Managing Jobs with the Command Line

On Windows: Any command line prefixed with "$SCHRODINGER/" should be executed without this prefix when using the Schrödinger Command Prompt.

Enter:

$SCHRODINGER/jsc --version

to print the version of the Job Server on your local computer (physical or virtual). The first two digits determine the release version (e.g. 55 corresponds to release 2021-3). For example:

jsc version 51*** revision=***********

To check the version of a Job Server on a remote cluster, enter:

$SCHRODINGER/jsc server-info <jobserver_host>[:<port>]

The version is printed in the same way as for a local Job Server

To list information about running jobs, enter:

$SCHRODINGER/jsc list

Use the --any-status option to list all jobs in the job database. You can filter the list with these options:

  • --status STATUS—list only jobs in the given status. You can use the --status option multiple times to list more than one status. STATUS can be one of the values listed in the Job Statuses table in the Evaluating the Status of a Job section.

  • --owner OWNER—list jobs started by the specified user (the “owner” of a job). If you want to list jobs from other users, your user account must be listed in the admin_users section in the Job Server configuration.

  • --server SERVER—list only jobs from the given Job Server:

  • --launch-dir DIR—list only jobs started from the given directory.

  • --created-before DATE and --created-after DATE—list jobs that were created before or after the given date. The supported formats for DATE are:

    2020-08-15            # defaults to 00:00:00
2020-08-15T15:40      # defaults to 15:40:00
				    2020-08-15T15:40:20

    If no date or month are specified, the current day or month is used. The timezone is the local timezone where the command was executed.

  • --has-downloadable-files and --no-downloadable-files—list only jobs that either have or do not have files in the file store that are ready for downloading.

You can also control how the list is displayed with these options:

  • --full-hostname—show the entire host name in the list, rather than a shorten version.

  • --full-jobname—show the entire job name in the list, rather than a shorted version.

  • --full-jobid—show the entire job ID in the list, rather than a shorted version.

  • --verbose—use this option to display more information about active jobs than what is included by default. The list includes additional fields such as Batch ID and when the job was started.

  • --vv—use this option to display the most information about active jobs and also any subjobs. The list displays all possible fields relevant to the running job and subjobs.

  • --id-only—show only the job ID with no header.

To display information about specific jobs, enter:

$SCHRODINGER/jsc info <jobid>

To display all available information about a specific job, use the --vv option.

To show the list of sub-jobs for a parent job, or all related sub-jobs, use the --tree option.

$SCHRODINGER/jsc info --tree <jobid>

Directories for subjobs are located in the subjobs directory of the parent job.

To inspect log files of running jobs, enter:

$SCHRODINGER/jsc tail-file <jobid>

Use the --follow option to keep monitoring the file as it is written (the equivalent of the Unix command tail -f). If there is more than one file to inspect, you can chose the file with the
--name FILENAME option.

To delete a completed job from the job database, enter:

$SCHRODINGER/jsc delete <jobid>
$SCHRODINGER/jsc tail-file <jobid>

To delete multiple jobs at once, enter:

$SCHRODINGER/jsc delete <jobid1> <jobid2> ...

To delete all completed jobs, enter:

$SCHRODINGER/jsc delete all

The "delete" action does not terminate running jobs. Use the "cancel" action to terminate running jobs. By default, jobs with results available for download are not deleted.

To delete all completed jobs, including jobs with downloadable files, use the
--with-downloadable-files option:

$SCHRODINGER/jsc delete all --with-downloadable-files

To delete jobs that were created before or after a certain date, use these options:

  • --created-before DATE and --created-after DATE—delete jobs that were created before or after the given date. The supported formats for DATE are:

    2020-08-15            # defaults to 00:00:00
2020-08-15T15:40      # defaults to 15:40:00
			    2020-08-15T15:40:20

    If no date or month are specified, the current day or month is used. The timezone is the local timezone where the command was executed.

    • To stop a running job and preserve its intermediate results, enter:

    $SCHRODINGER/jsc stop <jobid1> [<jobid 2> ...]

    Only jobs from Desmond, multisim, or bmin support this feature. To stop all running jobs, enter:

    $SCHRODINGER/jsc stop all

    To immediately terminate a single running job or jobs, enter:

    $SCHRODINGER/jsc cancel <jobid1> [<jobid 2> ...]

    To terminate all running jobs, enter:

    $SCHRODINGER/jsc cancel all

    To terminate problematic subjobs which do not respond to the cancel command, you can force cancellation using the --force option:

    $SCHRODINGER/jsc cancel --force <jobid1> [<jobid 2> ...]

    Canceling jobs discards their intermediate results. Canceling a parent job terminates and cleans up all subjobs

    Jobs are downloaded to the same machine from which the job was launched.

    Note that output files that have been successfully downloaded are automatically deleted from the Job Server’s internal storage (see the “File Store” section in the Architecture Overview). This means, in particular, that such files cannot be downloaded again.

    You can test the download speed of a server before downloading a job using the file-speedtest command. This command can also be used to troubleshoot any problems encountered when downloading or uploading to different servers. To display the addresses of all the known servers, enter:

    $SCHRODINGER/jsc admin file-speedtest

    To measure the download and upload speed of a particular server, use the server address:

    $SCHRODINGER/jsc admin file-speedtest <host:port>

    Jobs submitted from the command-line automatically start a background downloader process. This utility is also started by Maestro automatically if the "JOB_SERVER" feature flag is enabled.

    To check the status of the "downloaderd" service, enter:

    $SCHRODINGER/jsc download-status

    To stop the service yourself, enter:

    $SCHRODINGER/jsc download-stop

    To start the downloaderd service, enter:

    $SCHRODINGER/jsc download-start

    To list the downloadable files for a job, enter:

    $SCHRODINGER/jsc list-files <jobid>

    To download all available results when the "downloaderd" service isn't running, enter:

    $SCHRODINGER/jsc download

    This is a shortcut for the command "$SCHRODINGER/jsc download all". By default, results are downloaded into the same directory from where they were submitted. To download files into the current directory instead, enter:

    $SCHRODINGER/jsc download <jobid> --cwd

    To find the directory, from where a job was submitted, enter:

    $SCHRODINGER/jsc info --vv <jobid> | grep "launchDirectory"

    The job directory on the job host is where running jobs are located.

    To find the job host, enter:

    $SCHRODINGER/jsc info -v <jobid> | grep "Job Host"

    To find the job directory, enter:

    $SCHRODINGER/jsc info -v <jobid> | grep "Job Directory"

    The directory names of the running jobs in the job directory are the job IDs. You can cd into the by-name folder of the job directory to see the running jobs listed by job name instead.

    If the job fails, the job directory will be retained on the job host. You can review the contents of that directory, which can contain useful information as to why the job has failed.