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

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I used mpirun/mpiexec and it runs same job 32times
#1
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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
--------------------------------------------------------

Category: 
Compilation
Post Situation: 
Unsolved
Mon, 2020-09-21 00:53
leygkn
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Increase nstruct to the number of MPI cores you are using. 

Mon, 2020-09-21 07:25
jadolfbr
(Reply to #3)
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I increased nstruct number but, I have same symptom 

Mon, 2020-09-21 18:50
leygkn
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Hmm.  So, what is this option? -use-hwthread-cpus

Mon, 2020-09-21 20:57
jadolfbr
(Reply to #5)
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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

Tue, 2020-09-22 00:52
leygkn
(Reply to #6)
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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

Wed, 2020-09-23 22:55
leygkn
(Reply to #7)
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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. 

Thu, 2020-09-24 10:04
jadolfbr