UNIX Environment
Add the following line to your .cshrc file:
setenv PATH /usr/local/bin:${PATH}:/afs/slac/g/suncat/bin
Queues
Queue Name |
Comment |
Wallclock Duration (hours) |
---|---|---|
suncat-test |
16 cores, for quick "does-it-crash" test |
10 minutes |
suncat-short |
|
2 |
suncat-medium |
|
20 |
suncat-long |
|
50 |
suncat-xlong |
Requires JensN/Frank/Felix permission |
100 |
Submitting Jobs
It is important to have an "afs token" before submitting jobs. Check the status with the tokens commands. Renew every 24 hours with /usr/local/bin/kinit command.
Login to a suncat login server (suncatls1,suncatls2,suncatls3) to execute commands like these (notice they are similar for gpaw/dacapo/jacapo):
gpaw-bsub -o mo2n.log -q <qname> -n 8 mo2n.py dacapo-bsub -o Al-fcc-single.log -q <qname> -n 8 Al-fcc-single.py jacapo-bsub -o Al-fcc-single.log -q <qname> -n 8 co.py
NOTE: Because of a file-locking bug in afs, all output from GPAW should go to nfs. Our fileserver space is at /nfs/slac/g/suncatfs. You should always use the "/nfs" form of that name (the nfs automounter software often refers to it as "/a", but that syntax should not be in any of your scripts).
ANOTHER NOTE: The above commands "take control" and set all the environment, preventing the user from changing part of the environment (PATH, PYTHONPATH, etc.). If you want to take that fancier (but more error prone) approach, look at the 2 lines in the gpaw-bsub/dacapo-bsub scripts in /afs/slac/g/suncat/bin, and modify the environment after executing the "setupenv" command, and before executing the "bsub" command.
Useful Commands
Login to a suncat login server (suncatls1,suncatls2,suncatls3) to execute these. You can get more information about these commands from the man pages.
bjobs (shows your current list of batch jobs and jobIds) bjobs -d (shows list of your recently completed batch jobs) bjobs -u all | grep suncat (show jobs of all users in the suncat queues) bpeek <jobId> (examine logfile output from job that may not have been flushed to disk) bkill <jobId> (kill job) btop <jobId> (moves job priority to the top) bbot <jobId> (moves job priority to the bottom) bmod [options] <jobId> (modify job parameters after submission, e.g. priority (using -sp flag))