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)