Pegasus 2.4.0 Released

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Release Notes for PEGASUS 2.4.0

1) Support for Pegasus DAX 3.0 

   Pegasus now also can accept DAX'es in Pegasus 3.0 format 

   Some salient features of the new format are
   - Users can specify locations of the files in the DAX
   - Users can specify what executables to use in the DAX
   - Users can specify sub dax in the DAX using the dax element. The
     dax jobs result in a separate subworkflow being launched with the 
     appropriate pegasus-plan command as the prescript
   - Users can specify condor DAG's in the DAX using the dag
     element. The dag job is passed on the Condor DAGMAN as a SUBDAG
     for execution.

   A sample 3.0  DAX can be found at

   In the next Pegasus release ( Pegasus 3.0 ) a JAVA DAX API will be
   made available. Certain more extensions will be added to the
   schema. For feature requests email

2) Support for running workflows on EC2 using S3 for storage

   Users while running on Amazon EC2 can use S3 for storage backend
   for the workflow execution. The details below assume that a user
   configures a condor pool on the nodes allocated from EC3

   To enable Pegasus for S3 the following properties need to be set.

   - pegasus.execute.*.filesystem.local = true
   - pegasus.transfer.*.impl = S3
   - pegasus.transfer.sls.*.impl = S3
   - pegasus.dir.create.impl = S3
   - pegasus.file.cleanup.impl = S3
   - pegasus.gridstart = SeqExec
   - pegasus.transfer.sls.s3.stage.sls.file = false

   For data stagein and creating S3 buckets for workflows pegasus
   relies on the amazon provided s3cmd command line client.
   Pegasus looks for a transformation with namespace amazon and
   logical name as s3cmd in the transformation catalog to figure out
   the location of the s3cmd client. for e.g in the File based
   Transformation Catalog the full name for transformation will be 

   In order to enable stdtout and stderr streaming correctly from
   Condor on EC2 we recommend adding certain profiles in the site
   catalog for the cloud site.
   Here is a sample site catalog

   <site handle="ec2" sysinfo="INTEL32::LINUX">
      <profile namespace="env" key="PEGASUS_HOME">/usr/local/pegasus/default</profile>
      <profile namespace="env" key="GLOBUS_LOCATION">/usr/local/globus/default</profile>
      <profile namespace="env" key="LD_LIBRARY_PATH">/usr/local/globus/default/lib</profile>
       <!-- the directory where a user wants to run the jobs on the
   	nodes retrived from ec2 -->
       <profile namespace="env" key="wntmp">/mnt</profile>
       <profile namespace="pegasus" key="style">condor</profile>
       <!-- to be set to ensure condor streams stdout and stderr back
	to submit host -->	
       <profile namespace="condor" key="should_transfer_files">YES</profile>
       <profile namespace="condor" key="transfer_output">true</profile>
       <profile namespace="condor" key="transfer_error">true</profile>
       <profile namespace="condor" key="WhenToTransferOutput">ON_EXIT</profile>
       <profile namespace="condor" key="universe">vanilla</profile>

       <profile namespace="condor" key="requirements">(Arch==Arch)&amp;&amp;(Disk!=0)&amp;&amp;(Memory!=0)&amp;&amp;(OpSys==OpSys)&amp;&amp;(FileSystemDomain!="")</profile>
       <profile namespace="condor" key="rank">SlotID</profile>
       <lrc url="rls://"/>
       <gridftp url="s3://" storage="" major="2" minor="4" patch="3"/>
       <jobmanager universe="vanilla" url="" major="2" minor="4" patch="3"/>
       <jobmanager universe="transfer" url="" major="2" minor="4" patch="3"/>

       <!-- create a new bucket for each wf
           <workdirectory >/</workdirectory>
        <!-- use an existing bucket -->
   Relevant JIRA links

3) pegasus-analyzer

   There is a new tool called pegasus-analyzer. It helps the users to
   analyze the workflows after the workflow has finished executing. 

   It is not meant to be run while the workflow is still running. To
   track the status of a running workflow for now, the users are
   recommended to use pegasus-status. 

   pegasus-analyzer looks at the workflow submit directory and parses
   the condor dagman logs and the job.out files to print a summary of
   the workflow execution. 

   The tool prints out the following summary of the workflow

   Total jobs
   jobs succeeded
   jobs failed
   jobs unsubmitted

   For all the failed jobs the tool prints out the contents of job.out
   and job.err file. 

   The user can use the --quiet option to display only the paths to
   the .out and .err files. This is useful when the job output is
   particularly big or when kickstart is used to launch the jobs. 

   For pegasus 3.0 the tool will be updated to parse kickstart output
   files and provide a concise view rather than displaying the whole

4) Support for Condor Glite

   Pegasus now supports a new style named glite for generating the submit
   files. This allows pegasus to create submit files for a glite
   environment where a glite blahp talks to the scheduler instead of
   GRAM. At a minimum the following profiles need to be associated with
   the job. 

   pegasus profile style - value set to glite
   condor profile grid_resource - value set to the remote scheduler to
   	  	  		  which glite blahp talks to .

    This style should only be used when the condor on the submit host
    can directly talk to scheduler running on the cluster. In Pegasus
    site  catalog there should be a separate compute site that has
    this style associated with it. This style should not be specified
    for the local site. 

    As part of applying the style to the job, this style adds the
    following classads expressions to the job description 

    +remote_queue - value picked up from globus profile queue
    +remote_cerequirements - See below

    The remote CE requirements are constructed from the following
    profiles associated with the job. The profiles for a job are
    derived from various sources 

    - user properties
    - transformation catalog
    - site catalog
    - DAX

    Note it is upto the user to specify these or a subset of them.

    The following globus profiles if associated with the job are picked up

    hostcount -> PROCS
    count -> NODES
    maxwalltime-> WALLTIME

    The following condor profiles if associated with the job are picked up

    priority -> PRIORITY

    All the env profiles are translated to MYENV

    For e.g. the expression in the submit file may look as

    +remote_cerequirements = "PROCS==18 && NODES==1 && PRIORITY==10 && WALLTIME==3600
       && PASSENV==1 && JOBNAME==\"TEST JOB\" && MYENV ==\"FOO=BAR,HOME=/home/user\""
    All the jobs that have this style applied dont have a remote
    directory specified in the submit directory. They rely on
    kickstart to change to the working directory when the job is
    launched on the remote node. 

5) Generating a site catalog for OSG using OSGMM
   The pegasus-get-sites tool has been modified to query the OSGMM (
   OSG Match Maker) to generate a site catalog for a VO 

   It builds upon the earlier Engage implementation. It has now been
   generalized and renamed to OSGMM 

   To pegasus-get-sites the source option now needs to be OSGMM
   instead of Engage 

   Some of the changes are

   The condor collector host can be specified at command line or in
   properties by specifying the property .
   It defaults to 

   If a user is part of the Engage VO they should set

   The default VO used is LIGO. Can be overriden by specifying the
   --vo option to pegasus-get-sites , or specifying the property 

   By default the implementation always returns validated sites. 
   To retrieve all sites for a VO set to false.

   In case of multiple gatekeepers are associated with the same osg
   site, multiple site catalog entries are created in the site
   catalog. A suffix is added to the extra sites (__index , where
   index starts from 1) 

   Sample Usage
   pegasus-get-sites --source OSGMM --sc osg-sites.xml --vo LIGO --grid OSG

   Tracked in JIRA at

   Currently, there is no way to filter sites according to the grid ( OSG|OSG-ITB ) in OSGMM

   The site catalog generated has storage directories that have a VO component in them.

6) Generating a site catalog for OSG using MYOSG
   pegasus-get-sites has now been modified to generate a site catalog by querying MyOSG

   To use MYOSG as the backend the source option needs to be set to MYOSG

   Sample usage

   pegasus-get-sites --source MYOSG --sc myosg-sites-new.xml -vvvvv --vo  ligo --grid osg
   This was tracked in JIRA
   Pegasus Team recommends using OSGMM for generating a site catalog.

7) Separation of Symlink and Stagein Transfer Jobs

   The following transfer refiners
   - Default
   - Bundle
   - Cluster
   now support the separation of the symlink jobs from the stage in
   jobs. While using these refiners, the files that need to be
   symlinked against existing files on a compute site will have a
   separate symlink job. The files that need to be actually copied to
   a remote site, will appear in the stage_in_ jobs. 

   This distinction, allows for the users to stage in data using third
   party transfers that run on the submit host, and at the same time
   be able to symlink against existing datasets. 
   The symlink jobs run on the remote compute sites. Earlier this was
   not possible, and hence for a user to use symlinking they had to
   turn off third party transfers. This resulted in an increased load
   on the head node as the stage in jobs executed there. 

   By default, Pegasus will use the transfer executable shipped with
   the worker package to do the symbolic linking . 

   If the user wants to change the executable to use , they can set the following property


   The above also allows us to use separate executables for staging in
   data and for symbolic linking. 
   For e.g. we can use GUC to stage in data by setting

   pegasus.transfer.stagein.impl GUC

   To control the symlinking granularity in the Bundle and Cluster
   refiners the following Pegasus profile keys can be associated 


   The feature implementation was tracked in JIRA at

8) Bypassing First Level Staging of Files for worker node execution

   Pegasus now has  capability to bypass first level staging if the
   input files in the replica catalog have a pool attribute matching
   the site at which a job is being run. This applies in case of
   worker node execution. 

   The cache file generated in the submit directory is the transient
   replica catalog. It also now has locations of where the inpute
   files are staged on the remote sites. Earlier it was only the files
   that were generated by the workflow. 

   Tracked in JIRA here 

9) Resolving SRM URL's for file URL's on a filesystem
   There is now support to resolve the SRM urls in the replica catalog to
   the file url on a site. The user needs to specify the URL prefix
   and the mount point of the filesystem.

   This can be done by specifying the properties


   Pegasus will then map SRM URL's associate with site to a paht on
   the filesytem by replacing the service url component with the mount

   For example if user has this specified

   pegasus.transfer.srm.ligo-cit.service.url          srm://
   pegasus.transfer.srm.ligo-cit.service.mountpoint   /mnt/hadoop/
   then url
   will resolve to 


10) New Transfer implementation Symlink

   Pegasus has now support for a perl executable called symlink
   shipped with the Pegasus worker package, that can be used to create
   multiple symlinks against input datasets in a single invocation 

   The Transfer implementation that uses the transfer executable also
   has the same functionality. 
   However, the transfer executable complains if it cannot find the
   Globus client libraries. 

   In order to use this executable for the symlink jobs, users need to
   set the following property 
   pegasus.transfer.symlink.impl Symlink

   Later on ( pegasus 3.0 release onwards ) this will be made the
   default executable to be used for symlinking jobs. 

11) Passing options forward to pegasus-run in pegasus-plan

   Users can now pass forward option to pegasus-run invocation that is
   used to submit the workflows in case of successful mapping.

   There is a  --forward option[=value] to pegasus-plan . This option
   allows a user to forward options to pegasus-run.
   For e.g. nogrid option can be passed to pegasus-run as follows
   pegasus-plan --forward nogrid

   The option can be repeated multiple times to forward multiple
   options to pegasus-run. The longopt version should always be
   specified for pegasus-run. 

12) Passing extra arguments SLS transfer implementations

   Users now can specify pegasus.transfer.sls.arguments to pass extra
   options at runtime to the SLS Implementations used by Pegasus. 
   The following SLS transfer implementations accept the above property.


13) Passing non standard java options to dax jobs in DAX 3.0

   The non standard jvm options (-X[option]) can now be specified for
   the sub workflows in the arguments section for the dax jobs. 

   For example for the DAX jobs , user can set the java max heap size
   to 1024m by specifying -X1024m in the arguments for the DAX job 

14) Location of Condor Logs directory on the submit host
   By default, pegasus designates the condor logs to be created in the
   /tmp directory. This is done to ensure that the logs are created in
   a local directory even though the submit directory maybe on NFS. 

   In the submit directory the symbolic link to the appropriate log
   file in the /tmp exists. However, since /tmp is automatically
   purged in most cases, users may want to preserve their condor logs
   in a directory on the local filesystem other than /tmp 

   The new property


   allows a user to designate the logs directory on the submit host
   for condor logs. 

15) Removing profile keys as part of overriding profiles

   There is now a notion of empty profile key valus in Pegasus.  The
   default action on empty key value is to remove the key. Currently
   the following namespaces follow this convention 

       - Condor
       - Globus
       - Pegasus

   This allows a user to unset values as part of overriding
   profiles. Normally a user can only update a profile value i.e they
   can update the value of a key, but the key remains associated with
   the job This allows the user to remove the key from the profile

   For e.g.

   A user may have a profile X set in the site catalog.

   Now for a particular job a user does not want that profile key to
   be used. He can now specify the same profile X with empty value in
   the transformation catalog for that job. This results in the
   profile key X being removed from the job. 

16) Constructing Paths to Condor DAGMan for recursive/hierarichal

   The entry for condor::dagman is no longer required for site local
   in the transformation catalog. 
   Instead pegasus constructs path from the following environment

   The priority order is as follows

   1) CONDOR_HOME defined in the environment
   2) CONDOR_LOCATION defined in the environment
   3) entry for condor::dagman for site local

   This is useful when running workflows that refer to sub workflows
   as in the new DAX 3.0 format.

   This was tracked in JIRA

17) Constructing path to kickstart

   By default the path to kickstart is determined on the basis of the
   environment variable PEGASUS_HOME associated with a site entry in
   the site catalog. 

   However, in some cases a user might want to use their own modified
   version of kickstart. 

   In order to enable that

   The path to kickstart will be constructed according to the following rule	
   1) pegasus profile gridstart.path specified in the site catalog for
      the site in question. 
   2) If 1 is not specified, then a path is constructed on the basis
   of the environment variable PEGASUS_HOME for the site in the site

   The above was tracked in JIRA

18) Bulk Lookups to Replica Catalog using rc-client
   rc-client now can do bulk lookups similar to how it does bulk
   inserts and deletes

   Details at

19) Additions to show-job workflow visualization script

   show-job now has a --title option to list add a user provided title for the generated gantt chart.

   show-job can also visualize workflow of workflows

20) Absolute paths for certain properties in the properties file

   The properties file that is written out now in the submit directory
   has absolute paths specified for the following property values. 


   This is even though user may have specified relative paths in properties file.

21) The default horizontal clustering factor

   Updated the default clustering factor as collapse with value = 1, instead of earlier value of 3

   This ensures, that users can cluster only jobs of certain types,
   and let others remain unclustered. Another way was to specify the
   collapse factor as 1 explicitly for jobs that users dont want
   clustering for. 

1) Handling of standard universe in condor style
   In Condor style , standard universe if specified for a job is ONLY
   associated for compute jobs. This ensures that pegasus auxillary
   jobs never execute in standard universe. 

2) Bug Fix for replica selection bug 43
   Checked in the fix for JIRA bug 43

   The ReplicaLocation class now has a clone method that does a
   shallow clone 
   This clone method is called in the selectReplica methods in the replica selectors.

3) rc-client did not implement  pegasus.catalog.replica.lrc.ignore property
   This is now fixed.
   This bug was tracked in JIRA

4) DAX'es created while partitioning a workflow
   During the partitioning of the workflows , the DAX for a partition
   was created incorrectly as the register flags were not correctly
   parsed by the VDL DAX parser. 

   This was tracked in JIRA

5) Handling of initialdir and remote_initialdir keys
   Changed the internal handling for the initialdir and
   remote_initialdir keys. The initialdir key is now only associated
   for standard universe jobs. For glidein and condor style we now
   associate remote_initialdir unless it is a standard universe job. 

   This was tracked in JIRA

6) Querying RLI for non existent LFN using rc-client
   rc-client had inconsistent behavior when querying RLI for a LFN
   that does not exist in the RLS. 
   This affected the rc-client lookup command option.

   Details at

7) Running clustered jobs on the cloud in directory other than /tmp
   There was a bug whereby the clustered jobs executing in worker node
   execution mode did not honor the wntmp environment variable
   specified in the Site Catalog for the site. 

   The bug fix was tracked through JIRA

8) Bug Fix for worker package deployment
   The regex employed to determine the pegasus version from a URL to a
   worker package was insufficient. It only took care of x86 builds. 

   For e.g. it could not parse the following

   This is now fixed.
   Related to JIRA PM-33

9) Destination URL construction for worker package staging
   Earlier the worker package input files always had third party
   URL's, even if the worker package deployment job executed on the
   remote site ( in push / pull mode ). 

   Now, the third party URL's are only constructed if the worker
   package deployment job is actually run in third party mode.		
   In push-pull mode, the destination URL's are file URLs	 

   Tracked in JIRA at


1) User Guides
   The Running on different Grids Guide now has information on how to
   run workflows using glite.   
   - Pegasus Replica Selection

   The guides are checked in $PEGASUS_HOME/doc/guides

   They can be found online at
2) Property Document was updated with the new properties introduced.