I used mpirun/mpiexec and it runs same job 32times

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- September 21, 2020 at 7:53 am #3580
  Anonymous
  First, I’m sorry for my poor english.
  
  I compiled rosetta applications via mpi options
  
  (/home/ael/Desktop/rosetta_bin_linux_2020.28.61328_bundle/main/source/bin/relax.mpi.linuxgccrelease)
  
  and I tried to use relax application to prepare structure
  
  Then, when i start relax application, my cpus (16cores, 32threads) rus fully and it calculates same calculations 32times
  
  (one output pdbs and 32 scores in .sc file)
  
  how can i solve this problems?
  
  *I read this post but I can’t understand what they say
  
  https://www.rosettacommons.org/node/10669
  
  —my script—-
  
  mkdir Starting_PDB
  
  mpiexec -use-hwthread-cpus relax.mpi.linuxgccrelease -s ./D1Frag_PDB/3qwq_D1.pdb
  
  -out:suffix _prep -nstruct 1
  
  -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false
  
  -out:path:pdb ./Starting_PDB -out:path:score ./Starting_PDB
  
  —-score file
  
  SEQUENCE:
  
  SCORE: total_score coordinate_constraint dslf_fa13 fa_atr fa_dun fa_elec fa_intra_rep fa_intra_sol_xover4 fa_rep fa_sol hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb lk_ball_wtd omega p_aa_pp pro_close rama_prepro ref yhh_planarity description
  
  SCORE: -405.633 123.102 -2.780 -1458.619 456.389 -398.157 2.662 51.867 159.163 797.808 -41.637 -103.976 -20.028 -40.516 -26.510 19.702 -60.587 1.293 57.131 77.682 0.378 3qwq_D1_prep_0001
  
  SCORE: -405.580 123.080 -2.782 -1458.113 456.556 -397.907 2.662 51.870 158.796 797.500 -41.636 -103.955 -20.011 -40.542 -26.568 19.730 -60.597 1.292 57.075 77.682 0.289 3qwq_D1_prep_0001
  
  SCORE: -405.637 123.121 -2.787 -1458.404 456.443 -398.064 2.662 51.868 159.112 797.660 -41.628 -103.956 -20.014 -40.514 -26.579 19.707 -60.621 1.294 57.027 77.682 0.354 3qwq_D1_prep_0001
  
  SCORE: -405.496 122.701 -2.525 -1458.187 457.178 -398.226 2.639 51.830 158.226 797.851 -41.625 -103.890 -20.018 -40.705 -26.417 19.984 -60.709 1.277 57.207 77.682 0.232 3qwq_D1_prep_0001
  
  …..
  
  —mpi compilation script
  
  sudo apt install openmpi-bin (maybe?)
  
  sudo apt install mpich
  
  sudo apt install zlib1g-dev
  
  #Compiling Rosetta
  
  cd rosetta*/main/source
  
  ./scons.py -j30 bin mode=release extras=mpi
- September 21, 2020 at 2:25 pm #15509
  Anonymous
  Increase nstruct to the number of MPI cores you are using.
  - September 22, 2020 at 1:50 am #15512
    Anonymous
    I increased nstruct number but, I have same symptom
- September 22, 2020 at 3:57 am #15513
  Anonymous
  Hmm. So, what is this option? -use-hwthread-cpus
  - September 22, 2020 at 7:52 am #15515
    Anonymous
    It allows use hyperthreading
    
    If I don’t use that option, my cpu use only 16 threads (same symptom but do same job 16times)
    
    I use ryzen 9 3950x cpu (16cores, 32threads)
    
    so i think do same job 32times
  - September 24, 2020 at 5:55 am #15522
    Anonymous
    core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags core.init: (0) Rosetta version: rosetta.binary.linux.release-264 r264 2020.37+release.3ba1aaa 3ba1aaa69637d143d3e7a0497fe9e99a2b65f1eb https://www.rosettacommons.org 2020-09-09T03:36:18.109196 core.init: (0) command: relax.mpiserialization.linuxgccrelease -s ./frag_PDB/1i1a_ABC.pdb -include_sugars -alternate_3_letter_codes pdb_sugar -load_PDB_components false -auto_detect_glycan_connections -min_bond_length 1.1 -max_bond_length 1.7 -ignore_zero_occupancy false -ignore_unrecognized_res -out:suffix _prep -nstruct 1 -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -out:path:all ./Starting_PDB basic.random.init_random_generator: (0) 'RNG device' seed mode, using '/dev/urandom', seed=-879294153 seed_offset=0 real_seed=-879294153 basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=-879294153 RG_type=mt19937 core.init: (0) found database environment variable ROSETTA3_DB: /home/ael/rosetta_bin_linux_2020.37.61417_bundle/main/database 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.init: (0) Checking for fconfig files in pwd and ./rosetta/flags core.init: (0) Rosetta version: rosetta.binary.linux.release-264 r264 2020.37+release.3ba1aaa 3ba1aaa69637d143d3e7a0497fe9e99a2b65f1eb https://www.rosettacommons.org 2020-09-09T03:36:18.109196 core.init: (0) command: relax.mpiserialization.linuxgccrelease -s ./frag_PDB/1i1a_ABC.pdb -include_sugars -alternate_3_letter_codes pdb_sugar -load_PDB_components false -auto_detect_glycan_connections -min_bond_length 1.1 -max_bond_length 1.7 -ignore_zero_occupancy false -ignore_unrecognized_res -out:suffix _prep -nstruct 1 -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -out:path:all ./Starting_PDB basic.random.init_random_generator: (0) 'RNG device' seed mode, using '/dev/urandom', seed=359470823 seed_offset=0 real_seed=359470823 basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=359470823 RG_type=mt19937 core.init: (0) found database environment variable ROSETTA3_DB: /home/ael/rosetta_bin_linux_2020.37.61417_bundle/main/database 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.init: (0) Checking for fconfig files in pwd and ./rosetta/flags core.init: (0) Rosetta version: rosetta.binary.linux.release-264 r264 2020.37+release.3ba1aaa 3ba1aaa69637d143d3e7a0497fe9e99a2b65f1eb https://www.rosettacommons.org 2020-09-09T03:36:18.109196 core.init: (0) command: relax.mpiserialization.linuxgccrelease -s ./frag_PDB/1i1a_ABC.pdb -include_sugars -alternate_3_letter_codes pdb_sugar -load_PDB_components false -auto_detect_glycan_connections -min_bond_length 1.1 -max_bond_length 1.7 -ignore_zero_occupancy false -ignore_unrecognized_res -out:suffix _prep -nstruct 1 -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -out:path:all ./Starting_PDB
    
    some lines when i run my script
  - September 24, 2020 at 5:04 pm #15524
    Anonymous
    Looks like you are only running on on the head node. Try giving mpiexec the number of processors to use with the -np option. I think that may work.
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