Running Jchem in parallel environment:

User be4c1293dc

26-02-2010 06:20:03


Is it possibel to run jchem tools in a parallel environment? I would like to speed up the process of fingerprint/descriptor calculation and clustering process using multiprocessor machine.


Many thanks


ChemAxon efa1591b5a

04-03-2010 09:27:59

Hi Sangeetha,

I'm afraid that neither fingerprint generation nor clustering can make use of multiple processors yet.

For the generation you may split up the input and run several independent processes and then merge the results.

We certainly plan to 'go parallel', however, it's not so evident to foresee which way to go. Thus your suggestions and comments would be very highly appreciated in this matter. Do you plan to use a multicore CPU? Or multiple CPUs with shared memory? Or you'd prefer a cluster or grid solution?

Or the cloud? Would you be ready to throw your perhaps confidential structures in the cloud (using secure connection)?



User be4c1293dc

05-03-2010 05:55:16

Hi Miklos,

I am using a multi-core CPU. It would be beneficial for most of us to have programs to be run in a multi-core or even cluster set-up. Such solutions can make effective usage of CPU's. I have no experience using cloud and hence not sure about that.

Thankyou for the opportunity


ChemAxon efa1591b5a

17-03-2010 08:29:07

Hi Sangeetha,

Thank you for your response. It's quite likely that multicore will be the most typical parallel environment in the near future. We will try to address multiprocessing in JKlustor.