Merged the difference

Samo Penic

2016-07-09 eb706bf094cb94104536cd1bb827828db672df5d

 python/trisurf/trisurf.py

@@ -1,10 +1,8 @@
#!/usr/bin/python3

import configobj
import xml.etree.ElementTree as ET
import base64
import zlib
import io
import sys,io
import os
from itertools import islice
import mmap
@@ -84,6 +82,9 @@
      '''
      try:
         self.config=configobj.ConfigObj(tape)
         with open (tape, "r") as myfile:
            self.rawText=myfile.read() #read the file

      except:
         print("Error reading or parsing tape file!\n")
         exit(1)
@@ -91,6 +92,7 @@
   def setTape(self, string):
      '''Method setTape(string) parses the string in memory that hold the tape contents.'''
      self.config=configobj.ConfigObj(io.StringIO(string))
      self.rawText=string
      return

   def getValue(self,key):
@@ -199,14 +201,51 @@
      Internal method for determining the number of the lines in the most efficient way. Is it really the most efficient?
      '''
      f = open(self.fullname, "r+")
      buf = mmap.mmap(f.fileno(), 0)
      lines = 0
      readline = buf.readline
      while readline():
         lines += 1
      try:
         buf = mmap.mmap(f.fileno(), 0)
         lines = 0
         readline = buf.readline
         while readline():
            lines += 1
         f.close()
      except:
         lines=0
         f.close()
      return lines

   def tail(self,filename,n=2):
      with open(filename,'r') as myfile:
         lines=myfile.readlines()
      return [lines[len(lines)-2].replace('\n',''),lines[len(lines)-1].replace('\n','')]

   def read(self):
      try:
         lines=self.tail(self.fullname)
      except:
         return(False)
      if len(lines)<2:
         return(False)
      #print (line)
      fields=shlex.split(lines[0])
      epoch1=fields[0]
      n1=fields[1]
		
      fields=shlex.split(lines[1])
      epoch2=fields[0]
      n2=fields[1]
      try:
         self.dT=int(epoch2)-int(epoch1)
         self.last=n2
         #print(epoch1)
         #print(epoch2)
         #print(self.dT)
         #print(self.last)
         self.startDate=os.path.getmtime(os.path.join(self.path,'.lock'))
      except:
         return(False)
      return(True)

   def read_old(self):
      '''
      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.
      '''
@@ -287,7 +326,7 @@
      version=root.find('trisurfversion')
      self.tape=Tape()
      self.tape.setTape(tapetxt.text)
		

   def getPID(self):
      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
      #self.Dir.makeifnotexist()
@@ -311,7 +350,7 @@
      return int(status)

   def isCompleted(self):
      if (int(self.tape.getValue("iterations"))==self.getLastIteration()+1):
      if int(self.tape.getValue("iterations"))+int(self.tape.getValue("inititer"))==self.getLastIteration()+1:
         return True
      else:
         return False
@@ -324,8 +363,15 @@
         return TS_NOLOCK
      if(psutil.pid_exists(int(pid))):
         proc= psutil.Process(int(pid))
         if proc.name=="trisurf":
            if proc.status=="stopped":
         #psutil.__version__ == '3.4.2' requires name() and status(), some older versions reguire name, status
         if(psutil.__version__>='2.0.0'):
            procname=proc.name()
            procstat=proc.status()
         else:
            procname=proc.name
            procstat=proc.status
         if procname=="trisurf":
            if procstat=="stopped":
               return TS_STOPPED
            else:
               return TS_RUNNING
@@ -352,26 +398,34 @@
            else:
               try:
                  with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile:
                     myfile.write("#This is automatically generated tape file from snapshot\n")
                     myfile.write(str(self.tape))
                     #myfile.write("#This is automatically generated tape file from snapshot")
                     myfile.write(str(self.tape.rawText))
               except:
                  print("Error -- cannot make tapefile  "+ os.path.join(self.Dir.fullpath(),"tape")+" from the snapshot in the running directory")
                  exit(1)
               try:
                  os.symlink(os.path.abspath(self.snapshotFile), os.path.join(self.Dir.fullpath(),self.snapshotFile))
                  os.symlink(os.path.abspath(self.snapshotFile), os.path.join(self.Dir.fullpath(),"initial_snapshot.vtu"))
               except:
                  print("Error while symlinking "+os.path.abspath(self.snapshotFile)+" to "+os.path.join(self.Dir.fullpath(),self.snapshotFile))
      
         #check if the simulation has been completed. in this case notify user and stop executing.
         if(self.isCompleted() and ("--force-from-tape" not in self.runArgs) and ("--reset-iteration-count" not in self.runArgs)):
            print("The simulation was completed. Not starting executable at localhost in "+self.Dir.fullpath()+"\n")
            print("The simulation was completed. Not starting executable in "+self.Dir.fullpath())
            return

         cwd=Directory(maindir=os.getcwd())
         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.
         self.Dir.goto()
         print("Starting trisurf-ng executable at localhost in "+self.Dir.fullpath()+"\n")
         print("Starting trisurf-ng executable in "+self.Dir.fullpath())
         if(self.fromSnapshot==True):
            params=["trisurf", "--restore-from-vtk",self.snapshotFile]+self.runArgs
            #here we try to determine whether we should continue the simulation or start from last known VTU snapshot.
            if(lastVTU==None):
               initSnap="initial_snapshot.vtu"
            else:
               initSnap=lastVTU
               print("WARNING: Not using initial snapshot as starting point, but selecting "+initSnap+" as a starting vesicle")
            params=["trisurf", "--restore-from-vtk",initSnap]+self.runArgs
            print("InitSnap is: "+initSnap)
         else:
            #veify if dump exists. If not it is a first run and shoud be run with --force-from-tape
            if(os.path.isfile("dump.bin")==False):
@@ -380,17 +434,17 @@
         subprocess.Popen (params, stdout=subprocess.DEVNULL)
         cwd.goto()
      else:
         print("Process already running. Not starting\n")
         print("Process in "+self.Dir.fullpath()+" already running. Not starting.")
      return

   def stop(self):
      pass

   def setMaindir(self,prefix,variables):
      maindir=""
      for p,v in zip(prefix,variables):
         if(v=="xk0"):
            tv=str(round(float(self.tape.config[v])))
            if sys.version_info<(3,0):
               tv=str(int(float(self.tape.config[v])))
         else:
            tv=self.tape.config[v]
         maindir=maindir+p+tv
@@ -407,7 +461,8 @@
      self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
      pid=self.getPID()
      status=self.getStatus()
      ETA=str(datetime.timedelta(microseconds=(int(self.tape.config['iterations'])-int(self.statistics.last))*self.statistics.dT)*1000000)
      if(self.statistics.fileOK):
         ETA=str(datetime.timedelta(microseconds=(int(self.tape.config['iterations'])-int(self.statistics.last))*self.statistics.dT)*1000000)
      if(status==TS_NONEXISTANT or status==TS_NOLOCK):
         statustxt="Not running"
         pid=""
@@ -425,14 +480,27 @@
      if(self.statistics.fileOK):
         report=[time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(self.statistics.startDate))),ETA, statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
      else:
         report=["N/A","N/A\t",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
         report=["N/A","N/A",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
      return report


   def stop(self):
      p=psutil.Process(self.getPID())
      p.kill()

   def writeComment(self, data, mode='w'):
      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
      self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
      self.Comment.writefile(data,mode=mode)


   def getLastVTU(self):
      vtuidx=self.getLastIteration()-int(self.tape.getValue("inititer"))
      if vtuidx<0:
         return None
      else:
         return  'timestep_{:06d}.vtu'.format(vtuidx)

   def __str__(self):
      if(self.getStatus()==0):
         str=" not running."