Hi, The exception is OutOfMemoryError, but the message is "unable to create new native thread". I would assume it has to do with limits on number of threads or limit on number of open files (on unix-like systems, most things are files and this limit can often lead to unexpected error messages).
Please execute in your shell: $ ulimit -a You will see there limits for memory, number of open files, cpu time, number of processes, etc. If one of these is particularly low, then probably this would be the source of your problem. To address this issue, you'll need your admin to grant you more privileges or create a new privileged account for running Kepler or whatever your security policy demands :). Regards, Tomek On 10/25/11 at 08:19am, Christopher Brooks wrote: > HI Nathalie, > > I'll need more information. > 1. What actions do you take to cause the run? > 2. Does the error occur when you start up Kepler or when something > else happens? > 3. Are you running from the Kepler development source distribution > or from Kepler-2.2? > > When I run the Kepler development source distribution, I get: > [run] JVM Memory = 5m 768m > Your run has: > JVM Memory = 512m 512m > > For my set up, kepler/build-area/settings/memory.xml looks like: > > ><?xml version="1.0" encoding="UTF-8"?> > ><!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd";> > ><properties> > ><comment>Modified Memory Properties</comment> > ><entry key="max">768m</entry> > ><entry key="min">5m</entry> > ></properties> > Does your memory.xml file set the min to 512m? > > It turns out that the min value is not actually the minimum value > ./build-area/src/org/kepler/build/project/MemoryProperties.java > reads memory.xml > > ./build-area/src/org/kepler/build/Run.java uses the value: > jvmMinMemory = MemoryProperties.getMinMemory(); > ... > java.createJvmarg().setLine("-Xms" + jvmMinMemory); > > I set the min key to 512m and Kepler started up for me and I was > able to run a model. > > I'm not familiar with Scientific Linux, but Wikipedia says it is > based on RedHat Enterprise Linux, > which is what I'm running. Perhaps your machine does not have very > much memory? > > Under RedHat, the "free" command returns the amount of memory available: > > bash-3.2$ free > total used free shared buffers cached > Mem: 16015360 13872904 2142456 0 1239668 8394912 > -/+ buffers/cache: 4238324 11777036 > Swap: 2031608 280 2031328 > > Also, from the command line, try: > java -Xms512m -Xmx512m -version > > I get: > bash-3.2$ java -Xms512m -Xmx512m -version > java version "1.6.0_21" > Java(TM) SE Runtime Environment (build 1.6.0_21-b06) > Java HotSpot(TM) 64-Bit Server VM (build 17.0-b16, mixed mode) > > Note that requesting a very large amount of memory will fail: > bash-3.2$ java -Xms512000m -Xmx512000m -version > Error occurred during initialization of VM > Could not reserve enough space for object heap > > _Christopher > > On 10/25/11 2:05 AM, Nathalie RAVENEL wrote: > >Distribution scientific linux 57. > > > >kepler.sh > >basedir:/root/kepler > >JVM Memory = 512m 512m > >LD_LIBRARY_PATH: > >/usr/java/jdk1.6.0_26/jre/lib/i386/client:/usr/java/jdk1.6.0_26/jre/lib/i386:/usr/java/jdk1.6.0_26/jre/../lib/i386:/opt/switm/libAMD64.lib:/usr/java/latest/jre/lib/amd64/native_threads:/usr/java/latest/jre/lib/amd64/xawt:/usr/java/latest/jre/lib/amd64:/usr/java/latest/jre/lib/amd64/server:/root/m2009b/bin/glnxa64/root/kepler/r/lib:/root/kepler/common/lib > > [null] Checking for patches... > > [null] Building Kars... > > [null] Exception in thread "main" java.lang.OutOfMemoryError: > >unable to create new native thread > > [null] at java.lang.Thread.start0(Native Method) > > [null] at java.lang.Thread.start(Thread.java:640) > > [null] at java.lang.UNIXProcess$1.run(UNIXProcess.java:141) > > [null] at > >java.security.AccessController.doPrivileged(Native Method) > > [null] at java.lang.UNIXProcess.<init>(UNIXProcess.java:103) > > [null] at java.lang.ProcessImpl.start(ProcessImpl.java:65) > > [null] at java.lang.ProcessBuilder.start(ProcessBuilder.java:453) > > [null] at java.lang.Runtime.exec(Runtime.java:593) > > [null] at java.lang.Runtime.exec(Runtime.java:431) > > [null] at java.lang.Runtime.exec(Runtime.java:328) > > [null] at > > org.kepler.loader.PermissionManager.setAllExecutable(PermissionManager.java:62) > > [null] at > > org.kepler.loader.PermissionManager.makeNativeLibsExecutable(PermissionManager.java:52) > > [null] at org.kepler.Kepler.main(Kepler.java:209) > >Exception in thread "main" Java returned: 1 > > at > >org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:106) > > at org.kepler.build.runner.Kepler.main(Kepler.java:90) > >Caused by: Java returned: 1 > > at > >org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:106) > > at org.kepler.build.runner.Kepler.run(Kepler.java:159) > > at > >org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102) > > ... 1 more > >Caused by: Java returned: 1 > > at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108) > > at org.kepler.build.Run.runSuite(Run.java:312) > > at org.kepler.build.Run.run(Run.java:214) > > at > >org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102) > > ... 3 more > >--- Nested Exception --- > >Java returned: 1 > > at > >org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:106) > > at org.kepler.build.runner.Kepler.run(Kepler.java:159) > > at > >org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102) > > at org.kepler.build.runner.Kepler.main(Kepler.java:90) > >Caused by: Java returned: 1 > > at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108) > > at org.kepler.build.Run.runSuite(Run.java:312) > > at org.kepler.build.Run.run(Run.java:214) > > at > >org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102) > > ... 3 more > >--- Nested Exception --- > >Java returned: 1 > > at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108) > > at org.kepler.build.Run.runSuite(Run.java:312) > > at org.kepler.build.Run.run(Run.java:214) > > at > >org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102) > > at org.kepler.build.runner.Kepler.run(Kepler.java:159) > > at > >org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102) > > at org.kepler.build.runner.Kepler.main(Kepler.java:90) > > > > > > > >_______________________________________________ > >Kepler-users mailing list > >Kepler-users@kepler-project.org > >http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users > > -- > Christopher Brooks, PMP University of California > CHESS Executive Director US Mail: 337 Cory Hall > Programmer/Analyst CHESS/Ptolemy/Trust Berkeley, CA 94720-1774 > ph: 510.643.9841 (Office: 545Q Cory) > home: (F-Tu) 707.665.0131 cell: 707.332.0670 > > _______________________________________________ > Kepler-users mailing list > Kepler-users@kepler-project.org > http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users -- Tomasz Zok Poznan Supercomputing and Networking Center ul. Noskowskiego 10, 61-704 Poznan, POLAND http://www.man.poznan.pl _______________________________________________ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
