Running Schrodinger jobs on Stallo

This page contains info about how to submit Schrodinger jobs on Stallo, based on two sets of examples - one for docking and one for molecular dynamics - provided to us by users.

Submitting jobs through the maestro interface:

Log in to Stallo with either x11-tunnelling enabled or through stallo-gui.uit.no.

To get download the jobscript example(s), type the following:Direct log in via ssh:

$ module load notur
$ cd $runex/Schrodinger
$ cp -R * ~/

Note: This suite is quite extensive in its features, and we generally advice you to either join tutorial courses, talk to experts in your proximity or read the vendor-provided documentation if you have absolutely no knowledge about how to use this suite of software. Here we only provide a couple of rough startup examples to get you up running.

Then;

If you want to test the molecular dynamics package

Do the following:

$ ssh -Y c1-3
$ cd example_md
$ maestro -NOSGL

and start a Molecular Dynamics task from the Tasks menu bar. Load model system from file, choose desmond_md_example.cms

Set all settings to your satisfaction.

Open the job settings; you should only be presented the following options

  1. localhost (only for job-setups)
  2. batch-short (2 hrs walltime/200 cpus)
  3. batch-normal (2 days (=48hrs) of walltime/1000 cpus)
  4. batch-long (21 days (504 hrs) of walltime/1000cpus)

Make sure that only one option is highlighted (only one of the batch-XXX´s). Press the run button and supervise running.

(This test case is provided us by Vladimir Pomogaev.)

If you want to test the docking package

Do the following:

$ ssh -Y c1-3
$ cd example_docking
$ maestro -NOSGL

and start a Docking task from the Tasks menu bar.

Choose abl1-kinase-t316i_glide-grid.zip as grid

Use ligands from file; if you want to run a very short test - choose abl1-kinase-t316i_minimized.mae, for a longer test browse for SD and choose Asinex-50000-3D-minimized.sdf set of ligands. Set all settings to your satisfaction. For job settings, see example above.

(This test case is provided us by Bjorn Dalhus.)

If you want to run vsw routines from the command line:

The Schrodinger suite is shipped with scripts that connects the software installation with the system batch resource allocation setup, making it possible to submit glide jobs from the linux command line.

Examples of valid command line submissions using the vsw-tool on Stallo:

vsw *.inp -DRIVERHOST batch-normal -host_glide batch-normal:100 -NJOBS 1 –adjust

If you are worried that you will not refind your files for emergency startup:

Note the following details:

  1. When the Schrodinger module is loaded on Stallo, the Schrodinger software folder is set in path, making $SCHRODINGER unecessary.
  2. The Schrodinger setup on Stallo writes to the scratch file system by default, potentially making both the -LOCAL and the -SAVE flags uneccesary.
  3. We do not recommend the -REMOTEDRIVER flag due to the risk of loosing jobs related to the admin process running out allocated time.