The postmortem Utility (JOB CONTROL IS DEPRECATED)

The postmortem utility archives information that is useful for understanding why jobs do not run as expected. It creates a zip archive containing the current environment, file system information, a list of installed Schrodinger software packages, the schrodinger.hosts file, the queue support scripts, the license file, and information such as input and output for specified jobs. When contacting technical support regarding a job, it is highly recommended to run this utility, and upload the archive when you fill in the support request form on the web site (https://www.schrodinger.com/support/).

Note: You should ensure that no sensitive information is added to the archive, by using the options described below, and by inspecting the contents of the archive.

The syntax of the postmortem utility is as follows:

$SCHRODINGER/utilities/postmortem [options] [jobids]

The options can be listed by running the command with the -help option; they are also available in the postmortem Command Help topic. Options may be truncated to any unique abbreviation.

If job IDs are specified, the job records for those jobs are archived, along with any related files (batch scripts, qlog files, and so on) from the job database. Parent and subjobs of the specified jobs are included as well, unless the option -noparents or -nosubjobs is given. Finally, unless -nojobfiles is given, any log files and non-structural input or output files listed in the job record are saved as well. If you want to include structure files in the output, use the -struct option.

The archive can be quite large if all job files for a large job are included. You might want to use the -size option to check the total size of the files to be archived, first.

To find the job IDs for your jobs, use the jobcontrol command, or look in the Monitor panel.

For example the following command lists all of your completed jobs:

$SCHRODINGER/jobcontrol -list completed

If file and directory names contain sensitive information that you don’t want to reveal, you can use the -autoreplace option to have the program replace them in the archived files. You can specify particular string replacements using the -replace option, as well. A list of all string replacements that were done is written to a file called archive.names.

You can change the default behavior of postmortem by setting preferences. This allows you to run the postmortem command without any arguments and archive your preferred choice of information. These preferences are stored in your Schrödinger user resources directory, and are managed using postmortem command options. The preference names and values are given in Table 1. Unlike options, preference names must not be abbreviated.

Table 1. Preferences for the postmortem utility, with the corresponding option
Preference	Option	Values	Default
`location`	`-location`	String defining directory	Current directory
`jobfiles`	`-[no]jobfiles`	`1\|0`	`1` (`-jobfiles`)
`alljobs`	`-[no]alljobs`	`1\|0`	`0` (`-noalljobs`)
`structures`	`-[no]structures`	`1\|0`	`0` (`-nostructures`)
`datafiles`	`-[no]datafiles`	`1\|0`	`0` (`-nodatafiles`)
`parents`	`-[no]parents`	`1\|0`	`1` (`-parents`)
`subjobs`	`-[no]subjobs`	`1\|0`	`1` (`-subjobs`)
`verbose`	`-verbose`	`1\|0`	`1` (`-verbose`)

To set preferences, use the -pref option:
```
postmortem -pref structures=1
postmortem -pref parents=0
```
To see what preferences are currently in force, use the -prefs option,
```
postmortem -prefs
```
To see the value for a particular preference, use -pref without asigning a value:
```
postmortem -pref verbose
```
To remove a preference, use the -reset option, for example
```
postmortem -reset verbose
```
To remove all preferences, use -reset without specifying a preference name:
```
postmortem -reset
```