Running Jobs From the Command Line

See Using the Command Line with Schrodinger Platform for a quick reference sheet.

For most purposes, you can start jobs from Maestro. You can also run or submit jobs from the command line on Linux hosts or from a Schrödinger shell on Windows hosts (see below). The Job Control facility recognizes a number of command-line options that can be used to control the behavior of the job. These options are summarized in Table 1.

Table 1. Command options.
Option	Description
`-DISP` policy	Set the project incorporation policy for this job: `ignore`, `append`, `appendinplace`, or `replace`. Requires `-PROJ`, and overrides `SCHRODINGER_JOB_DISPOSITION`. The policies are described in Incorporation of Job Output. Default: `ignore`.
`-DRIVERHOST` host	For distributed jobs, specify the host on which to run the driver (“master job”). Must specify a single host.
`-HOST` host `-HOST` host`:`n `-HOST "`host1`:`n1 host2 ...`"`	Run a job on the specified host or submit a job to the specified batch queue. host is the value of a `name` entry in the hosts file or the actual address of a host. To specify multiple hosts, supply a blank-separated list in quotes. To specify the (maximum) number of subjobs to run on a host, append a colon and the number of subjobs to the host name. Default: run on the local host.
`-NICE`	Run the job at reduced priority. On Linux, the program is run with `nice -19`. On Windows, the program is run at “idle” priority. Overrides `SCHRODINGER_NICE`.
`-NOLAUNCH`	Perform all the steps necessary for launching the job, but stop short of actually launching it.
`-NONICE`	Do not run the job at reduced priority. Overrides `SCHRODINGER_NICE`.
`-NOSTARTUP`	In the process of launching the job, stop short of executing the application startup script. Mainly useful for debugging.
`-PROJ` projectname	Assign the job to a Maestro project. Overrides `SCHRODINGER_PROJECT`
`-QARGS` queue-args	Pass arguments to the queue manager. These arguments are appended to those specified by the `qargs` settings in the hosts file and the `SCHRODINGER_QUEUE_ARGS` environment variable.
`-SAVE`	Copy the archived contents of the job directory back to the submission directory after the job finishes, as jobid`-jobdir.zip`.
`-SUBHOST` host `-SUBHOST` host`:`n `-SUBHOST "`host1`:`n1 host2 ...`"`	For distributed jobs, specify the hosts on which the subjobs will run. The syntax is the same as for `-HOST`. Default: run subjobs on the hosts specified by `-HOST`.
`-TMPDIR` directory	Specify the scratch directory for the job. The job directory is created as a subdirectory of the scratch directory. Overrides any user setting of `SCHRODINGER_TMPDIR`
`-USER` username	Specify the user name to be used for remote jobs. Must be used with `‑HOST`. Default: use the same user name as on the submission host.

In addition to these options, the startup scripts for some programs support several other options. These options are summarized in Table 2. You should check which options are supported by entering the command

$SCHRODINGER/program -HELP

Table 2. Options supported by some programs
Option	Description
`-LOCAL`	Write temporary files in the submission directory instead of the scratch directory. Input and output files are not copied. Default: write temporary files in the scratch directory.
`-NOJOBID`	Run the job outside of Job Control. If you use this option, you are responsible for managing all the environment variables, file handling, and checking done by Job Control.
`-NOLOCAL`	Write temporary files in the scratch directory instead of the submission directory. Some programs and utilities write files locally when run on the local host; this option can be used to force the use of the scratch directory.
`-WAIT`	Wait for the job to finish before executing another command. In a terminal window, this means that the command prompt is not displayed until the job finishes. In a script, it means that the next command is not executed until the job finishes. Default: return control to the shell immediately.

Command-line options always take precedence over the corresponding environment variable. Some of the options from Table 1 and Table 2 are described in more detail in the topics listed below. You can also obtain information for each program about the hosts you can use. These options are listed in Table 3.

Table 3. Information options
Option	Description
`-DEBUG` `-DDEBUG`	Show the details of operation of the top-level script. Show the verbose details of operation of the top-level script.
`-ENTRY`	Show the section of the `schrodinger.hosts` file that will be used for this job.
`-HELP`	Display command syntax for the application.
`-HOSTS`	List the hosts that are available for calculations.

On Windows, you can run Unix (Linux) commands by opening a Schrödinger Command Prompt window from the Start menu, then entering the sh command. The unxutils package provides many of the commands available in a Unix shell.