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parallel_conversion.py
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parallel_conversion.py
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from datetime import date
import multiprocessing, os, sys, getopt, time
import numpy as np
import V2RhoT_gibbs_lib as lib
def worker(name, data, table,outdir: str) -> None:
print(f'Started worker {name}')
## run conversion here
systime = time.time()
#out_gibbs=lib.vel_to_temp(data[:,2],data[:,3],table)
out_gibbs=lib.vel_to_temp_prop_out(data[:,2],data[:,3],table)
out_save=np.zeros_like(data[:,1])
out_save=data[:,0]
out_save=np.column_stack((out_save,data[:,1]))
out_save=np.column_stack((out_save,out_gibbs[:,0]))
out_save=np.column_stack((out_save,out_gibbs[:,1]))
out_save=np.column_stack((out_save,out_gibbs[:,2]))
out_save=np.column_stack((out_save,out_gibbs[:,3]))
out_save=np.column_stack((out_save,out_gibbs[:,4]))
out_save=np.column_stack((out_save,out_gibbs[:,5]))
out_save=np.column_stack((out_save,out_gibbs[:,6]))
out_save=np.column_stack((out_save,out_gibbs[:,7]))
np.savetxt(str(outdir)+"/"+str(name)+'_vel_converted.txt',out_save,header="#x(km) y(km) depth(km) Pressure(bar) Temperature(oC) Density(kg/m3) Vp(km/s) Vs(km/s) Vs_diff(%) Pseudo-metls(%)",comments='',fmt='%10.3f')
#np.savetxt(str(outdir)+"/"+str(name)+'_vel_converted.txt',out_save,header="#x(km) y(km) depth(km) Pressure(bar) Temperature(oC) Density(kg/m3) Vp (km/s) Vs (km/s) Vs_diff(km/s)",comments='',fmt='%10.3f')
worker_time=(time.time()-systime)/60.0
print(f'{name} worker finished in {worker_time} min.')
def main(argv):
no_of_processes = int(1)
inputfile = str('')
outputfile = str('conversion_out.txt')
materialfile = str('DMM_HP')
inputdir = str('./data_tomo')
outputdir = str('./output')
atten_model = int(1)
grain_size = float(10.0)
oscillation_period = float(75.0)
COH_val = float(50.0)
#oscillation_period = 75
try :
opts,args = getopt.getopt(argv,"h:p:I:i:O:o:m:A:g:s:W:",["idir","ifile","odir","ofile","mfile","Amodel","gsize","operiod","water"])
#print(opts)
#print(args)
except getopt.GetoptError:
print('\n###########################################################################################')
print(' Simple run example: parallel_conversion.py -i <inputfile> -o <outputfile>\n\
Below are the available options which you can pass as a command line argument:\n\
-h : help\n\
-p : no of parts to run in parallel (e.g., no of available cores). Default is 1\n\
-I : input directory. Default is ./data_tomo\n\
-i : input file name in the data_tomo folder. Format x(*) y(*) depth(km) Vs(km/s)\n\
-O : output directory. Default is ./output\n\
-o : output file name which will be saved in output folder\n\
-m : name of the material file in databases folder. Default is DMM_HP\n\
-A : attenuation model flag: 1 for Jackson and Faul 2010, 2 for Behn et al., 2009. If you choose 2 then you will have to supply COH. See -H option.\n\
-g : grain size in mm. Default is 10mm\n\
-s : oscillation period in seconds. Default is 75 seconds\n\
-W : Water contnent in H/10**6Si. Defualt is 50 H/10**6Si which almost dry. Note this will be used if you choose attenuation model 2.\n\
-geo : Geology file in the data_geo folder. Format Format x(*) y(*) geo(codes). Note: This option is not active at the momemnt.\
\nAll of the input options will be written in the output file as comments.')
print('###########################################################################################\n')
sys.exit(2)
if (len(opts)!=0):
for opt, arg in opts:
if opt == '-h':
print('\n###########################################################################################')
print(' Simple run example: parallel_conversion.py -i <inputfile> -o <outputfile>\n\
Below are the available options which you can pass as a command line argument:\n\
-h : help\n\
-p : no of parts to run in parallel (e.g., no of available cores). Default is 1\n\
-i : input file name in the data_tomo folder. Format x(*) y(*) depth(km) Vs(km/s)\n\
-o : output file name which will be saved in output folder\n\
-I : input directory. Default is ./data_tomo\n\
-O : output directory. Default is ./output\n\
-m : name of the material file in databases folder. Default is DMM_HP\n\
-A : attenuation model flag: 1 for Jackson and Faul 2010 (default model), 2 for Behn et al., 2009. If you choose 2 then you will have to supply COH. See -H option.\n\
-g : grain size in mm. Default is 10mm\n\
-s : oscillation period in seconds. Default is 75 seconds\n\
-W : Water contnent in H/10**6Si. Defualt is 50 H/10**6Si which almost dry. Note this will be used if you choose attenuation model 2.\n\
-geo : Geology file in the data_geo folder. Format Format x(*) y(*) geo(codes). Note: This option is not active at the momemnt.\
\nAll of the input options will be written in the output file as comments.')
print('###########################################################################################\n')
sys.exit()
elif opt in ("-p", "--processes"):
no_of_processes = int(arg)
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-I", "--idir"):
inputdir = str(arg)
elif opt in ("-O", "--odir"):
outputdir =str(arg)
elif opt in ("-m", "--mfile"):
materialfile = arg
elif opt in ("-A", "--Amodel"):
atten_model = int(arg)
elif opt in ("-g", "--gsize"):
grain_size = float(arg)
elif opt in ("-s", "--operiod"):
oscillation_period = float(arg)
elif opt in ("-W", "--water"):
COH_val = float(arg)
else:
pass
print('\n###########################################')
print('Your options are:')
print('Total no of processes',no_of_processes)
print('Input file is', inputfile)
print('Output file is', outputfile)
print('Material file is', materialfile)
print('Input folder is', inputdir)
print('Output folder is', outputdir)
print('Attenuation model is', atten_model)
print('Grain size is', grain_size,'mm')
print('Oscillation period is', oscillation_period,'seconds')
print('COH is (used when Attenuation model is 2)', COH_val,'H/10**6Si')
print('\n###########################################')
### get current directory
path = os.getcwd()
isExist = os.path.exists(outputdir)
if not isExist:
print('\n###########################################')
print('Output directory does not exist. Making one for you.')
print('\n###########################################')
os.makedirs(outputdir)
else:
print('\n###########################################')
print('Output directory exists. It will be overwritten.')
'''
print('Output directory exists. To save it will be renamed with _bu appended to it.\n\
New output directory will be made for you new results. But re')
os.mkdirs(outdir,str(path)+"/back_ups")
os.move(outdir,str(path)+"/back_ups")
os.makedirs(outdir)
'''
print('\n###########################################')
####################################################
systime = time.time()
###############
# data format
# age(Ma) depth(km) Vs(km/s)
try:
tomo_in = np.loadtxt(inputdir+'/'+inputfile,comments='#')
except:
print('\n###########################################')
print('Could not find input tomography file',inputdir+'/'+inputfile,'\nMake sure you have this file.')
print('\n###########################################')
sys.exit()
#tomo_in = np.loadtxt('./data_tomo/V_mean.txt',comments='#')
#print("Time spent on loading data: {:.2f} sec".format(time.time()-tcalc))
# Load table
try:
DMM_no_atten = np.loadtxt(str(path)+'/databases/'+str(materialfile),comments='#')
#print('dwerwerwerwer')
#print(atten_model)
#table = lib.mantle_melt_atten_correction(DMM_no_atten,grain_size,oscillation_period)
if atten_model == 2:
print('Chose 2 Atten model.')
table = lib.mantle_melt_atten_correction_Behn2009(DMM_no_atten,grain_size,oscillation_period,COH_val)
elif atten_model == 1:
print('Chose 1 Atten model.')
table = lib.mantle_melt_atten_correction(DMM_no_atten,grain_size,oscillation_period)
else:
print('You choose wronge attenuation model.Available options are 1 and 2 . For help run with -h option')
sys.exit()
except:
print('\n###########################################')
print('Could not find the material file',str(path)+'/databases/'+str(materialfile),'\nMake sure you have this file.')
sys.exit(0)
print('\n###########################################')
print('\n###########################################')
print("Time spent on loading data: {:.2f} sec".format((time.time()-systime)))
print('\n###########################################')
#####################
# find number of processors
#no_processors = int(multiprocessing.cpu_count())
#print("Total number of available processors: "+str(no_processors))
#no_processors = 4
no_of_parts = int(len(tomo_in)/no_of_processes)
#no_of_parts = 1000
print('\n###########################################')
print("Length of the input model: "+str(len(tomo_in)))
print("Length of chunk to run on each processor: "+str(no_of_parts))
print('\n###########################################')
systime = time.time()
processes = []
for i in range(no_of_processes):
start_index = no_of_parts*i
# If the input file factorization is not whole numnber
# then what i am doing here is that i will put the last chunk start
# and untill the length of the input on the last core
if i == no_of_processes-1:
end_index = len(tomo_in)
else:
end_index = start_index + no_of_parts
process = multiprocessing.Process(target=worker,
args=(f'Process_{i+1}',tomo_in[start_index:end_index,:],table,outputdir))
processes.append(process)
process.start()
for proc in processes:
proc.join()
print('\n###########################################')
print("Total execution time: {:.1f} min".format((time.time()-systime)/60.0))
print('Hope that was fast enough for you. If not then maybe try increasing no of processes with -p option')
#print('There are lot of for loops in the code and could be improved.\n')
print('Enjoy your conversion results in the output folder :)')
print('\n###########################################')
###############
# gather all output
# make comments that includes all the parameters used for conversion and put in the final converted file
meta_data = "#Created on: " + str(date.today()) +"\n#Input file is: " + str(inputfile) +"\n#Output file is: " + str(outputfile) +"\n#Material file is: " + str(materialfile) +"\n#Attenuation model is: " + str(atten_model) +"\n#Grain size is: " + str(grain_size) +" mm"+"\n#Oscillation period is: " + str(oscillation_period) +" seconds\n#COH is: " + str(COH_val) +"H/10**6Si\n"
out_save = np.loadtxt(str(outputdir)+'/Process_1_vel_converted.txt',comments='#')
for i in range(1,no_of_processes):
out = np.loadtxt(str(outputdir)+'/Process_'+str(i+1)+'_vel_converted.txt',comments='#')
out_save=np.append(out_save,out,axis=0)
np.savetxt(str(outputdir)+'/'+str(outputfile),out_save,delimiter=',',header="#x(km), y(km), depth(km), Pressure(bar), Temperature(oC), Density(kg/m3), Vp(km/s), Vs(km/s), Vs_diff(%), Pseudo-melts(%)",comments=meta_data,fmt='%10.3f')
else:
print('\n###########################################')
print('You did not provide required input.')
print('Run the code with -h option for help.')
print('###########################################\n')
if __name__ == '__main__':
main(sys.argv[1:])