HECToRNews 8, March 2010

Welcome to the HECToR newsletter.


For the previous issues please see here.

Training Course Timetable

The current schedule is below:

These training courses run by NAG are provided free of charge to HECToR users and UK academics whose work is covered by the remit of one of the participating research councils (EPSRC, NERC and BBSRC).

For more information on HECToR training, including the most up to date schedule, please see here, or contact hector.training@nag.co.uk

Follow the HECToR CSE Team on Twitter

Regular updates on the HECToR CSE service including training and dCSE information are now available from the NAG HECToR CSE Team on Twitter by following hectorcse.

HECToR Phase2B Upgrade

Later on this year HECToR will be upgraded to an XT6 (or 'Baker') system giving the user 24 processing cores on each node. An early user service will be available around April but the XT4 will continue to provide the main service at this stage.

Further details of the upgrade will be confirmed nearer the time. The transition to 24 cores is an exciting prospect and if a user suspects that their code may need performance investigation prior to the upgrade, then they are encouraged to seek the help of the NAG CSE team by contacting the HECToR helpdesk. Help and advice can then be given on how the code might be able to get full benefit from the hardware upgrade.

X2 Access and Charging

Please be advised that charging on the 128 core vector machine, the X2 will remain suspended for another year. Any new or current HECToR PI wishing to the use the X2 should submit a Class 2 technical assessment form to the Helpdesk. This form should clearly state the project details. Please note that it is not necessary to calculate an AU requirement and this open access is not restricted to EPSRC users. All new X2 HECToR users will be required to attend a specific X2 training course

For more information on the training course in using the X2 please see the X2 course description.

HECToR Direct Access

A reminder that the closing date for the next round of this mode of access is the 27th May. EPSRC are piloting a new access class for the HECToR service called 'Direct Access' (Class 1B) where users can request significant amounts ( i.e. greater than 1,000,000 AUs ) of computing resource only. However, for this current round the resources must be used from the 17th July and be used up within a period of up to six months from this date. The Direct Access mechanism will provide successful applicants with discretionary access to the HECToR system in order to provide resource to cover activities such as:

  • Bridging access between grant applications,
  • Resource to trial application developments at scale,
  • Provide preliminary results in aid of grant applications via Responsive Mode or to a Call for Proposals;

The proposals are assessed by a Resource Allocation Panel (RAP) who will next meet in June. The deadline for the subsequent round of applications will be the 21st September 2010. Full details are available online here.

HECToR Access Tool

An online tool to help users apply for access to the HECToR facility has recently been designed by EPCC. This will help users apply for access by guiding them through a series of simple questions.

To try the new HECToR Access Tool please see here.

CLE 2.2 and Dynamic Shared Objects

The current version of the Cray Linux Environment (CLE) 2.1 is scheduled to be updated with CLE 2.2. This OS upgrade is currently planned to take place on April 7th but this will be confirmed nearer the date.

Please note that CLE 2.2 will enable the support of dynamic shared objects (DSOs) on HECToR. DSO libraries allow for use of multiple programs that require the same segment of memory address space to be used during linking and compiling. HECToR will then be able to run many previously unsupported applications, and it will also make the installation of many other packages much easier.

Using DSOs may reduce executable size and improve optimization of system resources as only one image of the object is required per node. Also, when shared libraries are changed or upgraded, users will not need to recompile dependent applications. To compile your code for using dynamic linking at runtime use the -dynamic option in the compilation e.g.

ftn -dynamic test_dyn.f90 -o test_dyn

Alternatively set the environment variable export XTPE_LINK_TYPE=dynamic instead of the -dynamic option.

However note that this does not supersede the current static method, and all makefiles and related installation procedures should continue to work after the upgrade.

Programming Environment issues

HECToR Archive Solution

A data archiving mechanism is now available on HECToR and users are encouraged to back up their work with this facility. The archiver is accessed from the user's work file system (/work) and can be used either by placing files in a pre-defined directory for automatic nightly archiving or via a direct command. Instructions on how to use the archive are here.

Any PIs who require access to the archive should contact the HECToR Helpdesk . All users are reminded that data on /work is not backed up and is therefore at risk. If you have large volumes of data residing on /work we would strongly recommend that this is now moved to the archive where multiple copies can be maintained. Data can be moved to and from the archive at any time.

Changes to Default Modules

Please note that the following module updates have recently been carried out.

Gcc 4.2.4 -> 4.4.2
Pathscale 3.1 -> 3.2
Java 1.6.0_13 -> 1.6.0_17
Pgi 8.0.2 -> 9.0.4
Xt-libsci 10.3.2 -> 10.4.1
Xt-mpt 3.1.0 -> 3.5.1

The previous versions will all remain on HECToR but will no longer be the default and will need to be specified if they are required. E.g.

module swap xt-mpt/3.5.1 xt-mpt/3.1.0

FFTW3 No Longer Loaded by Default

Please note that in the recent updates to the default modules, the default version of Xt-libsci is now 10.4.1 rather than 10.3.2. This newer version does not automatically load fftw3 as part of Xt-libsc 10.4.1. Therefore the user should invoke

module load fftw/3.1.1


module load fftw/

For version 3.1.1 or of fftw respectively. Please note that users cannot have both modules loaded at once as there is a conflict between them.

Alternatively, the user can revert back to Xt-libsci 10.3.2 with

module swap xt-libsci/10.4.1 xt-libsci/10.3.2


Cray Compiler Environment

The Cray x86 compiler environment 7.1.6 has now been installed on HECToR for permanent usage. This comes with full support for Unified Parallel C (UPC) and Co-Array Fortran (CAF) as well as Fortran and C compilers.

Use from a default login with module swap PrgEnv-pgi PrgEnv-cray

For more information on the Cray Fortran compiler please see here.

A useful tip for users of Cray's Fortran compiler has been suggested by Dr Ning Li of the NAG CSE team : If you are developing software with the Cray Fortran compiler on HECToR, there is a minor problem with MPI - the MPT library 3.3.0 and after was built using a later version of the compiler so you cannot have 'use MPI' in your application. Instead, you should either switch back to an older version of MPT or "include 'mpif.h'" in your code.


Git is a fast version control system focused on effectivity and real-world usability for large projects. Git 1.6.6 has now been installed for use on HECToR. If you are a Git user you may access the Git module with the following command

module load git

Distributed Support

This is also referred to as dCSE support and funding is available to provide extended help with improving the performance of existing HECToR codes and developing high-performance algorithmic improvements for them. Support is also available to port new codes from other systems to HECToR. Awards to support proposed projects are assessed via regular independent panel reviews.

There are thirty current projects that are underway and four new projects are scheduled to begin during 2010. The reports from the completed dCSE projects are available here along with examples of dCSE success stories arising from application codes whose performance has been dramatically improved through dCSE support. A new report is now available on a recently completed project which has improved the performance of the aerosol simulation code GLOMAP MODE MPI. This dCSE work was performed by an HPC expert from the NAG CSE team.

Further information on the dCSE support service can be found here. The next application deadline is the 21st June 2010. Applicants are advised to contact hector-helpdesk@nag.co.uk with a brief description of their proposed work well before the application deadline. All applicants for the current round will be informed of the outcome of their proposals late July 2010. NAG staff are available to visit institutions to talk about this service. If you are interested in a visit please contact hector-helpdesk@nag.co.uk