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
@@ -12,13 +10,15 @@
import psutil
import time
import datetime
from subprocess import call, Popen
import subprocess
import shutil

# Process status
TS_NOLOCK=0 # lock file does not exist
TS_NONEXISTANT=0 # process is not in the list of processes
TS_STOPPED=1 # the process is listed, but is in stopped state
TS_RUNNING=2 # process is running
TS_COMPLETED=3 #simulation is completed

class FileContent:
   '''
@@ -82,6 +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)
@@ -89,6 +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):
@@ -142,7 +146,9 @@
      '''Method makeifnotexist() creates directory if it does not exist.'''
      if(self.exists()==0):
         self.make()
      return
         return True
      else:
         return False

   def remove(self):
      '''Method remove() removes directory recursively. WARNING! No questions asked.'''
@@ -195,19 +201,62 @@
      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.
      '''
      if(self.exists()):
      #   epoch1=0
      #   epoch2=0
      #   n1=0
      #   n2=0
         nlines=self.mapcount()
         if nlines<2:
            return(False)
         try:
            with open(self.fullname, "r+") as fin:
               i=0;
@@ -228,8 +277,10 @@
      else:
         #print("File "+self.fullname+" does not exists.\n")
         return(False)

      self.dT=(int(epoch2)-int(epoch1))/(int(n2)-int(n1))
      try:
         self.dT=(int(epoch2)-int(epoch1))/(int(n2)-int(n1))
      except:
         self.dT=0
      self.last=n2
      self.startDate=epoch1
      return(True)
@@ -246,13 +297,13 @@
   '''
   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.
   '''
   def __init__(self, subdir='run0', tape='', snapshot='', runArgs=[]):
   def __init__(self, subdir='run0', tape=None, snapshot=None, runArgs=[]):
      self.subdir=subdir
      self.runArgs=runArgs
      self.fromSnapshot=False
      if(tape!=''):
      if(tape!=None):
         self.initFromTape(tape)
      if(snapshot!=''):
      if(snapshot!=None):
         self.initFromSnapshot(snapshot)
      return

@@ -260,6 +311,7 @@
   def initFromTape(self, tape):
      self.tape=Tape()
      self.tape.readTape(tape)
      self.tapeFile=tape

   def initFromSnapshot(self, snapshotfile):
      try:
@@ -277,7 +329,7 @@

   def getPID(self):
      self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
      self.Dir.makeifnotexist()
      #self.Dir.makeifnotexist()
      try:
         fp = open(os.path.join(self.Dir.fullpath(),'.lock'))
      except IOError as e:
@@ -286,14 +338,40 @@
      fp.close()
      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:
         return -1 #file probably does not exist. e==2??
      status=fp.readline()
      fp.close()
      return int(status)

   def isCompleted(self):
      if int(self.tape.getValue("iterations"))+int(self.tape.getValue("inititer"))==self.getLastIteration()+1:
         return True
      else:
         return False

   def getStatus(self):
      pid=self.getPID()
      if(self.isCompleted()):
         return TS_COMPLETED
      if(pid==0):
         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
@@ -303,30 +381,70 @@
         return TS_NONEXISTANT

   def start(self):
      if(self.getStatus()==0):
      if(self.getStatus()==0 or self.getStatus()==TS_COMPLETED):
         #check if executable exists
         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.makeifnotexist()
#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")
               except:
                  print("Error while symlinking "+os.path.abspath(self.tapeFile)+" 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))
               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(),"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 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 "+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):
               self.runArgs.append("--force-from-tape")
            params=["trisurf"]+self.runArgs
         Popen (params, stdout=False)
         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
@@ -341,27 +459,48 @@
      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();
      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(status==TS_NONEXISTANT or status==TS_NOLOCK):
         statustxt="Not running"
         pid=""
         ETA=""
      elif status==TS_STOPPED:
         statustxt="Stopped"
         ETA="N/A"
      elif status==TS_COMPLETED:
         statustxt="Completed"
         pid=""
         ETA=""
      else:
         statustxt="Running"

      if(self.statistics.fileOK):
         report=[time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(self.statistics.startDate))),str(datetime.timedelta(microseconds=(int(self.tape.config['iterations'])-int(self.statistics.last))*self.statistics.dT)*1000), statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
         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."