subm

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.
 -k Keep backslashes in input lines instead of converting them to
 forward slashes (see Vmstopy).
 -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年03月01日T19:51:51.9
 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 5.2.0 subm/submfg(1)