ARSC HPC Users' Newsletter 295, July 19, 2004

Decommission of Yukon, Chilkoot, and Icehawk

As announced elsewhere, ARSC is removing three major HPC systems from service this summer and fall.

  Icehawk (IBM Power 3 cluster) : Inaccessible after July 31
  Yukon (Cray T3E) :              Inaccessible after September 30
  Chilkoot (Cray SV1ex) :         Inaccessible after September 30

All icehawk users should already have migrated and tested their codes on iceberg or another appropriate system.


All yukon users should be checked out and ready to run on klondike (Cray X1) or iceberg (IBM Power 4 cluster), by August 31. You may continue using yukon through September 30th.


All chilkoot users should be checked out on the klondike (Cray X1) by September 15th. You may continue using chilkoot through September 30th.

If need assistance migrating or optimizing your codes, your first point of contact, as always, is If you don't speak up, we won't know to help you!

Specifying Your Project in X1 PBS Scripts

If you are a member of multiple allocated X1 projects, you should be sure each PBS batch jobs draws its hours from the appropriate project. In PBS, you can set the project with the qsub option:

  -W group_list=<<Unix_Group>>
Where "<<Unix_Group>>" is the Unix permission group associated with the desired project. On ARSC systems, you are a member of one permission group per project, where the names are equivalent except that the project name is upper-case and the Unix group is lower-case. For instance, a user who is a member of two projects AAAA1C1 and ZZZZ2Y2 would charge the latter project by including the following line in his/her list of PBS directives at the top of the qsub script:

  #PBS -W group_list=zzzz2y2
Alternately the project could be set at submit time, by adding the same option to the interactive qsub command:

  klondike%        qsub -W group_list=zzzz2y2 jobscript
If you don't specify the -W group_list option, your default project (which matches your default Unix group) will be charged. This will work fine for most users.


  • To determine all your projects (groups), execute the Unix command "groups":
        klondike%        groups 
  • To determine your default project, get the group id number by grepping the /etc/passwd file, and get the name of that group by grepping the /etc/group file:
        klondike%        grep <YOUR-USER-NAME> /etc/passwd
          (The fourth field is the default group id number.)
        klondike%        grep <DEFAULT-GROUP-ID-NUMER> /etc/group 
  • A contrived example, by a contrived user:
        % groups
        aaaa1c1  zzzz2y2
        % grep stomato /etc/passwd
        stomato:x:5454:7654:Steven T. Omato:/u1/uaf/stomato:/bin/ksh
        % grep 7654 /etc/group
        % qsub -W group_list=zzzz2y2 jobscript

Rimegate Permanent Shut-Down

The SX-6 was powered off on June 30. The front-end system, rimegate, remains available to users, but, as noted in "news downtime" will be shut down on Wednesday, July 21:

            machine(s): rimegate
            start time: 15:00
              end time: Never
                reason: End of service as front-end to rime, system wipe.
                        Move all data off rimegate, contact us with 
                        any concerns.

Please retrieve everything you will want later.

All X1 /tmp files to be DELETED; $WRKDIR Purging; Quotas

[ This is a copy of an email sent by consult to all ARSC users on June 28th. Re-"printed" here in an attempt to avoid surprises... ]

> Configuration changes affecting ALL USERS on Klondike, Chilkoot, Yukon,
> Iceberg, Iceflyer, and the SGIs will soon be made on ARSC systems.
> These changes will directly impact usage on these systems starting
> Wednesday, July 28th, 2004.  A full understanding of these changes and
> their effects is essential, so if there are any questions or concerns,
> please contact ARSC consult as soon as possible.  The changes are
> described below:
> Klondike (Cray X1) : Purging of $WRKDIR (/tmp) will be activated.
> Quotas on $WRKDIR and $HOME will be enforced.  Because /tmp will be
> enlarged, a one-time removal of all files will occur.  This file removal
> is planned for Saturday, July 31st, 2004.
> Chilkoot (Cray SV1-ex) : Purging of $WRKDIR (/tmp) will be activated.
> Yukon (Cray T3E) : Purging of $WRKDIR (/tmp) will be activated.
> Iceberg (IBM P6X) : Purging of $WRKDIR (/wrkdir) will be activated.
> Iceflyer (IBM Regatta) : Purging of $WRKDIR (/wrkdir) will be activated.
> SGIs : Purging of $WRKDIR (/scratch) will be activated.
> Purging will permanently remove any files that have not been accessed
> for 10 days prior to the purge.  As a reminder, the $WRKDIR filesystems
> are not backed up, and we recommend users transfer their data to and
> from the $ARCHIVE system to $WRKDIR.  The initial quotas will be set at
> 100 MB for $HOME, and 10 GB for $WRKDIR.
> If you have any questions or concerns, please contact ARSC Consult at
> (907)450-8602.

Quick-Tip Q & A

A: [[ I've gotten some Fortran code that's difficult to read. It could stand
   [[ consistent indentation, capitalization, etc...  Can someone recommend
   [[ a "pretty-printer" for Fortran?  Preferably one that can handle both
   [[ free- and fixed-form.

  # From Greg Newby:
  For C or C++, a good choice would be the "indent" program, available
  as part of the GNU collection.  For FORTRAN, I have two suggestions
  but don't know how we'll they'll do with your code, or how F90-aware
  they are:
    FORTRAN prettifier:

    Follow the download link, then compile the C program (gcc
    worked for me).  A .txt file provides usage information.


    Try the "emacs" editor in FORTRAN mode.  It should
    automatically enter this mode with a .f or .for filename
    extension.  To indent a section of code, go to the bottom
    of the file, set a mark, go to the top, then run "indent-region".
    The key sequence would be something like this:

            ESC->  (to bottom of file)
            CNTL-space   (set a mark)
            ESC-<  (to top of file)
            ESC-X indent-region  (type out the command)

    Try this on a copy of your file, in case it makes a mess of things!

Q: [ And, this week, a question from Greg: ]

  I've noticed that I can sometimes get colors to work with emacs, but
  other times I cannot.  Colors are great for syntax and variable

  A remote linux system + a Mac terminal window ($TERM=linux) does great
  with colors, but many other combinations do not (including the emacs
  that ships with the Macs).  Does anyone know good ways to find out
  whether color is available in a particular emacs installation, and if
  so how to get colors to display?

[[ Answers, Questions, and Tips Graciously Accepted ]]

Current Editors:
Ed Kornkven ARSC HPC Specialist ph: 907-450-8669
Kate Hedstrom ARSC Oceanographic Specialist ph: 907-450-8678
Arctic Region Supercomputing Center
University of Alaska Fairbanks
PO Box 756020
Fairbanks AK 99775-6020
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