我尝试了joblib,但是,我被困在设置处理器亲和力(如下所述((该错误与我的脚本一起显示(。
现在,我想知道是否还有其他选项或替代方案可以让我实现相同的目标,即使用我的8个内核(以类似于GNU并行的方式(并行运行相同的脚本。
错误:
AttributeError: 'Process' object has no attribute 'set_cpu_affinity'
我的脚本:
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)
最简单的事情就是只启动从例如命令行。要使每个过程都处理自己的文件,您可以在调用Python时通过它:
python myscript.py filename
然后,通过
在Python中可用filename
import sys
filename = sys.argv[1]