Job Management

This section describes how to submit scientific workload, i.e. “jobs”, to the Virtual Cluster. The assignment of jobs to computational resources, prioritization, etc. is handled by a workload management system. A user usually doesn’t interact with the workload management system directly, as the Schrödinger Suite offers a convenient layer to interact with the system called “Job Server”.

Warning

It is strongly recommended to use the commands described in this guide when interacting with jobs. Using the commands provided by the underlying workload management system can cause issues with the job-tracking mechanism of Job Server.

Jobs can be submitted from a remote client, e.g. a physical workstation or laptop, or from a virtual desktop or a remote shell session on the Virtual Cluster. Section Setup Remote Job Submission describes the required steps to configure remote job submission. If jobs are submitted directly on the Virtual Cluster the only step required is to select the Schrödinger Suite version to use for the job. This can be accomplished by executing the command

module load schrodinger/<VERSION>

where <VERSION> can be one of the Schrödinger Suite versions available on your Virtual Cluster. The available Schrödinger Suite versions can be displayed using the command

module avail schrodinger

To set a certain version of Schrödinger Suite as the default such that the module load command doesn't need to be executed every time logging in to the Virtual Cluster the command

module save

can be used.

Setup Remote Job Submission

In order to submit jobs from a client (e.g., laptop or desktop PC) to the Virtual Cluster a few setup steps are required on the client. This section guides through the setup process on the client.

Registration with Job Server

It is required that you authenticate against the Job Server installed on the Virtual Cluster. If your system administrator has configured the installation of Schrödinger Suite on your client to use the Virtual Cluster as a compute backend, Maestro will show a dialog which asks for your username and password. You need to provide the same username and password as used to log in to the Virtual Cluster with the web portal (see Web Application). Alternatively, you can authenticate with Job Server using the command prompt as described below.

Note

Is your client uses the Windows operating system the following command must be entered without the $SCHRODINGER/ prefix.

Enter the following command on a command prompt on your client (it is assumed that $SCHRODINGER points to the installation of the Schrödinger Suite on your client you want to use to submit jobs to the Virtual Cluster):

$SCHRODINGER/jsc cert get <DNS_NAME>:<PORT> [--user USERNAME]

where <DNS_NAME> is the DNS name of the Virtual Cluster, <PORT> is the port number of the Job Server (usually 8030). The --user option needs to be specified only if the username of your account on the Virtual Cluster and the username on your client is different.

Note

The version of the Schrödinger Suite on your client and on the Virtual Cluster must match, i.e., you can only submit jobs to the Virtual Cluster from Maestro (or from the command line) on your client if the exact same version of Schrödinger Suite is also installed on the Virtual Cluster.

Setting the JOB_SERVER Feature Flag

Currently, two feature flags need to be enabled on the client to submit jobs to a Virtual Cluster (and a remote Job Server in general). Enter the following commands on a command prompt on your client to enable the feature flag (it is assumed that $SCHRODINGER points to the installation of the Schrödinger Suite on your client you want to use to submit jobs to the Virtual Cluster):

$SCHRODINGER/feature_flags -e JOB_SERVER
$SCHRODINGER/feature_flags -e IGNORE_SCHRODINGER_HOSTS

Note

If you need to submit jobs to other cluster systems which are not yet configured for Job Server, it is possible to limit the scope of the setting to a single command or a single instance of Maestro by setting the environment variable SCHRODINGER_FEATURE_FLAGS to +JOB_SERVER+IGNORE_SCHRODINGER_HOSTS in the shell session used to start Maestro or any other Schrödinger program.

Testing Job Submission

It is recommended to test job submission after the client setup as described above has been completed. The command:

$SCHRODINGER/testapp -HOST <PARTITION_NAME>

Can be executed in order to test whether job submission to the Virtual Cluster works fine. If this command completes successfully and the output contains a job ID remote job submission to the Virtual Cluster works fine.

Schrödinger Suite Versions and Partitions Available on the Virtual Cluster

Information about the Schrödinger Suite installations available on a Virtual Cluster for job submission can be obtained using the command

$SCHRODINGER/jsc installations <DNS_NAME>:<PORT>

Information about the partitions available on a Virtual Cluster to which jobs can be submitted via command line or from within Maestro can be obtained using the command

$SCHRODINGER/jsc hosts list

Additional Documentation

Please refer to

the Job Server command line user guide

to learn more about how to manage jobs submitted to the Virtual Cluster from the command line. Please refer to the

Starting Jobs from Maestro section of the Schrödinger Suite documentation

to learn more about managing jobs from within Maestro.