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 | 138 ++++++++++++++++++++++++++++++++++------------
1 files changed, 102 insertions(+), 36 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index e3108b3..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
@@ -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):
@@ -210,8 +212,45 @@
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.
'''
@@ -263,10 +302,20 @@
'''
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
- self.fromSnapshot=False
+ self.isFromSnapshot=False
if(tape!=None):
self.initFromTape(tape)
if(snapshot!=None):
@@ -275,9 +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:
@@ -285,17 +334,15 @@
except:
print("Error reading snapshot file")
exit(1)
- self.fromSnapshot=True
+ 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 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:
@@ -305,8 +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:
@@ -316,7 +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
@@ -352,25 +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):
+ if(self.isFromSnapshot==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))
@@ -380,10 +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
+ 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):
@@ -395,16 +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
@@ -414,13 +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=""
@@ -435,17 +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."
--
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