It is my first time using an MPI executable to run the ddg_monomer. I tested it to mutate the first residue from D to A with different cores, which is compared to a serial job. The following is the results:
Core number, time, ddg prediction
1 (serial), 32 hours, -0.362
2, 25.433 hours, -1.722
4, 29.766 hours, 0.055
8, 24.68 hours, 0.239
24, 25.13 hours, -3.080
So can I ask:
1) As the ddg prediction vary a lot, is ddg_monomer reproducible?
2) More cores seem to be not so efficient, why is that?
3) I also tested pmut_scan_parallel.linuxgccrelease. When "-constant_seed" is removed, the outputs are always identical no matter whether "-jran" option is constant or not. So is pmut_scan_parallel better than ddg_monomer in terms of reproducibility?
One of the option files for the MPI job as well as its job script .sh file are attached. I would appreciate it if someone can help me that. Thank you very much.