Batch Jobs

One Time Setup

If you don't have a SLAC system ID (i.e. you are not in the SLAC Directory) apply for one electronically here.

After you have a SLAC system ID, if you don't have a SLAC account fill out the (unfortunately) non-electronic forms here and return them to the mighty administrator.

Email the administrator requesting access to the queues, along with your SLAC account name. It might take a couple of hours to add you to the appropriate permissions lists.

Add the following line to your .cshrc file:

setenv PATH /usr/local/bin:${PATH}:/afs/slac/g/suncat/bin

If you have a line like the following in .cshrc remove it:

eval `/usr/local/bin/environ /bin/tcsh -i${?prompt} -e emacs:vi`

Queues

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:

gpaw-bsub -o mo2n.log -q <qname> -n 8 gpaw-python 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))