Starting multiple IJC in the same computer

User b726e46c74

04-11-2015 10:59:17


Dear all,

I have perhaps a simple question.

Is it possible and if yes how to run multiple IJC on the same hardware?

I would like to see what is the substructure overlap between 3.5 million and 65 000 compounds. I have a small tower that has enough memory and processing power to run multiple IJCs. this would also increase significantly the time needed for such overlap calculations.

I am currently running web version IJC on Ubuntu 14.04 and the same version on Mac.

I am posting this question because no matter what I do always shows the already opened GUI window. 

I tried to started form different terminals, I also tried to copy the program files in different location and started from there .... nothing worked. I wander if this is made so deliberately or it is a side effect and if it can be overrun?  

Thank you in advance for your answer!




ChemAxon 26d92e5dcd

04-11-2015 14:28:42

Dear Tsonko,

it is not possible to run multiple instances of Instant JChem on the same system in parallel. However, for your usecase that you describe, I believe Overlap analysis should do the trick. See the documentation here.

Wishing all the best


ChemAxon 3b366b17e5

04-11-2015 14:42:24


there exists a way how to run two instances of IJC on the same system in parallel. You need to specify user dir for the second instance from commandline:

bin/instantjchem  --userdir <path_to_second_user_dir>


User b726e46c74

05-11-2015 10:51:15

Hi Petr,

That is a great news. I tested and it works nicely as you state it. 

It would be kind of waste of resources to put a single process on a server and expect results in a mount when I can get them in a couple of days :).

Thank you again for the fast answer!