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added first version of fmtomo_parallel script

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Marcel Paffrath 2016-05-02 12:08:58 +02:00
parent dbe47690eb
commit ec42e1bd15
1 changed files with 280 additions and 0 deletions
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pylot/core/active/fmtomoUtils.py
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@ -1,7 +1,287 @@
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import os
import sys import sys
import subprocess
import datetime
import numpy as np import numpy as np
class Tomo3d(object):
def __init__(self, nproc):
self.defParas()
self.nproc = nproc
self.sources = self.readSrcFile()
self.traces = self.readTraces()
def defParas(self):
self.fmm = 'fm3d'
self.cvg = 'vgrids.in'
self.cig = 'interfaces.in'
self.csl = 'sources.in'
self.pg = 'propgrid.in'
self.rec = 'receivers.in'
#self.ot = 'otimes.dat'
self.frech = 'frechet.in'
self.mode = 'mode_set.in'
self.cwd = subprocess.check_output(['pwd'])[0:-1] + '/'
self.folder = 'test_'
def runFmm(self, directory, logfile, processes):
os.chdir(directory)
processes.append(subprocess.Popen('fm3d', stdout = None))
# os.system('%s > %s &'%(self.fmm, logfile))
os.chdir(self.cwd)
return processes
def makeDIR(self, directory):
err = os.system('mkdir %s'%directory)
if err is 256:
response = raw_input('Warning: Directory already existing. Continue (y/n)?\n')
if response == 'y':
print('Overwriting existing files.')
else:
sys.exit('Aborted')
def readNsrc(self):
srcfile = open(self.csl, 'r')
nsrc = int(srcfile.readline())
srcfile.close()
return nsrc
def readNtraces(self):
recfile = open(self.rec, 'r')
nrec = int(recfile.readline())
recfile.close()
return nrec
def calcSrcPerKernel(self):
nsrc = self.readNsrc()
return nsrc/self.nproc, nsrc%self.nproc
def srcIDs4Kernel(self, procID):
proc = procID - 1
nsrc = self.readNsrc()
srcPK, remain = self.calcSrcPerKernel()
if procID > self.nproc:
sys.exit('STOP: Kernel ID exceeds available number.')
if proc < remain:
start = (srcPK + 1) * (proc) + 1
return range(start, start + srcPK + 1)
elif proc == remain:
start = (srcPK + 1) * (proc) + 1
return range(start, start + srcPK)
elif proc > remain:
start = (srcPK + 1) * remain + srcPK * (proc - remain) + 1
return range(start, start + srcPK)
def startTomo(self):
starttime = datetime.datetime.now()
processes = []
for procID in range(1, self.nproc + 1):
directory = self.getProcDir(procID)
log_out = self.cwd + 'fm3dlog_' + str(procID) + '.out'
self.makeDIR(directory) # Problem bei Iteration
self.writeSrcFile(procID, directory)
self.writeTracesFile(procID, directory)
os.system('cp %s %s %s %s %s %s %s'
%(self.cvg, self.cig, self.frech,
self.fmm, self.mode, self.pg, directory))
processes = self.runFmm(directory, log_out, processes)
for p in processes:
p.wait()
self.mergeOutput()
tdelta = datetime.datetime.now() - starttime
print('Finished after %s'%tdelta)
def readSrcFile(self):
nsrc = self.readNsrc()
srcfile = open(self.csl, 'r')
sources = {}
temp = srcfile.readline()
for index in range(nsrc):
teleflag = int(srcfile.readline())
coords = srcfile.readline().split()
numpaths = int(srcfile.readline())
steps = int(srcfile.readline())
interactions = srcfile.readline().split()
veltype = int(srcfile.readline())
if teleflag is not 0:
sys.exit('Script not yet usable for teleseismic.')
if numpaths is not 1:
sys.exit('Script not yet usable for more than one path per source.')
sources[index + 1] = {'teleflag': teleflag,
'coords': coords,
'numpaths': numpaths,
'steps': steps,
'interactions': interactions,
'veltype': veltype
}
return sources
def readTraces(self):
recfile = open(self.rec, 'r')
ntraces = self.readNtraces()
traces = {}
temp = recfile.readline()
for index in range(ntraces):
coords = recfile.readline().split()
paths = int(recfile.readline())
source = int(recfile.readline())
path = int(recfile.readline())
traces[index + 1] = { 'coords': coords,
'paths': paths,
'source': source,
'path': path
}
return traces
def writeSrcFile(self, procID, directory):
srcfile = open('%s/sources.in'%directory, 'w')
sourceIDs = self.srcIDs4Kernel(procID)
srcfile.writelines('%s\n'%len(sourceIDs))
for sourceID in sourceIDs:
source = self.sources[sourceID]
coords = source['coords']
interactions = source['interactions']
srcfile.writelines('%s\n'%source['teleflag'])
srcfile.writelines('%s %s %s\n'%(float(coords[0]), float(coords[1]), float(coords[2])))
srcfile.writelines('%s\n'%source['numpaths'])
srcfile.writelines('%s\n'%source['steps'])
srcfile.writelines('%s %s\n'%(int(interactions[0]), int(interactions[1])))
srcfile.writelines('%s\n'%source['veltype'])
def writeTracesFile(self, procID, directory):
recfile = open('%s/receivers.in'%directory, 'w')
sourceIDs = self.srcIDs4Kernel(procID)
traceIDs = self.getTraceIDs4Sources(sourceIDs)
recfile.writelines('%s\n'%len(traceIDs))
for traceID in traceIDs:
trace = self.traces[traceID]
coords = trace['coords']
source = int(trace['source']) - sourceIDs[0] + 1
recfile.writelines('%s %s %s\n'%(float(coords[0]), float(coords[1]), float(coords[2])))
recfile.writelines('%s\n'%trace['paths'])
recfile.writelines('%s\n'%source)
recfile.writelines('%s\n'%trace['path'])
def getTraceIDs4Sources(self, sourceIDs):
traceIDs = []
for traceID in self.traces.keys():
if self.traces[traceID]['source'] in sourceIDs:
traceIDs.append(traceID)
return traceIDs
def getTraceIDs4Source(self, sourceID):
traceIDs = []
for traceID in self.traces.keys():
if self.traces[traceID]['source'] == sourceID:
traceIDs.append(traceID)
return traceIDs
def readArrivals(self, procID):
directory = self.getProcDir(procID)
arrfile = open(directory + '/arrivals.dat', 'r')
sourceIDs = self.srcIDs4Kernel(procID)
arrivals = []
for sourceID in sourceIDs:
traceIDs = self.getTraceIDs4Source(sourceID)
for traceID in traceIDs:
line = arrfile.readline().split()
if line != []:
# recID and srcID for the individual processor will not be needed
recID_proc, srcID_proc, ray, normal, arrtime, diff, head = line
arrivals.append([traceID, sourceID, ray, normal, arrtime, diff, head])
return arrivals
def readFrechet(self, procID):
directory = self.getProcDir(procID)
frechfile = open(directory + '/frechet.dat', 'r')
sourceIDs = self.srcIDs4Kernel(procID)
frechet = {}
for sourceID in sourceIDs:
traceIDs = self.getTraceIDs4Source(sourceID)
for traceID in traceIDs:
line = frechfile.readline().split()
if line != []:
# recID and srcID for the individual processor will not be needed
PDEV = []
recID_proc, srcID_proc, ray, normal, NPDEV = line
for i in range(int(NPDEV)):
PDEV.append(frechfile.readline())
frechet[traceID] = {'sourceID': sourceID,
'raypath': ray,
'normal': normal,
'NPDEV': NPDEV,
'PDEV': PDEV
}
return frechet
def mergeArrivals(self):
arrivalsOut = open(self.cwd + '/arrivals.dat', 'w')
print('Merging arrivals.dat...')
for procID in range(1, self.nproc + 1):
arrivals = self.readArrivals(procID)
for line in arrivals:
arrivalsOut.writelines('%6s %6s %6s %6s %15s %5s %5s\n'%tuple(line))
def mergeFrechet(self):
print('Merging frechet.dat...')
frechetOut = open(self.cwd + '/frechet.dat', 'w')
for procID in range(1, self.nproc + 1):
frechet = self.readFrechet(procID)
traceIDs = frechet.keys()
traceIDs.sort()
for traceID in traceIDs:
frech = frechet[traceID]
frechetOut.writelines('%6s %6s %6s %6s %6s\n'%
(traceID,
frech['sourceID'],
frech['raypath'],
frech['normal'],
frech['NPDEV']))
for pdev in frech['PDEV']:
frechetOut.writelines(pdev)
def mergeRays(self):
print('Merging rays.dat...')
filenames = []
for procID in range(1, self.nproc + 1):
directory = self.getProcDir(procID)
filenames.append(directory + '/rays.dat')
with open(self.cwd + 'rays.dat', 'w') as outfile:
for fname in filenames:
with open(fname) as infile:
for line in infile:
outfile.write(line)
def getProcDir(self, procID):
return self.cwd + self.folder + str(procID)
def mergeOutput(self):
self.mergeArrivals()
self.mergeFrechet()
self.mergeRays()
def vgrids2VTK(inputfile='vgrids.in', outputfile='vgrids.vtk', absOrRel='abs', inputfileref='vgridsref.in'): def vgrids2VTK(inputfile='vgrids.in', outputfile='vgrids.vtk', absOrRel='abs', inputfileref='vgridsref.in'):
''' '''