RosettaCommons
UnfoldedStateEnergyCalculator.mpi.linuxgccrelease is not working in mpi compilation
The UnfoldedStateEnergyCalculator.mpi.linuxgccrelease is not working in mpi compilation , I tried it several times and I figured out that the UnfoldedStateEnergyCalculator.defaultlinuxgccrelease is the release mode is working normally with the same tasks, files, and commands. Please help to fix this issue. 3.14 and 3.13 versions used.
To help track down the issue, what's the error message you're seeing? (Or what else is letting you know it's not working.)
The following error message is from ROSETTA_CRASH.log upon running mpi release
[START_MESSAGE]
Segmentation Fault
[END_MESSAGE]
[END_CRASH_REPORT]
I used this command
mpirun -np 64 /Rosetta_3.14/main/source/bin/UnfoldedStateEnergyCalculator.mpi.linuxgccrelease \
-ignore_unrecognized_res \
-ex1 \
-ex2 \
-extrachi_cutoff 0 \
-l ../inputs/list \
-usec:residue_name VAL \
-mute all \
-unmute devel.UnfoldedStateEnergyCalculator \
-unmute protocols.jd2.PDBJobInputer \
-no_optH true \
-detect_disulf false >& ufsec_log_VAL
I also tried to use an output log level of 500 to track the error, but it was the same thing, I also tried to run the same command without mpirun it didn't return anything, finally I used the default release and I ran the command again off course without mpirun, it worked for a while and there were output with errors like the list bellow (which I'll be thankful if you help me with it also), then it exits with these errors (which is different of the first issue.
[FILE]: src/core/id/NamedAtomID_Map.hh
[LINE]: 390
[START_MESSAGE]
Residue outside res_map range
[FILE]: src/core/pack/task/ResidueLevelTask_.cc
[LINE]: 1138
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `! found_aa_difference` failed.
[FILE]: src/core/conformation/Conformation.cc
[LINE]: 1857
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: too many tries in fill_missing_atoms!
[FILE]: src/core/conformation/Residue.cc
[LINE]: 1376
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to fill in missing atoms.
File: src/numeric/xyzVector.hh:671
Cannot create normalized xyzVector from vector of length() zero. Error occurred when trying to normalize the vector between points A and B. A=[0.000000,0.000000,0.000000], B=[0.000000,0.000000,0.000000].
[START_MESSAGE]
Error in Stub::from_four_points():
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion ! lines.empty() failed.
Some of the errors from the log, has more details ( I followed the unfolded_state_energy_calculator tutorial):
ERROR: too many tries in fill_missing_atoms!
ERROR:: Exit from: src/core/conformation/Conformation.cc line: 1857
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job '1h16_0001'
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs
[ ERROR ]: Caught exception:
File: src/core/conformation/Conformation.cc:1857
[ ERROR ] UtilityExitException
ERROR: too many tries in fill_missing_atoms!
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
--------------------------------------------------------------------------------------------------------------
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job '1jet_0001'
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs
[ ERROR ]: Caught exception:
File: src/core/kinematics/Stub.cc:105
Error in Stub::from_four_points():
File: src/numeric/xyzVector.hh:671
Cannot create normalized xyzVector from vector of length() zero. Error occurred when trying to normalize the vector between points A and B. A=[0.000000,0.000000,0.000000], B=[0.000000,0.000000,0.000000].
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
--------------------------------------------------------------------------------------------------------------
ERROR: Can't add atom named `CS` to ResidueType pdb_SMC as it already has one with that name.
ERROR:: Exit from: src/core/chemical/MutableResidueType.cc line: 860
core.chemical.Patch: [ WARNING ] Patch C_methylamidated implies it can apply to residue type pdb_SMC, but actually applying it fails with error message:
core.chemical.Patch: [ WARNING ]
File: src/core/chemical/MutableResidueType.cc:860
[ ERROR ] UtilityExitException
ERROR: Can't add atom named `CS` to ResidueType pdb_SMC as it already has one with that name.
core.chemical.Patch: [ WARNING ] You may want to check your patch definitions.
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'TP7' from the PDB components dictionary for residue type 'pdb_TP7'
ERROR: Can't add atom named `CS` to ResidueType pdb_SMC as it already has one with that name.
ERROR:: Exit from: src/core/chemical/MutableResidueType.cc line: 860
core.chemical.Patch: [ WARNING ] Patch C_methylamidated implies it can apply to residue type pdb_SMC, but actually applying it fails with error message:
core.chemical.Patch: [ WARNING ]
File: src/core/chemical/MutableResidueType.cc:860
[ ERROR ] UtilityExitException
ERROR: Can't add atom named `CS` to ResidueType pdb_SMC as it already has one with that name.
--------------------------------------------------------------------------------------------------------------
ERROR: Assertion `! found_aa_difference` failed.
ERROR:: Exit from: src/core/pack/task/ResidueLevelTask_.cc line: 1138
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job '1hbn_0001'
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs
[ ERROR ]: Caught exception:
File: src/core/pack/task/ResidueLevelTask_.cc:1138
[ ERROR ] UtilityExitException
ERROR: Assertion `! found_aa_difference` failed.
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
So here there are 2 things, one for mpi and default excutables, another for the return of the default itself and the input pdbs
I just wanted to announce that the mpi build of this application is not working at all, in 3.14 version