Bulletin 162 - 2006 Sep 18

1. qsubnew upgraded
2. User selectable job priorities for SX-6 jobs
3. Router outage will affect all CSIRO usage: 20-Sep 6pm-8pm
4. New bioinformatics software on cherax

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

A new version of the qsubnew wrapper for qsub was installed on 13 Sep.

This allows default memory limits to be picked up, limits the number of nodes for multi-node jobs, and re-allows the -S option on jobs.

There is now little difference in behaviour between jobs with and without the -S parameter. Without the -S parameter, ksh users should be careful to include the -n parameter in any rsh usage.

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Users have the option of specifying a priority parameter on SX-6 jobs with the flag

      #PBS -p pri

The default value for pri is 0. Values can range from -1024 (lowest priority) to 1023 (highest priority.

ERS has been configured to take two actions with jobs with non-default priorities specified:

1. Alter the job priority (as shown by erstatj) to have values that range by about 100 between the lowest and highest priority. This alters the order of selection for running (and holding) of jobs). (For CSIRO nodes with over-commitment allowed, this also alters the execution priority of jobs).
2. Alter the ERS measures of resource consumption, which feed back into user rank and hence job priority. Values have been set so that usage measures are scaled by a factor of (1.0 + pri / 2048), giving a range of values from 0.5 (for pri = -1024), through 1.0 (for pri = 0) to 1.50 (for pri = 1023).

Users can select different priorities on jobs according to the priority of their work. For example, development work might be submitted with a high priority to get good turnaround, whereas jobs that can wait over a weekend might be submitted with low priority.

The higher the priority used for jobs, the higher will be the ERS usage measures, and future jobs will be less favoured by ERS scheduling compared to others in the same ERS class (URGENT, SPECIAL or NORMAL). This is to discourage users from using the highest priorities continually.

There will be no change to the usage as reported on the WWW pages.

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A change to a new router is necessary for CSIRO to connect to AARNet3. This has become urgent because our current link via Grangenet is being turned off months earlier than previously advised.

The change will take place this Wednesday, 20th September from 6pm to 8pm.

This will affect interconnection between CSIRO hosts in the computer room, as well as external connection. It is reasonable to expect that none of the CSIRO systems will be able to do anything productive during this time. The period of time set aside assumes that no serious difficulties are encountered.

Cherax will also have a software upgrade during this period which should have no additional user impact.

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• The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services. Setup your environment with "module load ncbi'.

• Bioperl versions 1.4.0 and 1.5.1 (default).

• you may need perl/5.8.8 which contains Bundle::Bioperl Setup your environment with "module load perl/5.8.8 bioperl'.

Please report any problems to hpchelp (see below). You can see more information about this and other CSIRO software by going to intra.hpsc.csiro.au/userguides and clicking the "software" button that takes you to our software information at the central APAC repository of such information. You can also subscribe to the HPSC blog for more discussion of this item:
http://intra.hpsc.csiro.au/weblog/HPSCblog/.

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