The HECToR Service is now closed and has been superceded by ARCHER.

Welcome to HECToRNews 3, February 2009

Featuring:

Introduction

This is the third Newsletter for HECToR users from the Computational Science and Engineering support (CSE) team of NAG Ltd. The HECToR newsletter intends to keep users updated with useful information on the National Supercomputing Service. You can also read the previous issues.

In this issue we have information on HECToR related training courses, general updates regarding the HECToR programming environment, support issues and information on the distributed support service.

Training (including Fortran 95)

The High Performance Computing (HPC) and HECToR training courses run by NAG Ltd. are provided free of charge to HECToR users and UK academics whose work is funded by one of the participating research councils (EPSRC, NERC and BBSRC). Over the coming months, the following courses are scheduled:

  • February 24-26, NAG Manchester - Fortran 95
  • March 23-25, University of Bristol - Parallel Programming with MPI
  • March 23-25, University of Southampton - Fortran 95
  • March 30 - April 1, University of Southampton - Parallel Programming with MPI
  • April 6-7, University of Southampton - OpenMP and Mixed-mode Programming
  • May 18-19, University of Cambridge - Introduction to Fortran 95
  • June 1-2, University of Cambridge - Introduction to MPI

The majority of the courses are aimed at HPC and HECToR. But, there is also training in scientific programming with the non-HPC Fortran 95 course. This is suitable for anyone who would like to learn the language from scratch or perhaps would like to update or build on their current knowledge. For more information on the course times and locations please see the training schedule or contact [Email address deleted]

Programming Environment Issues

Default Modules Update

During the HECToR maintenance session on Wednesday 4th March there will be an update to the modular software setup which will affect compilers, libraries and tools. There is a default version of each module which is automatically invoked unless the user specifies otherwise.

The plan is to update the default versions of these components to newer versions. This will have no effect until you recompile your code, at which point the newer versions will be used automatically. For example, with xt-mpt the new default version will be 3.1.0, but you may revert back to the older version with 

    module swap xt-mpt/3.1.0 xt-mpt/3.0.0

however, we recommend that you use the default versions. For more information please see the Using the module environment section of the HECToR User Guide.

Details of the changes mentioning the software components affected are available on the HECToR website.

CLE2.1 Upgrade - mpt2.0 will no longer be available

Please be advised that the HECToR operating system will be upgraded to CLE2.1 on March 18 2009. As of 18 March, binaries compiled under mpt2.x will not run on HECToR. These will be blocked automatically.

Any such binaries will have to be recompiled against mpt3.x prior to 18 March. You can identify such binaries with the command: 

  find . -type f -a -perm -100 -a -exec grep 
       'rs64\.REL_2[a-zA-Z0-9/_.]*xt_allreduce.c' {} \; -print

We would also recommend that CLE2.0 compiled executables using mpt3.x are recompiled after the upgrade. This recompile is for performance reasons only.

Inaccurate Timings

When benchmarking their codes, some users have reported unexpected fluctuations in their timing results. These can be attributed to the state of resources that are unique to their particular login session. Some factors which may influence this might be the interconnect contention between nodes and the actual node placement. This issue was discussed at the HECToR User Group meeting last September and it was agreed that users could request a dedicated slot on HECToR which would be available straight after a planned maintenance session. To request a slot, contact the HECToR Helpdesk.

Pre-flight Mode Health Check

As with any high performance machine HECToR is susceptible to node failure. In order to check that you have not been assigned to any failed nodes you can use the node health checking routine in the Checking the health of compute nodes section of the HECToR User Guide. If the return value of the script is non zero this indicates a problem with the nodes you have been assigned, in which case you should not run any jobs but contact the helpdesk with the appropriate output files. The weblink shows example shell script text which can be included within a PBS script to call the node health checker and abort the job submission if there are any problems detected.

New Applications

  • The linear-scaling code for quantum-mechanical calculations based on density-functional theory, ONETEP is now available at version 2.2.16. The software can be loaded with: 
       
     module load onetep
    This will only be available to current ONETEP license holders who should their details to the HECToR Helpdesk for access to the code.
  • For users of NetCDF, the NCO package is a set of command-line utilities for performing various operations on NetCDF data storage files. This software package has been installed on HECToR as a module. Users can access them with: 
    
    module load NCO
    You may need to use the serial queue when running this to process files.
  • The parallel data visualisation tool ParaView has recently been installed on HECToR by the NAG CSE team. Currently, this is ParaView 3.4.0 and is available in batch mode using the pvbatch executable for running ParaView batch scripts. The client server mode where both the ParaView GUI and the ParaView server run on HECToR is also available. For more information on the software and how to use it on HECToR please see the ParaView section of the HECToR User Guide.

Distributed Support

This is also referred to as dCSE support. dCSE funding is available to provide extended help with improving the performance of existing HECToR codes and developing high-performance algorithmic improvements. Support is also available to port new codes from other systems to HECToR. Awards for proposed dCSE projects are assessed via an independent review panel. For more information, please see the dCSE Section.

At the last panel meeting eight projects were allocated funding:

  • Full parallelisation of a CFD code which uses a 3D compressible unsteady Navier-Stokes model for turbulent flows.
  • Implementing a 2D FFT to replace the current 1D method in a fully spectral CFD code.
  • Implementing hybrid MPI-OpenMP techniques in a finite difference/spectral CFD code and replacing the current 1D FFT method with a 2D decomposition.
  • Extending the scientific capabilities for HPC and implementing hybrid MPI-OpenMP to a time-dependent electron scattering code.
  • Porting a visualisation package to HECToR to enable the handling of large data sets.
  • Improving the I/O performance in a widely used molecular simulation package.
  • Installing and testing an open-source CFD toolbox on HECToR.
  • Implementing time-dependent density functional theory into a code which models materials at the atomic level.

There is a list of the current projects that are underway on the HECToR website.

The next application deadline is the 30 March 2009. Applicants will be informed of the outcome of their proposals early May. NAG staff are available to visit institutions to talk about this service. If you are interested in a visit please contact us at [Email address deleted].

HECToR Scientific Advisory Committee

The HECToR Scientific Advisory Committee (HSAC) exists to advise the service providers and Research Councils on the scientific direction of the service and the way that it is being run. If you have any concerns about the service or suggestions about how it may be improved then you can bring them to the attention of HSAC by contacting your user representative as follows:

  • EPSRC users: Ken Badcock, University of Liverpool (K.J.Badcock@liverpool.ac.uk)
  • NERC users: John Brodholt, UCL (j.brodholt@ucl.ac.uk)
  • BBSRC users: Charlie Laughton, Nottingham University (charles.laughton@nottingham.ac.uk)
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