can't set up higher memory amount for generatemd

User a3accc027a

16-09-2005 10:06:12


i suffered an out of memory error while trying to run generatemd:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

I've read the JChem FAQ section 10 about this kind of error, but after checking file

generatemd.bat i didn't find variable HEAP_LIMIT defined inside.

Then i tried to set up an environment variable under my bash shell (export HEAP_LIMIT=128)

at my best guess on how should i specify the memory amount, but even after doing so still

got the same error. I even tried a further increase (export HEAP_LIMIT=256) but again ran

out of memory.

How do i set an increased memory amount for generatemd? Could you please provide more

details? I'm surely doing something wrong somewhere... I'm running JChem in a Linux box.

thank you very much

Guillem Plasencia.

ChemAxon efa1591b5a

19-09-2005 08:20:45

Hi Guillem,

the easiest way is to issue the command below:

export JCHEM_JAVA_OPTS="-Xmx512M'

this will increase java heap size to 512MB. The underlying mechanism works as follows: the variable JCHEM_JAVA_OPTS is passed to java when GenerateMD class is loaded and started by the generatemd script command. Any other options you need to pass to Java VM can be set the same way.

Hope this helps.


I am a bit concerned how generatemd could overflow the heap - it should not!! Can you tell me the size of your input data (fileformat and number of compounds) as well as the type and parameter configuration of the molecular descriptor being used?



ChemAxon efa1591b5a

20-09-2005 11:47:18

Yet another remark: if you are using JChem 3.1 or later, you can specify the -Xmx option in the command line of generatemd. So you can type sg. like this:

generatemd c -Xmx128M infile.sdf -k CF

Hope this helps.