From 5c3143e7b7d0979d6eed07b6dfbe9f214159bdbb Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 31 May 2016 19:42:00 +0000
Subject: [PATCH] Use nucleus displaced centre in vertex move
---
python/trisurf/trisurf.py | 134 ++++++++++++++++++++++++++++++++++++--------
1 files changed, 108 insertions(+), 26 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index 9018555..46a3624 100644
--- a/python/trisurf/trisurf.py
+++ b/python/trisurf/trisurf.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python3
-
import configobj
import xml.etree.ElementTree as ET
import base64
@@ -13,12 +11,14 @@
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:
'''
@@ -82,6 +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)
@@ -89,6 +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):
@@ -197,19 +201,30 @@
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 read(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;
@@ -230,8 +245,10 @@
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)
@@ -277,7 +294,7 @@
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()
@@ -289,14 +306,40 @@
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"))==self.getLastIteration()+1):
+ return True
+ else:
+ 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))
- if proc.name()=="trisurf":
- if proc.status()=="stopped":
+ #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
@@ -306,7 +349,11 @@
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)
#Symlinks tape file to the directory or create tape file from snapshot in the direcory...
if(self.Dir.makeifnotexist()):
@@ -319,31 +366,45 @@
else:
try:
with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile:
- myfile.write("#This is automatically generated tape file from snapshot\n")
- 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))
-
+
+ #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):
- 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):
+ 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=""
@@ -364,27 +425,48 @@
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();
+ 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))),str(datetime.timedelta(microseconds=(int(self.tape.config['iterations'])-int(self.statistics.last))*self.statistics.dT)*1000000), statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
+ 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\t",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
+ 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()
+ 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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