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 +201,56 @@
			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 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.
			'''
			@@ -258,6 +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
			@@ -270,9 +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:
			@@ -285,12 +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:
			@@ -300,8 +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:
			@@ -311,7 +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
			@@ -324,8 +374,15 @@
			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
			@@ -340,25 +397,24 @@
			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))
			#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))

			@@ -368,10 +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",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):
			@@ -383,16 +447,16 @@
			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])))
			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
			@@ -402,13 +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=""
			@@ -423,17 +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):
			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."