Rosetta dock parallel

[Anonymous]

I am attempting to run rosettadock in 8 parallel processes on an 8-core machine. After building using the extras=mpi flag in scons, I am able to successfully execute 8 processes using mpirun -np 8 dockingexecutable @flags. Unfortunately, when the process goes to write the output files, it returns errors because it is trying to write to “outdir_1”, “outdir_2″…”outdir_8”.

Because I would like to be able to retrieve the structure of the lowest scoring docking complex I have my flags set to write the fullatom pdb of the results. Adjusting the output file name, prefix, or path does not solve the error. If I create the directories “outdir_1″…etc in my working directory, the problem is solved and the output pdb files are distributed among the directories.

While this solution suffices for the small parallel task I am doing now, I would soon like to upgrade to a larger cluster. If I am using say 300 processors, will I have to create 300 directories (outdir_1….outdir_300) to collect my results? Please let me know if I am doing something wrong or missing something. Thank you.

Flags:

-database /home/mahajanr/Rosetta/rosetta_database
-s model.1.pdb
-nstruct 300
-dock_pert 3 8
-fake_native
-ex1
-unboundrot
-mute core.util.prof
-out:file:fullatom
-out:file:o modtest
-out:prefix modecoy
-out:path:pdb /home/username/test/

[Anonymous]

Thank you very much for the prompt response. A quick followup:

Am I correct in my approach to getting coordinates of the lowest energy structure by having the program write all the pdb files (using -out:file:fullatom flag)? I then look at the score file and find which of the written structures has the lowest energy.

Or is there a way to not write each pdb structure and instead only write pdb files for the structures you are interested in afterwards?

[Anonymous]

Hi mahajan, would it be possible to share the response to your first question please. and the second one as well when you get a response.
cheers.

> I am attempting to run rosettadock in 8 parallel processes on an 8-core machine. After building using the extras=mpi flag in scons, I am able to successfully execute 8 processes using mpirun -np 8 dockingexecutable @flags. Unfortunately, when the process goes to write the output files, it returns errors because it is trying to write to “outdir_1”, “outdir_2″…”outdir_8”.
>
> Because I would like to be able to retrieve the structure of the lowest scoring docking complex I have my flags set to write the fullatom pdb of the results. Adjusting the output file name, prefix, or path does not solve the error. If I create the directories “outdir_1″…etc in my working directory, the problem is solved and the output pdb files are distributed among the directories.
>
> While this solution suffices for the small parallel task I am doing now, I would soon like to upgrade to a larger cluster. If I am using say 300 processors, will I have to create 300 directories (outdir_1….outdir_300) to collect my results? Please let me know if I am doing something wrong or missing something. Thank you.
>
> Flags:
>
> -database /home/mahajanr/Rosetta/rosetta_database
> -s model.1.pdb
> -nstruct 300
> -dock_pert 3 8
> -fake_native
> -ex1
> -unboundrot
> -mute core.util.prof
> -out:file:fullatom
> -out:file:o modtest
> -out:prefix modecoy
> -out:path:pdb /home/username/test/
>
>
>

[Anonymous]

Something has eaten my original response – the first posting from “smlewis” above is not from me, this appears to be a response from mahajanr.

Anyway:

The response to the original question, which got overwritten: Yes, you have to make N directories to run on N processors. The docking executeable in Rosetta3 predates the more recent job distributor, and the maintainers have not ported it to the unified job distributor/MPI system.

I am not aware of a filtering option in the main docking executeable. I believe you can get filtering using the parser version instead (I believe the documentation calls it “dock-design” or something similar).

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