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jcman import error on linux command line

User 773d472e7f

09-07-2012 07:35:37

Dear ChemAxon Support,


I am creating a molecule database in linux/mysql using jcman on the commandline.


I have successfully used the following command on a local test server with (4GB RAM) using an SDFile containing 1000 structures. This local server has also imported an SDFile containing 1 million structures.


However the command fails on a vServer. The vServer has 4GB RAM. The command line feedback is copied below:




root@v14908:/# jcman a AKOS_MOLTABLE /akos/AKOS_1000_SMALL.sdf --driver com.mysql.jdbc.Driver --dburl jdbc:mysql://localhost:3306/akossamplesservice -l akossamples -p ********** -a


Collecting file information ...


 Done.


Importing structures from /akos/AKOS_1000_SMALL.sdf ...


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


Java HotSpot(TM) 64-Bit Server VM warning: Exception java.lang.OutOfMemoryError occurred dispatching signal SIGTERM to handler- the VM may need to be forcibly terminated


/root/ChemAxon/JChem/bin/jcman: line 177: 15560 Killed                  java $javaopts chemaxon.jchem.Command "$@"


root@v14908:/#


Many thanks for your help.


Bernard


ChemAxon aa7c50abf8

09-07-2012 07:48:31

Bernard,


Your system is likely to be running out of virtual memory. I suspect you will find references to oom-killer or oom_kill_process in the system logs.


Peter