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