splitcombine(1)             General Commands Manual            splitcombine(1)



NAME
       splitcombine - Produce command files for running volcombine in parallel

SYNOPSIS
       splitcombine  [options]  [Combine_command_file]

DESCRIPTION
       splitcombine will take a command file for combining pieces from two
       dual-axis tomograms and produce multiple command files that can be run
       in parallel by Processchunks.  The arguments are optional.  If no
       arguments are entered, the program will operate on volcombine.com, pro-
       ducing volcombine-start.com to do initial tasks, volcombine-NNN.com to
       produce individual pieces (e.g., volcombine-027.com to produce
       sum27.rec), and volcombine-finish.com to reassemble the pieces and
       clean up intermediate files.

       The program will modify the components of volcombine.com to place tem-
       porary files other than sum*.rec in a local temporary directory appro-
       priate for the machine running the command file.  However, there are no
       such files and no need for a local temporary directory after IMOD
       4.2.8.  This temporary directory is distinct from the temporary direc-
       tory that you can set up to do the combine operation in, which will be
       referred to as the master temporary directory.  The latter must be
       accessible from all machines.  If it is not accessible by the name
       present in the command file, it is necessary to enter a the -local and
       -global options with the local name and the name by which it is acces-
       sible from other machines.  However, if you set up your combine with a
       master temporary directory in /usr/tmp or /tmp, other machines will not
       be able to access this directory and the program will warn you that the
       operation cannot be run on multiple machines.


OPTIONS
       Splitcombine is a Python script and uses the PIP package for input (see
       the manual page for pip). Options can be specified either as command
       line arguments (with the -) or one per line in a command file (without
       the -).  Options can be abbreviated to unique letters; the currently
       valid abbreviations for short names are shown in parentheses.

       -comfile (-c) OR -CommandFile       File name
              Volcombine command file (default volcombine.com).  If this
              option is not entered and there is a non-option argument, it
              will be used for this filename.

       -local (-l) OR -LocalTempPath       File name
              The path to the master temporary directory that was placed into
              the command file by Setupcombine.  Only the portion of the
              path that differs from the globally accessible path needs to be
              supplied.

       -global (-g) OR -GlobalTempPath     File name
              The path by which all machines can access the master temporary
              directory.  Only the portion of the path that differs from the
              local path needs to be supplied

       -tempdir (-t) OR -TemporaryDirectory     File name
              Local directory for temporary files other than sum*.rec, which
              are no longer produced after IMOD 4.2.8.  The default is either
              a directory defined by the environment variable IMOD_TMPDIR, or
              /usr/tmp if it exists, or /tmp.  The local temporary directory
              was important for reducing network traffic and access of all
              machines to the same working directory.  This temporary direc-
              tory need not be accessible to all machines.

       -help (-h) OR -Usage
              Print usage summary

       -StandardInput
              Read parameter entries from standard input


FILES
       The finishing command file deletes the sum*.rec, as well as all command
       and log files for the pieces.

AUTHOR
       David Mastronarde  <mast at colorado dot edu>

SEE ALSO
       processchunks



IMOD                                 5.2.0                     splitcombine(1)