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run_pylith_lib.py
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import StringIO
from progressbar import ProgressBar
from collections import OrderedDict
import ConfigParser
import itertools
import numpy as np
import os
import netCDF4
import sys
import matplotlib.pyplot as plt
import time
import copy
import multiprocessing
import glob
import subprocess
import re
import csv
# ================== README ==================
#A sdb dico have 3 keys :
# 'name' : STRING, ex :'x' 'y' 'z' 'density' ...
# 'unit' : STRING, ex : 'kg/m**3' 'm/s' 'm/s' ...
# 'values' : LIST of the values
#
# ONE value type per dico (but severals values in the values list)
#
# a val dico have n keys ('x','y','density'...) + a entity_name key + entity_type key:
# param1 : [val1,val2 ...]
# param2 : [val1,val2 ...]
# ....
# paramn : [val1,val2 ...]
# +++
# entity_name : the name of the entity (thank you captain obvious)
# (all the annex keys must be removed in valdic2sdbdic_list)
#
# ONE block/interface per dico
# SEVERALS value type per dico
#
# a combi dico contains all information about ONE combinaition,
# the keys are like in the configfile '<name of the block/interface>.<name of the parameter>
#
# the discrimination of specific cases is in the configdic2valdic
# ________ ______ _____ _ _ _____ ______ _ _
# | ____\ \ / / __ \| __ \| | | |/ ____| | ____| | | (_)
# | |__ \ V / | | | | | | | | | (___ | |__ _ _ _ __ ___| |_ _ ___ _ __ ___
# | __| > <| | | | | | | | | |\___ \ | __| | | | '_ \ / __| __| |/ _ \| '_ \/ __|
# | |____ / . \ |__| | |__| | |__| |____) | | | | |_| | | | | (__| |_| | (_) | | | \__ \
# |______/_/ \_\____/|_____/ \____/|_____/ |_| \__,_|_| |_|\___|\__|_|\___/|_| |_|___/
#
#
def open_exodus(exodusin):
# print 'open a exodus'
if type(exodusin) is str:
exodusout = netCDF4.Dataset(exodusin, 'a')
else:
exodusout = exodusin
return exodusout
def make_exodusdic(exodusin):
if type(exodusin) is dict:
return exodusin # assuming the dico is a exodusdic
exodus = open_exodus(exodusin)
exodus_dic = {}
exodus_dic['title'] = str(exodus.title)
if type(exodusin) is str:
exodus_dic['filename'] = os.path.basename(exodusin)
else:
exodus_dic['filename'] = os.path.basename(str(exodus.title).split('(')[1].split(')')[0])
exodus_dic['blocks'] = blocksname_list(exodus)
exodus_dic['nodesets'] = nodesetname_list(exodus)
exodus_dic['X'] = exodus.variables['coordx'][:]
exodus_dic['Y'] = exodus.variables['coordy'][:]
exodus_dic['map'] = exodus.variables['node_num_map'][:]
for i in range(len(exodus_dic['nodesets'])):
exodus_dic['node_ns'+str(i+1)] = exodus.variables['node_ns'+str(i+1)][:]
return exodus_dic
def open_configfile(configfilein):
if type(configfilein) is str:
# print 'open a cf'
cfout = ConfigParser.ConfigParser()
cfout.optionxform = str
cfout.read(configfilein)
else:
cfout = configfilein
return cfout
def blocksname_list(exodus):
if type(exodus) is dict:
blocksnamelist = exodus['blocks']
elif type(exodus) is str or netCDF4.Dataset :
exodus = open_exodus(exodus)
nbblocks = len(exodus.dimensions['num_el_blk'])
blocksnamelist = []
for i in range(nbblocks):
blocksnamelist.append(''.join([x for x in exodus.variables['eb_names'][i,:] if type(x) is np.string_]))
return blocksnamelist
def nodesetname_list(exodus):
if type(exodus) is dict:
nodesetnamelist = exodus['nodesets']
elif type(exodus) is str or netCDF4.Dataset :
exodus = open_exodus(exodus)
nbnodesets = len(exodus.dimensions['num_node_sets'])
nodesetnamelist = []
for i in range(nbnodesets):
nodesetnamelist.append(''.join([x for x in exodus.variables['ns_names'][i,:] if type(x) is np.string_]))
return nodesetnamelist
def check_exodus_configfile(exodus,configfile):
# exodus = open_exodus(exodus)
exodus = make_exodusdic(exodus)
blkns_in_exodus = blocksname_list(exodus) + nodesetname_list(exodus)
cf = ConfigParser.ConfigParser()
cf.read(configfile)
sections = [s for s in cf.sections() if s.find('.') >= 0 ]
blkns_in_cf = list(set([ s.split('.')[0] for s in sections ]))
missing_e = []
for e in blkns_in_exodus:
if not e in blkns_in_cf:
missing_e.append(e)
if missing_e != []:
print ''
print " !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! "
print "WARN : missing parameters for blocs /nodesets in "
print configfile
print " "
for e in missing_e:
print e
print " !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! "
print " "
for e in blkns_in_cf:
if not e in blkns_in_exodus:
raise Exception(e + 'is not present in the exodus file !!!')
return None
def get_XY_of_nodeset_from_NETCDFexodus(exodus,nsdesc):
# from a EXODUS file imported with the NETCDF4 module
# and a nodeset descriptor (name or ID)
# retrun X & Y of the nodes, CUBIT's ID of the nodes and
# 'local' indices of the nodes in a pythonnic convention (start at 0)
exodus = open_exodus(exodus)
X = exodus.variables['coordx'][:]
Y = exodus.variables['coordy'][:]
mapp1 = exodus.variables['node_num_map'][:]
if type(nsdesc) is int:
nsid = nsdesc
elif type(nsdesc) is str:
nsid = nodesetname_list(exodus).index(nsdesc) + 1
nodesidlist = exodus.variables['node_ns'+str(nsid)][:] - 1
return X[nodesidlist],Y[nodesidlist],mapp1[nodesidlist],nodesidlist
def get_XY_of_nodeset_from_exodusdic(exodusdic,nsdesc):
X = exodusdic['X']
Y = exodusdic['Y']
mapp1 = exodusdic['map']
if type(nsdesc) is int:
nsid = nsdesc
elif type(nsdesc) is str:
nsid = exodusdic['nodesets'].index(nsdesc) + 1
nodesidlist = exodusdic['node_ns'+str(nsid)] - 1
return X[nodesidlist],Y[nodesidlist],mapp1[nodesidlist],nodesidlist
def get_XY_of_nodeset(exodusin,nsdesc):
if type(exodusin) is dict:
x,y,a,b = get_XY_of_nodeset_from_exodusdic(exodusin,nsdesc)
elif type(exodusin) is str or netCDF4.Dataset :
x,y,a,b = get_XY_of_nodeset_from_NETCDFexodus(exodusin,nsdesc)
else:
raise Exception('exodus is not a NETCDF or a dict' )
return x,y,a,b
# _____ _ _ ______ _ _
# / ____| | | | | ____| | | (_)
# | (___ _ __ ___ __ _| | | | |__ _ _ _ __ ___| |_ _ ___ _ __ ___
# \___ \| '_ ` _ \ / _` | | | | __| | | | '_ \ / __| __| |/ _ \| '_ \/ __|
# ____) | | | | | | (_| | | | | | | |_| | | | | (__| |_| | (_) | | | \__ \
# |_____/|_| |_| |_|\__,_|_|_| |_| \__,_|_| |_|\___|\__|_|\___/|_| |_|___/
#
def sort_XY_nodeset(x,y):
xy = np.vstack((x,y)).T
xy2 = (xy[xy[:,1].argsort()])
return np.flipud(xy2[:,0]), np.flipud(xy2[:,1].T)
def check_if_combiXY(combidic,entity):
for k,v in combidic.items():
if entity in k:
if 'combiXY' in k:
return True , v
return False , None
def product_on_dic(dicin):
varNames = sorted(dicin)
return [dict(zip(varNames, prod)) for prod in itertools.product(*(dicin[varName] for varName in varNames))]
def natural_sort(l):
convert = lambda text: int(text) if text.isdigit() else text.lower()
alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', key) ]
return sorted(l, key = alphanum_key)
def listofstr2str(listin):
outstr = '['
for s in listin:
outstr = outstr + s + ','
outstr = outstr[:-1] + ']'
return outstr
def flipper(X,Y):
# flip X,Y array in order to get the deepest point at the end of the array
if Y[-1] > Y[1]:
X = np.flipud(X)
Y = np.flipud(Y)
return X,Y
def dist(xa,ya,xb,yb):
return np.sqrt((xa-xb)**2 + (ya-yb)**2)
def cumul_dist(X,Y,i1,i2):
finaldist = 0
for i in range(i1,i2):
finaldist = finaldist + dist(X[i],Y[i],X[i+1],Y[i+1])
return finaldist
#
# _____ _ _ ______ _ _
# / ____| | | (_) | ____| | | (_)
# | | ___ _ __ ___ | |__ _ | |__ _ _ _ __ ___| |_ _ ___ _ __ ___
# | | / _ \| '_ ` _ \| '_ \| | | __| | | | '_ \ / __| __| |/ _ \| '_ \/ __|
# | |___| (_) | | | | | | |_) | | | | | |_| | | | | (__| |_| | (_) | | | \__ \
# \_____\___/|_| |_| |_|_.__/|_| |_| \__,_|_| |_|\___|\__|_|\___/|_| |_|___/
#
#
def unit_giver(namein,representative_value = 1 , limit_m_km = 100000 ):
if namein == 'x' or namein == 'y' or namein == 'z':
if representative_value < limit_m_km:
return 'km'
else:
return 'm'
elif namein == 'density':
return 'kg/m**3'
elif namein == 'vs':
return 'm/s'
elif namein == 'vp':
return 'm/s'
elif namein == 'viscosity':
return 'Pa*s'
elif namein == 'left-lateral-slip':
return 'cm/year'
elif namein == 'fault-opening':
return 'cm/year'
else:
return 'NoneUnit'
def make_combi_4_lockzone(Xin,Yin,ymax,lmin,stepmin,inunit='km',outunit='km'):
# ymax : the ultimate depth where is it supposed to be a locking
# lmin : minimal length of a locking zone in the same combi
# AND b/w 2 successive top point in 2 different combis
if inunit == 'km':
Xin = Xin * 1000
Yin = Yin * 1000
ymax = ymax * 1000
lmin = lmin * 1000
stepmin = stepmin * 1000
if outunit == 'km':
k = 1000
else:
k = 1
X,Y = Xin,Yin
# search if the first elt of X,Y is the top or the bottom of slab
X,Y = flipper(X,Y)
imax = np.min(np.flatnonzero(Y < ymax))
print 'making locking combinations'
print "ymax = " , ymax , " imax = " , imax
rangei = np.arange(imax)
xybound_list = []
ijbound_list = []
i_lasttoppt = 0
Ncombi_tot = 0
Ncombi_valid = 0
for c in list(itertools.combinations(rangei,2)):
Ncombi_tot += 1
# excluding locking zone with a too small l
if cumul_dist(X,Y,c[0],c[1]) < lmin:
continue
# excluding locking zone with a top point too close of the last one
if i_lasttoppt != c[0] and cumul_dist(X,Y,i_lasttoppt,c[0]) < stepmin:
continue
xybound_list.append(((X[c[0]]/k,Y[c[0]]/k),(X[c[1]]/k,Y[c[1]]/k)))
ijbound_list.append((c[0],c[1]))
i_lasttoppt = c[0]
Ncombi_valid += 1
print 'end of locking combinations, valid / total :' ,Ncombi_valid, '/', Ncombi_tot
return ijbound_list
def configfile2combidic_list(path,exodusin):
cf = ConfigParser.ConfigParser()
cf.read(path)
sections = cf.sections()
exodus_param = cf.get('Parameters','exodus_name')
exodus = open_exodus(exodusin)
check_exodus_configfile(exodus,path)
exodusdic = make_exodusdic(exodusin)
entity_name_lis = []
for s in sections:
if '.' in s:
entity_name_lis.append(s.split('.',1)[0])
entity_name_lis = list(set(entity_name_lis))
paramdic = {}
for e in entity_name_lis:
if cf.has_section(e + '.parameters'):
for param,val in cf.items(e + '.parameters'):
try:
val = eval(val)
except NameError:
val = val
if type(val) is list:
truemin = min(val[0:2])
truemax = max(val[0:2])
delta = val[2]
paramdic[e + '.' + param] = list(np.arange(truemin,truemax+1,delta))
if cf.has_option(e + '.general','spacing_mode'): # try for the special case of a exponetial progression
if cf.get(e + '.general','spacing_mode') == 'exp':
paramdic[e + '.' + param] = [ eval('1e+' + str(x)) for x in list(np.arange(truemin,truemax+1,delta))]
elif type(val) is str:
if val.strip()[0] == '-': # using a minus at the beginning of the string as marker for sign inversion
val2 = val.strip()[1:].replace(' ','')
paramdic[e + '.' + param] = [val2 + '.' + param +'-'] # putting the minus at the end
else:
paramdic[e + '.' + param] = [val.strip() + '.' + param]
#temporary value when the current val have to have another one
# change a few lines after
elif type(val) is float or int : # this test MUST be the last one
paramdic[e + '.' + param] = [val]
# MAKING THE COMBINATIONS OF THE LOCKING ZONE
faultlist = [s.split('.')[0] for s in cf.sections() if cf.has_option(s,'locked') and cf.getboolean(s,'locked') ]
for faultname in faultlist:
print faultname
ymax = cf.getfloat(faultname +'.general','maxi_locked_depth')
lmin = cf.getfloat(faultname +'.general','mini_locked_length')
stepmin = cf.getfloat(faultname +'.general','mini_locked_step')
out_dist_units = cf.get('Parameters','out_dist_units')
inp_dist_units = cf.get('Parameters','inp_dist_units')
if inp_dist_units == 'km':
kk = 1000
else:
kk = 1
X,Y,_,_ = get_XY_of_nodeset(exodus,faultname)
paramdic[faultname + '.combiXY'] = make_combi_4_lockzone(X/kk,Y/kk, \
ymax,lmin,stepmin,inunit=inp_dist_units,outunit=out_dist_units)
# SPECIFIC
# for badfield in [ k for k in configdic.keys() if 'maxi_locked_depth' in k ]:
# configdic.pop(badfield,None)
# ===== CARTESIAN PRODUCT OF A CONFIG DIC => MANY COMBIDIC =====
combidiclis = product_on_dic(paramdic)
# ==============================================================
print "total combinations for " + exodusdic['filename'] + ": ", len(combidiclis)
if len(combidiclis) == 0:
print "if total combinations == 0, check if imax == 0 too"
print "in this case ymax badly defined : problem of units (km <=> m) ?"
# REPLACING TEMP STR VAL BY THE FINAL ONE
for combidic in combidiclis:
for k,v in combidic.items():
if type(v) is str:
try:
if v[-1] == '-': # discrimination in case of a minus inversion
combidic[k] = - combidic[v[:-1]]
else:
combidic[k] = combidic[v]
except:
print "replacement of the " + k + " key per " + v + " failed in configfile2combidic_list"
return combidiclis,paramdic
def combidic2valdic2_list(combidic,configfile,exodusin):
start = time.time()
cf = open_configfile(configfile)
exodus = make_exodusdic(exodusin)
outunit = cf.get('Parameters','out_dist_units')
if outunit == 'm':
kk = 1
elif outunit == 'km':
kk = 1000
else:
kk = 1000
entity_name_lis = []
# getting the name of all entity (block/nodesets) in the combidico
# (for the moment the keys are <entity>.<parameter>)
# NB : Parameters without dot are naturally excluded
for k,v in combidic.iteritems():
entity_name_lis.append(k.split('.',1)[0])
list(set(entity_name_lis))
# iterating over all the entities
valdic_lis = []
for e in entity_name_lis:
tempdico = {}
for p,v in combidic.items() :
if e in p:
tempdico[p.split('.')[1]] = v
valdic = OrderedDict()
valdic['entity_name'] = e
valdic['x'] = []
valdic['y'] = []
# TYPE BLOCK => only ONE line
if cf.get(e + '.general','type') in ('bloc','block'):
valdic['x'] = [0]
valdic['y'] = [0]
for p,v in tempdico.items():
valdic[p] = [v]
# TYPE INTERFACE
elif cf.get(e + '.general','type') in ('interface'):
# LOCKED CASE => speed = nominal speed and 0
if cf.has_option(e + '.general','locked') and cf.getboolean(e + '.general','locked'):
if not 'combiXY' in tempdico.keys():
raise Exception('ERR : ' + ' is a locked interface but have no locking boundary (combiXY)')
X,Y,_,_ = get_XY_of_nodeset(exodus,e)
X,Y = flipper(X,Y)
X = X/kk
Y = Y/kk
valdic['x'] = list(X)
valdic['y'] = list(Y)
for p,v in tempdico.items():
if p == 'combiXY':
continue
elif p == 'left-lateral-slip':
valdic[p] = []
i = combidic[e + '.combiXY'][0]
j = combidic[e + '.combiXY'][1]
for n,(x,y) in enumerate(zip(X,Y)):
if i <= n <= j:
valdic[p].append(0)
else:
valdic[p].append(v)
else:
valdic[p] = [v] * len(valdic['x'])
# NOT LOCKED CASE => speed = nominal speed
else:
# case where the left lateral slip == 0
if tempdico['left-lateral-slip'] == 0:
valdic['x'] = [0,0]
valdic['y'] = [9999,-999999]
for p,v in tempdico.items():
valdic[p] = [v] * len(valdic['x'])
else: # case where the left lateral slip != 0
X,Y,_,_ = get_XY_of_nodeset(exodus,e)
X,Y = flipper(X,Y)
X = X/kk
Y = Y/kk
valdic['x'] = list(X)
valdic['y'] = list(Y)
for p,v in tempdico.items():
valdic[p] = [v] * len(valdic['x'])
valdic_lis.append(valdic)
# print "exec. time combidic2valdic :" , time.time() - start
return valdic_lis
def valdic2sdbdic_list(valdicin):
outlistofdic = []
for k,v in valdicin.iteritems():
if k == 'entity_name':
continue
if k == 'entity_type':
continue
dic = OrderedDict()
if type(v) is list:
dic['values'] = v
else:
dic['values'] = [v]
dic['name'] = k
dic['unit'] = unit_giver(dic['name'],np.max(np.abs(dic['values'])))
outlistofdic.append(dic)
entity_name = valdicin['entity_name']
return outlistofdic,entity_name
def write_spatialdb(valdicin,outpath):
listofdic , _ = valdic2sdbdic_list(valdicin)
outname = valdicin['entity_name']
# entitytype = valdicin['entity_name']
strm = StringIO.StringIO()
# ----- numloc -----
protonumloc = list(set([len(d['values']) for d in listofdic ]))
if len(protonumloc) != 1:
print "WARN : write_spatialdb : differents numlocs"
print "e.g. x : [1,2,3,4], vp : [10,20]"
for d in listofdic:
print d['name'],d['values']
numlocs = protonumloc[0]
# ----- datadim -----
if len( valdicin['x'] ) == 1 and len( valdicin['y'] ) == 1:
datadim = 0
elif len(list(set(valdicin['x']))) != 1 and len(list(set(valdicin['x']))) != 1:
datadim = 2
else:
datadim = 1
# ----- spacedim ------
if sum([d['name'] == 'z' for d in listofdic]) != 0:
spacedim = 3
else:
spacedim = 2
# ----- unitcoef ------
# finding the X value for the unit :
unitcoef = 1
for d in listofdic:
if d['name'] == 'x':
if d['unit'] == 'km':
unitcoef = 1000
# write usual header
strm.write('#SPATIAL.ascii 1\n')
strm.write('SimpleDB {\n')
strm.write(' num-values = {}\n'.format(len(listofdic) - spacedim))
namestr = ''
unitstr = ''
for d in listofdic:
# we must exclude the x,y,z name in the header
if d['name'] in ('x','y','z'):
continue
namestr = namestr + ' ' + d['name']
namestr = namestr.replace('_','-')
unitstr = unitstr + ' ' + d['unit']
strm.write(' value-names = {}\n'.format(namestr))
strm.write(' value-units = {}\n'.format(unitstr))
strm.write(' num-locs = {}\n'.format(numlocs))
strm.write(' data-dim = {}\n'.format(datadim))
strm.write(' space-dim = {}\n'.format(spacedim))
strm.write(' cs-data = cartesian {\n')
strm.write(' to-meters = {}\n'.format(unitcoef))
strm.write(' space-dim = {}\n'.format(spacedim))
strm.write(' } \n')
strm.write('} \n')
stdformat = '{:12.3f} '
for line in zip(*[ d['values'] for d in listofdic ]):
tempstr = stdformat * len(listofdic) + '\n'
strm.write(tempstr.format(*line))
fil = open(outpath + '/' + outname + '.spatialdb','w')
fil.write(strm.getvalue())
fil.close()
return strm
# __ __ _ ______ _ _
# | \/ | (_) | ____| | | (_)
# | \ / | __ _ _ _ __ | |__ _ _ _ __ ___| |_ _ ___ _ __ ___
# | |\/| |/ _` | | '_ \ | __| | | | '_ \ / __| __| |/ _ \| '_ \/ __|
# | | | | (_| | | | | | | | | |_| | | | | (__| |_| | (_) | | | \__ \
# |_| |_|\__,_|_|_| |_| |_| \__,_|_| |_|\___|\__|_|\___/|_| |_|___/
def main_experience_generator(configfile):
cf_objt = open_configfile(configfile)
outpath = cf_objt.get('Parameters','output_path')
local_cfg_generic = cf_objt.get('Parameters','local_generic')
main_cfg_generic = cf_objt.get('Parameters','main_generic')
output_cfg_local = cf_objt.get('Parameters','output_local')
output_cfg_main = cf_objt.get('Parameters','output_main')
outdirprefix = cf_objt.get('Parameters','output_dir_prefix')
# Loading config files
if not os.path.isfile(local_cfg_generic):
raise Exception('generic config file ' + local_cfg_generic + " don't exist")
if not os.path.isfile(main_cfg_generic):
raise Exception('generic config file ' + main_cfg_generic + " don't exist")
local_cfg_generic_objt = open_configfile(local_cfg_generic)
main_cfg_generic_objt = open_configfile(main_cfg_generic)
exodus_path = cf_objt.get('Parameters','exodus_name')
if os.path.isfile(exodus_path):
exodusdic = make_exodusdic(exodus_path)
exodusdiclis = [exodusdic]
elif os.path.isdir(exodus_path):
exodusdiclis = []
for protoexodus in glob.glob( exodus_path + '/' + '*.exo'):
exodusdic = make_exodusdic(protoexodus)
exodusdiclis.append(exodusdic)
else:
raise Exception('exodus file/folder ' + main_cfg_generic + " don't exist/is empty !")
i = 0
for exodusdic in exodusdiclis:
print ''
print ' ==============================================================='
print "processing combinations for " + exodusdic['filename']
combidiclis,confdic = configfile2combidic_list(configfile,exodusdic)
# L is the number of combis, for folders creation
L = str(len(str(len(combidiclis))))
frmtstr = '{:0>' + L + 'd}'
pbar = ProgressBar(maxval=len(combidiclis)+1)
pbar.start()
ipbar = 0
for combidic in combidiclis:
start = time.time()
i = i+1
ipbar = ipbar + 1
# print i
valdiclis = combidic2valdic2_list(combidic,cf_objt,exodusdic)
for valdic in valdiclis:
outdirectory = outpath + '/' + outdirprefix + '_' + frmtstr.format(i) + '/'
if not os.path.exists(outdirectory):
os.makedirs(outdirectory)
write_spatialdb(valdic, outdirectory)
# writing the pylith config files for each combi
write_configfile(cf_objt,copy.copy(local_cfg_generic_objt),copy.copy(main_cfg_generic_objt),outdirectory,output_cfg_local,output_cfg_main,exodusdic)
# writing a summary file of the combi
sumfile = open(outdirectory + '/' + outdirprefix + '_' + str(i) +'.sum', "w")
sumfile.write('exodus_title , ' + exodusdic['title'] + '\n')
sumfile.write('exodus_filename , ' + exodusdic['filename'] + '\n')
w = csv.writer(sumfile)
for key, val in OrderedDict(sorted(combidic.items())).items():
w.writerow([key, val])
sumfile.close()
pbar.update(ipbar)
pbar.finish()
# print 'execution combi :' , time.time() - start
print ''
print "FINISHING COMBINATION & CONFIGFILES WRITING PROCESS"
print "total combinations for " + outdirprefix + ' : ' + str(i)
return None
def main_run_pylith_multi(configfile):
if not os.path.isfile(configfile) :
raise Exception("ERR: CONFIG FILE DON'T EXIST !!!")
cf_objt = ConfigParser.ConfigParser()
cf_objt.read(configfile)
maindir = cf_objt.get('Parameters','output_path')
outdirprefix = cf_objt.get('Parameters','output_dir_prefix')
output_local = cf_objt.get('Parameters','output_local')
output_h5_name = cf_objt.get('Parameters','output_h5_name')
erase_existing = cf_objt.getboolean('Parameters','erase_existing')
# defining a valid path
pylith_path= cf_objt.get('Parameters','pylith_path')
dic_env = os.environ
dic_env['PATH'] = pylith_path+'/bin:'+ dic_env['PATH']
dic_env['PYTHONPATH'] = pylith_path+'/lib/python2.7/site-packages:'+ pylith_path +'/lib64/python2.7/site-packages:'#+ dic_env['PYTHONPATH']
dic_env['LD_LIBRARY_PATH'] = pylith_path+'lib:'+pylith_path+'lib64:' #+os.environ['LD_LIBRARY_PATH']
dirlist = natural_sort([ d for d in os.listdir(maindir) if d.startswith(outdirprefix) ])
cfwildcard = output_local
errbig_file_path = maindir + "/err_summary.log"
if os.path.isfile(errbig_file_path):
os.remove(errbig_file_path)
err_iter_list = []
process_args_list = []
pool = multiprocessing.Pool(processes=8)
for d in dirlist:
curdir = maindir + '/' + d
os.chdir(curdir)
if not os.path.exists('output'):
os.makedirs('output')
for cf in sorted(glob.glob(cfwildcard)):
args = [cf,curdir,output_h5_name,pylith_path,dic_env,erase_existing,errbig_file_path]
process_args_list.append(args)
# ===== MULTI PROCESS PART
start_pool = time.time()
# results = [ pool.apply(process_unit,args = (a,)) for a in process_args_list ]
results = pool.map(process_unit,process_args_list)
results = sorted(results)
errbig_file = open( errbig_file_path , "a")
#for f,std,err in results:
#if err != '':
#errbig_file.write('error log not empty for : '+ f +'\n')
errbig_file.write('total exec. time : ' + str(time.time() - start_pool))
# ===== CLASSIC MONO PART
# print '----------------------------------'
# print "running : " + cf + ' in ' + curdir
# if os.path.isfile('./output/' + output_h5_name + '.h5') and not erase_existing:
# print './output/' + output_h5_name + '.h5 exists , skiping ...'
# continue
# start = time.time()
# p = subprocess.Popen('',executable='/bin/bash', stdin=subprocess.PIPE , stdout=subprocess.PIPE , stderr=subprocess.PIPE ,env=dic_env)
# command = pylith_path +"/bin/pylith " + curdir + '/' + cf
# stdout,stderr = p.communicate( command )
# std_file = open("std.log", "w")
# err_file = open("err.log", "w")
# std_file.write(stdout)
# err_file.write(stderr)
# std_file.close()
# err_file.close()
# print "exec. time : " + str(time.time() - start) + ' s.'
# if stderr != '':
# print "err.log is not empty, must be checked !"
# err_iter_list.append(curdir)
#
# for e in err_iter_list:
# errbig_file.write(e+'\n')
# errbig_file.close()
return None
def process_unit(ain):
cf,curdir,output_h5_name,pylith_path,dic_env,erase_existing,errbig_file_path = ain
print '---------------- START ------------------'
os.chdir(curdir)
print "running : " + cf + ' in ' + curdir
if os.path.isfile( curdir + '/output/' + output_h5_name + '.h5') and not erase_existing:
print './output/' + output_h5_name + '.h5 exists , skiping ...'
return curdir ,'',''
print ''
start = time.time()
p = subprocess.Popen('',executable='/bin/bash', stdin=subprocess.PIPE , stdout=subprocess.PIPE , stderr=subprocess.PIPE ,env=dic_env)
command = pylith_path +"/bin/pylith " + curdir + '/' + cf
stdout,stderr = p.communicate( command )
std_file = open("std.log", "w")
err_file = open("err.log", "w")
std_file.write(stdout)
err_file.write(stderr)
std_file.close()
err_file.close()
print '---------------- END ------------------'
print "exec. time : " + str(time.time() - start) + ' s. for ' + os.path.basename(curdir)
if stderr != '':
print "err.log is not empty, must be checked !"
print stderr
errbig_file = open(errbig_file_path,'a')
errbig_file.write('error log not empty for : '+ curdir +'\n')
errbig_file.close()
print ''
return curdir , stdout , stderr
# _ _ __ _ __ _ _
# (_) | / _(_) / _(_) |
# __ ___ __ _| |_ ___ ___ ___ _ __ | |_ _ __ _| |_ _| | ___ ___
# \ \ /\ / / '__| | __/ _ \ / __/ _ \| '_ \| _| |/ _` | _| | |/ _ \/ __|
# \ V V /| | | | || __/ | (_| (_) | | | | | | | (_| | | | | | __/\__ \
# \_/\_/ |_| |_|\__\___| \___\___/|_| |_|_| |_|\__, |_| |_|_|\___||___/
# __/ |
# |___/
def remove_sections_beg(substring,config_obj):
list_remove=[string for string in config_obj.sections() if string.startswith(substring)]
[config_obj.remove_section(section) for section in list_remove]
def nodeset_type_from_configfile(configfilein,typein):
cf = open_configfile(configfilein)
outlist = []
for s in cf.sections():
if ( cf.has_option(s,'type') and cf.get(s,'type')==typein):
outlist.append(s.split('.')[0])
return outlist
def write_configfile(input_cfgfile,local_generic,main_generic,outpath,output_local,output_main,exodusdic):
# This function must have many args (and not only the configfile)
# because of speed of execution (openning many files with only the config file)
# here the files are opened before
######## Checking and opening blocks
### Check if output path exist and open file for writing
if not os.path.isdir(outpath):
os.mkdir(outpath)
if type(local_generic) is str:
if not os.path.isfile(local_generic):
raise Exception('generic config file ' + local_generic + " don't exist")
if type(main_generic) is str:
if not os.path.isfile(main_generic):
raise Exception('generic config file ' + main_generic + " don't exist")
out_local=outpath + '/' + output_local # for the local.cfg file
fic_out_local=open(out_local,'w')
out_main=outpath + '/' + output_main # for the main.cfg file
fic_out_main=open(out_main,'w')
### Check and open generic files
if type(local_generic) is str and type(main_generic) is str:
if ( not os.path.isfile(local_generic) or not os.path.isfile(main_generic)):
print 'WARNING: generic configuration files were not found, change path below and try again! \n' + local_generic
raise Exception
### Read generic files and Exodus
config_local = open_configfile(local_generic)
config_main = open_configfile(main_generic)
cfginput = open_configfile(input_cfgfile)
#exodus_name=cfginput.get('Parameters','exodus_name')
exodus_name= cfginput.get('Parameters','exodus_name') + '/' + exodusdic['filename']
### Change settings
list_of_blocks = blocksname_list(exodusdic)
total_time=float(cfginput.get('Parameters','total_time'))
dt=float(cfginput.get('Parameters','dt'))
config_local.set('pylithapp.timedependent.formulation.time_step','total_time',"%.1f*year" %total_time)
config_local.set('pylithapp.timedependent.formulation.time_step','dt',"%.1f*year" %dt)
### Get lists for bc and interfaces nodesets
nodeset_bc=nodeset_type_from_configfile(cfginput,'bc')
nodeset_interface=nodeset_type_from_configfile(cfginput,'interface')
config_local.set('pylithapp.timedependent','bc',listofstr2str(nodeset_bc))
config_local.set('pylithapp.timedependent','interfaces',listofstr2str(nodeset_interface))
### Remove unwanted sections
remove_sections_beg('pylithapp.timedependent.bc',config_local)
remove_sections_beg('pylithapp.timedependent.interfaces',config_local)
remove_sections_beg('pylithapp.problem',config_local)
remove_sections_beg('pylithapp.timedependent.materials',config_local)
### Start defining
for nodeset in nodeset_bc:
section_name='pylithapp.timedependent.bc.'+ nodeset
config_local.add_section(section_name)
config_local.set(section_name,'bc_dof',cfginput.get(nodeset + '.general','bc_dof'))
config_local.set(section_name,'label',nodeset)
config_local.set(section_name,'db_initial.label','Dirichlet BC')
### Set the Type
k=0
config_local.add_section('pylithapp.timedependent.interfaces')
for nodeset in nodeset_interface:
config_local.set('pylithapp.timedependent.interfaces',nodeset,'pylith.faults.FaultCohesiveKin')
section_name='pylithapp.timedependent.interfaces.'+ nodeset
config_local.add_section(section_name)
config_local.set(section_name,'label',nodeset)
config_local.set(section_name,'id',100+k)
k=k+1
config_local.set(section_name,'quadrature.cell','pylith.feassemble.FIATSimplex')
config_local.set(section_name,'quadrature.cell.dimension',1)
config_local.add_section(section_name+'.eq_srcs.rupture')
config_local.set(section_name+'.eq_srcs.rupture','slip_function','pylith.faults.ConstRateSlipFn')
config_local.add_section(section_name+'.eq_srcs.rupture.slip_function')
config_local.set(section_name+'.eq_srcs.rupture.slip_function','slip_time','spatialdata.spatialdb.UniformDB')
config_local.set(section_name+'.eq_srcs.rupture.slip_function','slip_time.label','Slip time')
config_local.set(section_name+'.eq_srcs.rupture.slip_function','slip_time.values','[slip-time]')
config_local.set(section_name+'.eq_srcs.rupture.slip_function','slip_time.data','[0.0*year]')
if cfginput.get(nodeset + '.general','spatialdb')=='file':
spatialdb_name=nodeset+'.spatialdb'
config_local.set(section_name+'.eq_srcs.rupture.slip_function','slip_rate.iohandler.filename',spatialdb_name)
config_local.set(section_name+'.eq_srcs.rupture.slip_function','slip_rate.query_type','linear')
config_local.set(section_name+'.eq_srcs.rupture.slip_function','slip_rate.label','Final Slip')
elif cfginput.get(nodeset + '.general','spatialdb')=='uniform':
config_local.set(section_name+'.eq_srcs.rupture','slip_rate.label','Final Slip')
config_local.set(section_name+'.eq_srcs.rupture','slip_rate.values','[left-lateral-slip,fault-opening]')
left_lateral_slip=cfginput.getfloat(nodeset + '.parameters','left-lateral-slip')
fault_opening=cfginput.getfloat(nodeset + '.parameters','fault-opening')
config_local.set(section_name+'.eq_srcs.rupture','slip_rate.data','[%.1f*cm/year, %.1f*cm/year]'%(left_lateral_slip,fault_opening))
####### OUTPUTS
#### Write output files for domains and subdomains
section_name='pylithapp.problem.formulation.output.domain'
config_local.add_section(section_name)
config_local.set(section_name,'writer.filename','output/'+cfginput.get('Parameters','output_h5_name')+'.h5')
section_name='pylithapp.problem.formulation.output.subdomain'
config_local.add_section(section_name)
config_local.set(section_name,'writer.filename','output/'+cfginput.get('Parameters','surface_nodeset_name')+'.h5')
#### Write output files for faults
for nodeset in nodeset_interface:
section_name='pylithapp.problem.interfaces.'+nodeset+'.output'
config_local.add_section(section_name)
config_local.set(section_name,'writer','pylith.meshio.DataWriterHDF5')
config_local.set(section_name,'writer.filename','output/'+nodeset+'.h5')
for block in list_of_blocks:
section_name='pylithapp.timedependent.materials.'+block+'.output'
config_local.add_section(section_name)
config_local.set(section_name,'writer.filename','output/'+block+'.h5')
config_local.write(fic_out_local)
fic_out_local.close()
################################################
######## Do the main generic file
################################################
### Define the exodus file
config_main.set('pylithapp.mesh_generator.reader','filename',exodus_name)
config_main.set('pylithapp.mesh_generator.reader','coordsys.space_dim',2)
config_main.set('pylithapp.timedependent','materials',listofstr2str(list_of_blocks))
remove_sections_beg('pylithapp.timedependent.materials',config_main)
config_main.add_section('pylithapp.timedependent.materials')
for block in list_of_blocks:
if cfginput.has_option(block + '.general','type_material'):
if cfginput.get(block + '.general','type_material')=='elastic':
config_main.set('pylithapp.timedependent.materials',block,'pylith.materials.ElasticPlaneStrain')
elif cfginput.get(block + '.general','type_material')=='maxwell':
config_main.set('pylithapp.timedependent.materials',block,'pylith.materials.MaxwellPlaneStrain')
else:
print "WARN : no type_material defined for " + block + ", elastic by default"
config_main.set('pylithapp.timedependent.materials',block,'pylith.materials.ElasticPlaneStrain')
else:
print "WARN : no type_material defined for " + block + ", elastic by default"
config_main.set('pylithapp.timedependent.materials',block,'pylith.materials.ElasticPlaneStrain')
section_name='pylithapp.timedependent.materials.'+block
id_block = list_of_blocks.index(block) + 1
config_main.add_section(section_name)
config_main.set(section_name,'label',block)
config_main.set(section_name,'id',id_block)
config_main.set(section_name,'db_properties.label',block+' properties')
config_main.set(section_name,'db_properties.iohandler.filename',block+'.spatialdb')
config_main.set(section_name,'quadrature.cell','pylith.feassemble.FIATSimplex')
config_main.set(section_name,'quadrature.cell.dimension','2')
section_output='pylithapp.timedependent.materials.'+block+'.output'
config_main.add_section(section_output)
config_main.set(section_output,'cell_filter','pylith.meshio.CellFilterAvg')
config_main.set(section_output,'output_freq','time_step')
config_main.set(section_output,'time_step','9.99999*year')
config_main.set(section_output,'writer','pylith.meshio.DataWriterHDF5')
surf_nodeset=cfginput.get('Parameters','surface_nodeset_name')
config_main.set('pylithapp.problem.formulation.output.subdomain','label',surf_nodeset)
#### Write PETSC
# Nothing to write
### Write to output
config_main.write(fic_out_main)
fic_out_main.close()
return None
# _______ _ _ ______ ______ _ _ _____