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ReplicaDock2.0 demo fails with MPIFileBufJobDistributor: (1) [ ERROR ]

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ReplicaDock2.0 demo fails with MPIFileBufJobDistributor: (1) [ ERROR ]
#1

Dear all,

I'm really struggeling to repeat the published procedures to run ReplicaDock2.0 (Local and Global), let alone adopt it to my needs.

I followed the protocol as descibed by Harmalkar et al.  and running the examples from /rosetta/rosetta.source.release-314/main/demos/public/replicadock2". To be able to start the run, I needed to remove '''<AddEncounterConstraintMover name="encounter_cst" gap="8" />''' and '''<Add mover_name="encounter_cst"/>'''. This allowed me to start the run using 

mpirun -np 26 $ROSETTA/main/source/bin/rosetta_scripts.mpi.linuxgccrelease @local_flags

(with nstruct 8 and n_replica 3 as flags) and interestingly, the run ends without any problems. But unfortunatley, there is also no real output. Instead, I have l 26 log files of which only 4 contain data:

  • logs/log_2 and logs/log_3 end with the CitationManager - all good.
  • logs/log_0 ends in the middle:
    [...]
    core.scoring.motif: (0) preload_motif_data
    core.pack.dunbrack.RotamerLibrary: (0) shapovalov_lib_fixes_enable option is true.
    core.pack.dunbrack.RotamerLibrary: (0) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
    core.pack.dunbrack.RotamerLibrary: (0) Binary rotamer library selected: /rosetta/rosetta.source.release-314/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
    core.pack.dunbrack.RotamerLibrary: (0) Using Dunbrack library binary file '/rosetta/rosetta.source.release-314/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
    core.pack.dunbrack.RotamerLibrary: (0) Dunbrack 2010 library took 0.092613 seconds to load from binary
    core.pack.pack_rotamers: (0) built 22 rotamers at 1 positions.
    core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
    protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ...
    

     

  • logs/log_1 ends with an error:
    core.scoring.motif: (1) preload_motif_data
    core.pack.dunbrack.RotamerLibrary: (1) shapovalov_lib_fixes_enable option is true.
    core.pack.dunbrack.RotamerLibrary: (1) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
    core.pack.dunbrack.RotamerLibrary: (1) Binary rotamer library selected: /rosetta/rosetta.source.release-314/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
    core.pack.dunbrack.RotamerLibrary: (1) Using Dunbrack library binary file '/rosetta/rosetta.source.release-314/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
    core.pack.dunbrack.RotamerLibrary: (1) Dunbrack 2010 library took 0.099069 seconds to load from binary
    core.pack.pack_rotamers: (1) built 22 rotamers at 1 positions.
    core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph
    protocols.evaluation.ChiWellRmsdEvaluatorCreator: (1) Evaluation Creator active ...
    protocols.jd2.MPIFileBufJobDistributor: (1) [ ERROR ] TIME_STAMP: Mon Aug  8 14:24:45 2022 assign job 1 batch: 00000
    protocols.jd2.MPIFileBufJobDistributor: (1) Starting JobDistribution with 8 worker processes
    protocols.jd2.MPIFileBufJobDistributor: (1) [ ERROR ] TIME_STAMP: Mon Aug  8 14:24:45 2022 assign job 2 batch: 00000
    protocols.jd2.MPIFileBufJobDistributor: (1) [ ERROR ] TIME_STAMP: Mon Aug  8 14:24:45 2022 assign job 3 batch: 00000
    protocols.jd2.MPIFileBufJobDistributor: (1) [ ERROR ] TIME_STAMP: Mon Aug  8 14:24:45 2022 assign job 4 batch: 00000
    protocols.jd2.MPIFileBufJobDistributor: (1) [ ERROR ] TIME_STAMP: Mon Aug  8 14:24:45 2022 assign job 5 batch: 00000
    protocols.jd2.MPIFileBufJobDistributor: (1) [ ERROR ] TIME_STAMP: Mon Aug  8 14:24:45 2022 assign job 6 batch: 00000
    protocols.jd2.MPIFileBufJobDistributor: (1) [ ERROR ] TIME_STAMP: Mon Aug  8 14:24:45 2022 assign job 7 batch: 00000
    protocols.jd2.MPIFileBufJobDistributor: (1) [ ERROR ] TIME_STAMP: Mon Aug  8 14:24:45 2022 assign job 8 batch: 00000
    protocols.jd2.JobDistributor: (1) no more batches to process...
    protocols.jd2.MPIFileBufJobDistributor: (1) Master Node: Finished sending spin down signals to slaves
    protocols.jd2.MPIFileBufJobDistributor: (1) Master Node stats: jobs-send out: 8  returned: 8  bad input jobs: 0
    

     

It is repeatly always like this, no matter how many times I repeat the run and change parameters. Again, this is happening for both GlobalDock and LocalDock. I really spend a lot of time to try and fix this, but now I'm stuck. I hope somebody from the community can provide with some advice her.

Thank you in advance,
Erwin

Category: 
Post Situation: 
Tue, 2022-08-09 05:42
erpannec

Hello,

Sorry to hear that you have been having issues running it. To start with, removing EncounterConstraintMover is a good way to get around the issue. We realized it recently that the mover is in the developer version, so we will move it to public repositories soon. (It shouldn't affect your docking performance much, so removing it should be okay).

After you run the script, are you able to generate .out files. These are silent output files that actually contain all the docking data (i.e. scores + PDB structures). You can grep the scores using the following bash script in the output directory (I am hoping you have 8 of the trajectory files named in this fashion).

for i in {1..8}; do echo decoys_P_000$i\_traj.out; cat decoys_P_000$i\_traj.out | grep SCORE: >> decoys_1.fsc ; done; sort -n -k13 decoys_1.fsc

Hope this helps! Let me know if there are any issues and I would be happy to help!

Tue, 2022-08-09 16:01
Ameya

Dear Ameya,

Thank you already for this respons. 

I don't get any PBDs as output, not even when I add "out:pdb" to the flags file. What is created, is decoys.out and scores.fsc. So no decoy per nstruct. This is probably in line with the JobDistributor throwing an error for all job batches?


Thanks for the help!
Erwin

Fri, 2022-08-12 01:20
erpannec

Dear Ameya,

Do you need more information to help me troubleshoot these issues?

 

Thank you in advance,
Erwin

Tue, 2022-08-23 21:00
erpannec

Dear Ameya,

Do you have any update on this matter?

Kind regards,
Erwin

Thu, 2022-09-15 05:17
erpannec