2

I'm running joblib and having the same problem as here, it only uses 2 cores out of 8. I tried setting the CPU affinity as described here. I'm using psutil version 5.4.3. I still run into this error:

AttributeError: 'Process' object has no attribute 'set_cpu_affinity'

This is my script:

from datetime import datetime
from subprocess import call 
from joblib import Parallel, delayed
import multiprocessing
import psutil
import os

startTime = datetime.now()

pdb_name_list = []
for filename in os.listdir('/home/labusr/Documents/python_scripts/Spyder/Refinement'):
   if filename.endswith(".pdb"):     
       pdb_name_list.append(filename)

num_cores = multiprocessing.cpu_count()
p = psutil.Process(os.getpid())
p.set_cpu_affinity(range(num_cores))
print(p.get_cpu_affinity())

inputs = range(2) 

def strcuture_refine(file_name,i):
    print('Refining strcuture %s round %s......\n' %(file_name, i))
    call(['/home/labusr/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease',
          '-in::file::s', '/home/labusr/Documents/python_scripts/Spyder/_Refinement/%s' %file_name,
          '-parser::protocol', '/home/labusr/Documents/A_asymm_refine.xml',
          '-parser::script_vars', 'denswt=35', 'rms=1.5', 'reso=4.3', 'map=/home/labusr/Documents/tubulin_exercise/masked_map_center.mrc', 
          'testmap=/home/labusr/Documents/tubulin_exercise/mmasked_map_top_centered_resampled.mrc',
          '-in:ignore_unrecognized_res',
          '-edensity::mapreso', '4.3',
          '-default_max_cycles', '200',
          '-edensity::cryoem_scatterers',
          '-beta',
          '-out::suffix', '_%s' %i,
          '-crystal_refine'])
    print('Time for refining %s round %s is: \n' %(file_name, i), datetime.now() - startTime)

for file_name in pdb_name_list:
    Parallel(n_jobs=num_cores)(delayed(strcuture_refine)(file_name,i) for i in inputs)
ahmadkhalifa
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1 Answers1

0

The function set_cpu_affinity() is now deprecated.

Instead the function cpu_affinity() acts as both a getter and a setter. If you don't supply an argument, it will return the current affinity and if you supply and argument it will set it.

e.g.

$ pid.cpu_affinity() 
[0,1,2,3,4,5,6,7]

$ pid.cpu_affinity([0,1])

$ pid.cpu_affinity()
[0,1]
Acapulco
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Conor
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