Hello, I am trying the score app in the tutorials and meet an fatal error.
I work on CentOS 7 and my rosetta version is rosetta_src_2019.40.60963_bundle.
At first, I just used the command given by the instruction, it is:
score.mpi.linuxgccrelease -in:file:s input_files/1qys.pdb -in:file:native input_files/from_rcsb/1qys.pdb -ignore_waters
however, it stoped after a few seconds and the last lines of log is:
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
protocols.jobdist.main: (0) PDB Output Mode
protocols.jobdist.JobDistributors: (0) Node: 0 next_job()
protocols.jobdist.JobDistributors: (0) Master Node -- Waiting for job request; tag_ = 1
I tried several times and it was always waiting even 1 hour later. I had to interrupt it.
when restarting, I used the mpirun -np 2 to enable multiple processes, the commond is:
mpirun -np 2 --allow-run-as-root score.mpi.linuxgccrelease -in:file:s input_files/1qys.pdb -in:file:native input_files/from_rcsb/1qys.pdb -ignore_waters
And the last log is:
protocols.jobdist.main: (1) Starting 1qys_0001 ...
core.import_pose.import_pose: (1) File 'input_files/1qys.pdb' automatically determined to be of type PDB
protocols.jobdist.main: (1) Finished 1qys_0001 in 1 seconds.
protocols.jobdist.JobDistributors: (0) Master Node --available job? 0
protocols.jobdist.JobDistributors: (0) Master Node -- Spinning down node 1
protocols.jobdist.JobDistributors: (0) Node 0 -- ready to call mpi finalize
protocols.jobdist.JobDistributors: (1) Node: 1 next_job()
protocols.jobdist.JobDistributors: (1) Slave Node 1 -- requesting job from master node; tag_ 1
protocols.jobdist.JobDistributors: (1) Node 1 -- ready to call mpi finalize
protocols.jobdist.main: (0) Finished all 0 structures in 3 seconds.
Warning: (0) [ WARNING ] No structures processed. Existing output files may have been skipped, did you mean to delete them or to use the -overwrite flag?
protocols.jobdist.main: (1) Finished all 1 structures in 2 seconds.
But it gave no result or output file, things were all the same when I retried and added -overwrite.
Then I tried 3 or more processes, such as:
mpirun -np 3 --allow-run-as-root score.mpi.linuxgccrelease -in:file:s input_files/1qys.pdb -in:file:native input_files/from_rcsb/1qys.pdb -ignore_waters
And the last log is:
core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph
protocols.jobdist.main: (1) PDB Output Mode
protocols.jobdist.JobDistributors: (1) Node: 1 next_job()
protocols.jobdist.JobDistributors: (1) Slave Node 1 -- requesting job from master node; tag_ 1
protocols.jobdist.JobDistributors: (0) Master Node --available job? 0
protocols.jobdist.JobDistributors: (0) Master Node -- Spinning down node 1
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jobdist.main: (2) Finished 1qys_0001 in 1 seconds.
protocols.jobdist.JobDistributors: (0) Master Node -- Spinning down node 2 with 1 remaining nodes.
protocols.jobdist.JobDistributors: (0) Node 0 -- ready to call mpi finalize
protocols.jobdist.JobDistributors: (2) Node: 2 next_job()
protocols.jobdist.JobDistributors: (2) Slave Node 2 -- requesting job from master node; tag_ 1
protocols.jobdist.JobDistributors: (2) Node 2 -- ready to call mpi finalize
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 3985 on node localhost exited on signal 11 (Segmentation fault).
It still did not work.
I do not know why it always failed and how to fix this problem. It is really appreciated if it can be solved.
Thanks a lot!