Dear friends,
I am trying to use “ddg_monomer.linuxgccrelease” in our university cluster.
However, since my protein is too large (a dimer, each monomer contains 663 residues), the calculation ends because of the wall-time (72 hours) before it finishes.
I am here to ask if it is possible to restart the program. Or is there a method to make the program faster, like using MPI?
Thanks.
Category:
Post Situation:
I don't see any indication of checkpointing or restart behavior in the ddg_monomer application. Also, it doesn't look like there's any support for MPI.
The one thing I think would be possible would be to split out the mutations which you're testing into separate resfiles or mutfiles (https://www.rosettacommons.org/docs/latest/application_documentation/analysis/ddg-monomer#input-files). Given the range syntax of the resfile (https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles), it shouldn't be too hard to put together a set of resfiles which break up the protein into appropriately sized segments. You can then launch multiple runs of the program, each focusing on a small section of the protein. You'd then need to combine the results after the fact.