Submitting a Schrodinger Job to SGE

Schrodinger jobs use their own internal job controller, and this must be taken into account when running one of the Schrodinger applications on a CRC system.

The control of a job can be done in the following ways listed by order of preference:

  • with the Maestro GUI to control job from the menu Applications->Monitor_Jobs

From there users can check the status of their jobs in more details. They can kill any jobs also (it will kill jobs from SGE scheduler job list as well)

  • with the jobcontrol command line
jobcontrol -list to see all your job

jobcontrol -kill  opteron-0-46ba1f76 (in the following glide example) to kill it

jobcontrol -g to access a simple GUI
  • with regular SGE command
qdel #job_id

Glide job

To submit a Glide use the following syntax:

para_glide -HOST localhost:10 -n 10 -x -i {inputfile.inp} 

The para_glide application splits the Glide job specified in the input-file into smaller subjobs for distributed execution. The ligands from firstlig to lastlig are separated into njobs equal-sized batches. In the previous example, 10 njobs will be scheduled on any available CRC nodes. That parameter needs to match (or at least to be smaller) than the number following 'serial:' command

A successful submission should look like the following:

$ para_glide -HOST localhost:10 -x -i 1E5Mtopxp.inp -n 10
JobId: opteron-0-46ba1f76 (that number is the job ID for the Schrodinger job control)

$ qstat -u afs_id
job-ID  prior name       user         state submit/start at     queue    master  ja-task-ID
---------------------------------------------------------------------------------------------
 358107     0 j1E5Mtopxp afs_id       r     08/08/2007 16:12:12 dcopt002.q MASTER
 358106     0 j1E5Mtopxp afs_id       r     08/08/2007 16:12:12 dcopt017.q MASTER
 358105     0 j1E5Mtopxp afs_id       r     08/08/2007 16:12:12 dcopt046.q MASTER
 358108     0 j1E5Mtopxp afs_id       r     08/08/2007 16:12:27 dcopt092.q MASTER
 358103     0 j1E5Mtopxp afs-id       r     08/08/2007 16:12:11 ddcopt092. MASTER
 358104     0 j1E5Mtopxp afs_id       r     08/08/2007 16:12:12 ddcopt092. MASTER
 358109     0 j1E5Mtopxp afs_id       r     08/08/2007 16:12:27 ddcopt113. MASTER
 358110     0 j1E5Mtopxp afs_id       r     08/08/2007 16:12:27 ddcopt113. MASTER
 358111     0 j1E5Mtopxp afs_id       r     08/08/2007 16:12:27 ddcopt113. MASTER
 358112     0 j1E5Mtopxp afs_id       r     08/08/2007 16:12:27 ddcopt113. MASTER

Liaison job

To submit a Liaison job using Maestro, please refer to the documentation $SCHRODINGER/doc/liaison/user_manual.

At some point you will be see the following window: Liaison Image

If the job uses only NPROC=1 processor , select 'serial' in the host field instead of localhost.

If the job uses NPROC=8 processors, select 'mpi-8' in the pe field.

For a command-line submission, you can find more details at page 36 of the documentation. Use -HOST control job option as documented previously in the Glide job section.


For further information about Schrodinger suite (http://www.schrodinger.com/), please refer to the documentations located in $SCHRODINGER/doc.