From 96b0a0ac783d35fbf4e764fe8e610ddc2a79af27 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 04 Jan 2017 22:03:25 +0000
Subject: [PATCH] Added even more readability...
---
python/trisurf/trisurf.py | 385 +++++++++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 329 insertions(+), 56 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index 2d67a74..92b138b 100644
--- a/python/trisurf/trisurf.py
+++ b/python/trisurf/trisurf.py
@@ -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
@@ -12,41 +10,98 @@
import psutil
import time
import datetime
+import subprocess
+import shutil
-'''
-This is a trisurf instance manager written in python
+# 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"
@@ -55,22 +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:
@@ -79,11 +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())
@@ -93,6 +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:
@@ -101,7 +172,17 @@
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)
@@ -109,23 +190,78 @@
return
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 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;
@@ -146,33 +282,51 @@
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)
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=''):
+
+ @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
- if(tape!=''):
+ self.runArgs=runArgs
+ self.isFromSnapshot=False
+ if(tape!=None):
self.initFromTape(tape)
- if(snapshot!=''):
+ if(snapshot!=None):
self.initFromSnapshot(snapshot)
return
def initFromTape(self, tape):
- self.tape=Tape()
- self.tape.readTape(tape)
+ self.Tape=Tape()
+ self.Tape.readTape(tape)
+ self.tapeFilename=tape
def initFromSnapshot(self, snapshotfile):
try:
@@ -180,48 +334,129 @@
except:
print("Error reading snapshot file")
exit(1)
-
+ self.isFromSnapshot=True
+ self.snapshotFile=snapshotfile
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 getStatus(self):
- self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
- self.Dir.makeifnotexist()
-# self.Dir.goto()
+ def getPID(self):
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();
- if(psutil.pid_exists(int(pid))):
- return 1
+ pid=fp.readline()
+ fp.close()
+ return int(pid)
+
+ def getLastIteration(self):
+ 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 0
+ 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))
+ #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):
- self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
- self.Dir.makeifnotexist()
-# self.Dir.goto()
- print("Starting trisurf-ng executable at "+self.Dir.fullpath()+"\n")
+ 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)
+#Symlinks tape file to the directory or create tape file from snapshot in the direcory...
+ if(self.Dir.makeifnotexist()):
+ if(self.isFromSnapshot==False):
+ try:
+ os.symlink(os.path.abspath(self.tapeFilename), self.Dir.fullpath()+"/tape")
+ except:
+ 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.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 in "+self.Dir.fullpath())
+ if(self.isFromSnapshot==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])))
+ 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
@@ -231,14 +466,52 @@
return
def getStatistics(self, statfile="statistics.csv"):
- self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
- self.statistics=Statistics(self.Dir.fullpath(), statfile)
- if(self.statistics.fileOK):
- report=time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(self.statistics.startDate)))+"\t"+str(datetime.timedelta(microseconds=(int(self.tape.config['iterations'])-int(self.statistics.last))*self.statistics.dT)*1000)+" ETA\t"+"STATUS"
+ 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:
- report="N/A\tN/A\t"+"STATUS"
+ 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):
+ 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.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."
--
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