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pegasus-plan(1) [debian man page]

PEGASUS-PLAN(1) 														   PEGASUS-PLAN(1)

NAME
pegasus-plan - runs Pegasus to generate the executable workflow SYNOPSIS
pegasus-plan [-v] [-q] [-V] [-h] [-Dprop=value...]] [-b prefix] [--conf propsfile] [-c cachefile[,cachefile...]] [-C style[,style...]] [--dir dir] [--force] [--force-replan] [--inherited-rc-files] [-j prefix] [-n] [-o site] [-s site1[,site2...]] [--staging-site s1=ss1[,s2=ss2[..]] [--randomdir[=dirname]] [--relative-dir dir] [--relative-submit-dir dir] -d daxfile DESCRIPTION
The pegasus-plan command takes in as input the DAX and generates an executable workflow usually in form of condor submit files, which can be submitted to an execution site for execution. As part of generating an executable workflow, the planner needs to discover: data The Pegasus Workflow Planner ensures that all the data required for the execution of the executable workflow is transferred to the execution site by adding transfer nodes at appropriate points in the DAG. This is done by looking up an appropriate Replica Catalog to determine the locations of the input files for the various jobs. At present the default replica mechanism used is RLS. The Pegasus Workflow Planner also tries to reduce the workflow, unless specified otherwise. This is done by deleting the jobs whose output files have been found in some location in the Replica Catalog. At present no cost metrics are used. However preference is given to a location corresponding to the execution site The planner can also add nodes to transfer all the materialized files to an output site. The location on the output site is determined by looking up the site catalog file, the path to which is picked up from the pegasus.catalog.site.file property value. executables The planner looks up a Transformation Catalog to discover locations of the executables referred to in the executable workflow. Users can specify INSTALLED or STAGEABLE executables in the catalog. Stageable executables can be used by Pegasus to stage executables to resources where they are not pre-installed. resources The layout of the sites, where Pegasus can schedule jobs of a workflow are described in the Site Catalog. The planner looks up the site catalog to determine for a site what directories a job can be executed in, what servers to use for staging in and out data and what jobmanagers (if applicable) can be used for submitting jobs. The data and executable locations can now be specified in DAX'es conforming to DAX schema version 3.2 or higher. OPTIONS
Any option will be displayed with its long options synonym(s). -Dproperty=value The -D option allows an experienced user to override certain properties which influence the program execution, among them the default location of the user's properties file and the PEGASUS home location. One may set several CLI properties by giving this option multiple times. The -D option(s) must be the first option on the command line. A CLI property take precedence over the properties file property of the same key. -d file, --dax file The DAX is the XML input file that describes an abstract workflow. This is a mandatory option, which has to be used. -b prefix, --basename prefix The basename prefix to be used while constructing per workflow files like the dagman file (.dag file) and other workflow specific files that are created by Condor. Usually this prefix, is taken from the name attribute specified in the root element of the dax files. -c file[,file,...], --cache file[,file,...] A comma separated list of paths to replica cache files that override the results from the replica catalog for a particular LFN. Each entry in the cache file describes a LFN , the corresponding PFN and the associated attributes. The pool attribute should be specified for each entry. LFN_1 PFN_1 pool=[site handle 1] LFN_2 PFN_2 pool=[site handle 2] ... LFN_N PFN_N [site handle N] To treat the cache files as supplemental replica catalogs set the property pegasus.catalog.replica.cache.asrc to true. This results in the mapping in the cache files to be merged with the mappings in the replica catalog. Thus, for a particular LFN both the entries in the cache file and replica catalog are available for replica selection. -C style[,style,...], --cluster style[,style,...] Comma-separated list of clustering styles to apply to the workflow. This mode of operation results in clustering of n compute jobs into a larger jobs to reduce remote scheduling overhead. You can specify a list of clustering techniques to recursively apply them to the workflow. For example, this allows you to cluster some jobs in the workflow using horizontal clustering and then use label based clustering on the intermediate workflow to do vertical clustering. The clustered jobs can be run at the remote site, either sequentially or by using MPI. This can be specified by setting the property pegasus.job.aggregator. The property can be overridden by associating the PEGASUS profile key collapser either with the transformation in the transformation catalog or the execution site in the site catalog. The value specified (to the property or the profile), is the logical name of the transformation that is to be used for clustering jobs. Note that clustering will only happen if the corresponding transformations are catalogued in the transformation catalog. PEGASUS ships with a clustering executable seqexec that can be found in the $PEGASUS_HOME/bin directory. It runs the jobs in the clustered job sequentially on the same node at the remote site. In addition, an MPI wrapper mpiexec, is distributed as source with PEGASUS. It can be found in the $PEGASUS_HOME/src/tools/cluster directory. The wrapper is run on every MPI node, with the first one being the master and the rest of the ones as workers. The number of instances of mpiexec that are invoked is equal to the value of the Globus RSL key nodecount. The master distributes the smaller constituent jobs to the workers. For e.g. If there were 10 jobs in the clustered job and nodecount was 5, then one node acts as master, and the 10 jobs are distributed amongst the 4 slaves on demand. The master hands off a job to the slave node as and when it gets free. So initially all the 4 nodes are given a single job each, and then as and when they get done are handed more jobs till all the 10 jobs have been executed. By default, seqexec is used for clustering jobs unless overridden in the properties or by the pegasus profile key collapser. The following type of clustering styles are currently supported: o horizontal is the style of clustering in which jobs on the same level are aggregated into larger jobs. A level of the workflow is defined as the greatest distance of a node, from the root of the workflow. Clustering occurs only on jobs of the same type i.e they refer to the same logical transformation in the transformation catalog. Horizontal Clustering can operate in one of two modes. a. Job count based. The granularity of clustering can be specified by associating either the PEGASUS profile key clusters.size or the PEGASUS profile key clusters.num with the transformation. The clusters.size key indicates how many jobs need to be clustered into the larger clustered job. The clusters.num key indicates how many clustered jobs are to be created for a particular level at a particular execution site. If both keys are specified for a particular transformation, then the clusters.num key value is used to determine the clustering granularity. 1. Runtime based. To cluster jobs according to runtimes user needs to set one property and two profile keys. The property pegasus.clusterer.preference must be set to the value runtime. In addition user needs to specify two Pegasus profiles. a. clusters.maxruntime which specifies the maximum duration for which the clustered job should run for. b. job.runtime which specifies the duration for which the job with which the profile key is associated, runs for. Ideally, clusters.maxruntime should be set in transformation catalog and job.runtime should be set for each job individually. o label is the style of clustering in which you can label the jobs in your workflow. The jobs with the same level are put in the same clustered job. This allows you to aggregate jobs across levels, or in a manner that is best suited to your application. To label the workflow, you need to associate PEGASUS profiles with the jobs in the DAX. The profile key to use for labeling the workflow can be set by the property pegasus.clusterer.label.key. It defaults to label, meaning if you have a PEGASUS profile key label with jobs, the jobs with the same value for the pegasus profile key label will go into the same clustered job. --conf propfile The path to properties file that contains the properties planner needs to use while planning the workflow. --dir dir The base directory where you want the output of the Pegasus Workflow Planner usually condor submit files, to be generated. Pegasus creates a directory structure in this base directory on the basis of username, VO Group and the label of the workflow in the DAX. By default the base directory is the directory from which one runs the pegasus-plan command. -f, --force This bypasses the reduction phase in which the abstract DAG is reduced, on the basis of the locations of the output files returned by the replica catalog. This is analogous to a make style generation of the executable workflow. --force-replan By default, for hierarichal workflows if a DAX job fails, then on job retry the rescue DAG of the associated workflow is submitted. This option causes Pegasus to replan the DAX job in case of failure instead. -g, --group The VO Group to which the user belongs to. -h, --help Displays all the options to the pegasus-plan command. --inherited-rc-files file[,file,...] A comma separated list of paths to replica files. Locations mentioned in these have a lower priority than the locations in the DAX file. This option is usually used internally for hierarchical workflows, where the file locations mentioned in the parent (encompassing) workflow DAX, passed to the sub workflows (corresponding) to the DAX jobs. -j prefix, --job-prefix prefix The job prefix to be applied for constructing the filenames for the job submit files. -n, --nocleanup This results in the generation of the separate cleanup workflow that removes the directories created during the execution of the executable workflow. The cleanup workflow is to be submitted after the executable workflow has finished. If this option is not specified, then Pegasus adds cleanup nodes to the executable workflow itself that cleanup files on the remote sites when they are no longer required. -o site, --o site The output site where all the materialized data is transferred to. By default the materialized data remains in the working directory on the execution site where it was created. Only those output files are transferred to an output site for which transfer attribute is set to true in the DAX. -q, --quiet Decreases the logging level. -r[dirname], --randomdir[=dirname] Pegasus Worfklow Planner adds create directory jobs to the executable workflow that create a directory in which all jobs for that workflow execute on a particular site. The directory created is in the working directory (specified in the site catalog with each site). By default, Pegasus duplicates the relative directory structure on the submit host on the remote site. The user can specify this option without arguments to create a random timestamp based name for the execution directory that are created by the create dir jobs. The user can can specify the optional argument to this option to specify the basename of the directory that is to be created. The create dir jobs refer to the dirmanager executable that is shipped as part of the PEGASUS worker package. The transformation catalog is searched for the transformation named pegasus::dirmanager for all the remote sites where the workflow has been scheduled. Pegasus can create a default path for the dirmanager executable, if PEGASUS_HOME environment variable is associated with the sites in the site catalog as an environment profile. --relative-dir dir The directory relative to the base directory where the executable workflow it to be generated and executed. This overrides the default directory structure that Pegasus creates based on username, VO Group and the DAX label. --relative-submit-dir dir The directory relative to the base directory where the executable workflow it to be generated. This overrides the default directory structure that Pegasus creates based on username, VO Group and the DAX label. By specifying --relative-dir and --relative-submit-dir you can have different relative execution directory on the remote site and different relative submit directory on the submit host. -s site[,site,...], --sites site[,site,...] A comma separated list of execution sites on which the workflow is to be executed. Each of the sites should have an entry in the site catalog, that is being used. To run on the submit host, specify the execution site as local. In case this option is not specified, all the sites in the site catalog are picked up as candidates for running the workflow. --staging-site s1=ss1[,s2=ss2[..]] A comma separated list of key=value pairs , where the key is the execution site and value is the staging site for that execution site. In case of running on a shared filesystem, the staging site is automatically associated by the planner to be the execution site. If only a value is specified, then that is taken to be the staging site for all the execution sites. e.g --staging-site local means that the planner will use the local site as the staging site for all jobs in the workflow. -s, --submit Submits the generated executable workflow using pegasus-run script in $PEGASUS_HOME/bin directory. By default, the Pegasus Workflow Planner only generates the Condor submit files and does not submit them. -v, --verbose Increases the verbosity of messages about what is going on. By default, all FATAL, ERROR, CONSOLE and WARN messages are logged. The logging hierarchy is as follows: 1. FATAL 2. ERROR 3. CONSOLE 4. WARN 5. INFO 6. CONFIG 7. DEBUG 8. TRACE For example, to see the INFO, CONFIG and DEBUG messages additionally, set -vvv. -V, --version Displays the current version number of the Pegasus Workflow Management System. RETURN VALUE
If the Pegasus Workflow Planner is able to generate an executable workflow successfully, the exitcode will be 0. All runtime errors result in an exitcode of 1. This is usually in the case when you have misconfigured your catalogs etc. In the case of an error occurring while loading a specific module implementation at run time, the exitcode will be 2. This is usually due to factory methods failing while loading a module. In case of any other error occurring during the running of the command, the exitcode will be 1. In most cases, the error message logged should give a clear indication as to where things went wrong. PEGASUS PROPERTIES
This is not an exhaustive list of properties used. For the complete description and list of properties refer to $PEGASUS_HOME/doc/advanced-properties.pdf pegasus.selector.site Identifies what type of site selector you want to use. If not specified the default value of Random is used. Other supported modes are RoundRobin and NonJavaCallout that calls out to a external site selector. pegasus.catalog.replica Specifies the type of replica catalog to be used. If not specified, then the value defaults to RLS. pegasus.catalog.replica.url Contact string to access the replica catalog. In case of RLS it is the RLI url. pegasus.dir.exec A suffix to the workdir in the site catalog to determine the current working directory. If relative, the value will be appended to the working directory from the site.config file. If absolute it constitutes the working directory. pegasus.catalog.transformation Specifies the type of transformation catalog to be used. One can use either a file based or a database based transformation catalog. At present the default is Text. pegasus.catalog.transformation.file The location of file to use as transformation catalog. If not specified, then the default location of $PEGASUS_HOME/var/tc.data is used. pegasus.catalog.site Specifies the type of site catalog to be used. One can use either a text based or an xml based site catalog. At present the default is XML3. pegasus.catalog.site.file The location of file to use as a site catalog. If not specified, then default value of $PEGASUS_HOME/etc/sites.xml is used in case of the xml based site catalog and $PEGASUS_HOME/etc/sites.txt in case of the text based site catalog. pegasus.data.configuration This property sets up Pegasus to run in different environments. This can be set to sharedfs If this is set, Pegasus will be setup to execute jobs on the shared filesystem on the execution site. This assumes, that the head node of a cluster and the worker nodes share a filesystem. The staging site in this case is the same as the execution site. nonsharedfs If this is set, Pegasus will be setup to execute jobs on an execution site without relying on a shared filesystem between the head node and the worker nodes. condorio If this is set, Pegasus will be setup to run jobs in a pure condor pool, with the nodes not sharing a filesystem. Data is staged to the compute nodes from the submit host using Condor File IO. pegasus.code.generator The code generator to use. By default, Condor submit files are generated for the executable workflow. Setting to Shell results in Pegasus generating a shell script that can be executed on the submit host. FILES
$PEGASUS_HOME/etc/dax-3.3.xsd is the suggested location of the latest DAX schema to produce DAX output. $PEGASUS_HOME/etc/sc-3.0.xsd is the suggested location of the latest Site Catalog schema that is used to create the XML3 version of the site catalog $PEGASUS_HOME/etc/tc.data.text is the suggested location for the file corresponding to the Transformation Catalog. $PEGASUS_HOME/etc/sites.xml3 | $PEGASUS_HOME/etc/sites.xml is the suggested location for the file containing the site information. $PEGASUS_HOME/lib/pegasus.jar contains all compiled Java bytecode to run the Pegasus Workflow Planner. SEE ALSO
pegasus-sc-client(1), pegasus-tc-client(1), pegasus-rc-client(1) AUTHORS
Karan Vahi <vahi at isi dot edu> Gaurang Mehta <gmehta at isi dot edu> Pegasus Team http://pegasus.isi.edu 05/24/2012 PEGASUS-PLAN(1)

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