Is it possible to restart the ddg_monomer.linuxgccrelease?

[Anonymous]

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. 

[Anonymous]

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.

[Author]

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