multisim Command Help

Command: $SCHRODINGER/utilities/multisim

Multisim workflow program

Usage:
* To run a new job:
  $SCHRODINGER/utilities/multisim [<options>] {-m <file>.msj} {<file>.cms|<file>.mae}

* To restart a previous job:
  $SCHRODINGER/utilities/multisim [<options>] {-RESTART <multisim_checkpoint_file>}
  You normally also need to specify the '-d' option.

I/O options:
 -i       <input file>   input structure file in the .cms or .mae format
                         (This option has been DEPRECATED, please specify the
                         .cms or .mae file without the -i flag in the future)
 -m       <input_file>   input .msj file defining the basic workflow
 -RESTART <input_file>   multisim checkpoint file for restarting a job.
 -r       <input file>   multisim checkpoint file for restarting a job.
                         (This option has been DEPRECATED, please use -RESTART
                         instead in the future)
 -d       <input_file>   stage data file from the previous job and usually with
                         the .tgz suffix. This option should be used only in
                         restarting a job with multisim checkpoint file.
 -c       <input_file>   set configuration parameters for a family of stages.
 -ADD_FILE <input_file>  Additional input file to copy to the working directory
                         of this multisim job
 -ALT_DIR <directory>    Alternative directory where to look for input files
 -o       <output_file>  output .cms or .mae file. This file can be incorporated
                         into Maestro.

Workflow options:
 -m       <input_file>   input .msj file defining the basic workflow
 -c       <input_file>   set configuration parameters for a family of stages.
 -set     <string>       modify the basic workflow defined by the .msj file.

Job options:
 -JOBNAME <job_name>     name of this multisim job
 -HOST    <host_name>    host machine to run the multisim main job (default is
                         localhost)
 -SUBHOST <host_name>    host machine to run subjobs
 -host    <host_name>    host machine to run subjobs.
                         (This option has been DEPRECATED, please use -SUBHOST
                         instead in the future)
 -RETRIES <number>       maximum times to retry failed subjobs (default is 3).
 -max_retries <number>   maximum times to retry failed subjobs (default is 3).
                         (This option has been DEPRECATED, please use -RETRIES
                         instead in the future)
 -TMPDIR  <dir>          specify a tmpdir setting for this job
 -WAIT                   do not return until the job completes.
 -SAVE                   return zip archive of job directory at job completion.
 -NICE                   run the job at reduced priority.
 -maxjob  <number>       maximum number of simultaneous subjobs (default is 1)
 -mode    {umbrella}     run in non-default execution mode. Currently, there is
                         only 1 valid value: umbrella. In umbrella mode, subjobs
                         will run on the nodes allocated to the main job.
 -max-walltime <number>  number of seconds to run the job and then checkpoint.

Other options:
 -description <text>     job description to print to the log
 -nopref                 ignore the multisim preference file.
 -probe                  probe a checkpoint file and quit.
 -quiet                  light log information (default)
 -verbose                heavy log information
 -debug                  turn on multisim debug mode.
 -DEBUG                  turn on both multisim and jobcontrol debug modes.
 -v, -version            show the program's version and exit.

 -h, -help, -HELP [<topic>]
                         show help and quit. User can optionally specify a topic
                         for help. Valid topics are the following: @all, @doc,
                         @<flag> (where <flag> represents the flag of any valid
                         option, e.g. @-help), @example, and @deprecated.
                         For more detail see help of the '@-help' topic.