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User Mailing

ICHEC mail #5

Posted: 2005-10-07

Dear ICHEC users,


1. ICHEC courses
2. Software packages now available at ICHEC
3. New debugging tool: DDT
4. Updated scheduling policies
5. Charging mechanism / requesting additional resources
6. Development queues on walton / interactive use
7. 50 project milestone

1 - ICHEC courses

We are glad to announce that the first ICHEC courses will take place on 25th, 26th and 27th October at University College Dublin (UCD). Registration is free but essential as places are limited and will be allocated on a first come first served basis. So register early to avoid disappointment.

See http://www.ichec.ie/news/1128520772 for further information and access to the registration form.

Courses will be organised at UCC Cork and NUI,Galway in November, and a second series of courses may be organised in Dublin in early December if demand is sufficient.

These courses will consist in a general introduction to High-Performance Computing on Day 1 and an introduction to the Message Passing Interface (MPI) on Day 2 and 3.

2 - Software packages now available at ICHEC

We would like to remind you that a number of packages are now available on hamilton and walton. These include well-known commercial packages such as Gaussian and MSC.Marc. The full list can be obtained from http://www.ichec.ie/software.

Note that many of these packages have licensing terms which prevent us from opening access to all users by default (some are conditional on signing a sub-license agreement, or confirming that you have read and understood the terms of the licenses such as using standard acknowledgements in publications). We have therefore restricted access via a UNIX group mechanism.

Please contact the ICHEC helpdesk at https://www.ichec.ie/helpdesk/ to be added to the relevant group(s).

3 - New debugging tool: DDT

We have recently acquired a floating license for Allinea's DDT (Distributed Debugging Tool - see www.allinea.com) on hamilton and walton. This debugger offers powerful features (such as memory debugging,visualising data in 3D with a multi-dimensional array viewer, etc.) all available through an intuitive GUI. DDT supports all mainstream languages (f90/f95 C/C++) as well as parallel libraries (MPI and OpenMP).

DDT can be found at /opt/packages/ddt-1.9.1b on both systems. We are currently updating our documentation to include a "Getting started" guide on debugging with DDT.

4 - Updated scheduling policies

We have recently modified our scheduling policies to allow a better utilisation of our resources. Changes are as follows:

On Hamilton:

a/ Production region increased from 16 CPUs up to 20 CPUs (and obviously development region down from 16 CPUs to only 12 CPUs).

b/ So-called "week-end queues" have been deleted as their usage was non-existent.

On Walton:

a/ The minimum number of CPUs available for the development region has been brought down to only 1 node (2 CPUs) to allow pre- post-processing jobs. Serial production runs should *not* be submitted to walton unless they are grouped within a task farm (minimum number of CPUs: 8).

b/ So-called "week-end queues" have been deleted as their usage was non-existent.

5 - Charging mechanism / requesting additional resources

We would like to remind you that accounting is not currently in operation on our systems. In other words current usage is "free for all". An accounting software will be deployed and configured in late October / early November. However, we keep logs of all jobs and will produce a detailed analysis of the utilisation profile to our funding agency.

Once the accounting software is in place, PI may request additional resources without the need to re-submit a new proposal. Such requests must however be made in writing, through the ICHEC helpdesk.

6 - Development queues on walton / interactive use

Many users have requested further information on how to use the development queues interactively on walton. Indeed, parallel jobs must be run with "mpiexec", which can only be started through PBS with "qsub". However, PBS can be used in interactive mode using the -I flag, for instance:

qsub -I -l walltime=0:05:00,nodes=4:ppn=2 -d=`pwd`

will start a shell to run an interactive parallel job on 8 CPUs. Once you are on the prompt, simply start your application in the usual manner, e.g.:

mpiexec ./hello-mpi.exe

will start my application "hello-mpi.exe" on the 8 CPUs reserved earlier. Once you have finished using your application, simply type "exit" to deallocate the resources you have obtained through the call to qsub.

As the queues on walton are filling up quickly, we would strongly encourage you to make an accurate description of your requirements (e.g., in terms of maximum runtime) rather than systematically specifying the maximum allowed runtime time. More specifically, many jobs currently submitted as "production" could be run in the "night" queues, which would result in a better utilisation of our resources and improved turn around time for your application.

7- 50 project milestone

We are proud to announce that we have just reached a new milestone with our 50th project being granted access to hamilton/walton. Further information about current research projects can be found at http://www.ichec.ie/research

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