Processor use

User e59cb00a69

18-06-2008 21:57:49


I recently imported the NCI dataset into instant jchem, and during the SDF import I check to see how much CPU power the program is using for the task.

It seems that instant jchem is only using 20% of available processing power. Is there a way to devote more processor to instant j chem?

Also I'm having problems with LibraryMCS. I get the error "heap space". How can I increase the heap space in LibraryMCS?

Thanks so much,


ChemAxon fa971619eb

19-06-2008 11:38:57

Most of the time is probably spent with disk IO (if you are using a local database) or network IO (if using a remote database).

Also, if you are using a multi-procesor and/or a multi-core machine then not all operations can utilise the available processors/cores, though in general IJC is fairly effiicent in doing so.


User e59cb00a69

19-06-2008 14:16:22


What about the heap space problem?

ChemAxon fa971619eb

19-06-2008 14:40:26

you should be able to increase the amount of memory available (heap space etc.) using the startup options.

Look in the libmcs startup stripts (e.g bin/libmcs.bat) and look for the HEAP_LIMIT variable.


ChemAxon efa1591b5a

20-06-2008 06:49:42

You can pass -Xmx to the batch/shell script programs that launch libmcs.

Btw, what's the size of your input?