Statistical & Genetics Software Available on Light and Group

**** software list are subjected to change upon user's requests and vendor upgrade.

Sources for Additional Software:

• Genetic Analysis: http://linkage.rockefeller.edu/soft/list.html
• CMU StatLib: http://lib.stat.cmu.edu
• GNU Website: http://www.gnu.org

Miscellaneous UNIX Utilities & Compiliers:

• PBSPro_5.4.1.41640(Portable Batch System)
• GNU: a2ps, bison, ghostscript(gs)
• C++: gcc-3.2.3.54
• Perl-5.8.0
• File editing: latex/tetex, emacs, pico, & vi

Tips:

• Make sure that /usr/bin & /usr/local/bin is in your path to use these programs
• Server "Light" and "Group" are configured to be identical for the Linux cluster for users to submit batch jobs on 7 executable hosts.
• each single user can submit as many as 10 jobs for execution at the same time.
• See http://www.vipbg.vcu.edu/lub for details
• To run an intensive job: "nice sas8 myjob &"

How to use pbs on light or group:

1.  use existing scripts to submit jobs for mx, sas or merlin:

• qmx <FILENAME>
• qsas <FILENAME>
• qR <FILENAME>

2. check the submitted job status:

• qstat -n
• "R" states for "Running"; "E" states for "existing"  If you have a long job to run but get "E" right away, your data or script may have some errors, contact sys admin for solution.

3. to delete a submitted job:

• qdel <JOBID>
• qstat to check if the job is deleted

How to use Samba to map your Unix home directory to window file manager

• Make sure that you have had server information plus samba account and password set up by system administrator
• in windows xp, open "My Computer", then "Tools", select "Map Network Drive"
• select an available letter you prefer to be mapped, in Folder box, type: \\128.172.85.5\YOURNAME
• check the box for reconnect at logon if you want to.
• click on "Finish", it will prompt you your username and password for samba connection if they are different from your windows username and password.