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| | | import xml.etree.ElementTree as ET |
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| | | import base64 |
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| | | import zlib |
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| | | import io |
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| | | import sys,io |
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| | | import os |
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| | | from itertools import islice |
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| | | import mmap |
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| | |
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| | | lines=0 |
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| | | f.close() |
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| | | return lines |
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| | | |
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| | | |
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| | | def tail(self,filename,n=2): |
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| | | with open(filename,'r') as myfile: |
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| | | lines=myfile.readlines() |
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| | | return [lines[len(lines)-2].replace('\n',''),lines[len(lines)-1].replace('\n','')] |
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| | | |
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| | | def read(self): |
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| | | try: |
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| | | lines=self.tail(self.fullname) |
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| | | except: |
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| | | return(False) |
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| | | if len(lines)<2: |
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| | | return(False) |
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| | | #print (line) |
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| | | fields=shlex.split(lines[0]) |
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| | | epoch1=fields[0] |
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| | | n1=fields[1] |
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| | | |
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| | | fields=shlex.split(lines[1]) |
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| | | epoch2=fields[0] |
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| | | n2=fields[1] |
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| | | try: |
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| | | self.dT=int(epoch2)-int(epoch1) |
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| | | self.last=n2 |
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| | | #print(epoch1) |
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| | | #print(epoch2) |
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| | | #print(self.dT) |
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| | | #print(self.last) |
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| | | self.startDate=os.path.getmtime(os.path.join(self.path,'.lock')) |
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| | | except: |
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| | | return(False) |
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| | | return(True) |
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| | | |
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| | | def read_old(self): |
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| | | ''' |
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| | | Method read() reads the statistics if it exists. It sets local variable dT storing the time differential between two intervals of simulation (outer loops). It also stores last simulation loop and the start of the run. |
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| | | ''' |
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| | |
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| | | return int(status) |
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| | | |
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| | | def isCompleted(self): |
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| | | if (int(self.tape.getValue("iterations"))==self.getLastIteration()+1): |
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| | | if int(self.tape.getValue("iterations"))+int(self.tape.getValue("inititer"))==self.getLastIteration()+1: |
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| | | return True |
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| | | else: |
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| | | return False |
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| | |
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| | | return |
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| | | |
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| | | cwd=Directory(maindir=os.getcwd()) |
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| | | lastVTU=self.getLastVTU() #we get last VTU file in case we need to continue the simulation from last snapshot. Need to be done before the Dir.goto() call. |
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| | | self.Dir.goto() |
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| | | print("Starting trisurf-ng executable in "+self.Dir.fullpath()) |
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| | | if(self.fromSnapshot==True): |
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| | | params=["trisurf", "--restore-from-vtk","initial_snapshot.vtu"]+self.runArgs |
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| | | #here we try to determine whether we should continue the simulation or start from last known VTU snapshot. |
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| | | if(lastVTU==None): |
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| | | initSnap="initial_snapshot.vtu" |
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| | | else: |
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| | | initSnap=lastVTU |
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| | | print("WARNING: Not using initial snapshot as starting point, but selecting "+initSnap+" as a starting vesicle") |
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| | | params=["trisurf", "--restore-from-vtk",initSnap]+self.runArgs |
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| | | print("InitSnap is: "+initSnap) |
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| | | else: |
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| | | #veify if dump exists. If not it is a first run and shoud be run with --force-from-tape |
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| | | if(os.path.isfile("dump.bin")==False): |
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| | |
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| | | print("Process in "+self.Dir.fullpath()+" already running. Not starting.") |
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| | | return |
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| | | |
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| | | def stop(self): |
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| | | pass |
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| | | |
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| | | def setMaindir(self,prefix,variables): |
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| | | maindir="" |
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| | | for p,v in zip(prefix,variables): |
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| | | if(v=="xk0"): |
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| | | tv=str(round(float(self.tape.config[v]))) |
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| | | if sys.version_info<(3,0): |
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| | | tv=str(int(float(self.tape.config[v]))) |
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| | | else: |
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| | | tv=self.tape.config[v] |
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| | | maindir=maindir+p+tv |
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| | |
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| | | report=["N/A","N/A",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()] |
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| | | return report |
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| | | |
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| | | |
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| | | def stop(self): |
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| | | p=psutil.Process(self.getPID()) |
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| | | p.kill() |
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| | | |
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| | | def writeComment(self, data, mode='w'): |
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| | | self.Dir=Directory(maindir=self.maindir,simdir=self.subdir) |
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| | | self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment")) |
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| | | self.Comment.writefile(data,mode=mode) |
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| | | |
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| | | |
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| | | def getLastVTU(self): |
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| | | vtuidx=self.getLastIteration() #-int(self.tape.getValue("inititer"))+1 |
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| | | if vtuidx<0: |
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| | | return None |
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| | | else: |
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| | | return 'timestep_{:06d}.vtu'.format(vtuidx) |
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| | | |
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| | | def __str__(self): |
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| | | if(self.getStatus()==0): |
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| | | str=" not running." |
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