code rearrange and minor processing changes
This commit is contained in:
parent
2bb2ddbc7b
commit
019b801603
@ -6,15 +6,28 @@ 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, iterations):
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def __init__(self, nproc, iterations, citer = 0, overwrite = False):
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'''
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Class build from FMTOMO script tomo3d. Can be used to run several instances of FMM code in parallel.
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:param: nproc, number of parallel processes
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:type: integer
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:param: iterations, number of iterations
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:type: integer
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:param: citer, current iteration (default = 0: start new model)
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:type: integer
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'''
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self.setCWD()
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self.defParas()
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self.nproc = nproc
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self.iter = iterations # number of iterations
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self.citer = 0 # current iteration
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self.citer = citer # current iteration
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self.sources = self.readSrcFile()
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self.traces = self.readTraces()
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self.directories = []
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self.overwrite = overwrite
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def defParas(self):
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self.defFMMParas()
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@ -29,6 +42,7 @@ class Tomo3d(object):
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self.pg = 'propgrid.in'
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self.rec = 'receivers.in'
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self.frech = 'frechet.in'
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self.frechout = 'frechet.dat'
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self.ot = 'otimes.dat'
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self.ttim = 'arrivals.dat'
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self.mode = 'mode_set.in'
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@ -53,7 +67,7 @@ class Tomo3d(object):
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self.resout = 'residuals.dat'
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def copyRef(self):
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# Attention: Copies reference grids to used grids (e.g. sourcesref.in to sources.in)
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# Copies reference grids to used grids (e.g. sourcesref.in to sources.in)
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os.system('cp %s %s'%(self.ivg, self.cvg))
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os.system('cp %s %s'%(self.iig, self.cig))
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os.system('cp %s %s'%(self.isl, self.csl))
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@ -65,6 +79,30 @@ class Tomo3d(object):
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def runFrech(self):
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os.system(self.frechgen)
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def runTOMO3D(self):
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starttime = datetime.datetime.now()
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print('Starting TOMO3D on %s parallel processes for %s iteration(s).'
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%(self.nproc, self.iter))
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if self.citer == 0:
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self.makeInvIterDir()
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self.startForward(self.cInvIterDir)
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self.raiseIter()
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while self.citer <= self.iter:
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self.makeInvIterDir()
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self.startInversion()
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self.saveVgrid()
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self.startForward(self.cInvIterDir)
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self.raiseIter()
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if self.citer > self.iter:
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self.removeDirectories()
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self.unlink(os.path.join(self.cwd, self.frechout))
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self.unlink(os.path.join(self.cwd, self.ttim))
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tdelta = datetime.datetime.now() - starttime
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print('runTOMO3D: Finished %s iterations after %s.'%(self.iter, tdelta))
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def runFmm(self, directory, logfile, processes):
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os.chdir(directory)
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fout = open(logfile, 'w')
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@ -73,6 +111,47 @@ class Tomo3d(object):
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os.chdir(self.cwd)
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return processes
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def startForward(self, logdir):
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self._printLine()
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print('Starting forward simulation for iteration %s.'%(self.citer))
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if self.citer == 0:
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self.copyRef()
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self.runFrech()
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self.makeDirectories()
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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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logfn = 'fm3dlog_' + str(procID) + '.out'
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log_out = os.path.join(logdir, logfn)
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self.writeSrcFile(procID, directory)
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self.writeTracesFile(procID, directory)
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os.system('cp {cvg} {cig} {mode} {pg} {frechin} {dest}'
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.format(cvg=self.cvg, cig=self.cig, frechin=self.frech,
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mode=self.mode, pg=self.pg, dest=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(self.cInvIterDir)
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self.clearDirectories()
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self.copyArrivals()
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if self.citer == 0:
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self.copyArrivals(self.rtrav)
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self.calcRes()
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tdelta = datetime.datetime.now() - starttime
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print('Finished Forward calculation after %s'%tdelta)
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def startInversion(self):
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print('Calling %s...'%self.inv)
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os.system(self.inv)
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def calcRes(self):
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resout = os.path.join(self.cwd, self.resout)
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if self.citer == 0:
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@ -85,111 +164,91 @@ class Tomo3d(object):
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RMS, var, chi2 = residuals[-1].split()
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print('Residuals: RMS = %s, var = %s, Chi^2 = %s.'%(RMS, var, chi2))
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def runTOMO3D(self):
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starttime = datetime.datetime.now()
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print('Starting TOMO3D on %s parallel processes for %s iteration(s).'
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%(self.nproc, self.iter))
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if self.citer == 0:
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self.startForward()
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self.raiseIter()
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while self.citer <= self.iter:
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self.startInversion()
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self.startForward()
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self.raiseIter()
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tdelta = datetime.datetime.now() - starttime
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print('runTOMO3D: Finished %s iterations after %s.'%(self.iter, tdelta))
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def _printLine(self):
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print('----------------------------------------')
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def raiseIter(self):
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self.citer +=1
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self._printLine()
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invfile = open(self.cwd + '/inviter.in', 'w')
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invfile.write('%s'%self.citer)
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invfile.close()
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def startInversion(self):
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print('Calling %s...'%self.inv)
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os.system(self.inv)
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def startForward(self):
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self._printLine()
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print('Starting forward simulation for iteration %s.'%(self.citer))
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self.makeDirectories()
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starttime = datetime.datetime.now()
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processes = []
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if self.citer == 0:
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self.copyRef()
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self.runFrech()
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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.writeSrcFile(procID, directory)
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self.writeTracesFile(procID, directory)
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os.system('cp {cvg} {cig} {mode} {pg} {frechout} {dest}'
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.format(cvg=self.cvg, cig=self.cig, frechout=self.frech,
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mode=self.mode, pg=self.pg, dest=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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self.clearDirectories()
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self.copyArrivals()
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if self.citer == 0:
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self.copyArrivals(self.rtrav)
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self.calcRes()
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tdelta = datetime.datetime.now() - starttime
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print('Finished Forward calculation after %s'%tdelta)
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def copyArrivals(self, target = None):
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if target == None:
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target = self.mtrav
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os.system('cp %s %s'%(self.ttim, target))
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def makeDIR(self, directory):
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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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if err is 0:
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self.directories.append(directory)
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def clearDIR(self, directory):
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err = os.system('rm -r %s'%directory)
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return
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if err is 256:
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if self.overwrite == True:
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print('Overwriting existing files.')
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self.clearDir(directory)
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self.directories.append(directory)
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return
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raise RuntimeError('Could not create directory: %s'%directory)
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def makeDirectories(self):
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for procID in range(1, self.nproc + 1):
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directory = self.getProcDir(procID)
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self.makeDIR(directory)
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self.makeDir(directory)
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def makeInvIterDir(self):
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invIterDir = self.cwd + '/it_%s'%(self.citer)
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err = os.system('mkdir %s'%invIterDir)
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if err is 256:
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if self.overwrite:
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self.clearDir(invIterDir)
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elif err is not 0:
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raise RuntimeError('Could not create directory: %s'%invIterDir)
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self.cInvIterDir = invIterDir
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def clearDir(self, directory):
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print('Wiping directory %s...'%directory)
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for filename in os.listdir(directory):
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filenp = os.path.join(directory, filename)
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os.remove(filenp)
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def clearDirectories(self):
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for directory in self.directories:
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self.clearDIR(directory)
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self.clearDir(directory)
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def rmDir(self, directory):
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print('Removing directory %s...'%directory)
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return os.rmdir(directory)
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def removeDirectories(self):
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for directory in self.directories:
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self.rmDir(directory)
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self.directories = []
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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 getProcDir(self, procID):
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return os.path.join(self.cwd, self.folder) + str(procID)
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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 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 copyArrivals(self, target = None):
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if target == None:
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target = os.path.join(self.cwd, self.mtrav)
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os.system('cp %s %s'%(os.path.join(
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self.cInvIterDir, self.ttim), target))
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def saveVgrid(self):
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vgpath = os.path.join(self.cwd, 'vgrids.in')
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os.system('cp %s %s'%(vgpath, self.cInvIterDir))
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def calcSrcPerKernel(self):
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nsrc = self.readNsrc()
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if self.nproc > nsrc:
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raise ValueError('Number of spawned processes higher than number of sources')
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return nsrc/self.nproc, nsrc%self.nproc
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def srcIDs4Kernel(self, procID):
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@ -208,6 +267,18 @@ class Tomo3d(object):
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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 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 readSrcFile(self):
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nsrc = self.readNsrc()
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srcfile = open(self.csl, 'r')
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@ -258,6 +329,62 @@ class Tomo3d(object):
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return traces
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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 readRays(self, procID):
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directory = self.getProcDir(procID)
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raysfile = open(directory + '/rays.dat', 'r')
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sourceIDs = self.srcIDs4Kernel(procID)
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rays = {}
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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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line1 = raysfile.readline().split()
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if line1 != []:
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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, nsec = line1
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raysecs = {}
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for sec in range(int(nsec)):
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line2 = raysfile.readline().split()
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npoints, region, diff, head = line2
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raypoints = []
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for j in range(int(npoints)):
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raypoints.append(raysfile.readline() + '\n')
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raysecs[sec] = {'npoints': npoints,
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'region': region,
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'diff': diff,
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'head': head,
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'raypoints': raypoints
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}
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rays[traceID] = {'sourceID': sourceID,
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'raypath': ray,
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'normal': normal,
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'nsec': nsec,
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'raysections': raysecs
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}
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return rays
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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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@ -289,154 +416,44 @@ class Tomo3d(object):
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recfile.write('%s\n'%source)
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recfile.write('%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 mergeArrivals(self):
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arrivalsOut = open(os.path.join(self.cwd, self.ttim), 'w')
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def mergeArrivals(self, directory):
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arrfn = os.path.join(directory, self.ttim)
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arrivalsOut = open(arrfn, '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.write('%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.write('%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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os.system('ln -fs %s %s'%(arrfn, os.path.join(self.cwd, self.ttim)))
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def readRays(self, procID):
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directory = self.getProcDir(procID)
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raysfile = open(directory + '/rays.dat', 'r')
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sourceIDs = self.srcIDs4Kernel(procID)
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rays = {}
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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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line1 = raysfile.readline().split()
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if line1 != []:
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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, nsec = line1
|
||||
raysecs = {}
|
||||
|
||||
for sec in range(int(nsec)):
|
||||
line2 = raysfile.readline.split()
|
||||
npoints, region, diff, head = line2
|
||||
raypoints = []
|
||||
|
||||
for j in range(int(npoints)):
|
||||
raypoints.append(raysfile.readline() + '\n')
|
||||
|
||||
raysecs[sec] = {'npoints': npoints,
|
||||
'region': region,
|
||||
'diff': diff,
|
||||
'head': head,
|
||||
'raypoints': raypoints
|
||||
}
|
||||
|
||||
|
||||
rays[traceID] = {'sourceID': sourceID,
|
||||
'raypath': ray,
|
||||
'normal': normal,
|
||||
'nsec': nsec,
|
||||
'raysections': raysecs
|
||||
}
|
||||
return rays
|
||||
|
||||
def mergeRays(self):
|
||||
def mergeRays(self, directory):
|
||||
print('Merging rays.dat...')
|
||||
with open(self.cwd + 'rays.dat', 'w') as outfile:
|
||||
with open(directory + '/rays.dat', 'w') as outfile:
|
||||
for procID in range(1, self.nproc + 1):
|
||||
rays = self.readRays(procID)
|
||||
for traceID in rays:
|
||||
ray = rays[traceID]
|
||||
outfile.write('%6s %6s %6s %6s %6s'%(traceID,
|
||||
outfile.write('%6s %6s %6s %6s %6s\n'%(traceID,
|
||||
ray['sourceID'],
|
||||
ray['raypath'],
|
||||
ray['normal'],
|
||||
ray['nsec']))
|
||||
for sec in range(int(ray['nsec'])):
|
||||
raysec = ray['raysections'][sec]
|
||||
outfile.write('%6s %6s %6s %6s'%(raysec['npoints'],
|
||||
outfile.write('%6s %6s %6s %6s\n'%(raysec['npoints'],
|
||||
raysec['region'],
|
||||
raysec['diff'],
|
||||
raysec['head']))
|
||||
outfile.writelines(raysec['raypoints'])
|
||||
|
||||
|
||||
# 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 mergeFrechet(self):
|
||||
def mergeFrechet(self, directory):
|
||||
print('Merging frechet.dat...')
|
||||
|
||||
with open(self.cwd + '/frechet.dat', 'w') as outfile:
|
||||
frechfnout = os.path.join(directory, self.frechout)
|
||||
with open(frechfnout, 'w') as outfile:
|
||||
for procID in range(1, self.nproc + 1):
|
||||
filename = self.getProcDir(procID) + '/frechet.dat'
|
||||
filename = os.path.join(self.getProcDir(procID), self.frechout)
|
||||
with open(filename) as infile:
|
||||
for sourceID in self.srcIDs4Kernel(procID):
|
||||
for traceID in self.getTraceIDs4Source(sourceID):
|
||||
@ -445,15 +462,18 @@ class Tomo3d(object):
|
||||
for index in range(int(NPDEV)):
|
||||
outfile.write(infile.readline())
|
||||
|
||||
os.system('ln -fs %s %s'%(frechfnout, os.path.join(self.cwd, self.frechout)))
|
||||
|
||||
def getProcDir(self, procID):
|
||||
return os.path.join(self.cwd, self.folder) + str(procID)
|
||||
def mergeOutput(self, directory):
|
||||
self.mergeArrivals(directory)
|
||||
self.mergeFrechet(directory)
|
||||
self.mergeRays(directory)
|
||||
|
||||
def mergeOutput(self):
|
||||
self.mergeArrivals()
|
||||
self.mergeFrechet()
|
||||
self.mergeRays()
|
||||
def unlink(self, filepath):
|
||||
return os.system('unlink %s'%filepath)
|
||||
|
||||
def _printLine(self):
|
||||
print('----------------------------------------')
|
||||
|
||||
def vgrids2VTK(inputfile='vgrids.in', outputfile='vgrids.vtk', absOrRel='abs', inputfileref='vgridsref.in'):
|
||||
'''
|
||||
|
||||
Loading…
Reference in New Issue
Block a user