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
			@@ -13,12 +11,14 @@
			import time
			import datetime
			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):
			@@ -197,19 +201,67 @@
			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.
			'''
			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;
			@@ -230,8 +282,10 @@
			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)
			@@ -248,6 +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
			@@ -277,9 +341,9 @@
			version=root.find('trisurfversion')
			self.tape=Tape()
			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'))
			@@ -289,14 +353,40 @@
			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
			@@ -306,8 +396,12 @@
			return TS_NONEXISTANT

			def start(self):
			if(self.getStatus()==0):
			self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
			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)
			#Symlinks tape file to the directory or create tape file from snapshot in the direcory...
			if(self.Dir.makeifnotexist()):
			if(self.fromSnapshot==False):
			@@ -319,37 +413,53 @@
			else:
			try:
			with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile:
			myfile.write("#This is automatically generated tape file from snapshot\n")
			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))


			#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
			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
			@@ -361,30 +471,55 @@
			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();
			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)1000000), 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\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):
			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."