From 56016c6fbb33395c5a06a0cd3f144934782ef5a2 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Thu, 07 Jul 2016 14:35:16 +0000
Subject: [PATCH] Fixed a bug in getting the last value when running 2.7
---
python/trisurf/trisurf.py | 100 +++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 83 insertions(+), 17 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index ac8abaf..8e60d69 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):
@@ -199,14 +201,51 @@
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.
'''
@@ -311,7 +350,7 @@
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
@@ -325,8 +364,14 @@
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 proc.name()=="trisurf":
- if proc.status()=="stopped":
+ 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
@@ -353,13 +398,13 @@
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))
@@ -369,10 +414,18 @@
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
+ #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):
@@ -384,14 +437,14 @@
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
@@ -430,11 +483,24 @@
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"))+1
+ 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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