SDSC Thread Graphic Issue 13, April 2007

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User Services Director:
Anke Kamrath

Subhashini Sivagnanam

Graphics Designer:
Diana Diehl

Application Designer:
Fariba Fana

Help Desk: User Questions

Frequently Asked Questions from Our Users

—Ella Xiong

Dear SDSC Consulting,

It seems as though on Blue Gene some users' jobs do not need to go through the queue, while other users' jobs wait a very long time before running. Can you tell me how the BlueGene scheduler works? Are special preferences given to certain jobs or users?


Actually, no special preferences are given to BlueGene jobs. Jobs are run on a first come, first served basis; no other priorities are given. However, due to the layout of the BlueGene partitions, you might want to be a little careful regarding which partitions you request. An efficient way to make use of BlueGene partitions is to check which partitions are busy and which are free before submitting a job. In order to do this, you can use the /usr/local/apps/utils/showq command.

See our User Guide for a more detailed partition layout on BlueGene.

Please also note that the smaller partitions are contained within the larger partitions. Hence, if there is a job running on the bot128-1 partition, then the bot64-1, bot64-2, bot256-1, bot, and rack partitions will be unavailable in addition to the bot128-1 partition. Similarly, if there is a job running on the rack partition all the other partitions will be unavailable. Therefore, if you have a small job please, choose the smallest possible partition which fits your job to enable users to run on other partitions.

Dear SDSC Consulting,
How can I get access to SAS software on Thor ( as announced in SDSC User News?


SAS Enterprise Miner is a data mining tool recently installed on Thor. In order to use SAS, you must have an account on Thor in addition to a valid SDSC account and login and an SDSC compute or data allocation. To request an account on Thor, submit a ticket through the online form.

After you obtain your account, follow these steps to start your SAS session:

  1. Log on to
  2. Navigate to /opt/SAS/SASAPCore/apps/EnterpriseMiner/bin/
  3. Run em
    % cd /opt/SAS/SASAPCore/apps/EnterpriseMiner/bin/
    % ./em
  4. When the Enterprise Miner environment launches, select the Personal Workstation option.

or there is an alternate SAS environment:

  1. Log on to
  2. Navigate to /opt/SAS/SAS_9.1/bin
  3. Launch sas_en

For more information, visit our SAS help page

Ella Xiong is reachable via e-mail at

Did you know ..?

that SDSC has limited the core file size to 32MB.
To make good use of the core file size it is recommneded using the MP_COREFILE_FORMAT environment variable (or its associated command-line flag -corefile_format) to set the format of corefiles to lightweight corefiles.
See Thread article Issue 4, February 2006 for more details.