processchunks(1)                                              processchunks(1)



NAME
       processchunks - Run command files in parallel on multiple processors

SYNOPSIS
       processchunks [options] <machine list> <root name of command files>

       processchunks [options] -q # <queue command and arguments> <root name>

DESCRIPTION
       processchunks will process a set of command files in parallel on multi-
       ple machines or processors that have access to a common filesystem.  It
       can also be used to run a single command file on a remote machine.


   Command Files
       The command files should be in the format runnable with Vmstocsh
       (e.g., using subm) and be named like files produced by Chunksetup.
       Specifically, the files for processing individual components should be
       named rootname-001.com, rootname-002.com, etc., where "rootname" is the
       root name of the command files, entered as the last command line argu-
       ment.  If the command files create temporary files, they must be named
       uniquely, such as by ending their names in .$$ and placing them in
       /usr/tmp.  (See Chunksetup for an alternative using hostnames).  The
       temporary files should be removed by the individual command files with
       statements like
       $if (-e /usr/tmp/tmpfil.$$) rm -f /usr/tmp/tmpfil.$$

       In addition to the files for individual chunks, there may also be two
       additional files: rootname-start.com, to perform initial tasks, and
       rootname-finish.com, for final assembly and cleanup.  If the start file
       exists, Processchunks will run this on the first machine before start-
       ing to distribute the chunks; and if the finish file exists, it will
       also be run on the first machine when all chunks are finished.

       It is also possible to execute groups of command files in parallel,
       then run one command file when all of these are done, then go on to
       another group of files in parallel.  This is done by adding "-sync"
       after the number for each file to be run for synchronization.  The
       files should all still have unique, sequential numbers.  For example,
       if the 10th and 20th files are named rootname-010-sync.com and root-
       name-020-sync.com, then files 1 to 9 will be run to completion in par-
       allel, then rootname-010-sync.com will be run alone on the first
       machine, then 11 to 19 will be run in parallel, then root-
       name-020-sync.com will be run alone, then all remaining files will be
       run in parallel.

       To run any single command file on a remote machine, simply use the -s
       option and provide the machine name and the name of the command file.


   Running Processchunks
       The machine list provided on the command line should be a list of
       machine names or IP addresses, separated by commas and with no embedded
       spaces.  Machines with multiple processors should be entered as many
       times as the number of processors that you want to use.  The local
       machine on which you are running Processchunks can be identified by its
       hostname or as "localhost"; in either case the command will be run
       directly on the machine.  If this is the only machine, then it can be
       identified by a single number specifying the number of processors to
       use.  For example, you can enter "4" instead of "localhost,local-
       host,localhost,localhost".  For all other machines, the command will be
       run with ssh.  You must be set up to log into each of the machines with
       ssh without having to enter a password (see below).  Each machine must
       have access to the current directory.  The -w option can be used to
       specify the path by which remote machines can access the current direc-
       tory.

       Processchunks first probes all of the machines to see if connections
       can be established and to show you the first line of the "w" output on
       each machine (or the output of "imodwincpu" on a Windows machine).
       This will also allow you to provide any one-time interactive confirma-
       tion needed by ssh, such as when you first log in to the machine.  If
       the "w" or "imodwincpu" command cannot be run on a machine, it is auto-
       matically removed from the list.  After this probe, the program asks
       you to confirm that you want to proceed with this list of machines
       (unless you use the -g option to skip this confirmation).  Thus, you
       could run Processchunks with a large list of machines, examine this
       output, then exit and restart after eliminating machines with too much
       load.

       After the confirmation, Processchunks starts jobs on all of the
       machines and watches for completion.  It detects successful completion
       by adding a command to the end of each file to write "CHUNK DONE" into
       the log.  Jobs are started with "nice".  When the job on a machine fin-
       ishes, that machine is given another job and the program reports the
       total number of chunks done so far.  When a job appears to have failed,
       the job is started again.  Initially the job may tend to be restarted
       on the same machine where it failed, but near the end when there are
       other machines free, it will be sent to another machine.

       Except on Windows, if you type "Esc" and "Enter" at the beginning of a
       line, the program will give you four choices: killing any running jobs
       and terminating, stopping after letting any running jobs finish,
       attempting to restart with the current list of machines, or just con-
       tinuing.  If you choose to terminate or restart, existing jobs will
       first be killed to avoid having the same job running twice at the same
       time.  When you rerun this program after stopping in this way, be sure
       to use the -r option so that existing results will be retained.  This
       method of interacting with the program replaces the use of Ctrl-C with
       the earlier script version of processchunks.

       On Windows, interaction in the terminal running the program is not pos-
       sible, and the program is automatically run in the background via an
       alias to protect it from being interrupted with Ctrl-C.  Thus the only
       way to issue instructions to it is by entering them into a file that
       the program watches.  The default name of this file is "process-
       chunks.input" but you can set a different name with the -c option.


   Running on a Cluster Queue
       Processchunks can submit all command files to a cluster queue instead
       of running them on specific machines with ssh, provided that there is a
       program that can perform the operations needed to place a chunk on the
       queue and kill jobs.  IMOD contains a script, Queuechunk, which can
       do these operations for some specific queue types.  For other queues or
       variations, this script would have to be modified or replaced.  To use
       a queue, enter the -q option with the maximum number of jobs to be
       placed on the queue at any time, and replace the list of machine name
       with the command that Processchunks needs to issue, e.g.:
          "queuechunk -t pbs -q fast"
       Note that the command will contain multiple words and must be enclosed
       in quotes as above.  With the version distributed in IMOD, the type
       must be specified with -t, and there is an option -q to specify the
       name of the queue, and an option -h to specify the name of the head
       node, which would then be contacted via ssh.


   Initial Configuration
       To set up ssh keys for access without passwords, simply run
          ssh-keygen -t dsa
       and type Enter for all of the queries.  Then enter:
          cp $HOME/.ssh/id_dsa.pub $HOME/.ssh/authorized_keys
       If necessary, distribute this authorized_keys file to the .ssh directo-
       ries on other machines that do not have the same home directory.  The
       three different kinds of platforms (Linux/Unix, Mac OSX, Windows) may
       require separately generated keys.  If this seems to be the case, run
       ssh-keygen once on each type of machine then combine the
       .ssh/id_dsa.pub files from each into one authorized_keys file.  Dis-
       tribute this combined authorized_keys file to the .ssh directories.

       Processchunks runs jobs via ssh by starting a non-interactive bash
       login shell on the remote computer.  Any programs to be run must be on
       your path when logging in as a bash user.  If you use only IMOD pro-
       grams in the command file and IMOD has been installed by the default
       method, there should be no problem.  However, if you set up the IMOD
       environment in your own startup files instead of in the default way,
       you need to make sure that the environment is defined when running this
       bash shell.  Specifically, you need to set the IMOD_DIR environment
       variable then source $IMOD_DIR/IMOD-....sh in your ~/.bash_profile and
       not just in your ~/.bashrc, since the latter is not run by the non-
       interactive shell.  Similarly, if you are running programs outside IMOD
       whose environment is set up in your own startup files, you need to do
       that in to set environment only in ~/.bash_profile.  Thus, the recom-
       mended approach is to set the environment in ~/.bashrc and source that
       file from ~/.bash_profile.

       To diagnose problems, there are a few tests that you can run by issuing
       the same kind of command that Processchunks uses to run jobs, of the
       form:
          ssh -x machine bash --login -c \'"command"\'
       where the command can be relatively complex because of the quoting; but
       the quoting can be omitted for simple commands.  Specifically, use
          ssh -x machine bash --login -c \'"cd directory"\'
       to test if you can change to the given directory.  Use
          ssh -x machine bash --login -c imodinfo
       to test if the remote machine can run IMOD this way, and use
          ssh -x machine bash --login -c env > env.out
       to collect the environment if there is trouble running IMOD.

       Parallel processing through eTomo uses Processchunks.  The available
       machines are generally defined in a file "cpu.adoc" that is located in
       the directory pointed to by the environment variable IMOD_CALIB_DIR
       (default /usr/local/ImodCalib).  See the example cpu.adoc file in
       $IMOD_DIR/autodoc and the manual page for cpuadoc for full details
       on configuring this file.  For a single machine with multiple CPUs,
       there are three simple options for enabling the parallel processing:
          1) In eTomo, open the Settings dialog from the Options menu, check
       "Enable Parallel processing" and enter the number of processors.
          2) Make a file /usr/local/ImodCalib/cpu.adoc with these two lines:
              [Computer = localhost]
              number = 4
       where the number should be set to the number of processors.
           3) set the environment variable IMOD_PROCESSORS to the number of
       processors, e.g.,
           setenv IMOD_PROCESSORS 4     (for tcsh users)
           export IMOD_PROCESSORS=4     (for bash users)


   Options
       Processchunks 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 -):

       -r     Resume processing and retain all existing log files.  The
              default is to remove all existing log files, run rootname-
              start.com if it exists, and then run all of the individual com-
              mand files, finishing with rootname-finish.com if it exists.
              With this option, the program will not rerun any command files
              whose corresponding log files end with "CHUNK DONE", including
              the start and finish files.

       -s     Run a single command file on a remote machine (i.e., the first
              machine in machine list).  The command file is not required to
              be numbered.  The rootname given on the command line can be
              either the full name or the name excluding ".com".

       -g     Go start processing after probing the machines, without waiting
              for confirmation from the user.

       -n    Integer
              Run jobs with "niceness" set to the given value, which can range
              from 0 for no reduction in priority to 19 for maximum reduction.
              The default nice value is 18.

       -w    File name
              The full path for reaching the current directory on the remote
              machines.  This entry is needed when working on a local disk
              whose mounted path on the other machines is different from its
              path (as given by pwd) on the local machine.

       -d    Integer
              Drop a machine from the list if it fails this number of times in
              a row.  The default criterion is 5.

       -e    Integer
              Quit if a chunk gives a processing error (as opposed to failing
              to start) this number of times.  All running jobs will be
              killed.  The default limit is 5.

       -c    File name
              Check the given file periodically for lines with commands to
              quit, pause, or drop a machine (Q, P, or D machine_name).  The
              default name of this file is "processchunks.input".

       -q    Integer
              Put chunks on a cluster queue instead of sending them to indi-
              vidual machines via ssh.  The given value indicates the maximum
              number of chunks to submit at any one time.  With this option,
              the list of machine names must be replaced by the command needed
              to interact with the queue.

       -Q    Text string
              When running on a queue, this option can be used to specify the
              name that Processchunks will use when it reports chunks being
              started and finishing.
               The entry must be a single word with no embedded spaces.  It
              need not match the actual name of the queue; the default is
              "queue".

       -P     Output process ID.  When this option is entered together with
              "-g", the program will skip probing machine loads.

       -v     Verbose output

       -V    Text string
              This option enables debugging output from a specific class or
              function.  It has no effect if "-v" is not entered too.  The
              entry has the form "?|?,2|class,[function,[...]][,2]|2" where 2
              means more verbose and ?  lists the functions that have informa-
              tion to print.

       -help  Print usage message

       -StandardInput
              Read parameter entries from standard input


FILES
       Log files will be generated for all command files that are run.  The C-
       shell script produced by Vmstocsh for rootname-nnn.com is saved to
       rootname-nnn.csh.  This file is removed after the command file com-
       pletes.

BUGS
       Ctrl-C cannot be blocked on Windows, so the program needs to be run in
       the background to protect it from being killed inadvertently.


AUTHOR
       Sue Held  <sueh at colorado dot edu>

HISTORY
       Up until IMOD 4.2.8, processchunks was a script written in C shell.  It
       is now a program in C++ using Qt.

SEE ALSO
       chunksetup, vmstocsh, queuechunk, cpuadoc



BL3DEMC                              4.3.7                    processchunks(1)