Hello,
The Rosetta program was frozen at "protocols.jobdist.JobDistributors: (0) Master Node -- Waiting for job request; tag_ = 1" when I was trying to predict structure of a sequence. Dose anybody know how to solve this problem?
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IU-Quota version 1.2 loaded.
xy32@elogin1:~> :~> module unload PrgEnv-intel
:~: command not found
xy32@elogin1:~> module unload PrgEnv-intel
xy32@elogin1:~> module load PrgEnv-gnu
xy32@elogin1:~> module load openmpi/gnu/4.0.2
openmpi version 4.0.2 loaded.
xy32@elogin1:~> module load rosetta
rosetta version 2019.35 loaded.
xy32@elogin1:~> ls
1ELW.fasta aat000_03_05.200_v1_3 flags t000_.psipred_ss2
1elw.pdb aat000_09_05.200_v1_3
xy32@elogin1:~> /N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/source/bin/AbinitioRelax.mpi.linuxgccrelease @flags
core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags
core.init: (0) Rosetta version: rosetta.source.release-231 r231 2019.35+release.767c1ea 767c1ea25c572fbc078db45ad65dddb507240ad3 https://www.rosettacommons.org 2019-08-30T10:52:08.483471
core.init: (0) command: /N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/source/bin/AbinitioRelax.mpi.linuxgccrelease @flags
basic.random.init_random_generator: (0) 'RNG device' seed mode, using '/dev/urandom', seed=-53430990 seed_offset=0 real_seed=-53430990
basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=-53430990 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 980 residue types
core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 1.03723 seconds.
core.import_pose.import_pose: (0) File './1elw.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: (0) Loading (but possibly not actually using) 'NI' from the PDB components dictionary for residue type 'pdb_NI'
core.chemical.GlobalResidueTypeSet: (0) Loading (but possibly not actually using) 'TRS' from the PDB components dictionary for residue type 'pdb_TRS'
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU:NtermProteinFull 1
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU:NtermProteinFull 1
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU:NtermProteinFull 1
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU:NtermProteinFull 1
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue MET:NtermProteinFull 122
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: SD on residue MET:NtermProteinFull 122
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue MET:NtermProteinFull 122
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 123
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 123
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 123
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 123
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 231
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 231
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 231
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 231
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue MET:CtermProteinFull 236
core.pack.pack_missing_sidechains: (0) packing residue number 1 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 122 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 123 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 231 because of missing atom number 6 atom name CG
core.pack.task: (0) Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015
core.scoring.etable: (0) Starting energy table calculation
core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: (0) Finished calculating energy tables.
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: (0) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: (0) Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: (0) Read 40 countpair representative atoms
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: /N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: (0) Using Dunbrack library binary file '/N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: (0) Dunbrack 2010 library took 0.154166 seconds to load from binary
core.pack.pack_rotamers: (0) built 63 rotamers at 4 positions.
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.chemical.GlobalResidueTypeSet: (0) Finished initializing centroid residue type set. Created 62 residue types
core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 0.029976 seconds.
core.chemical.residue_support: (0) [ WARNING ] Atom type 'Ni' on atom 'NI' from residue type 'NI' does not have a centroid mode equivalent: assuming CAbb.
core.chemical.GlobalResidueTypeSet: (0) Loading (but possibly not actually using) 'NI' from the PDB components dictionary for residue type 'pdb_NI'
core.chemical.GlobalResidueTypeSet: (0) Loading (but possibly not actually using) 'TRS' from the PDB components dictionary for residue type 'pdb_TRS'
protocols.abinitio.AbrelaxApplication: (0) read fasta sequence: 120 residues
GCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEARD
core.import_pose.import_pose: (0) File './1elw.pdb' automatically determined to be of type PDB
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU:NtermProteinFull 1
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU:NtermProteinFull 1
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU:NtermProteinFull 1
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU:NtermProteinFull 1
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue MET:NtermProteinFull 122
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: SD on residue MET:NtermProteinFull 122
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue MET:NtermProteinFull 122
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 123
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 123
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 123
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 123
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 231
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 231
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 231
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 231
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue MET:CtermProteinFull 236
core.pack.pack_missing_sidechains: (0) packing residue number 1 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 122 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 123 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 231 because of missing atom number 6 atom name CG
core.pack.task: (0) Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015
core.pack.pack_rotamers: (0) built 63 rotamers at 4 positions.
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ...
core.io.fragments: (0) reading fragments from file: ./aat000_09_05.200_v1_3 ...
core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader...
core.fragments.ConstantLengthFragSet: (0) finished reading top 25 9mer fragments from file ./aat000_09_05.200_v1_3
core.io.fragments: (0) reading fragments from file: ./aat000_03_05.200_v1_3 ...
core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader...
core.fragments.ConstantLengthFragSet: (0) finished reading top 200 3mer fragments from file ./aat000_03_05.200_v1_3
core.fragment: (0) compute strand/loop fractions for 117 residues...
protocols.abinitio.AbrelaxApplication: (0) run ClassicAbinitio.....
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth
basic.io.database: (0) Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth
core.scoring.ScoreFunction: (0) ATOM_VDW set to CENTROID_ROT_MIN
core.scoring.ramachandran: (0) shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: (0) Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
basic.io.database: (0) Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt
basic.io.database: (0) Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt
basic.io.database: (0) Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt
basic.io.database: (0) Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt
core.scoring.AtomVDW: (0) Openning alternative vdw file: /N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/database/chemical/atom_type_sets/centroid_rot//min.txt
core.scoring.ScoreFunction: (0) ATOM_VDW set to CENTROID_ROT_MIN
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015
protocols.jobdist.JobDistributors: (0) Node: 0 next_job()
protocols.jobdist.JobDistributors: (0) Master Node -- Waiting for job request; tag_ = 1
Killed
It looks like you're running an MPI compilation of Rosetta without using mpirun or srun. As such, you're only launching one process, and it's sitting there waiting for worker processes (that don't exist) to ask it for work.
Depending on your cluster, you need to use mpirun or srun to launch MPI programs. See https://kb.iu.edu/d/awrz#mpi for the Indiana State University's cluster.