An error with score app

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!