out of memory in MarvinView

I have got an out of memory error when I try to load thousands of molecules into MarvinView.

Code:

mview -n 10000 smiles10K.smi

Increasing the limit of the importable structures is not enough. You have to provide more memory for Java. Normally, the JVM's memory usage is limited to 64M: this is the maximum heap size. You can increase it with the -Xmx parameter in the JVM. Increasing the inital heap size is also recommended to avoid other potential out of memory error in the JVM. Use the -Xms parameter to do it.


The following configuration seems to be enough for 10K structures:

Code:

mview -Xms150m -Xmx150m -n 10000 smiles10K.smi

You play with these values, e.g.:

Code:

mview -Xms400m -Xmx600m -n 30000 input.smi

(where the heap size is 400MB at the beginning and Java can increase it until 600MB)





To check the settings, start MarvinView, and select menu item Help->About Java VM and see the Memory settings.





By the way, we plan to decrease the memory demand of MarvinView, so that it will be able to handle huge molecule files without the need for setting these parameters.