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| | | #!/usr/bin/python3 |
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| | | import configobj |
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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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| | | ''' |
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| | | try: |
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| | | self.config=configobj.ConfigObj(tape) |
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| | | with open (tape, "r") as myfile: |
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| | | self.rawText=myfile.read() #read the file |
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| | | |
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| | | except: |
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| | | print("Error reading or parsing tape file!\n") |
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| | | exit(1) |
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| | | def setTape(self, string): |
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| | | '''Method setTape(string) parses the string in memory that hold the tape contents.''' |
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| | | self.config=configobj.ConfigObj(io.StringIO(string)) |
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| | | self.rawText=string |
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| | | return |
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| | | |
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| | | def getValue(self,key): |
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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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| | | 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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| | | else: |
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| | | try: |
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| | | with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile: |
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| | | myfile.write("#This is automatically generated tape file from snapshot") |
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| | | myfile.write(str(self.tape)) |
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| | | #myfile.write("#This is automatically generated tape file from snapshot") |
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| | | myfile.write(str(self.tape.rawText)) |
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| | | except: |
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| | | print("Error -- cannot make tapefile "+ os.path.join(self.Dir.fullpath(),"tape")+" from the snapshot in the running directory") |
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| | | exit(1) |
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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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