MacroModel Reference Manual - ISP

Chapter 2: Running MacroModel2.2 Job ControlSchrödinger’s job control facility controls the execution of MacroModel jobs, including remoteand distributed MacroModel jobs (see Section 2.3 on page 19). Whether a job is started fromthe shell or from Maestro, the job control procedures can be carried out either from the shell, asdescribed below, or from the Monitor panel in Maestro. For a complete description of jobcontrol, see Chapter 3 of the Job Control Guide.The $SCHRODINGER/jobcontrol script provides a variety of mechanisms for obtaining informationabout jobs and for interacting with running jobs. The script can be run either interactivelyor as a shell command. Executing the command:$SCHRODINGER/jobcontrolwithout arguments invokes the interactive use of the facility; the -HELP option describes usage.The -stop jobid option stops a job gracefully. The -pause and -resume options suspend andrestart jobs, and the -update option causes the running job to perform an update to its log file.These functions supersede the former behavior of the .stp, .hlt, and .upt files (described inSection 2.2.1 on page 17) which no longer have an effect unless DEBG 931 is specified.Note:While the -kill option can be used to stop a job immediately, its use with distributedMacroModel jobs might on occasion not kill all of the processes associated with therun. We recommend using the -stop option to avoid this problem.The job control utility maintains a database containing the status of all jobs in $HOME/.schrodinger/.jobdb. Normally, when running MacroModel jobs from Maestro’s projectfacility, the database is cleared when jobs are incorporated into projects. Otherwise, the.jobdb directory could become quite full over time. The jobcontrol utility can be used topurge the job database. For example, to purge the entire database, use the -purge all option.Of course, you should not purge jobs that you expect to incorporate into Maestro projects.Completed jobs are purged by default after a week. The job control utility checks for old jobswhenever a job is initiated. To change the threshold for purging jobs, set the environment variableSCHRODINGER_JOBDB_CLEANUP to the desired value in seconds.2.2.1 Interacting With a Running MacroModel Job Via FilesThe job control facility can be run either from Maestro or from the command line, and can beused to interact with running MacroModel jobs. Using the job-control facility is the recommendedmethod for interacting with running MacroModel jobs, but file-based methods forcontrolling running MacroModel jobs are described below.MacroModel 9.7 Reference Manual 17