Added many changes to trisurf.py. Mostly readability. Great fix in class Ru...

Samo Penic

2017-01-04 61ad95ca712a374f6e58127fda738b67c57d743d

 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
@@ -296,7 +343,7 @@
      self.tape.setTape(tapetxt.text)

   def getPID(self):
      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
#      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
      #self.Dir.makeifnotexist()
      try:
         fp = open(os.path.join(self.Dir.fullpath(),'.lock'))
@@ -307,7 +354,7 @@
      return int(pid)

   def getLastIteration(self):
      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
#      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
      #self.Dir.makeifnotexist()
      try:
         fp = open(os.path.join(self.Dir.fullpath(),'.status'))
@@ -318,7 +365,7 @@
      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
@@ -354,7 +401,7 @@
         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)
#         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):
@@ -382,10 +429,18 @@
            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):
@@ -397,14 +452,14 @@
         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
@@ -416,13 +471,13 @@
      return

   def getStatistics(self, statfile="statistics.csv"):
      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
      self.statistics=Statistics(self.Dir.fullpath(), statfile)
#      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=""
@@ -437,17 +492,34 @@
      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):
      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.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."