|
|
||||
|
Bulletin 156 - 2006 May 26
1. CSIRO HPSC staff changes CSIRO HPSC welcomes Dr Aaron McDonough, formerly with NEC, who has joined CSIRO HPSC to provide applications support. [ page top ] 2. HPCCC Seminars Please see http://www.hpccc.gov.au/seminars/ for information about future seminars.
10.00 Wed 31 May 2006
10.00 Wed 21 June 2006 It is planned to repeat the recent seminar on Subversion at CSIRO Aspendale soon. [ page top ] 3. Updated WWW - User Guides, photo, conference papers The HPCCC and HPSC User Guides have had major revisions and re-organisation, and are at http://www.hpccc.gov.au/hpccc/userguides/ and http://www.hpsc.csiro.au/userguides/ . Various articles of documentation developed by HPCCC and NEC/A have been linked into the revised guides and the userguide faq, some of which have been migrated from the Local Supplementary Information section of the NEC SX-6/TX7 User Manuals page: http://www.hpccc.gov.au/hpccc/userdocs/index_user.shtml . A new photo of HPCCC, HPSC and NEC staff appears at http://www.hpccc.gov.au/ . A paper from the recent NEC User Group conference by Mathis Rosenhauer of DKRZ entitled "Fine Grained Performance Measurement of Parallel Kernels using SX Hardware Counters" is available from http://www.hpccc.gov.au/hpccc/seminars/ under the heading " Conference Proceedings". Some papers from a recent SGI Computational Chemistry Workshop are available from http://intra.hpsc.csiro.au/user/links/ under the heading "Training Courses, Seminars, Conferences". [ page top ] 4. Documentation on the use of GFS on gale Gale users now have direct access to many of the SX-6/TX7 file systems through the use of uGFS. There are GFS filesystems mounted in /SX/bm with uGFS, but special i/o libraries are needed to access them. There are uGFS aware utilities in /SX/local/bin (sxcat, sxcp, sxtar, sxmv, ...) and a 'rungfs' command to enable other executables to pre-load appropriate libraries and become uGFS capable, e.g. rungfs myprog /SX/bm/data/myid/myfile > mylocalresult A guide to using uGFS on gale has been prepared by NEC, and is in the userguide faq: http://www.hpccc.gov.au/hpccc/userguides/faq/localguide.php#uGFS [ page top ] 5. NQSII qsub wrapper The HPCCC qsub wrapper script allows the use of warning time limits, but not warning memory limits for jobs. For example, #PBS -l cputim_job="80,50"works, but not #PBS -l memsz_job="450MB,500MB"- the latter results in the message "Request not queued.". [ page top ] 6. burnet - changing the OS on the compute nodes to sles9 - CHANGE On burnet, some nodes are currently only available to a 'test' queue. Some of these nodes have native 64-bit capability and are running a 64-bit version of sles9 which will allow compiling and running 64-bit executables. This may have significant performance improvements for some applications. 32-bit executables should still run fine. To run on the nodes with the new Configurations, jobs currently must be submitted to the queue "test". To direct jobs only to the i686 or x86_64 nodes add the qsub option "-q test -l arch=i686" or "-q test -l arch=x86_64". Some users have already run tests and no major problems have been reported so far. Feedback to hpchelp@csiro.au would be welcome, including information about changes in both correctness of results and changes in performance. On Tuesday 6th June, nodes with the new configuration will be made generally available. Then nodes will be progressively rebuilt for the new configuration as the become idle. If you can run some tests first, you may avoid an inconvenient surprise. During the period when nodes with both SLES9 and CentOS operating systems are available, you can choose one type of OS or the other with the qsub option "-l opsys=sles9" or "-l opsys=rhas3". There are compilers for x86_64 which can/must be run on the x86_64 nodes to use the right linker. To setup your environment to use the x86_64 Intel compilers run: "pkgenv icc-8.1e ifort-8.1e" before you compile. For further information, contact Gareth Williams. [ page top ] 7. burnet - new version 9.0, 9.1 Intel compilers New version 9.0, 9.1 Intel compilers have been installed on burnet. They have pkgenv settings:
Note that some of these settings are aliases for others, e.g. ifort->ifort-9.1->ifort-9.1.032 The 'e' signifies EM64T/x86_64 and these versions must be run on one of the new configuration x86_64, sles9 blades to use the right linker. You can do your compile in a batch job, or run an interactive batch job with: "qsub -I -l arch=x86_64,walltime=30:00". Note the you currently also need "-q test", but later on that will be undesirable. For further information, contact Gareth Williams. [ page top ] 8. burnet - reduced limits on number of processes on head node There have been problems over the last few weeks with several users' jobs spawning large numbers of processes on burnet's head node. This has pushed the load on burnet too high, and resulted in long waits for users doing interactive work. Because of this, on 16th May, we limited the number of processes users can run on burnet's head node to a soft limit of 50 processes, and a hard limit of 80 processes. The compute nodes have no limit on the number of processes that can be run, and if users needs to run an application interactively that needs more processes than this, they can start an interactive job on a compute node by using: qsub -I -l walltime=0:30:00 or similar. [ page top ]
|
|
Comments to: © Copyright 2010, CSIRO Australia Use of this web site and information available from it is subject to our Legal Notice and Disclaimer and Privacy Statement |