites proposals for project access to Tier-1 resources, via DECI,
the Distributed European Computing Initiative, providing single project
cross-national access to national (Tier-1) HPC-resources.

The DECI-12 call is supported and managed by the PRACE-3IP project in addition
to the Parties participating in the Non-binding memorandum of understanding
(MoU) on interim Tier-1 exchange programme. PRACE-3IP receives EC funding
(RI-312763) and enhances the implementation of the HPC Research Infrastructure
PRACE. PRACE-3IP is responsible for the Tier-1 access through the DECI calls
until its end. After the end of the PRACE-3IP project, Tier-1 access and
reduced support for users is offered in kind by the Parties of the Tier-1
exchange programme MoU.

o Opening date: 18th December 2013, 12:00 CET
o Closing date: 20th January 2014, 17:00 CET
o Allocation start date: 1st May, 2014
o Allocation period: 1 year for Project Access
o Type of access: DECI (Tier-1)

Tier-1 machines available: Cray XE/XC, and a range of large clusters including
GPU resources made available from Cyprus, Finland, Hungary, Ireland, Italy,
Poland, Serbia, Sweden, Switzerland, the Czech Republic, the Netherlands,
the United Kingdom and Turkey.

DECI provides single project cross-national access to European Tier-1 resources
(national systems). Access will be awarded for a period of 12 months, beginning
1st May 2014. Resources are available on the following architectures: Cray XE6,
Cray XC30, IBM Blue Gene/Q, Intel clusters (various processor and memory
configurations) and hybrid systems (clusters with GPGPU accelerators).
Applicants need not specify a particular machine or architecture, but if they
do, we will endeavour to take these preferences into account.

Scope of the Tier-1 call and criteria for access

DECI enables European researchers to obtain access to the most powerful
national (Tier-1) computing resources in Europe regardless of their country of
origin or employment and to enhance the impact of European science and
technology at the highest level. Proposals must deal with complex, demanding,
innovative simulations that would not be possible without Tier-1 access. Please
note that, in addition to offering access to computing resources,
applications-enabling and porting, assistance from experts at the leading
European HPC centres is offered (on request and depending on availability) to
enable projects to be run on the most appropriate Tier-1 platforms in PRACE.
Note that after the end of the PRACE-3IP project limited support will be
provided on a best effort basis from parties of the Tier-1 resource exchange MoU.

Eligibility for Tier-1

Proposals from academia and industry are eligible, as long as the project
leader is undertaking non-proprietary research in a European country (European
Union, candidates, associated countries and PRACE member countries). Project
leaders will typically be employed in research organisations (academic or
industrial). Individual HPC centres may have further restrictions on who is
eligible to use the machines, e.g. due to US export rules. Further
information is available on request.

Tier-1 Computing Resources offered in this call

Cray Large Cray XE6 systems are available at SNIC-KTH (Sweden) and CSCS
(Switzerland). The largest of these machines has a peak performance of 400
TeraFlops and a total of 47,872 cores. At CSC (Finland) a 11,776-core (Sandy
Bridge) machine and at EPCC (UK) a 72,192-core (Ivy Bridge) machine, both with
XC30 architectures are available. Around 50% of the total DECI resource
(equating to 38 million XE6 or XC30 compute core hours) is available on Cray
architecture. IBM Blue Gene/Q access is available at the STFC Hartree Centre
and this system has a Linpack performance of just over one Pflop/s with 98,304
cores. Around 10% of the total DECI resource (equating to 25 million Blue
Gene/Q compute core hours) is available on this architecture. Clusters –
clusters are available CaSToRC (Cyprus, Westmere cluster plus GPGPU), CINECA
(Italy, Westmere cluster plus GPGPU), CYFRONET (Intel Xeon), ICHEC (Ireland,
x86 Cluster with shared memory and accelerator partitions), ICM (Poland,
IBM Power 7), IPB (Serbia, Intel Sandy Bridge plus GPGPU cluster), NIIFI
(Hungary, HP Magny-Cours Cluster), PSNC (Poland, SGI SMP cluster), SURFsara
(the Netherlands, Bullx Ivy Bridge Cluster), UHEM (Turkey, Nehalem cluster),
VSB-TUO (Bull Intel Xeon) and WCSS (Poland, Intel Xeon). Around 40% of the
total DECI resource (equating to 25 million cluster compute core hours) is
available on this class of architecture.

How to apply to DECI-12

Applicants should apply to DECI via our submission tool:

https://deci-peer-review.cines.fr/login.

The DECI support team is available to answer questions by email while the call
is open and applicants are encouraged to contact us if they have any questions.
Late applications cannot be accepted. In the case of technical difficulties,
the decision of the DECI Peer Review Team as to whether an application can be
accepted is final. Applicants are advised to submit as early as possible before
the deadline. The deadline for submission of proposals for Tier-1 systems is
20th January, 2014, at 17:00 CET.

Process details and deadlines for Tier-1 DECI proposals

The call will close at 17:00 CET on the 20th January 2014. The DECI Peer Review
Team will perform an administrative validation check. In case of administrative
inaccuracies the applicant will receive an email asking for administrative
details. The deadline for the applicant to provide such details is 27th January
2014 at 17:00 CET. Anything received after 27th January 2014 at 17:00 CET will
NOT be accepted nor considered in the review process. Between 20th January 2014
and 27th January 2014 the DECI Peer Review Team will accept modified proposals
ONLY when these supply further details in reply to requests from PRACE. Several
submissions of the same proposal before the submission deadline are permitted,
but only the last one will be considered. By 17:00 CET on 27th January 2014,
all applicants will receive confirmation that their proposals have been
correctly submitted and that they meet the eligibility criteria. From 27th
January the projects will be technically and scientifically peer reviewed. The
DECI proposals will be peer-reviewed by national peer-review panels. The
applicants will be informed of the review results in early April 2014.

Terminology

Core hour: Elapsed time (wall clock time) in which a core is allocated to the
user.

Timetable for DECI 12th Call for Project Access proposals

o Opening date: 18th December, 2013, 12:00
o Closing date: 20th January, 2014, 17:00 CET
o Anticipated allocation decisions: Early April 2014
o Allocation start date of awarded proposals: 1st May 2014
o Allocation end date of award: 30th April 2015

Contacts

For any queries related to applications or eligibility please contact:
deci-support@prace-ri.eu

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.

About PRACE

The Partnership for Advanced Computing in Europe (PRACE) is an international
non-profit association with its seat in Brussels. The PRACE Research
Infrastructure provides a persistent world-class high performance computing
service for scientists and researchers from academia and industry in Europe.
The computer systems and their operations accessible through PRACE are
provided by 4 PRACE members (BSC representing Spain, CINECA representing
Italy, GCS representing Germany and GENCI representing France). The
Implementation Phase of PRACE receives funding from the EU’s Seventh Framework
Programme (FP7/2007-2013) under grant agreements RI-261557, RI-283493 and
RI-312763. For more information, see:
http://www.prace-ri.eu

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

If you would like to stay up to date with all activities at ICHEC please
follow our twitter or facebook accounts:

http://twitter.com/ichec
http://facebook.com/ichec

Finally, the ICHEC Team would like to take this opportunity to thank you for
your support during 2013, the year we launched Fionn and quadrupled the compute
power available to researchers in Ireland plus giving access to some exciting
new technologies. We would also like to wish you a happy Christmas and a
prosperous New Year.

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Dr. Martin Peters
User support Activity Leader

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