import configobj
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import xml.etree.ElementTree as ET
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import base64
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import zlib
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import sys,io
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import os
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from itertools import islice
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import mmap
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import shlex
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import psutil
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import time
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import datetime
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import subprocess
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import shutil
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# Process status
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TS_NOLOCK=0 # lock file does not exist
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TS_NONEXISTANT=0 # process is not in the list of processes
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TS_STOPPED=1 # the process is listed, but is in stopped state
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TS_RUNNING=2 # process is running
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TS_COMPLETED=3 #simulation is completed
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class FileContent:
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'''
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Class is helpful for reading and writting the specific files.
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'''
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def __init__(self,filename):
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''' The instance is done by calling constructor FileContent(filename)
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The object then reads filename if it exists, otherwise the data is empty string.
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User may force to reread file by calling the readline() method of the class.
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Filename is stored in local variable for future file operations.
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'''
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self.filename=filename
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self.readfile()
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def readfile(self):
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'''Force reread of the file and setting the data'''
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self.data=""
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try:
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with open (self.filename, "r") as myfile:
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self.data=myfile.read().replace('\n', '') #read the file and remove newline from the text
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except:
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pass # does nothing if error occurs
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def writefile(self, data, mode='w'):
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'''File may be updated by completely rewritting the file contents or appending the data to the end of the file.
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this is achieved by calling writefile(data, mode) method, where data is the string data to be written and
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mode can be 'a' for append and 'w' for writting the file anew.
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'''
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with open (self.filename, mode) as myfile:
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myfile.write(data)
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def getText(self):
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'''
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Method getText() or calling the object itself returns string of data
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'''
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return self.data
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def __str__(self):
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'''
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Method getText() or calling the object itself returns string of data
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'''
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return self.getText()
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class Tape:
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'''
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Special class that manages configuration of trisurf (commonly named tape). It can read and parse configuration from disk or parse it from string.
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'''
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def __init__(self):
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'''The object is instatiated by calling Tape() constructor without parameters'''
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return
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def readTape(self, tape='tape'):
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'''
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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.
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If the tape cannot be read, it prints error and exits.
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'''
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try:
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self.config=configobj.ConfigObj(tape)
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with open (tape, "r") as myfile:
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self.rawText=myfile.read() #read the file
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except:
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print("Error reading or parsing tape file!\n")
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exit(1)
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def setTape(self, string):
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'''Method setTape(string) parses the string in memory that hold the tape contents.'''
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self.config=configobj.ConfigObj(io.StringIO(string))
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self.rawText=string
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return
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def getValue(self,key):
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'''Method getValue(key) returns value of a single parsed setting named "key".'''
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return self.config[key]
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def __str__(self):
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'''Calling the object itself, it recreates the tape contents from parsed values in form of key=value.'''
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retval=""
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for key,val in self.config.iteritems():
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retval=retval+str(key)+" = "+str(val)+"\n"
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return retval
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class Directory:
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'''
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Class deals with the paths where the simulation is run and data is stored.
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'''
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def __init__(self, maindir=".", simdir=""):
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'''Initialization Directory() takes two optional parameters, namely maindir and simdir. Defaults to current directory. It sets local variables maindir and simdir accordingly.'''
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self.maindir=maindir
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self.simdir=simdir
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return
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def fullpath(self):
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'''
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Method returns string of path where the data is stored. It combines values of maindir and simdir as maindir/simdir on Unix.
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'''
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return os.path.join(self.maindir,self.simdir)
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def exists(self):
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''' Method checks whether the directory specified by fullpath() exists. It return True/False on completion.'''
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path=self.fullpath()
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if(os.path.exists(path)):
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return True
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else:
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return False
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def make(self):
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''' Method make() creates directory. If it fails it exits the program with error message.'''
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try:
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os.makedirs(self.fullpath())
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except:
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print("Cannot make directory "+self.fullpath()+"\n")
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exit(1)
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return
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def makeifnotexist(self):
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'''Method makeifnotexist() creates directory if it does not exist.'''
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if(self.exists()==0):
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self.make()
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return True
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else:
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return False
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def remove(self):
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'''Method remove() removes directory recursively. WARNING! No questions asked.'''
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if(self.exists()):
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try:
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os.rmdir(self.fullpath())
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except:
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print("Cannot remove directory "+self.fullpath()+ "\n")
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exit(1)
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return
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def goto(self):
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'''
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Method goto() moves current directory to the one specified by fullpath(). WARNING: when using the relative paths, do not call this function multiple times.
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'''
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try:
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os.chdir(self.fullpath())
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except:
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print("Cannot go to directory "+self.fullpath()+"\n")
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return
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class Statistics:
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'''
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Class that deals with the statistics file from the simulations.
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File is generally large and not all data is needed, so it is dealt with in a specific way.
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'''
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def __init__(self,path,filename="statistics.csv"):
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'''
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At the initialization call it receives optional filename parameter specifying the path and filename of the statistics file.
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The local variables path, filename, fullname (joined path and filename) and private check if the file exists are stored.
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'''
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self.path=path
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self.filename=filename
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self.fullname=os.path.join(path,filename)
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self.fileOK=self.read()
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return
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def exists(self):
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'''Method check if the statistics file exists.'''
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if(os.path.isfile(self.fullname)):
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return True
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else:
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return False
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def mapcount(self):
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'''
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Internal method for determining the number of the lines in the most efficient way. Is it really the most efficient?
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'''
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f = open(self.fullname, "r+")
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try:
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buf = mmap.mmap(f.fileno(), 0)
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lines = 0
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readline = buf.readline
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while readline():
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lines += 1
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f.close()
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except:
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lines=0
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f.close()
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return lines
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def tail(self,filename,n=2):
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with open(filename,'r') as myfile:
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lines=myfile.readlines()
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return [lines[len(lines)-2].replace('\n',''),lines[len(lines)-1].replace('\n','')]
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def read(self):
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try:
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lines=self.tail(self.fullname)
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except:
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return(False)
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if len(lines)<2:
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return(False)
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#print (line)
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fields=shlex.split(lines[0])
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epoch1=fields[0]
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n1=fields[1]
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fields=shlex.split(lines[1])
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epoch2=fields[0]
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n2=fields[1]
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try:
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self.dT=int(epoch2)-int(epoch1)
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self.last=n2
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#print(epoch1)
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#print(epoch2)
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#print(self.dT)
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#print(self.last)
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self.startDate=os.path.getmtime(os.path.join(self.path,'.lock'))
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except:
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return(False)
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return(True)
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def read_old(self):
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'''
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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.
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'''
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if(self.exists()):
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# epoch1=0
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# epoch2=0
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# n1=0
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# n2=0
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nlines=self.mapcount()
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if nlines<2:
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return(False)
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try:
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with open(self.fullname, "r+") as fin:
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i=0;
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for line in fin:
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if(i==1):
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#print (line)
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fields=shlex.split(line)
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epoch1=fields[0]
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n1=fields[1]
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if(i==nlines-1):
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fields=shlex.split(line)
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epoch2=fields[0]
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n2=fields[1]
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i=i+1
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except:
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#print("Cannot read statistics file in "+self.fullname+"\n")
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return(False)
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else:
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#print("File "+self.fullname+" does not exists.\n")
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return(False)
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try:
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self.dT=(int(epoch2)-int(epoch1))/(int(n2)-int(n1))
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except:
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self.dT=0
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self.last=n2
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self.startDate=epoch1
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return(True)
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def __str__(self):
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'''
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Prints the full path with filename of the statistics.csv file
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'''
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return(str(self.fullname))
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class Runner:
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'''
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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.
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'''
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def __init__(self, subdir='run0', tape=None, snapshot=None, runArgs=[]):
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self.subdir=subdir
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self.runArgs=runArgs
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self.fromSnapshot=False
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if(tape!=None):
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self.initFromTape(tape)
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if(snapshot!=None):
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self.initFromSnapshot(snapshot)
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return
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def initFromTape(self, tape):
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self.tape=Tape()
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self.tape.readTape(tape)
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self.tapeFile=tape
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def initFromSnapshot(self, snapshotfile):
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try:
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tree = ET.parse(snapshotfile)
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except:
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print("Error reading snapshot file")
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exit(1)
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self.fromSnapshot=True
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self.snapshotFile=snapshotfile
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root = tree.getroot()
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tapetxt=root.find('tape')
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version=root.find('trisurfversion')
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self.tape=Tape()
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self.tape.setTape(tapetxt.text)
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def getPID(self):
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self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
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#self.Dir.makeifnotexist()
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try:
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fp = open(os.path.join(self.Dir.fullpath(),'.lock'))
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except IOError as e:
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return 0 #file probably does not exist. e==2??
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pid=fp.readline()
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fp.close()
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return int(pid)
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def getLastIteration(self):
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self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
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#self.Dir.makeifnotexist()
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try:
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fp = open(os.path.join(self.Dir.fullpath(),'.status'))
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except IOError as e:
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return -1 #file probably does not exist. e==2??
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status=fp.readline()
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fp.close()
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return int(status)
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def isCompleted(self):
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if int(self.tape.getValue("iterations"))+int(self.tape.getValue("inititer"))==self.getLastIteration()+1:
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return True
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else:
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return False
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def getStatus(self):
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pid=self.getPID()
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if(self.isCompleted()):
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return TS_COMPLETED
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if(pid==0):
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return TS_NOLOCK
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if(psutil.pid_exists(int(pid))):
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proc= psutil.Process(int(pid))
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#psutil.__version__ == '3.4.2' requires name() and status(), some older versions reguire name, status
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if(psutil.__version__>='2.0.0'):
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procname=proc.name()
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procstat=proc.status()
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else:
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procname=proc.name
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procstat=proc.status
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if procname=="trisurf":
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if procstat=="stopped":
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return TS_STOPPED
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else:
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return TS_RUNNING
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else:
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return TS_NONEXISTANT
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else:
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return TS_NONEXISTANT
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def start(self):
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if(self.getStatus()==0 or self.getStatus()==TS_COMPLETED):
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#check if executable exists
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if(shutil.which('trisurf')==None):
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print("Error. Trisurf executable not found in PATH. Please install trisurf prior to running trisurf manager.")
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exit(1)
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self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
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#Symlinks tape file to the directory or create tape file from snapshot in the direcory...
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if(self.Dir.makeifnotexist()):
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if(self.fromSnapshot==False):
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try:
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os.symlink(os.path.abspath(self.tapeFile), self.Dir.fullpath()+"/tape")
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except:
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print("Error while symlinking "+os.path.abspath(self.tapeFile)+" to "+self.Dir.fullpath()+"/tape")
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exit(1)
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else:
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try:
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with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile:
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#myfile.write("#This is automatically generated tape file from snapshot")
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myfile.write(str(self.tape.rawText))
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except:
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print("Error -- cannot make tapefile "+ os.path.join(self.Dir.fullpath(),"tape")+" from the snapshot in the running directory")
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exit(1)
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try:
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os.symlink(os.path.abspath(self.snapshotFile), os.path.join(self.Dir.fullpath(),"initial_snapshot.vtu"))
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except:
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print("Error while symlinking "+os.path.abspath(self.snapshotFile)+" to "+os.path.join(self.Dir.fullpath(),self.snapshotFile))
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#check if the simulation has been completed. in this case notify user and stop executing.
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if(self.isCompleted() and ("--force-from-tape" not in self.runArgs) and ("--reset-iteration-count" not in self.runArgs)):
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print("The simulation was completed. Not starting executable in "+self.Dir.fullpath())
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return
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cwd=Directory(maindir=os.getcwd())
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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.
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self.Dir.goto()
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print("Starting trisurf-ng executable in "+self.Dir.fullpath())
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if(self.fromSnapshot==True):
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#here we try to determine whether we should continue the simulation or start from last known VTU snapshot.
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if(lastVTU==None):
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initSnap="initial_snapshot.vtu"
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else:
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initSnap=lastVTU
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print("WARNING: Not using initial snapshot as starting point, but selecting "+initSnap+" as a starting vesicle")
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params=["trisurf", "--restore-from-vtk",initSnap]+self.runArgs
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print("InitSnap is: "+initSnap)
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else:
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#veify if dump exists. If not it is a first run and shoud be run with --force-from-tape
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if(os.path.isfile("dump.bin")==False):
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self.runArgs.append("--force-from-tape")
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params=["trisurf"]+self.runArgs
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subprocess.Popen (params, stdout=subprocess.DEVNULL)
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cwd.goto()
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else:
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print("Process in "+self.Dir.fullpath()+" already running. Not starting.")
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return
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def setMaindir(self,prefix,variables):
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maindir=""
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for p,v in zip(prefix,variables):
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if(v=="xk0"):
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tv=str(round(float(self.tape.config[v])))
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if sys.version_info<(3,0):
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tv=str(int(float(self.tape.config[v])))
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else:
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tv=self.tape.config[v]
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maindir=maindir+p+tv
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self.maindir=maindir
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return
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def setSubdir(self, subdir="run0"):
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self.subdir=subdir
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return
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def getStatistics(self, statfile="statistics.csv"):
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self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
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self.statistics=Statistics(self.Dir.fullpath(), statfile)
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self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
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pid=self.getPID()
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status=self.getStatus()
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if(self.statistics.fileOK):
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ETA=str(datetime.timedelta(microseconds=(int(self.tape.config['iterations'])-int(self.statistics.last))*self.statistics.dT)*1000000)
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if(status==TS_NONEXISTANT or status==TS_NOLOCK):
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statustxt="Not running"
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pid=""
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ETA=""
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elif status==TS_STOPPED:
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statustxt="Stopped"
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ETA="N/A"
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elif status==TS_COMPLETED:
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statustxt="Completed"
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pid=""
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ETA=""
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else:
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statustxt="Running"
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if(self.statistics.fileOK):
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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()]
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else:
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report=["N/A","N/A",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
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return report
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def stop(self):
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p=psutil.Process(self.getPID())
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p.kill()
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def writeComment(self, data, mode='w'):
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self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
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self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
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self.Comment.writefile(data,mode=mode)
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|
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def getLastVTU(self):
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vtuidx=self.getLastIteration()-int(self.tape.getValue("inititer"))
|
if vtuidx<0:
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return None
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else:
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return 'timestep_{:06d}.vtu'.format(vtuidx)
|
|
def __str__(self):
|
if(self.getStatus()==0):
|
str=" not running."
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else:
|
str=" running."
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return(self.Dir.fullpath()+str)
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