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
@@ -245,6 +245,11 @@
         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.
@@ -297,6 +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
@@ -328,7 +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'))
@@ -339,7 +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'))
@@ -350,7 +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
@@ -386,7 +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):
@@ -443,6 +458,8 @@
      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
@@ -454,13 +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=""
@@ -475,25 +492,29 @@
      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.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()
      vtuidx=self.getLastIteration()-int(self.tape.getValue("inititer"))
      if vtuidx<0:
         return None
      else: