trisurf-ng.git - Gitblit

			@@ -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.
			'''
			@@ -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
			@@ -325,8 +364,14 @@
			if(psutil.pid_exists(int(pid))):
			proc= psutil.Process(int(pid))
			#psutil.__version__ == '3.4.2' requires name() and status(), some older versions reguire name, status
			if proc.name()=="trisurf":
			if proc.status()=="stopped":
			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
			@@ -353,13 +398,13 @@
			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))
			#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))

			@@ -369,10 +414,18 @@
			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",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):
			@@ -384,14 +437,14 @@
			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
			@@ -430,11 +483,24 @@
			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"))+1
			if vtuidx<0:
			return None
			else:
			return 'timestep_{:06d}.vtu'.format(vtuidx)

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