Out of memory error IJchem 6.0.3

I am using IJchem version 6.0.3.

When i try to perform substructure search on a database of 2126706 compounds i get the error:

ERROR: Tbale "APP.PART" could not fit into str. cache (out of memory)

I am currently running it on a 4 GB RAM machine.

Whats is the max. number of compounds i can search with this memory  limitation? Alternately what would be the memory requirements for the number of compounds i have ?

-Manali

Dear Manali,

I suppose that you are using Windows machine. The maximum memory allocation in this case is left to Java Virtual Machine heurestic algorithms. In your case, it will be better to set the maximum memory manually. See the documentation here and here for the proper memory size. 

For the amount of structures that you mention, 200-300 MB should be enough. For smooth operation, I would however advise to set the maximum memory to 512 MB. You can do that either via IJC (documentation here) or manually in instantjchem.conf file which is located in the \etc foler in the installation directory of IJC (C:\Program Files\ChemAxon\InstantJChem\etc), where you add the J-Xmx512m option into the "default_options" section of the file.

Wishing all the best

David

I changed the C:\Program Files\ChemAxon\InstantJChem\etc file  from

-J-Xmx512m to -J-Xmx1024m

and yet i get the same problem.

Am i missing something ?

Dear Manali,

did you add the -J-Xmx512m option into the default_options, or did you just change the already existing -J-Xmx512m option in the default_mac_options to -J-Xmx1024m? Please see attached screenshot for reference.

The default_mac_options is used only when the operating system is Mac OS X, which is not your case, so if your memory setting was done in the default_mac_options, it was not reflected to your Windows installation.

Could you please confirm against the screenshot?

Wishing all the best

David

You were absolutely correct, i pasted it at the wrong place.

It works fine now.

Thanks