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Comments (7)

This is not a question, per se - I suppose it's more of an observation.

We recently upgraded LSF on one of our clusters to v9.0.1, and quickly discovered that Queue can't submit jobs. The reaction was rather violent - the entire JVM crashed, and the stack trace showed it dying in lsb_submit(). We downgraded LSF to v8.3.0, and everything is working fine (so far).

I know Queue is compiled against the LSF v7.0.6 API, it would appear that it's not binary-compatible with LSF 9.x.

Hope this helps others in the future...

Comments (6)

I had no problem to run GATK two weeks ago. But today, when I run the following GATK command, I got error message. It seems it cannot load library " liblsf.so". Please see below. Is there any change recently on GATK library?

2:15pm qyu@vbronze /bit/data01/projects/GC_coverage $ java -Xmx4g -Djava.io.tmpdir=/broad/hptmp/vdauwera -jar /humgen/gsa-scr1/vdauwera/gatk/walker/dist/Queue.jar -S /bit/data01/projects/GC_coverage/src/IntervalCovGG.scala -i /humgen/gsa-hpprojects/GATK/data/genes_of_interest.exon_targets.interval_list -b /bit/data01/projects/GC_coverage/testGCcoverage/data/DEV-2129.list -o /bit/data01/projects/GC_coverage/testGCcoverage/DEV-2129.gatkreport -m 16 -sc 100 -bsub -jobQueue priority -startFromScratch -run

The error shows:

ERROR 14:13:06,238 QGraph - Uncaught error running jobs. 
java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot 
open shared object file: No such file or directory
        at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
        at org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:9
0)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf
706JobRunner.scala:233)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.<clinit>(L
sf706JobRunner.scala)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf7
06JobRunner.scala:47)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf
706JobManager.scala:35)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf
706JobManager.scala:33)
        at org.broadinstitute.sting.queue.engine.QGraph.newRunner(QGraph.scala:6
32)
        at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:408
)
        at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:131)
        at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scal
a:127)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command
LineProgram.java:236)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command
LineProgram.java:146)
        at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:
62)
        at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load librar
y 'lsf': liblsf.so: cannot open shared object file: No such file or directory
        at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
        at org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:9
.........

Thanks, Qing

Comments (7)

Hi,

I am testing queue scripts with new installed LSF v8.3. The test script is:

java -Djava.io.tmpdir=/tmp -jar jar2216/Queue.jar -S Queue-2.2-16-g9f648cb/resources/ExampleCountReads.scala -R Queue-2.2-16-g9f648cb/resources/exampleFASTA.fasta -I Queue-2.2-16-g9f648cb/resources/exampleBAM.bam --bsub -run

where I get error message as follows:

'java' '-Xmx1024m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/data/cmb/wxing/gatk/.queue/tmp' '-cp' '/data/cmb/wxing/gatk/jar2216/Queue.jar' 'org.broadinstitute.sting.gatk. CommandLineGATK' '-T' 'CountReads' '-I' '/data/cmb/wxing/gatk/Queue-2.2-16-g9f648cb/resources/exampleBAM.bam' '-R' '/data/cmb/wxing/gatk/Queue-2.2-16-g9f648cb/resources/exampleFASTA.fasta' java.lang.UnsatisfiedLinkError: Error looking up function 'ls_getLicenseUsage': /usr/local/lsf/8.3/linux2.6-glibc2.3-x86_64/lib/liblsf.so: undefined symbol: ls_getLicenseUsage at com.sun.jna.Function.(Function.java:179) at com.sun.jna.NativeLibrary.getFunction(NativeLibrary.java:344) at com.sun.jna.NativeLibrary.getFunction(NativeLibrary.java:324) at com.sun.jna.Native.register(Native.java:1341) at com.sun.jna.Native.register(Native.java:1018) at org.broadinstitute.sting.jna.lsf.v7_0_6.LibLsf.(LibLsf.java:86) at java.lang.J9VMInternals.initializeImpl(Native Method) at java.lang.J9VMInternals.initialize(J9VMInternals.java:200) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.unitDivisor(Lsf706JobRunner.scala:401) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.org$broadinstitute$sting$queue$engine$lsf$Lsf706JobRunner$$convertUnits(Lsf706JobRunner.scala:416) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner.start(Lsf706JobRunner.scala:98) at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:83) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:432) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:154) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:145) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)

Any clues on the issue "java.lang.UnsatisfiedLinkError: Error looking up function 'ls_getLicenseUsage': /usr/local/lsf/8.3/linux2.6-glibc2.3-x86_64/lib/liblsf.so: ". Or anyone had similar problems?

Anyone think it could be the version of our LSF (v8.3) as the code seem based on version 706?

Many thanks, Wei