This page is still under construction and may contain incorrect information
Pegasus Tutorial
This is based on Tutorial note, but it is tailored to run Pegasus and montage.dax example on a local condor pool, with MyProxy.
Prerequisites for this node
- Condor (running condor_master and condor_schedd). It comes with Condor-G.
- condor_submit working (Refer to the Condor Submit Test in these notes).
- Linux user accounts on the local machine.
- Globus installed as the 2nd node and working as client.
(Copied the /etc/grid-security/certificates etc.) - Globus usercerts were made on the Globus MyProxy sever.
- The user authentication entries are made in /etc/grid-security/gridmapfile on local and central server.
# vim /etc/grid-security/grid-mapfile --insert-- "/O=Grid/OU=GlobusTest/OU=simpleCA-grid2.ramscommunity.org/OU=ramscommunity.org/CN=Yoichi Takayama" yoichi "/O=Grid/OU=GlobusTest/OU=simpleCA-grid2.ramscommunity.org/OU=ramscommunity.org/CN=Luke Foxton" lfoxton
- Pegasus Mapper was installed on this host.
- NFS is mounted.
- Pegasus Worker is installed on NFS.
- Montage is installed on NFS.
Pegasus Init
This has been defined in /etc/profile
unset CLASSPATH ... ... export PEGASUS_HOME=/usr/local/pegasus/2.2.0 source $PEGASUS_HOME/setup.sh $ env | grep PEGASUS PEGASUS_HOME=/usr/local/pegasus/2.2.0 $ env | grep CLASSPATH CLASSPATH=/usr/local/pegasus/2.2.0/lib/xmlParserAPIs.jar:/usr/local/pegasus/2.2.0/lib/cryptix-asn1.jar:/usr/local/pegasus/2.2.0/lib/mysql-connector-java-5.0.5-bin.jar:/usr/local/pegasus/2.2.0/lib/preservcsl.jar:/usr/local/pegasus/2.2.0/lib/java-getopt-1.0.9.jar:/usr/local/pegasus/2.2.0/lib/postgresql-8.1dev-400.jdbc3.jar:/usr/local/pegasus/2.2.0/lib/puretls.jar:/usr/local/pegasus/2.2.0/lib/cryptix32.jar:/usr/local/pegasus/2.2.0/lib/exist.jar:/usr/local/pegasus/2.2.0/lib/commons-logging.jar:/usr/local/pegasus/2.2.0/lib/xmldb.jar:/usr/local/pegasus/2.2.0/lib/jce-jdk13-125.jar:/usr/local/pegasus/2.2.0/lib/pegasus.jar:/usr/local/pegasus/2.2.0/lib/log4j-1.2.8.jar:/usr/local/pegasus/2.2.0/lib/xmlrpc.jar:/usr/local/pegasus/2.2.0/lib/accessors.jar:/usr/local/pegasus/2.2.0/lib/commons-pool.jar:/usr/local/pegasus/2.2.0/lib/cog-jglobus.jar:/usr/local/pegasus/2.2.0/lib/xercesImpl.jar:/usr/local/pegasus/2.2.0/lib/globus_rls_client.jar:/usr/local/pegasus/2.2.0/lib/jakarta-oro.jar:/usr/local/pegasus/2.2.0/lib/exist-optional.jar:/usr/local/pegasus/2.2.0/lib/junit.jar:/usr/local/pegasus/2.2.0/lib/cryptix.jar:/usr/local/pegasus/2.2.0/lib/resolver.jar:/usr/local/pegasus/2.2.0/lib/wings.jar
Get Pegasus tutorial package.
cd $HOME
$ wget http://pegasus.isi.edu/tutorial/issgc08/pegasus-wms-issgc08.tar.gz
$ tar -xzvf pegasus-wms-issgc08.tar.gz
$ cd pegasus-wms
$ ls -l total 64 drwxr-xr-x 2 yoichi yoichi 4096 Sep 11 18:46 config drwxr-xr-x 3 yoichi yoichi 4096 Aug 23 12:54 dags drwxr-xr-x 2 yoichi yoichi 4096 Aug 23 12:37 dax -rw-r--r-- 1 yoichi yoichi 113 May 6 10:49 partitiondax -rw-r--r-- 1 yoichi yoichi 147 Jun 7 03:29 pegasus-plan-grid -rw-r--r-- 1 yoichi yoichi 151 Jun 7 03:29 pegasus-plan-grid-defer -rw-r--r-- 1 yoichi yoichi 145 May 1 10:01 pegasus-plan-local -rw-r--r-- 1 yoichi yoichi 48 Jun 6 04:40 proxy-logon
Input data
Got the tutorial input data from ISI site and installed in /nfs/shared-scratch/tutorial/pegasus-wms/.
# mkdir /nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage # mv inputdata/0.2degree /nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage # chmod -R 1777 /nfs/shared-scratch # ls -l /nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree total 12536 -rwxrwxrwt 1 condor condor 2111040 Aug 28 23:54 2mass-atlas-990502s-j1420186.fits -rwxrwxrwt 1 condor condor 2111040 Aug 28 23:54 2mass-atlas-990502s-j1420198.fits -rwxrwxrwt 1 condor condor 2111040 Aug 28 23:54 2mass-atlas-990502s-j1430080.fits -rwxrwxrwt 1 condor condor 2111040 Aug 28 23:54 2mass-atlas-990502s-j1430092.fits -rwxrwxrwt 1 condor condor 2111040 Aug 28 23:54 2mass-atlas-990502s-j1440186.fits -rwxrwxrwt 1 condor condor 2111040 Aug 28 23:54 2mass-atlas-990502s-j1440198.fits -rwxrwxrwt 1 condor condor 1294 Aug 28 23:54 cimages.tbl -rwxrwxrwt 1 condor condor 33426 Aug 28 23:54 dag.xml -rwxrwxrwt 1 condor condor 1229 Aug 28 23:54 diffs.tbl -rwxrwxrwt 1 condor condor 2750 Aug 28 23:54 images.tbl -rwxrwxrwt 1 condor condor 1294 Aug 28 23:54 pimages.tbl -rwxrwxrwt 1 condor condor 304 Aug 28 23:54 region.hdr -rwxrwxrwt 1 condor condor 1376 Aug 28 23:54 rimages.tbl -rwxrwxrwt 1 condor condor 431 Aug 28 23:54 statfile.tbl -rwxrwxrwt 1 condor condor 1360 Aug 28 23:54 url.list
Properties and Catalog files
Pegasus needs 1 properties file and 3 catalog files to run. The properties file indicates which catalog files to use (and it contains other properties, too).
- Replica catalog - files names and locations.
- Sites catalog - Grid pool site def (host names, service names & locations).
- Transformation catalog - Grid applications (names and locations).
Properties file
> cat config/properties
##########################
# PEGASUS USER PROPERTIES
##########################
## SELECT THE REPLICAT CATALOG MODE AND URL
pegasus.catalog.replica = SimpleFile
pegasus.catalog.replica.file = ${user.home}/pegasus-wms/config/rc.data
#pegasus.catalog.replica.url=rlsn://smarty.isi.edu
## SELECT THE SITE CATALOG MODE AND FILE
pegasus.catalog.site = XML
pegasus.catalog.site.file = ${user.home}/pegasus-wms/config/sites.xml
## SELECT THE TRANSFORMATION CATALOG MODE AND FILE
pegasus.catalog.transformation = File
pegasus.catalog.transformation.file = ${user.home}/pegasus-wms/config/tc.data
## SET UP THE WORK AND INVOCATION DATABASE
#pegasus.catalog.work = Database
#pegasus.catalog.provenance = InvocationSchema
## Database related properties
#pegasus.catalog..db.driver = MySQL
#pegasus.catalog.*.db.url = jdbc:mysql://smarty.isi.edu/osg2008
#pegasus.catalog.*.db.user = osg2008user
#pegasus.catalog.*.db.password = Osg2008
## USE DAGMAN RETRY FEATURE FOR FAILURES
pegasus.dagman.retry=2
## STAGE ALL OUR EXECUTABLES OR USE INSTALLED WHEREVER THEY EXIST
# pegasus.catalog.transformation.mapper = All
# Use All for genera use
# pegasus.catalog.transformation.mapper = Installed
# Use Installed for diamond.dax example
pegasus.catalog.transformation.mapper = Staged
# Staged means pegasus will deploy a worker package
# into the working directory of the workflow
# which must be on the nfs and shared.
# Otherwise Worker packages must be installed
# at the same locations on all
# Worker nodes as specified in the tc.data.
## CHECK JOB EXIT CODES FOR FAILURE
pegasus.exitcode.scope=all
pegasus.exitcode.arguments= -e
## OPTIMZE DATA & EXECUTABLE TRANSFERS
pegasus.transfer.refiner=Bundle
#STAGE DATA AND EXECUTABLES USING GRIDFTP 3rd PARTY MODE
pegasus.transfer.*.thirdparty.sites=*
pegasus.transfer.*.impl GUC
## WORK AND STORAGE DIR
pegasus.dir.storage = ${user.name}/storage
pegasus.dir.exec = ${user.name}/exec
# JOB Priorities
pegasus.job.priority=10
pegasus.transfer.*.priority=100
#JOB CATEGORIES
pegasus.dagman.projection.maxjobs 2
Replica catalog
Edit the ./config/rc.in file to reflect the change of the file locations. This includes diamond.dax input/output files. Local input files are located in /scratch/tutorial/inputdata. The output files are located in local /scratch/storage. Network files are located in /nfs/shared-scratch/tutorial/pegasus-wms/inputdata.
$ vi config/rc.in -- insert -- # file-based replica catalog: 2008-09-24T01:58:11.069-07:00 f.a gsiftp://grid1.ramscommunity.org/scratch/tutorial/inputdata/diamond/f.a pool="local" 2mass-atlas-990502s-j1420198.fits gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/2mass-atlas-990502s-j1420198.fits pool="local" 2mass-atlas-990502s-j1430092.fits gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/2mass-atlas-990502s-j1430092.fits pool="local" images_20080505_143233_14944.tbl gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/images.tbl pool="local" 2mass-atlas-990502s-j1430080.fits gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/2mass-atlas-990502s-j1430080.fits pool="local" 2mass-atlas-990502s-j1440198.fits gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/2mass-atlas-990502s-j1440198.fits pool="local" 2mass-atlas-990502s-j1440186.fits gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/2mass-atlas-990502s-j1440186.fits pool="local" 2mass-atlas-990502s-j1420186.fits gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/2mass-atlas-990502s-j1420186.fits pool="local" cimages_20080505_143233_14944.tbl gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/cimages.tbl pool="local" dag_20080505_143233_14944.xml gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/dag.xml pool="local" region_20080505_143233_14944.hdr gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/region.hdr pool="local" pimages_20080505_143233_14944.tbl gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/pimages.tbl pool="local" statfile_20080505_143233_14944.tbl gsiftp://grid1.ramscommunity.org/nfs/shared-scratch/tutorial/pegasus-wms/inputdata/montage/0.2degree/statfile.tbl pool="local" f.c2 gsiftp://grid1.ramscommunity.org/scratch/yoichi/storage/f.c2 pool="local" f.c1 gsiftp://grid1.ramscommunity.org/scratch/yoichi/storage/f.c1 pool="local" f.d gsiftp://grid1.ramscommunity.org/scratch/yoichi/storage/f.d pool="local" mosaic_20080505_143233_14944_area.fits gsiftp://grid1.ramscommunity.org/scratch/yoichi/storage/mosaic_20080505_143233_14944_area.fits pool="local" mosaic_20080505_143233_14944.fits gsiftp://grid1.ramscommunity.org/scratch/yoichi/storage/mosaic_20080505_143233_14944.fits pool="local" shrunken_20080505_143233_14944.fits gsiftp://grid1.ramscommunity.org/scratch/yoichi/storage/shrunken_20080505_143233_14944.fits pool="local" montage.jpg gsiftp://grid1.ramscommunity.org/scratch/yoichi/storage/montage.jpg pool="local"
Clear the old catalog/rc.data (if it exists) and create a new rc.data from rc.in as follows:
$ rc-client -Dpegasus.user.properties=config/properties list local $ rc-client -Dpegasus.user.properties=config/properties clear $ rc-client -Dpegasus.user.properties=config/properties --insert config/rc.in $ rc-client -Dpegasus.user.properties=config/properties list local
Sites catalog
Next, edit the ./config/sites.txt to reflect changes. Back up the old one and make a new sites.txt with: (Globus is installed on this host at /usr/local/globus. The Pegasus Mapper is installed at /usr/local/pegasus. The Pegasus Worker is accessible for Execute node from /nfs/software/pegasus. GridFTP is accessible for the rams Condor pool from grid2. GridFTP is also installed on grid1.)
site rams{
sysinfo "INTEL32::LINUX"
gridlaunch "/nfs/software/pegasus/2.0.2/bin/kickstart"
workdir "/nfs/shared-scratch/"
gridftp "gsiftp://grid2.ramscommunity.org/nfs/shared-scratch" "4.2.0"
universe transfer "grid2.ramscommunity.org/jobmanager-fork" "4.2.0"
universe vanilla "grid2.ramscommunity.org/jobmanager-condor" "4.2.0"
lrc "rlsn://smarty.isi.edu"
profile env "GLOBUS_LOCATION" "/usr/local/globus"
profile env "LD_LIBRARY_PATH" "/usr/local/globus/lib"
profile env "PEGASUS_HOME" "/nfs/software/pegasus/2.0.2"
profile pegasus "bundle.stagein" "1"
profile pegasus "bundle" "1"
}
site local{
sysinfo "INTEL32::LINUX"
gridlaunch "/usr/local/pegasus/2.0.2/bin/kickstart"
workdir "/scratch"
gridftp "gsiftp://grid1.ramscommunity.org/scratch" "4.2.0"
universe transfer "grid1.ramscommunity.org/jobmanager-fork" "4.2.0"
universe vanilla "grid1.ramscommunity.org/jobmanager-condor" "4.2.0"
lrc "rlsn://smarty.isi.edu"
profile env "GLOBUS_LOCATION" "/usr/local/globus"
profile env "LD_LIBRARY_PATH" "/usr/local/globus/lib"
profile env "PEGASUS_HOME" "/usr/local/pegasus/2.0.2"
}
NB: The local host is also a part of the rams Condor pool in this case.
Make sure that the user can read/write to /scratch and /nfs/shared-scratch.
lrc "rlsc://smarty.ramscommunity.org" is about a replica catalog service. It is commented out in the property file, since we are using the SimpleFile catalog. The manual seems to imply that any valid URL may do, but I am not certain. However, it has to be mentioned in sites.txt, or you get an error.
Parse this with sc-client to generate sites.xml.
$ sc-client -f config/sites.txt -o config/sites.xml 2008.11.18 12:37:48.323 EST: [INFO] event.pegasus.sc-client pegasus.version 2.2.0cvs - STARTED 2008.11.18 12:37:48.389 EST: [INFO] Reading config/sites.txt 2008.11.18 12:37:48.460 EST: [INFO] Reading config/sites.txt -DONE 2008.11.18 12:37:48.470 EST: [INFO] Written out the converted file to config/sites.xml 2008.11.18 12:37:48.471 EST: [INFO] Time taken to execute is 0.116 seconds 2008.11.18 12:37:48.471 EST: [INFO] event.pegasus.sc-client pegasus.version 2.2.0cvs - FINISHED
Transformation catalog
(Note: These worked with 2.0.1 but they don't work with 2.2.0 we are using now)
Copy the tc.data to tc.data.old
Delete the old tc.data, by: (assuming that you are in pegasus-wms)
$ tc-client -Dpegasus.user.properties=config/properties -q -B $ tc-client -Dpegasus.user.properties=config/properties -d -BPRELST 2008.09.11 19:18:33.931 EST: [INFO] Deleted the entire tc succesfullytc-client $ tc-client -Dpegasus.user.properties=config/properties -q -B
Or, simply delete the tc.data file
Create a new config/tc.in with:
local condor::dagman /nfs/software/condor/7.0.4/bin/condor_dagman INSTALLED INTEL32::LINUX NULL local diamond::analyze:2.0 /nfs/software/pegasus/2.0.2/bin/keg INSTALLED INTEL32::LINUX NULL local diamond::findrange:2.0 /nfs/software/pegasus/2.0.2/bin/keg INSTALLED INTEL32::LINUX local diamond::preprocess:2.0 /nfs/software/pegasus/2.0.2/bin/keg INSTALLED INTEL32::LINUX rams bin/mDiff gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mDiff STATIC_BINARY INTEL32::LINUX ENV::MONTAGE_HOME="." rams bin/mFitplane gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mFitplane STATIC_BINARY INTEL32::LINUX NULL rams mAdd:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mAdd STATIC_BINARY INTEL32::LINUX NULL rams mBackground:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mBackground STATIC_BINARY INTEL32::LINUX NULL rams mBgModel:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mBgModel STATIC_BINARY INTEL32::LINUX NULL rams mConcatFit:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mConcatFit STATIC_BINARY INTEL32::LINUX NULL rams mDiffFit:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mDiffFit STATIC_BINARY INTEL32::LINUX ENV::MONTAGE_HOME="." rams mImgtbl:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mImgtbl STATIC_BINARY INTEL32::LINUX NULL rams mJPEG:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mJPEG STATIC_BINARY INTEL32::LINUX NULL rams mProject:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mProjectPP STATIC_BINARY INTEL32::LINUX CONDOR::priority="25" rams mProjectPP:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mProjectPP STATIC_BINARY INTEL32::LINUX CONDOR::priority="25" rams mShrink:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mShrink STATIC_BINARY INTEL32::LINUX NULL
Make a new catalog/tc.data file with:
$ tc-client -Dpegasus.user.properties=config/properties -a -B -f config/tc.in (check it with) $ tc-client -Dpegasus.user.properties=config/properties -q -B
MyProxy
(# su - yoichi)
($ cd pegasus-wms)
$ myproxy-logon -s grid2
Enter MyProxy pass phrase:
A credential has been received for user yoichi in /tmp/x509up_u500.
GRAM2 gatekeeper
Pegasus requires Globus gatekeeper, which is pre-ws GRAM2.
This has been set up with the GRAM2 section with Globus installation and test.
Submitting a job to rams Condor pool
$ pegasus-plan -Dpegasus.user.properties=`pwd`/config/properties --dir `pwd`/dags \ --sites rams --output local --nocleanup --force --cluster horizontal \ --dax `pwd`/dax/montage.dax 2008.11.18 13:08:56.574 EST: [INFO] event.pegasus.planner planner.version 2.2.0cvs - STARTED 2008.11.18 13:08:57.447 EST: [INFO] event.pegasus.parse.dax dax.id /home/yoichi/pegasus-wms/dax/montage.dax - STARTED 2008.11.18 13:08:57.600 EST: [INFO] event.pegasus.parse.dax dax.id /home/yoichi/pegasus-wms/dax/montage.dax - FINISHED 2008.11.18 13:08:57.670 EST: [INFO] event.pegasus.siteselection dax.id montage_0 - STARTED 2008.11.18 13:08:57.731 EST: [INFO] event.pegasus.siteselection dax.id montage_0 - FINISHED 2008.11.18 13:08:57.749 EST: [INFO] event.pegasus.cluster dax.id montage_0 - STARTED 2008.11.18 13:08:57.845 EST: [INFO] event.pegasus.cluster dax.id montage_0 - FINISHED 2008.11.18 13:08:57.845 EST: [INFO] Grafting transfer nodes in the workflow 2008.11.18 13:08:57.846 EST: [INFO] event.pegasus.generate.transfer-nodes dax.id montage_0 - STARTED 2008.11.18 13:09:02.535 EST: [INFO] event.pegasus.generate.transfer-nodes dax.id montage_0 - FINISHED 2008.11.18 13:09:02.542 EST: [INFO] event.pegasus.generate.workdir-nodes dax.id montage_0 - STARTED 2008.11.18 13:09:02.549 EST: [INFO] event.pegasus.generate.workdir-nodes dax.id montage_0 - FINISHED 2008.11.18 13:09:02.549 EST: [INFO] event.pegasus.generate.cleanup-wf dax.id montage_0 - STARTED 2008.11.18 13:09:02.552 EST: [INFO] event.pegasus.generate.cleanup-wf dax.id montage_0 - FINISHED 2008.11.18 13:09:02.565 EST: [INFO] Generating codes for the concrete workflow 2008.11.18 13:09:04.024 EST: [INFO] Generating codes for the concrete workflow -DONE 2008.11.18 13:09:04.026 EST: [INFO] Generating code for the cleanup workflow 2008.11.18 13:09:04.080 EST: [INFO] Generating code for the cleanup workflow -DONE 2008.11.18 13:09:04.085 EST: [INFO] I have concretized your abstract workflow. The workflow has been entered into the workflow database with a state of "planned". The next step is to start or execute your workflow. The invocation required is pegasus-run -Dpegasus.user.properties=/home/yoichi/pegasus-wms/dags/yoichi/pegasus/montage/run0001/pegasus.9270.properties --nodatabase /home/yoichi/pegasus-wms/dags/yoichi/pegasus/montage/run0001 2008.11.18 13:09:04.086 EST: [INFO] Time taken to execute is 7.491 seconds 2008.11.18 13:09:04.086 EST: [INFO] event.pegasus.planner planner.version 2.2.0cvs - FINISHED
$ pegasus-run -Dpegasus.user.properties=/home/yoichi/pegasus-wms/dags/yoichi/pegasus/montage/run0001/pegasus.9270.properties --nodatabase /home/yoichi/pegasus-wms/dags/yoichi/pegasus/montage/run0001 Rescued /tmp/montage-09271.log as /tmp/montage-09271.log.000 Checking all your submit files for log file names. This might take a while... Done. ----------------------------------------------------------------------- File for submitting this DAG to Condor : montage-0.dag.condor.sub Log of DAGMan debugging messages : montage-0.dag.dagman.out Log of Condor library output : montage-0.dag.lib.out Log of Condor library error messages : montage-0.dag.lib.err Log of the life of condor_dagman itself : montage-0.dag.dagman.log Condor Log file for all jobs of this DAG : /tmp/montage-09271.log -no_submit given, not submitting DAG to Condor. You can do this with: "condor_submit montage-0.dag.condor.sub" ----------------------------------------------------------------------- Submitting job(s). Logging submit event(s). 1 job(s) submitted to cluster 6. I have started your workflow, committed it to DAGMan, and updated its state in the work database. A separate daemon was started to collect information about the progress of the workflow. The job state will soon be visible. Your workflow runs in base directory. cd /home/yoichi/pegasus-wms/dags/yoichi/pegasus/montage/run0001 *** To monitor the workflow you can run *** pegasus-status -w montage-0 -t 20081118T130856+1100 or pegasus-status /home/yoichi/pegasus-wms/dags/yoichi/pegasus/montage/run0001 *** To remove your workflow run *** pegasus-remove -d 6.0 or pegasus-remove /home/yoichi/pegasus-wms/dags/yoichi/pegasus/montage/run0001
$ pegasus-status /home/yoichi/pegasus-wms/dags/yoichi/pegasus/montage/run0001
-- Submitter: grid1.ramscommunity.org : <137.111.246.175:9650> : grid1.ramscommunity.org
ID OWNER/NODENAME SUBMITTED RUN_TIME ST PRI SIZE CMD
6.0 yoichi 11/18 13:09 0+00:01:04 R 0 4.9 condor_dagman -f -
7.0 |-montage_0_r 11/18 13:10 0+00:00:07 R 10 0.1 kickstart -n pegas
$ condor_status
Name OpSys Arch State Activity LoadAv Mem ActvtyTime
grid1.ramscommunit LINUX INTEL Owner Idle 0.060 249 0+00:50:05
grid4.ramscommunit LINUX INTEL Unclaimed Idle 0.000 503 0+00:55:04
Total Owner Claimed Unclaimed Matched Preempting Backfill
INTEL/LINUX 2 1 0 1 0 0 0
Total 2 1 0 1 0 0 0
$ pegasus-status /home/yoichi/pegasus-wms/dags/yoichi/pegasus/montage/run0001
-- Submitter: grid1.ramscommunity.org : <137.111.246.175:9650> : grid1.ramscommunity.org
ID OWNER/NODENAME SUBMITTED RUN_TIME ST PRI SIZE CMD
CVS 2.2.0 nightly-build problem
The CVS 2.2.0 nightly-build had some problem.
$ pegasus-version -f
2.2.0cvs-x86_cent_4.2-20081016052128Z
$ tc-client -Dpegasus.user.properties=config/properties -q -B
Exception in thread "main" java.util.EmptyStackException
at java.util.Stack.peek(Stack.java:85)
at edu.isi.pegasus.common.logging.format.AbstractLogFormatter.add(AbstractLogFormatter.java:146)
at edu.isi.pegasus.common.logging.format.Simple.add(Simple.java:52)
at edu.isi.pegasus.common.logging.LogManager.log(LogManager.java:411)
at org.griphyn.common.catalog.toolkit.TCClient.executeCommand(TCClient.java:247)
at org.griphyn.common.catalog.toolkit.TCClient.main(TCClient.java:381)
This may be contributing to some problems.
Although this error was fixed, it is not yet available as a binary package apparently and I was advised to build from the SVN source.
SVN is not installed, so first it must be installed.
# yum install subversion.i386 ... ... Installed: subversion.i386 0:1.4.2-2.el5 Complete!
Checking out the latest trunk:
# svn checkout https://smarty.isi.edu/svn/repo1/pegasus/trunk pegasus Error validating server certificate for 'https://smarty.isi.edu:443': - The certificate is not issued by a trusted authority. Use the fingerprint to validate the certificate manually! Certificate information: - Hostname: smarty.isi.edu - Valid: from Sep 2 23:58:13 2008 GMT until Sep 2 23:58:13 2009 GMT - Issuer: Certificate Authorities, DOEGrids, org - Fingerprint: bc:2f:1c:49:44:13:36:71:02:e0:65:e5:79:17:5d:dd:c5:5c:ab:cd (R)eject, accept (t)emporarily or accept (p)ermanently? p ... ... Checked out revision 1059.
Building:
# unset CLASSPATH # export PEGASUS_HOME=/root/pegasus # source $PEGASUS_HOME/setup-devel.sh # cd $PEGASUS_HOME # ant dist-worker dist # cd dist # ls -l total 30272 drwxr-xr-x 14 root root 4096 Nov 18 18:40 pegasus-2.2.0cvs -rw-r--r-- 1 root root 15466833 Nov 18 18:41 pegasus-binary-2.2.0cvs-x86_cent_5.2.tar.gz -rw-r--r-- 1 root root 15466848 Nov 18 18:44 pegasus-worker-2.2.0cvs-x86_cent_5.2.tar.gz
Replacing the Pagasus-Mapper:
# rm -rf pegasus-2.2.0cvs
# tar -xzvf pegasus-binary-2.2.0cvs-x86_cent_5.2.tar.gz
...
...
# rm -rf /usr/local/pegasus/2.2.0/*
# mv pegasus-2.2.0cvs/* /usr/local/pegasus/2.2.0
# ls -l /usr/local/pegasus/2.2.0
total 184
drwxr-xr-x 2 root root 4096 Nov 18 18:40 bin
drwxr-xr-x 10 root root 4096 Nov 18 18:40 contrib
drwxr-xr-x 5 root root 4096 Nov 18 18:40 doc
drwxr-xr-x 2 root root 4096 Nov 18 18:40 etc
drwxr-xr-x 2 root root 4096 Nov 18 18:40 examples
-rw-r--r-- 1 root root 5096 Nov 18 18:31 GTPL
drwxr-xr-x 3 root root 4096 Nov 18 18:40 lib
drwxr-xr-x 2 root root 4096 Nov 18 18:40 libexec
-rw-r--r-- 1 root root 11368 Nov 18 18:31 LICENSE
drwxr-xr-x 3 root root 4096 Nov 18 18:39 man
-rw-r--r-- 1 root root 4106 Nov 18 18:31 MIGRATING_FROM_VDS
-rw-r--r-- 1 root root 2714 Nov 18 18:31 README
-rw-r--r-- 1 root root 12175 Nov 18 18:31 RELEASE_NOTES
-rwxr-xr-x 1 root root 2212 Nov 18 18:31 setup.csh
-rwxr-xr-x 1 root root 2217 Nov 18 18:31 setup.sh
drwxr-xr-x 2 root root 4096 Nov 18 18:40 share
drwxr-xr-x 2 root root 4096 Nov 18 18:40 sql
-rw-r--r-- 1 root root 29 Nov 18 18:38 stamp
drwxr-xr-x 7 root root 4096 Nov 18 18:40 test
drwxr-xr-x 2 root root 4096 Nov 18 18:40 var
Replacing the Pegasus-Worker:
# tar -xzvf pegasus-worker-2.2.0cvs-x86_cent_5.2.tar.gz
pegasus-2.2.0cvs/
...
...
# rm -rf /nfs/software/pegasus/2.2.0/*
# ls -l /nfs/software/pegasus/2.2.0/
total 0
# mv pegasus-2.2.0cvs/* /nfs/software/pegasus/2.2.0/
# ls -l /nfs/software/pegasus/2.2.0/
total 184
drwxr-xr-x 2 root root 4096 Nov 18 18:43 bin
drwxr-xr-x 10 root root 4096 Nov 18 18:40 contrib
drwxr-xr-x 5 root root 4096 Nov 18 18:40 doc
drwxr-xr-x 2 root root 4096 Nov 18 18:40 etc
drwxr-xr-x 2 root root 4096 Nov 18 18:40 examples
-rw-r--r-- 1 root root 5096 Nov 18 18:31 GTPL
drwxr-xr-x 3 root root 4096 Nov 18 18:40 lib
drwxr-xr-x 2 root root 4096 Nov 18 18:40 libexec
-rw-r--r-- 1 root root 11368 Nov 18 18:31 LICENSE
drwxr-xr-x 3 root root 4096 Nov 18 18:39 man
-rw-r--r-- 1 root root 4106 Nov 18 18:31 MIGRATING_FROM_VDS
-rw-r--r-- 1 root root 2714 Nov 18 18:31 README
-rw-r--r-- 1 root root 12175 Nov 18 18:31 RELEASE_NOTES
-rwxr-xr-x 1 root root 2212 Nov 18 18:31 setup.csh
-rwxr-xr-x 1 root root 2217 Nov 18 18:31 setup.sh
drwxr-xr-x 2 root root 4096 Nov 18 18:40 share
drwxr-xr-x 2 root root 4096 Nov 18 18:40 sql
-rw-r--r-- 1 root root 29 Nov 18 18:43 stamp
drwxr-xr-x 7 root root 4096 Nov 18 18:40 test
drwxr-xr-x 2 root root 4096 Nov 18 18:40 var
Test
# su - yoichi $ cd pegasus-wms $ tc-client -Dpegasus.user.properties=config/properties -q -B #RESID LTX PTX TYPE SYSINFO PROFILES local condor::dagman /nfs/software/condor/7.0.4/bin/condor_dagman INSTALLED INTEL32::LINUX NULL local diamond::analyze:2.0 /nfs/software/pegasus/2.2.0/bin/keg INSTALLED INTEL32::LINUX NULL local diamond::findrange:2.0 /nfs/software/pegasus/2.2.0/bin/keg INSTALLED INTEL32::LINUX NULL local diamond::preprocess:2.0 /nfs/software/pegasus/2.2.0/bin/keg INSTALLED INTEL32::LINUX NULL rams bin/mDiff gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mDiff STATIC_BINARY INTEL32::LINUX ENV::MONTAGE_HOME="." rams bin/mFitplane gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mFitplane STATIC_BINARY INTEL32::LINUX NULL rams mAdd:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mAdd STATIC_BINARY INTEL32::LINUX NULL rams mBackground:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mBackground STATIC_BINARY INTEL32::LINUX NULL rams mBgModel:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mBgModel STATIC_BINARY INTEL32::LINUX NULL rams mConcatFit:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mConcatFit STATIC_BINARY INTEL32::LINUX NULL rams mDiffFit:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mDiffFit STATIC_BINARY INTEL32::LINUX ENV::MONTAGE_HOME="." rams mImgtbl:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mImgtbl STATIC_BINARY INTEL32::LINUX NULL rams mJPEG:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mJPEG STATIC_BINARY INTEL32::LINUX NULL rams mProject:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mProjectPP STATIC_BINARY INTEL32::LINUX CONDOR::priority="25" rams mProjectPP:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mProjectPP STATIC_BINARY INTEL32::LINUX CONDOR::priority="25" rams mShrink:3.0 gsiftp://grid2.ramscommunity.org/nfs/software/montage/3.0/bin/mShrink STATIC_BINARY INTEL32::LINUX NULL
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