Added even more readability in using the trisurf.py's runner class

Samo Penic

2017-01-04 3fc0ef33e7a09a04a9f9055f9085e64255e62299

 python/trisurf/trisurf.py

@@ -2,7 +2,7 @@
import xml.etree.ElementTree as ET
import base64
import zlib
import io
import sys,io
import os
from itertools import islice
import mmap
@@ -212,8 +212,45 @@
         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 readText(self):
      with open(self.fullname, 'r+') as fin:
         cont=fin.read()
      return cont

   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.
      '''
@@ -265,6 +302,16 @@
   '''
   Class Runner consists of a single running or terminated instance of the trisurf. It manages starting, stopping, verifying the running process and printing the reports of the configured instances.
   '''

   @property
   def Dir(self):
      return Directory(maindir=self.maindir,simdir=self.subdir)


   @property
   def Statistics(self):
      return Statistics(self.Dir.fullpath(), "statistics.csv")

   def __init__(self, subdir='run0', tape=None, snapshot=None, runArgs=[]):
      self.subdir=subdir
      self.runArgs=runArgs
@@ -277,9 +324,9 @@


   def initFromTape(self, tape):
      self.tape=Tape()
      self.tape.readTape(tape)
      self.tapeFile=tape
      self.Tape=Tape()
      self.Tape.readTape(tape)
      self.tapeFilename=tape

   def initFromSnapshot(self, snapshotfile):
      try:
@@ -292,12 +339,10 @@
      root = tree.getroot()
      tapetxt=root.find('tape')
      version=root.find('trisurfversion')
      self.tape=Tape()
      self.tape.setTape(tapetxt.text)
      self.Tape=Tape()
      self.Tape.setTape(tapetxt.text)

   def getPID(self):
      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
      #self.Dir.makeifnotexist()
      try:
         fp = open(os.path.join(self.Dir.fullpath(),'.lock'))
      except IOError as e:
@@ -307,8 +352,6 @@
      return int(pid)

   def getLastIteration(self):
      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
      #self.Dir.makeifnotexist()
      try:
         fp = open(os.path.join(self.Dir.fullpath(),'.status'))
      except IOError as e:
@@ -318,7 +361,7 @@
      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
@@ -354,20 +397,19 @@
         if(shutil.which('trisurf')==None):
            print("Error. Trisurf executable not found in PATH. Please install trisurf prior to running trisurf manager.")
            exit(1)
         self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
#Symlinks tape file to the directory or create tape file from snapshot in the direcory...
         if(self.Dir.makeifnotexist()):
            if(self.fromSnapshot==False):
               try:
                  os.symlink(os.path.abspath(self.tapeFile), self.Dir.fullpath()+"/tape")
                  os.symlink(os.path.abspath(self.tapeFilename), self.Dir.fullpath()+"/tape")
               except:
                  print("Error while symlinking "+os.path.abspath(self.tapeFile)+" to "+self.Dir.fullpath()+"/tape")
                  print("Error while symlinking "+os.path.abspath(self.tapeFilename)+" to "+self.Dir.fullpath()+"/tape")
                  exit(1)
            else:
               try:
                  with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile:
                     #myfile.write("#This is automatically generated tape file from snapshot")
                     myfile.write(str(self.tape.rawText))
                     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)
@@ -382,10 +424,18 @@
            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 in "+self.Dir.fullpath())
         if(self.fromSnapshot==True):
            params=["trisurf", "--restore-from-vtk","initial_snapshot.vtu"]+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):
@@ -402,9 +452,11 @@
      maindir=""
      for p,v in zip(prefix,variables):
         if(v=="xk0"):
            tv=str(round(float(self.tape.config[v])))
            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]
            tv=self.Tape.config[v]
         maindir=maindir+p+tv
      self.maindir=maindir
      return
@@ -414,13 +466,11 @@
      return

   def getStatistics(self, statfile="statistics.csv"):
      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
      self.statistics=Statistics(self.Dir.fullpath(), statfile)
      self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
      pid=self.getPID()
      status=self.getStatus()
      if(self.statistics.fileOK):
         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=""
@@ -435,22 +485,33 @@
      else:
         statustxt="Running"

      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()]
      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",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
      return report


   def stop(self):
      p=psutil.Process(self.getPID())
      p.kill()
      try:
         p=psutil.Process(self.getPID())
         p.kill()
      except:
         print("Could not stop the process. Is the process running? Do you have sufficient privileges?")


   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."