PEGASUS-CLUSTER(1)														PEGASUS-CLUSTER(1)

NAME

       pegasus-cluster - run a list of applications

SYNOPSIS

       pegasus-cluster [-d] [-e | -f] [-S ec] [-s fn] [-R fn] [-n nr] [inputfile]

DESCRIPTION

       The pegasus-cluster tool executes a list of application in the order specified (assuming sequential mode.) It is generally used to do
       horizontal clustering of independent application, and does not care about any application failures. Such failures should be caught by using
       pegasus-kickstart to start application.

       In vertical clustering mode, the hard failure mode is encouraged, ending execution as soon as one application fails. When running a complex
       workflow through pegasus-cluster , the order of applications in the input file must be topologically sorted.

       Applications are usually using pegasus-kickstart to execute. In the pegasus-kickstart case, all invocations of pegasus-kickstart except the
       first should add the pegasus-kickstart option -H to supress repeating the XML preamble and certain other headers of no interest when
       repeated.

       pegasus-cluster permits shell-style quoting. One level of quoting is removed from the arguments. Please note that pegasus-kickstart will
       also remove one level of quoting.

ARGUMENTS

       -d
	   This option increases the debug level. Debug message are generated on stdout . By default, debugging is minimal.

       -e
	   This flag turns on the old behavior of pegasus-cluster to always run everything and return success no matter what. The -e flag is
	   mutually exclusive with the -f flag. By default, all applications are executed regardles of failures. Any detected application failure
	   results in a non-zero exit status from pegasus-cluster.

       -f
	   In hard failure mode, as soon as one application fails, either through a non-zero exit code, or by dying on a signal, further execution
	   is stopped. In parallel execution mode, one or more other applications later in the sequence file may have been started already by the
	   time failure is detected.  Pegasus-cluster will wait for the completion of these applications, but not start new ones. The -f flag is
	   mutually exclusive with the -e flag. By default, all applications are executed regardless of failures. Any detected application failure
	   results in a non-zero exit status from pegasus-cluster.

       -h
	   This option prints the help message and exits the program.

       -s fn
	   This option will send protocol message (for Mei) to the specified file. By default, all message are written to stdout .

       -R fn
	   The progress reporting feature, if turned on, will write one event record whenever an application is started, and one event record
	   whenever an application finished. This is to enable tracking of jobs in progress. By default, track logs are not written, unless the
	   environment variable SEQEXEC_PROGRESS_REPORT is set. If set, progress reports are appended to the file pointed to by the environment
	   variable.

       -S ec
	   This option is a multi-option, which may be used multiple times. For each given non-zero exit-code of an application, mark it as a form
	   of success. In -f mode, this means that pegasus-cluster will not fail when seeing this exit code from any application it runs. By
	   default, all non-zero exit code constitute failure.

       -n nr
	   This option determines the amount of parallel execution. Typically, parallel execution is only recommended on multi-core systems, and
	   must be deployed rather carefully, i.e. only completely independent jobs across of whole inputfile should ever be attempted to be run
	   in parallel. The argument nr is the number of parallel jobs that should be used. In addition to a non-negative integer, the word auto
	   is also understood. When auto is specified, pegasus-cluster will attempt to automatically determine the number of cores available in
	   the system. Strictly sequential execution, as if nr was 1, is the default. If the environment variable SEQEXEC_CPUS is set, it will
	   determine the default number of CPUs.

       inputfile
	   The input file specifies a list of application to run, one per line. Comments and empty lines are permitted. The comment character is
	   the octothorpe (#), and extends to the end of line. By default, pegasus-cluster uses stdin to read the list of applications to execute.

RETURN VALUE

       The pegasus-cluster tool returns 1, if an illegal option was used. It returns 2, if the status file from option -s cannot be opened. It
       returns 3, if the input file cannot be opened. It does not return any failure for failed applications in old-exit -e mode. In default and
       hard failure -f mode, it will return 5 for true failure. The determination of failure is modified by the -S option.

       All other internal errors being absent, pegasus-cluster will always return 0 when run without -f . Unlike shell, it will not return the
       last application's exit code. In default mode, it will return 5, if any application failed. Unlike shell, it will not return the last
       application's exit code. However, it will execute all applications. The determination of failure is modified by the -S flag. In -f mode,
       *pegasus-cluster returns either 0 if all main sequence applications succeeded, or 5 if one failed; or more than one in parallel execution
       mode. It will run only as long as applications were successful. As before, the *-S flag determines what constitutes a failure.

       The pegasus-cluster application will also create a small summary on stdout for each job, and one for itself, about the success and failure.
       The field failed reports any exit code that was not zero or a signal of death termination. It does not include non-zero exit codes that
       were marked as success using the -S option.

TASK SUMMARY

       Each task executed by pegasus-cluster generates a record bracketed by square brackets like this (each entry is broken over two lines for
       readability):

	   [seqexec-task id=1, start="2011-04-27T14:31:25.340-07:00", duration=0.521,
	    status=0, line=1, pid=18543, app="/bin/usleep"]
	   [seqexec-task id=2, start="2011-04-27T14:31:25.342-07:00", duration=0.619,
	    status=0, line=2, pid=18544, app="/bin/usleep"]
	   [seqexec-task id=3, start="2011-04-27T14:31:25.862-07:00", duration=0.619,
	    status=0, line=3, pid=18549, app="/bin/usleep"]

       Each record is introduced by the string seqexec-task with the following constituents, where strings are quoted:

       id
	   This is a numerical value for main sequence application, indicating the application's place in the sequence file. The setup task uses
	   the string setup , and the cleanup task uses the string cleanup .

       start
	   is the ISO 8601 time stamp, with millisecond resolution, when the application was started. This string is quoted.

       duration
	   is the application wall-time duration in seconds, with millisecond resolution.

       status
	   is the raw exit status as returned by the wait family of system calls. Typically, the exit code is found in the high byte, and the
	   signal of death in the low byte. Typically, 0 indicates a successful execution, and any other value a problem. However, details could
	   differ between systems, and exit codes are only meaningful on the same os and architecture.

       line
	   is the line number where the task was found in the main sequence file. Setup- and cleanup tasks don't have this attribute.

       pid
	   is the process id under which the application had run.

       app
	   is the path to the application that was started. As with the progress record, any pegasus-kickstart will be parsed out so that you see
	   the true application.

PEGASUS-CLUSTER SUMMARY
       The final summary of counts is a record bracketed by square brackets like this (broken over two lines for readability):

	   [seqexec-summary stat="ok", lines=3, tasks=3, succeeded=3, failed=0, extra=0,
	    duration=1.143, start="2011-04-27T14:31:25.338-07:00", pid=18542, app="./seqexec"]

       The record is introduced by the string seqexec-summary with the following constituents:

       stat
	   The string fail when pegasus-cluster would return with an exit status of 5. Concretely, this is any failure in default mode, and first
	   failure in -f mode. Otherwise, it will always be the string ok , if the record is produced.

       lines
	   is the stopping line number of the input sequence file, indicating how far processing got. Up to the number of cores additional lines
	   may have been parsed in case of -f mode.

       tasks
	   is the number of tasks processed.

       succeeded
	   is the number of main sequence jobs that succeeded.

       failed
	   is the number of main sequence jobs that failed. The failure condition depends on the -S settings, too.

       extra
	   is 0, 1 or 2, depending on the existence of setup- and cleanup jobs.

       duration
	   is the duration in seconds, with millisecond resolution, how long *pegasus-cluster ran.

       start
	   is the start time of pegasus-cluster as ISO 8601 time stamp.

SEE ALSO

       pegasus-kickstart(1)

CAVEATS

       The -S option sets success codes globally. It is not possible to activate success codes only for one specific application, and doing so
       would break the shell compatibility. Due to the global nature, use success codes sparingly as last resort emergency handler. In better
       plannable environments, you should use an application wrapper instead.

EXAMPLE

       The following shows an example input file to pegasus-cluster making use of pegasus-kickstart to track applications.

	   #
	   # mkdir
	   /path/to/pegasus-kickstart -R HPC -n mkdir /bin/mkdir -m 2755 -p split-corpus split-ne-corpus
	   #
	   # drop-dian
	   /path/to/pegasus-kickstart -H -R HPC -n drop-dian -o '^f-new.plain' /path/to/drop-dian /path/to/f-tok.plain /path/to/f-tok.NE
	   #
	   # split-corpus
	   /path/to/pegasus-kickstart -H -R HPC -n split-corpus /path/to/split-seq-new.pl 23 f-new.plain split-corpus/corpus.
	   #
	   # split-corpus
	   /path/to/pegasus-kickstart -H -R HPC -n split-corpus /path/to/split-seq-new.pl 23 /path/to/f-tok.NE split-ne-corpus/corpus.

ENVIRONMENT VARIABLES

       A number of environment variables permits to influence the behavior of pegasus-cluster during run-time.

       SEQEXEC_PROGRESS_REPORT
	   If this variable is set, and points to a writable file location, progress report records are appended to the file. While care is taken
	   to atomically append records to the log file, in case concurrent instances of pegasus-cluster are running, broken Linux NFS may still
	   garble some content.

       SEQEXEC_CPUS
	   If this variable is set to a non-negative integer, that many CPUs are attempted to be used. The special value auto permits to
	   auto-detect the number of CPUs available to pegasus-cluster on the system.

       SEQEXEC_SETUP
	   If this variable is set, and contains a single fully-qualified path to an executable and arguments, this executable will be run before
	   any jobs are started. The exit code of this setup job will have no effect upon the main job sequence. Success or failure will not be
	   counted towards the summary.

       SEQEXEC_CLEANUP
	   If this variable is set, and contains a single fully-qualified path to an executable and arguments, this executable will be before
	   pegasus-cluster quits. Failure of any previous job will have no effect on the ability to run this job. The exit code of the cleanup job
	   will have no effect on the overall success or failure state. Success or failure will not be counted towards the summary.

HISTORY

       As you may have noticed, pegasus-cluster had the name seqexec in previous incantations. We are slowly moving to the new name to avoid
       clashes in a larger OS installation setting. However, there is no pertinent need to change the internal name, too, as no name clashes are
       expected.

AUTHORS

       Jens-S. Vockler <voeckler at isi dot edu>

       Pegasus http://pegasus.isi.edu/

								    05/24/2012							PEGASUS-CLUSTER(1)