===============================
Release Notes for PEGASUS 2.3.0
===============================
NEW FEATURES
--------------
1) Regex Based Replica Selection
Pegasus now allows users to use regular expression based replica
selection. To use this replica selector, users need to set the
following property
pegasus.selector.replica Regex
The Regex replica selector allows the user allows the user to
specifiy the regex expressions to use for ranking various PFNs
returned from the Replica Catalog for a particular LFN. This
replica selector selects the highest ranked PFN i.e the replica
with the lowest rank value.
The regular expressions are assigned different rank, that determine
the order in which the expressions are employed. The rank values
for the regex can expressed in user properties using the property.
pegasus.selector.replica.regex.rank.[value]
The value is an integer value that denotes the rank of an
expression with a rank value of 1 being the highest rank.
For example, a user can specify the following regex expressions
that will ask Pegasus to prefer file URL's over gsiftp url's from
example.isi.edu
pegasus.selector.replica.regex.rank.1 file://.*
pegasus.selector.replica.regex.rank.2 gsiftp://example\.isi\.edu.*
User can specify as many regex expressions as they want.
Since Pegasus is in Java , the regex expression support is what
Java supports. It is pretty close to what is supported by
Perl. More details can be found at
http://java.sun.com/j2se/1.5.0/docs/api/java/util/regex/Pattern.html
There is documentation about the new replica selector in the
properties document . It can also be found at
$PEGASUS_HOME/etc/sample.properties
To use this set pegasus.selector.replica Regex
2) Automatic Determination of pool attributes in RLS Replica Catalog
Pegasus can now associate a pool attribute with the replica catalog
entries returned from querying a LRC if the pool attribute is not
already specified.
This is achieved by associating the site handles with corresponding
LRC url's in the properties file. This mapping tells us what
default pool attribute should be assigned while querying a
particular LRC. For example
pegasus.catalog.replica.lrc.site.llo rls://ldas.ligo-la.caltech.edu:39281
pegasus.catalog.replica.lrc.site.lho rls://ldas.ligo-wa.caltech.edu:39281
tells Pegasus that all results from LRC
rls://ldas.ligo-la.caltech.edu:39281 are associated with site llo
Using this feature only makes sense, when a LRC *ONLY* contains
mapping for data on one site, as in case of LIGO LDR deployment.
3) Pegasus auxillary jobs on submit host now execute in local universe
All the scheduler universe jobs are now executed in local
universe. Also any job planned for site local will by default run
in local universe instead of scheduler universe.
Additionally, extra checks were put in to handle the Condor File
Transfer Mechansim issues in case local/scheduler universe. This
was tracked in bugzilla at
http://vtcpc.isi.edu/bugzilla/show_bug.cgi?id=40
A user can override the local universe generation by specifying the
condor profile key universe and setting it to the value desired.
4) Python API for generating DAX and PDAX
Pegasus now includes a Python API for generating DAXes and PDAXes.
An example can be found online at
http://vtcpc.isi.edu/pegasus/index.php/ChangeLog#Added_Python_API_for_DAX_and_PDAX
For more information on the DAX API type: pydoc Pegasus.DAX2
For more information on the PDAX API type: pydoc Pegasus.PDAX2
5) Interface to Engage VO for OSG
There is a new Site Catalog Implementation called Engage that
interfaces with the Engage VO to discover resource information
about OSG from the information published in RENCI glue classads.
To use it set
pegasus.catalog.site Engage
To generate a site catalog using pegasus-get-sites set the source
option to Engage
pegasus-get-sites --source Engage --sc engage.sc.xml
6) Gensim now reports Seqexec Times and Seqexec Delays
Gensim script ($PEGASUS_HOME/contrib/showlog/gensim) now reports
the seqexec time and the seqexec delay for the clustered jobs.
There are two new columns in the jobs file created by seqexec
- seqexec
- seqexec delay.
The seqexec time is determined from the last line of the .out file
of the clustered jobs. E.g format [struct stat="OK", lines=4,
count=4, failed=0,
duration=21.836,start="2009-02-20T16:14:56-08:00"]
The seqexec delay is the seqexec time - kickstart time.
This useful for analyzing large scale workflow runs.
7) Properties to turn on or off the seqexec progress logging
The property pegasus.clusterer.job.aggregator.seqexec.hasgloballog
is now deprecated.
It has been replaced by two boolean properties
- pegasus.clusterer.job.aggregator.seqexec.log whether to log
progress or not
- pegasus.clusterer.job.aggregator.seqexec.log.global whether to
log progress to global file or not.
The pegasus.clusterer.job.aggregator.seqexec.log.global only
comes into effect when
pegasus.clusterer.job.aggregator.seqexec.log is set to true
8) Passing of the DAX label to kickstart invocation
Now, the kickstart invocation for the jobs is always passed the dax
label using the -L option. To disable the passing of the DAX label,
user needs to set pegasus.gridstart.label to false
Additionally, the basename option to pegasus-plan overrides the
label value retrieved from the DAX.
9) show-job works on MAC OSX platform
$PEGASUS_HOME/contrib/showlog/show-job now does not fail on
unavailability of convert program. It only logs a warning and
creates the EPS File , but not the png files. This allows us to
run show-job on MAC OSX systems.
10) Enabling InPlace cleanup in deferred planning
By default in case of deferred planning cleanup is turned off as
the cleanup algorithm does not work across partitions.
However, in scenarios where the partitions themseleves are
independant ( i.e. dont share files ), user can safely turn on
cleanup.
This can now be done by setting
pegasus.file.cleanup.scope deferred
If the property is set to deferred, and the users wants to disable
cleanup , they can still specify --nocleanup option on command
line and that is honored.
However in case of scope fullahead for deferred planning, the
command line options are ignored and always nocleanup is set.
11) New Pegasus Job Classad
Pegasus now publishes a job runtime classad with the jobs. The
class ad key name is pegasus_job_runtime. The value passed to it
is picked up from the Pegasus Profile runtime. If the Pegaus
Profile is not associated, then the globus maxwalltime profile key
is used. If both are not set, then a value of zero is published.
This job classad can be used for users in case of glidein, to
ensure that the jobs complete before the nodes expire.
For the coral glidein service the sub expression to job
requirement swould look something like this
(CorralTimeLeft > MY.pegasus_job_runtime)
12) [workflow].job.map file
Pegasus now creates a [workflow].job.map file that links jobs in
the DAG with the jobs in the DAX. The contents of the file are in
netlogger format.
The [workflow] is replaced by the name of the workflow i.e. same
prefix as the .dag file
In the file there are two types of events.
a) pegasus.job
b) pegasus.job.map
pegasus.job - This event is for all the jobs in the DAG. The
following information is associated with this event.
- job.id the id of the job in the DAG
- job.class an integer designating the type of the job
- job.xform the logical transformation which the job refers to.
- task.count the number of tasks associated with the job. This is
equal to the number of pegasus.job.task events created for that
job.
pegasus.job.map - This event allows us to associate a job in the
DAG with the jobs in the DAX. The following information is
associated with this event.
-task.id the id of the job in the DAG
-task.class an integer designating the type of the job
-task.xform the logical transformation which the job refers to.
13) Source Directory for Worker Package Staging
Users now can specify the property
pegasus.transfer.setup.source.base.url to specify the URL to the
source directory containing the pegasus worker packages. If it is
not specified, then the worker packages are pulled from the http
server at pegasus.isi.edu during staging of executables.
BUGS FIXED
----------
1) Critical Bug Fix to rc-client
SCEC reported a bug with the rc-client while doing bulk inserts
into RLS. The bug was related to how logging is initialized
internally in the client.
Details of the bug fix can be found at
http://vtcpc.isi.edu/bugzilla/show_bug.cgi?id=38
2) Bug Fix to tailstatd for parsing jobnames with . in them
There was a bug where tailstatd incorrectly generated events in
the jobstate.log while parsing condor logs. This was due to an
errorneous regex expression for determining the event
POST|PRE SCRIPT STARTED.
The earlier expression did not allow for . in jobnames. This is
especially prevalent in LIGO workflows where the DAX labels have
. in them.
An example of the problem line in DAGMan log
1/24 10:11:21 Running POST script of Node
inspiral_hipe_eobinj_cat2_veto.EOBINJ_CAT_2_VETO.daxlalapps_sire_ID000731...
Earlier the job id was parsed as inspiral_hipe_eobinj_cat2_veto
instead of
inspiral_hipe_eobinj_cat2_veto.EOBINJ_CAT_2_VETO.daxlalapps_sire_ID000731
3) Pegasus Builds on FC10
Earlier the Pegasus builds were failed on FC10 as the invoke c tool
did not build correctly. This is now fixed.
Details at
http://vtcpc.isi.edu/bugzilla/show_bug.cgi?id=41
4) tailstatd killing jobs by detecting starvation
tailstatd removes a job after four hours when the job has been
waiting in the queue WITHOUT being marked as EXECUTE in the condor
log. To override tailstatd has an option of setting starvation time
to 0 via command line or via pegasus.max.idletime property. The if
condition in the perl script was not accepting 0 as a value when
trying to override the default 4 hour starvation time. This fix
allows the value to be set to 0 (turn of starvation checks) or any
other value via the property pegasus.max.idletime.
This was tracked in pegasus jira as bug 40
http://pegasus.isi.edu/jira/browse/PM-40
Documentation
--------------
1) User Guides
The release has new user guides about the following
- Pegasus Job Clustering
- Pegasus Profiles
- Pegasus Replica Selection
The guides are checked in $PEGASUS_HOME/doc/guides
They can be found online at
http://pegasus.isi.edu/mapper/doc.php
2) Property Document was updated with the new properties introduced.
Pegasus 2.3.0 Released
on April 22, 2009
with No Comments