trisurf-ng.git - Gitblit

			@@ -1,47 +1,107 @@
			#!/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
			'''
			This is a trisurf instance manager written in python
			import shlex
			import psutil
			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:
			'''
			Class is helpful for reading and writting the specific files.
			'''
			def __init__(self,filename):
			''' The instance is done by calling constructor FileContent(filename)

			The object then reads filename if it exists, otherwise the data is empty string.
			User may force to reread file by calling the readline() method of the class.

			Filename is stored in local variable for future file operations.
			'''

			self.filename=filename
			self.readfile()

			def readfile(self):
			'''Force reread of the file and setting the data'''
			self.data=""
			try:
			with open (self.filename, "r") as myfile:
			self.data=myfile.read().replace('\n', '') #read the file and remove newline from the text
			except:
			pass # does nothing if error occurs


			Invoke with:
			tsmgr [-t tape \| -r snapshot.vtu] [-s subdirectory]
			def writefile(self, data, mode='w'):
			'''File may be updated by completely rewritting the file contents or appending the data to the end of the file.
			this is achieved by calling writefile(data, mode) method, where data is the string data to be written and
			mode can be 'a' for append and 'w' for writting the file anew.
			'''
			with open (self.filename, mode) as myfile:
			myfile.write(data)

			If tape is specified, the trisurf wilt start from tape with initial distribution, if snapshot is specified the trisurf will be restored from given snapshot file and simulation will continue.
			def getText(self):
			'''
			Method getText() or calling the object itself returns string of data
			'''
			return self.data

			'''


			def __str__(self):
			'''
			Method getText() or calling the object itself returns string of data
			'''
			return self.getText()

			class Tape:
			'''Has all the info on the tape'''
			'''
			Special class that manages configuration of trisurf (commonly named tape). It can read and parse configuration from disk or parse it from string.
			'''

			def __init__(self):
			'''The object is instatiated by calling Tape() constructor without parameters'''
			return

			def readTape(self, tape='tape'):
			'''
			Tape is read and parsed by calling the readTape() method with optional tape parameter, which is full path to filename where the configuration is stored.
			If the tape cannot be read, it prints error and exits.
			'''
			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)

			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):
			'''Method getValue(key) returns value of a single parsed setting named "key".'''

			return self.config[key]

			def __str__(self):
			'''Calling the object itself, it recreates the tape contents from parsed values in form of key=value.'''
			retval=""
			for key,val in self.config.iteritems():
			retval=retval+str(key)+" = "+str(val)+"\n"
			@@ -50,22 +110,31 @@


			class Directory:
			'''
			Class deals with the paths where the simulation is run and data is stored.
			'''
			def __init__(self, maindir=".", simdir=""):
			'''Initialization Directory() takes two optional parameters, namely maindir and simdir. Defaults to current directory. It sets local variables maindir and simdir accordingly.'''
			self.maindir=maindir
			self.simdir=simdir
			return

			def fullpath(self):
			'''
			Method returns string of path where the data is stored. It combines values of maindir and simdir as maindir/simdir on Unix.
			'''
			return os.path.join(self.maindir,self.simdir)

			def exists(self):
			''' Method checks whether the directory specified by fullpath() exists. It return True/False on completion.'''
			path=self.fullpath()
			if(os.path.exists(path)):
			return 1
			return True
			else:
			return 0
			return False

			def make(self):
			''' Method make() creates directory. If it fails it exits the program with error message.'''
			try:
			os.makedirs(self.fullpath())
			except:
			@@ -74,11 +143,15 @@
			return

			def makeifnotexist(self):
			'''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.'''
			if(self.exists()):
			try:
			os.rmdir(self.fullpath())
			@@ -88,6 +161,9 @@
			return

			def goto(self):
			'''
			Method goto() moves current directory to the one specified by fullpath(). WARNING: when using the relative paths, do not call this function multiple times.
			'''
			try:
			os.chdir(self.fullpath())
			except:
			@@ -96,59 +172,138 @@


			class Statistics:
			'''
			Class that deals with the statistics file from the simulations.
			File is generally large and not all data is needed, so it is dealt with in a specific way.
			'''

			def __init__(self,path,filename="statistics.csv"):
			'''
			At the initialization call it receives optional filename parameter specifying the path and filename of the statistics file.

			The local variables path, filename, fullname (joined path and filename) and private check if the file exists are stored.
			'''
			self.path=path
			self.filename=filename
			self.fullname=os.path.join(path,filename)
			self.read()
			self.fileOK=self.read()
			return

			def __str__(self):
			return(str(self.fullname))

			def exists(self):
			'''Method check if the statistics file exists.'''
			if(os.path.isfile(self.fullname)):
			return True
			else:
			return False

			def mapcount(self):
			'''
			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;
			for line in fin:
			if(i==1):
			print (line)
			#print (line)
			fields=shlex.split(line)
			epoch1=fields[0]
			n1=fields[1]
			if(i==nlines-1):
			print (line)
			fields=shlex.split(line)
			epoch2=fields[0]
			n2=fields[1]
			i=i+1
			except:
			print("Cannot read statistics file in "+self.fullname+"\n")
			exit(1)
			#print("Cannot read statistics file in "+self.fullname+"\n")
			return(False)
			else:
			print("File "+self.fullname+" does not exists.\n")
			exit(1)
			#print("File "+self.fullname+" does not exists.\n")
			return(False)
			try:
			self.dT=(int(epoch2)-int(epoch1))/(int(n2)-int(n1))
			except:
			self.dT=0
			self.last=n2
			self.startDate=epoch1
			return(True)

			def __str__(self):
			'''
			Prints the full path with filename of the statistics.csv file
			'''
			return(str(self.fullname))



			class Runner:
			'''
			Class Runner consists of a single running or terminated instance of the trisurf
			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=''):
			def __init__(self, subdir='run0', tape=None, snapshot=None, runArgs=[]):
			self.subdir=subdir
			if(tape!=''):
			self.runArgs=runArgs
			self.fromSnapshot=False
			if(tape!=None):
			self.initFromTape(tape)
			if(snapshot!=''):
			if(snapshot!=None):
			self.initFromSnapshot(snapshot)
			return

			@@ -156,6 +311,7 @@
			def initFromTape(self, tape):
			self.tape=Tape()
			self.tape.readTape(tape)
			self.tapeFile=tape

			def initFromSnapshot(self, snapshotfile):
			try:
			@@ -163,34 +319,132 @@
			except:
			print("Error reading snapshot file")
			exit(1)

			self.fromSnapshot=True
			self.snapshotFile=snapshotfile
			root = tree.getroot()
			tapetxt=root.find('tape')
			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.makeifnotexist()
			try:
			fp = open(os.path.join(self.Dir.fullpath(),'.lock'))
			except IOError as e:
			return 0 #file probably does not exist. e==2??
			pid=fp.readline()
			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):
			return 0
			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))
			#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
			else:
			return TS_NONEXISTANT
			else:
			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):
			#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="./"
			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
			@@ -202,8 +456,50 @@
			return

			def getStatistics(self, statfile="statistics.csv"):
			self.statistics=Statistics("", statfile) # we are already in the running directory, so local path is needed!
			return
			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(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))),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()

			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):