subm/submfg(1)              General Commands Manual             subm/submfg(1)



NAME
       subm/submfg - Run an IMOD command file in the background or foreground

SYNOPSIS
       submfg  [options]  command_file  [command_file ...]

DESCRIPTION
       subm runs the operations in one or more IMOD command files in the back-
       ground.  When multiple files are given, they are run in sequence.  The
       script that runs the command files is actually named submfg, and if
       invoked with this name, the operations will run in the foreground.  The
       IMOD startup scripts on all systems define an alias "subm" that will
       run submfg in the background.  There is also a separate script, "subm",
       that simply starts submfg as a background process.  "subm" will thus
       work even from an IMOD-capable Command Prompt window in Windows, and on
       systems where the alias is not available (e.g., some Ubuntu systems).

       A command file is converted to a Python script and run with Vmstopy;
       see that man page for a description of the allowed format.  The full
       command file name can be given, or the extension can be omitted if it
       is ".com" or ".pcm".  A log file is automatically made for each command
       file; by default the name is the root of the command file name with the
       extension ".log", and an existing copy of that file becomes a backup
       with "~" added to the name.  This behavior can be modified (see -l
       option).  When each command file is started, the process ID will be
       printed to terminal.  When a command file completes, there is a comple-
       tion message, which can be modified by setting the environment variable
       SUBM_MESSAGE.  If a command file exits with an error, vmstopy extracts
       an error message from the log if possible, or prints the last few lines
       of the log if not.

       There are two options for terminating submfg and the job started by it.
       If submfg was started with the alias, the best way is to bring it to
       the foreground by entering "fg" and interrupt it by typing "Ctrl-C".
       This method will clean up the temporary file used to run the script.
       The second way, and the only way if invoking with script instead of the
       alias, is to use
           imodkillgroup  PID
       where PID is the process ID printed when each job starts.  This method
       will leave behind the temporary file.

OPTIONS
       -c     Continue with the next command file even if one command file
              fails; the default is to stop after a failure.

       -t     Print the elapsed real and CPU time when each command file fin-
              ishes.

       -s     Convert the command files to C-shell scripts with Vmstocsh
              and run with csh.  See that man page for the allowed format.

       -n #   Run the jobs with a "niceness" increment set to the given num-
              ber.

       -l #   Set the type of numbered or time-stamped log file names to use.
              The options are:
                    1 - 4 for sequential numbers with 1 to 4 digits
                   -1 for date-time stamps like Mar-01-195046.4
                   -2 for date-time stamps like 20120301-195121.9
                   -3 for date-time stamps like 2012-03-01T19:51:51.9
              There is also an environment variable, SUBM_LOG_TYPE, that can
              be set to one of these values to define the default log type.
              In that case, "-l 0" can be used to override this default and
              get a plain log.

AUTHOR
       David Mastronarde,  mast at colorado dot edu

SEE ALSO
       processchunks

FILES
       The program makes a temporary file named submtemp.PID where PID is the
       process ID.  This file will be left behind if the process is killed.



IMOD                                4.10.10                     subm/submfg(1)