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

Member Site › Forums › Rosetta 3 › Rosetta 3 – General › I used mpirun/mpiexec and it runs same job 32times

Viewing 2 reply threads
  • Author
    Posts
    • 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. 

                • Author
                  Posts
                Viewing 2 reply threads
                • You must be logged in to reply to this topic.