Last modified: 2014-09-10 20:26:16 UTC
Running a tool via crontab with jsub results in the following error: Picked up _JAVA_OPTIONS: -Xmx150M Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit. Error occurred during initialization of VM Could not reserve enough space for object heap The tool ~toolserverdb/ns-updater/startNSUpdate.sh works on tools-login though.
Have you tried to add more mem to sge runtime environment for the job? Also some of my simple java tools need at least 4G mem (-l h_vmem=4000M).
Unfortunatelly the original parameters of SGE as well as you suggested one do not work.
Could you specify the exact command line you are using to run the tool?
tools.toolserverdb@tools-login:~$ sh -x ~/ns-updater/startUpdate.sh + which java + JAVA=/usr/bin/java + export _JAVA_OPTIONS=-Xmx150M + CONFIG=/data/project/toolserverdb/ns-updater/conf/config.properties + LOG4JCONFIG=/data/project/toolserverdb/ns-updater/conf/log4j.xml + [ -z /usr/bin/java ] + /usr/bin/java -Dlog4j.configuration=file:/data/project/toolserverdb/ns-updater/conf/log4j.xml -jar /data/project/toolserverdb/ns-updater/Updater.jar /data/project/toolserverdb/ns-updater/conf/config.properties Picked up _JAVA_OPTIONS: -Xmx150M 2014-09-10 20:22:24,068 INFO TSUpdater [] Maximum thread-number: 2 + exit 0 and then I do a jsub ns-updater/startUpdate.sh and get a Picked up _JAVA_OPTIONS: -Xmx150M Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.
