so, i'm trying to get nightly.sh to run on pads with coasters and i'm not quite sure where this is falling apart. so far the only thing i've edited is providers/ssh-pbs-coasters/sites.template.xml (allowing it to take the PROJECT and QUEUE variables). from what i can tell the sites.xml file does get generated correctly but then according to the test output it times out during submission:<br>
<br>[skenny@login1 tests]$ ./nightly.sh -c -g -s groups/group-ssh.sh<br>
RUNNING_IN: /ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/run-2011-01-10<br>HTML_OUTPUT: /ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/run-2011-01-10/tests-2011-01-10.html<br>which: no ifconfig in (/ci/projects/cnari/apps/freesurfer64/bin:/ci/projects/cnari/apps/freesurfer64/fsfast/bin:/ci/projects/cnari/apps/freesurfer64/mni/bin:/ci/projects/cnari/usr/bin:/ci/projects/cnari/apps/afni:/ci/projects/cnari/apps/swift/bin:/soft/java-1.6.0_11-sun-r1/bin:/soft/java-1.6.0_11-sun-r1/jre/bin:/software/common/gx-map-0.5.3.3-r1/bin:/soft/apache-ant-1.7.1-r1/bin:/soft/condor-7.0.5-r1/bin:/soft/globus-4.2.1-r2/bin:/soft/globus-4.2.1-r2/sbin:/usr/kerberos/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/local/bin:/software/common/softenv-1.6.0-r1/bin:/home/skenny/bin/linux-rhel5-x86_64:/home/skenny/bin:/soft/maui-3.2.6p21-r1/bin:/soft/maui-3.2.6p21-r1/sbin:/soft/openmpi-1.4.2-gcc4.1-r1/bin)<br>
GROUPLISTFILE: groups/group-ssh.sh<br><br>Prolog: Build<br><br>Executing (part 1)<br>/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests<br>Executing (part 2)<br>/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift<br>
14815 pts/27 00:00:00 nightly.sh<br>monitor(1): killing test process...<br>touch: cannot touch `killed_test': Stale NFS file handle<br>monitor(1): killed process_exec (TERM)<br>process_exec_trap()<br>killing all swifts...<br>
++ echo 13685<br>13685<br>++ ps -f<br>UID PID PPID C STIME TTY TIME CMD<br>skenny 14815 1 0 15:49 pts/27 00:00:00 /bin/bash ./nightly.sh -c -g -s groups/group-ssh.sh<br>skenny 14816 1 0 15:49 pts/27 00:00:00 /bin/bash ./nightly.sh -c -g -s groups/group-ssh.sh<br>
skenny 14879 1 0 15:49 pts/27 00:00:04 java -Xmx2048M -Djava.endorsed.dirs=/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/<br>skenny 15473 23767 0 15:55 pts/27 00:00:00 /bin/bash ./nightly.sh -c -g -s groups/group-ssh.sh<br>
skenny 15503 15473 7 15:55 pts/27 00:00:08 /soft/java-1.6.0_11-sun-r1/jre/bin/java -classpath /soft/apache-ant-1.7.1-r1/lib/ant-launcher.jar -Dant.home=/soft/apache-ant-1.7.1-r1 -Dant.<br>skenny 15890 14815 0 15:57 pts/27 00:00:00 ps -f<br>
skenny 23767 23760 0 13:53 pts/27 00:00:00 -bash<br>./nightly.sh: line 588: 14819 Killed "$@" > $OUTPUT 2>&1<br>+++ ps -f<br>+++ grep '.*java'<br>+++ grep -v grep<br>++ kill_this skenny 14879 1 0 15:49 pts/27 00:00:04 java -Xmx2048M -Djava.endorsed.dirs=/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/endorsed -DUID=1195 -DGLOBUS_TCP_PORT_RANGE=50000,51000 -DGLOBUS_HOSTNAME=<a href="http://login1.pads.ci.uchicago.edu" target="_blank">login1.pads.ci.uchicago.edu</a> -DCOG_INSTALL_PATH=/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/.. -Dswift.home=/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/.. -Djava.security.egd=file:///dev/urandom -classpath /ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../etc:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../libexec:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/addressing-1.0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/antlr-2.7.5.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/axis.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/axis-url.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/backport-util-concurrent.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/coaster-bootstrap.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-abstraction-common-2.4.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-axis.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-grapheditor-0.47.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-jglobus-1.7.0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-karajan-0.36-dev.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-clref-gt4_0_0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-coaster-0.3.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-dcache-0.1.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-gt2-2.4.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-gt4_0_0-2.5.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-local-2.2.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-localscheduler-0.4.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-ssh-2.4.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-webdav-2.1.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-resources-1.0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-swift-svn.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-trap-1.0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-url.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-util-0.92.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/commonj.jar:/ci/projects/cnari/soft/swift_latest/cog/mo skenny 15503 15473 7 15:55 pts/27 00:00:08 /soft/java-1.6.0_11-sun-r1/jre/bin/java -classpath /soft/apache-ant-1.7.1-r1/lib/ant-launcher.jar -Dant.home=/soft/apache-ant-1.7.1-r1 -Dant.library.dir=/soft/apache-ant-1.7.1-r1/lib org.apache.tools.ant.launch.Launcher -cp :./ -quiet dist<br>
++ '[' -n 14879 ']'<br>++ /bin/kill -KILL 14879<br>++ set +x<br>Executing Package (part 3)<br>/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift<br>Executing Package (part 4)<br>
/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/lib<br>Executing Package (part 5)<br>/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/lib<br>
Executing Package (part 6)<br>/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests<br>/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/swift<br><br>Part 1: SSH with PBS and Coasters Configuration Test<br>
<br>Using: /ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/tests/providers/ssh-pbs-coasters/sites.template.xml<br>Using: /ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/tests/providers/ssh-pbs-coasters/tc.template.data<br>
`/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/etc/swift.properties' -> `./swift.properties'<br>`/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/tests/providers/ssh-pbs-coasters/001-catsn-ssh-pbs-coasters.swift' -> `./001-catsn-ssh-pbs-coasters.swift'<br>
Executing /ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/tests/providers/ssh-pbs-coasters/001-catsn-ssh-pbs-coasters.swift (part 1)<br>16623 pts/27 00:00:00 nightly.sh<br>monitor(1): killing test process...<br>
monitor(1): killed process_exec (TERM)<br>process_exec_trap()<br>killing all swifts...<br>++ echo 15473<br>15473<br>++ ps -f<br>UID PID PPID C STIME TTY TIME CMD<br>skenny 15473 23767 0 15:55 pts/27 00:00:00 /bin/bash ./nightly.sh -c -g -s groups/group-ssh.sh<br>
skenny 16623 15473 0 15:58 pts/27 00:00:00 /bin/bash ./nightly.sh -c -g -s groups/group-ssh.sh<br>skenny 16624 15473 0 15:58 pts/27 00:00:00 /bin/bash ./nightly.sh -c -g -s groups/group-ssh.sh<br>skenny 16687 1 0 15:58 pts/27 00:00:04 java -Xmx2048M -Djava.endorsed.dirs=/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/<br>
skenny 17414 16623 0 16:06 pts/27 00:00:00 ps -f<br>skenny 23767 23760 0 13:53 pts/27 00:00:00 -bash<br>./nightly.sh: line 588: 16627 Killed "$@" > $OUTPUT 2>&1<br>+++ ps -f<br>
+++ grep '.*java'<br>+++ grep -v grep<br>++ kill_this skenny 16687 1 0 15:58 pts/27 00:00:04 java -Xmx2048M -Djava.endorsed.dirs=/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/endorsed -DUID=1195 -DGLOBUS_TCP_PORT_RANGE=50000,51000 -DGLOBUS_HOSTNAME=<a href="http://login1.pads.ci.uchicago.edu" target="_blank">login1.pads.ci.uchicago.edu</a> -DCOG_INSTALL_PATH=/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/.. -Dswift.home=/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/.. -Djava.security.egd=file:///dev/urandom -classpath /ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../etc:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../libexec:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/addressing-1.0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/antlr-2.7.5.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/axis.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/axis-url.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/backport-util-concurrent.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/coaster-bootstrap.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-abstraction-common-2.4.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-axis.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-grapheditor-0.47.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-jglobus-1.7.0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-karajan-0.36-dev.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-clref-gt4_0_0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-coaster-0.3.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-dcache-0.1.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-gt2-2.4.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-gt4_0_0-2.5.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-local-2.2.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-localscheduler-0.4.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-ssh-2.4.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-provider-webdav-2.1.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-resources-1.0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-swift-svn.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-trap-1.0.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-url.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/cog-util-0.92.jar:/ci/projects/cnari/soft/swift_latest/cog/modules/swift/tests/cog/modules/swift/dist/swift-svn/bin/../lib/commonj.jar:/ci/projects/cnari/soft/swift_latest/cog/mo<br>
++ '[' -n 16687 ']'<br>++ /bin/kill -KILL 16687<br>++ set +x<br>kill 16624: No such process<br>TOOK: 500<br>FAILED<br>Swift svn swift-r3921 (swift modified locally) cog-r3013<br><br>RunID: 20110110-1558-ojtlnxfb<br>
Progress:<br>Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>
Progress: Selecting site:9 Initializing site shared directory:1<br>
Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>
Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>
Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>Progress: Selecting site:9 Initializing site shared directory:1<br>
nightly.sh: monitor(1): killed: exceeded 500 seconds<br>FAILED<br>++ seq --format %04.f 1 1 10<br>+ for count in '`seq --format "%04.f" 1 1 10`'<br>+ '[' -f catsn.0001.out ']'<br>+ exit 1<br>
<br>----------------------------------------------------------------<br><br>i'm running this directly on the pads login and seeing this in the swift log:<br><br>2011-01-10 16:33:18,539-0600 INFO TransportProtocolCommon The Transport Protocol thread failed <br>
java.io.IOException: The socket is EOF <br> at com.sshtools.j2ssh.transport.TransportProtocolInputStream.readBufferedData(TransportProtocolInputStream.java:183) <br>
at com.sshtools.j2ssh.transport.TransportProtocolInputStream.readMessage(TransportProtocolInputStream.java:226) <br> at com.sshtools.j2ssh.transport.TransportProtocolCommon.processMessages(TransportProtocolCommon.java:1440) <br>
at com.sshtools.j2ssh.transport.TransportProtocolCommon.startBinaryPacketProtocol(TransportProtocolCommon.java:1034) <br> at com.sshtools.j2ssh.transport.TransportProtocolCommon.run(TransportProtocolCommon.java:393) <br>
at java.lang.Thread.run(Thread.java:619) <br><br><br>you can view the test output here:<br><br><a href="http://www.ci.uchicago.edu/~skenny/swift_tests/run-2011-01-10/tests-2011-01-10.html">http://www.ci.uchicago.edu/~skenny/swift_tests/run-2011-01-10/tests-2011-01-10.html</a><br>
<br>anyway, thought i'd post this in case there's something that might jump out at any of you that i can tweak...<br><br>~sk<br><br><br>