Job Control Environment Variables (JOB CONTROL IS DEPRECATED)

There are a number of environment variables that can be used to specify the location of resources, manage the job database, and control various aspects of job execution. Some of these environment variables provide alternate means of specifying the resource; others are the sole means of specifying a resource or of overriding a default value.

 

Variable

Purpose

SCHROD_LICENSE_FILE

LM_LICENSE_FILE

 

Specify the license file or a list of license files to use if the license file is not installed in $SCHRODINGER. The list must be separated by colons on Unix and semicolons on Windows. The SCHROD_LICENSE_FILE definition supersedes any other definition. Both of these environment variables are FlexLM environment variables.
Use SCHROD_LICENSE_FILE when LM_LICENSE_FILE does not point to a license file containing Schrödinger licenses.

SCHRODINGER

Specify the installation directory.

SCHRODINGER_AUTO_SAVE

If set to 1, force the contents of the job directory to be archived and copied back to the submission host only for those jobs that have died (whose exit status is “died”). It is also possible to force such copying for all jobs (see

SCHRODINGER_SAVE_JOBDIR).

SCHRODINGER_DEATH_THRESHOLD

Time threshold after which an active but unreachable job is considered dead.

SCHRODINGER_HOSTS

Specify the hosts file. See Location of the Hosts File for a Job.

SCHRODINGER_JOB_DEBUG

Control debugging output. Allowed values are:

0

No debugging output

1

Standard debugging output (same as entering -DEBUG from the command line)

2

Detailed debugging output (same as entering -DDEBUG from the command line)

SCHRODINGER_JOB_DISPOSITION

Specify how to incorporate job results into the project

(same as entering -DISP from the command line)

Available values are:

append—add entries to project in an entry group

appendinplace—add entries immediately after source entries

replace—replace project entries with new entries

ignore—do not incorporate entries

Default: ignore

See Incorporation of Job Output.

SCHRODINGER_JOBDB2

Specify the full path name for the job database.
Default: ~/.schrodinger/.jobdb2

See The Job Database (JOB CONTROL IS DEPRECATED).

SCHRODINGER_JOBDB_CLEANUP

Specify how long the job record of a completed job is kept in the job database before being automatically deleted. For example, one day can be expressed as 86400, 1440m, 24h, or 1d. A value of 0 turns off automatic cleanup. The value is overridden by any jnanny setting, so you should use jnanny instead if possible.
Default: 7 days.

See Purging the Job Database (JOB CONTROL IS DEPRECATED) and Performing Actions on Jobs with jnanny (JOB CONTROL IS DEPRECATED).

SCHRODINGER_JOBDB_MAXSIZE

Specify the maximum number of job records to be kept in the job database. If this number is exceeded, job records of completed jobs are purged, starting with the oldest, at the next cleanup time.

Default: 2000 records.

SCHRODINGER_JMONITOR_PORT

Specify the port or range of ports that jmonitor may use. Ports can be specified as comma or colon-separated lists without spaces. Ranges can specified with a dash, for example, 5987:5989-5992:5994. Set this variable if there is a firewall that allows connections to ports within a given range only. The number of ports should be twice the number of jmonitor processes (jobs).

SCHRODINGER_JPROXY

Regulate the use of jproxy for the job. If set to 1, jproxy is used; if set to 0, it is not. By default (if not set), jproxy is used for batch jobs.

SCHRODINGER_JPROXY_PORT

Specify the port or range of ports that jproxy may use. Overrides any setting of proxyport in the hosts file.
The syntax is the same as for SCHRODINGER_JSERVER_PORT.
If this environment variable is not set, the values set in SCHRODINGER_JSERVER_PORT apply to jproxy as well. Therefore, it is generally not advisable to specify only one port in SCHRODINGER_JSERVER_PORT, as this will make it impossible for jserver and jproxy to run on the same machine, which may be necessary.

SCHRODINGER_JSERVER

Regulate the use of jserver for the job. If set to 1, jserver is used; if set to 0, it is not. By default (if not set), jserver is used for remote and batch jobs.

SCHRODINGER_JSERVER_LOGSIZE

Set the size threshold for the jserver log file in bytes. Units of kilobytes and megabytes can be used by appending K or M to the value. The five most recent log files are kept, with extensions .1 through .5. When the file size exceeds this threshold, the files are rotated, the .log.5 file is discarded if it exists, and a new log file is started.

SCHRODINGER_JSERVER_PORT

Specify the port or range of ports that jserver may use. Ports can be specified as comma or colon-separated lists without spaces. Ranges can specified with a dash, for example, 5987:5989-5992:5994. Setting this variable is useful if there is a firewall that allows connections to ports within a given range only.

SCHRODINGER_LICENSE_DEBUG

Turns on debugging related to license usage. Any nonzero integer value turns on debugging.

SCHRODINGER_LICENSE_RETRY

Specify how long to keep trying to obtain a license. The time interval between license checkout attempts can either be doubling, or constant. To use doubling time intervals, provide an integer to specify the time in seconds, or an integer value with a time unit, such as 7200s, 120m, 2h. An attempt to obtain a license is made at intervals that double after each try, starting at 10s. The final attempt is made at the specified maximum time.

To use a constant time interval between license checkout attempts, provide a colon-separated pair of a time and an integer. For example, SCHRODINGER_LICENSE_RETRY=10m:5 will try to check out a license every 10 minutes up to 5 times.

 

Default: 1 minute.

SCHRODINGER_LOGFILE_CLEANUP

Clean up (remove) jserver and jproxy log files that are older than the specified age. The value can be an integer value in seconds, or an integer value with a time unit, such as 7200s, 120m, 2h.

Default: 1 month.

SCHRODINGER_MAX_RETRIES

Specify the number of times a failed subjob from a distributed job is rerun before exiting with a failure. Only supported for distributed Glide and workflow jobs.

Default: 3.

SCHRODINGER_MONITOR_INTERVAL

Set the interval at which monitored files are copied back to the launch directory.

SCHRODINGER_NICE

Lower the priority of Schrödinger jobs. If it is unset or set to a null string, the priority is not lowered. The value local lowers the priority on jobs and subjobs submitted to the local host, but does not lower the priority of jobs or subjobs submitted to a remote host. Any other value lowers the priority of all jobs. Jobs run on the local host from Maestro are run with reduced priority; this behavior cannot be changed by unsetting SCHRODINGER_NICE or setting it to a null string.

Equivalent to using the -NICE command-line option.

SCHRODINGER_NO_NFS

If set, avoid using NFS mounts for file transfers between the job directory and the submission (output) directory, if possible.

SCHRODINGER_NODEFILE

Specify the path to a file containing a list of hosts and the number of CPUs to use on each host. Each line in the file must have the format:
host:numberofCPUs

You can list a host multiple times rather than provide the number of CPUs; this may affect the execution of parallel jobs.

 

This environment variable is used to pass an explicit list of hosts to the driver for a parallel or distributed job. It is not used by Job Control directly; as such, the meaning of the file depends on the product that uses it. For a parallel job, such as parallel Jaguar or Desmond, the names in the file must be actual host names, not entries in the hosts file. For distributed jobs, like Glide docking, the names must be entries in the hosts file, since they are used for launching subjobs.

 

Ordinarily, the hosts to use for a distributed or parallel job would be supplied using command line arguments, as explained elsewhere in this document. This variable is provided to allow the usual mechanism to be overridden when necessary.

SCHRODINGER_PROJECT

Specify the path name of the Maestro project into which the results of the job should be incorporated

(same as entering -PROJ from the command line)

See Incorporation of Job Output.

SCHRODINGER_QLOGDIR

Specify the path to the directory where queue log files (.qlog) for batch jobs are to be written. The default is the job database directory; however, if that directory is not mounted on the queue host, an alternative path needs to be specified, or the queueing system will not be able to write those log files.

SCHRODINGER_QUEUE_ARGS

Specify queue arguments for job submission to a queueing system. These arguments are also used when subjobs are submitted by a master job. Queue arguments specified with this environment variable are appended to those read from schrodinger.hosts.

SCHRODINGER_RETAIN_JOBDIR

If set to 1, when the job finishes and the output files are copied back, the job directory is not removed. By default, it is removed if it did not exist already.

SCHRODINGER_SAVE_JOBDIR

If set to 1, archive the contents of the job directory and copy it back to the submission host when the job finishes. The archive appears in the output directory as jobid-jobdir.zip. It is also possible to force such copying only for jobs that have died (see SCHRODINGER_AUTO_SAVE).

Equivalent to using the -SAVE command-line option.
SCHRODINGER_SSH_IDENTITY (Windows only) Full path to the file used for ssh connection. This can be used to communicate the location to Job Control when the file is not in the default location (%HOMEPATH%\%USERNAME%.ppk).

SCHRODINGER_STRANDED_INTERVAL

Time interval for checking for stranded jobs by jnanny. Default: 10 minutes.

SCHRODINGER_STRANDED_THRESHOLD

Check whether an active job is still running if its job record has not been updated for this length of time. Default: 10 minutes.

SCHRODINGER_SUBMITTED_INTERVAL

Time interval for checking on submitted and launched jobs by jnanny to ensure that they are progressing. Default: 10 minutes.

SCHRODINGER_SUBMITTED_THRESHOLD

Check whether a submitted job is still in the queue if its job record has not been updated for this length of time. Default: 5 minutes.

SCHRODINGER_TMPDIR

Specify the full path name for the directory in which run time temporary job directories are created. Overrides the tmpdir setting specified in the schrodinger.hosts file (The tmpdir Setting in the Hosts File).