Bulletin 172 - 2007 September 24

1. Traffic Lights
2. SUPER-UX 17.1
3. MPI SX6 settings for SUPER-UX R17.1
4. Passing environment variables to batch jobs
5. OPeNDAP Workshops
6. Upgraded software cherax and burnet
7. New Software cherax and burnet
8. Change to using HPSC licenses from outside HPSC

Note: "CSIRO" items can apply to BoM users of cherax and burnet

A new version of the traffic light display was recently installed.

This version gives access to more details of some of the services, e.g. batch queues.

See http://intra.hpsc.csiro.au/ or http://www.hpccc.gov.au/hpccc/system_status/

(Because of the growth in the size of the traffic light display, it may be useful to click with the right mouse button on the display, and select the option "This Frame" and "Open Frame in New Tab", or whatever your favourite browser offers.)

[ page top ]

There have been no reported user problems with the SUPER-UX 17.1 upgrade on the SX-6s.

After the upgrade is complete, the interim "2" queues which give access to the upgraded nodes will remain for a while, but will be de-activated on 1st November.

[ page top ]

To initialise your csh and ksh environment for MPI/SX under the upgraded R17.1 Operating System (OS), please remove the R15.1 runtime module, and the default MPI/SX R17.1 runtime module will automatically be available.

Comment out the following line from the module initialisation code in your ~/.cshrc and ~/.profile files.

          # module load mpirt/r151-7.2.0

• For csh-shell user-login script, the modules initialisation code becomes:

            if ( "`uname`" == "SUPER-UX" ) then
               source  /usr/local/Modules/3.1.6/init/csh
               # module load mpirt/r151-7.2.0
            endif
  

• For korn-shell user-login script, the modules initialisation code becomes:

            if [ "`uname`" = "SUPER-UX" ]
                then
                     .  /usr/local/Modules/3.1.6/init/ksh
                     # module load mpirt/r151-7.2.0
            fi
  

[ page top ]

The recent update of NQSII includes a fix for a problem with passing environment variables into a batch job.

Passing variables to batch jobs is good for chaining together a sequence of jobs and using one script to run similar jobs for multiple sets of input data.

With the recent update, if you want to pass the variables "VAR1" and "VAR2" into a job, you can use the qsub option "-v VAR1,VAR2" (as documented in the man page). You can also use the directive "#PBS -v VAR1,VAR2" in the header of your script.

The workaround that was recommended will still work (on the command line use the option "-v VAR1=$VAR1,VAR2=$VAR2" but that will not work in a directive.

The same syntax also works for the torque batch system on cherax and burnet.

[ page top ]

Please forward the enclosed OPeNDAP workshop series information to interested staff, collaborators, and communities.

More information is available from: http://opendap.bom.gov.au/opendap_workshops/

IT security officers are invited to the OPeNDAP System Admin. workshop to hear more detail information regarding the software security audit checks for the Hyrax server. The Hyrax developer's encourage the early engagement of IT security in the assessment of the service for your organization.

For more information contact Tim Pugh:

[ page top ]

• Intel Math Kernel Library 9.1 for Linux (for C++ and Fortran).

  For product details see http://intra.hpsc.csiro.au/user/userdocs/ax

  You can access Intel MKL 9.1 on cherax and burnet by doing:

          module load intel-mkl/9.1
  

  For more details on usage visit the APAC software map http://nf.apac.edu.au/facilities/software/index.php?l=&site=CSIRO

[ page top ]

• Intel Integrated Performance Primitives v5.2 for Linux (for C++)

  Intel IPP is a software library which provides a broad range of functionality including general signal, image, speech, graphics, data compression, cryptography, text strings and audio processing, vector manipulation and matrix math, as well as more sophisticated primitives for construction of audio, video and speech codecs.

  For product details see http://intra.hpsc.csiro.au/user/userdocs/ax

  You can access Intel IPP on cherax and burnet by doing:

          module load intel-ipp
  

  For more details on usage visit the APAC software map http://nf.apac.edu.au/facilities/software/index.php?l=&site=CSIRO

• Intel(R) Threading Building Blocks v2.0

  Intel TBB is a runtime-based parallel programming model for C++ code that uses threads. It consists of a template-based runtime library that allows you to write scalable applications that specify tasks instead of threads, emphasize data parallel programming, and take advantage of concurrent collections and parallel algorithms.

  For product details see http://intra.hpsc.csiro.au/user/userdocs/ax

  You can access Intel TBB on cherax and burnet by doing:

         module load intel-tbb
  

  For more details on usage visit the APAC software map http://nf.apac.edu.au/facilities/software/index.php?l=&site=CSIRO

[ page top ]

CSIRO HPSC is migrating license serving to a new host: lm.hpsc.csiro.au where possible (matlab first!). For most usage the transition will be transparent. For use of HPSC hosted licenses on external platforms, changes will be required, and we will directly contact recent users. If you have problems with using licensed software please contact us.

[ page top ]