From 8b8845e452b45b765c0c74a388296d10e91787fc Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 28 Nov 2017 21:03:17 +0000
Subject: [PATCH] Changed the executabe to tssystem ;)
---
trisurf/trisurf.py | 167 +++++++++++++++++++++++++++++++------------------------
1 files changed, 95 insertions(+), 72 deletions(-)
diff --git a/trisurf/trisurf.py b/trisurf/trisurf.py
index 92b138b..2212c8e 100644
--- a/trisurf/trisurf.py
+++ b/trisurf/trisurf.py
@@ -186,7 +186,6 @@
self.path=path
self.filename=filename
self.fullname=os.path.join(path,filename)
- self.fileOK=self.read()
return
def exists(self):
@@ -196,7 +195,7 @@
else:
return False
- def mapcount(self):
+ def lineCount(self):
'''
Internal method for determining the number of the lines in the most efficient way. Is it really the most efficient?
'''
@@ -213,19 +212,26 @@
f.close()
return lines
- def tail(self,filename,n=2):
- with open(filename,'r') as myfile:
+ def tail(self):
+ with open(self.fullname,'r') as myfile:
lines=myfile.readlines()
return [lines[len(lines)-2].replace('\n',''),lines[len(lines)-1].replace('\n','')]
- def read(self):
+ def checkFileValidity(self):
try:
- lines=self.tail(self.fullname)
+ lines=self.tail()
except:
return(False)
if len(lines)<2:
return(False)
- #print (line)
+ return(True)
+
+ def getSimulationDeltaTime(self):
+ try:
+ lines=self.tail()
+ except:
+ return 0
+
fields=shlex.split(lines[0])
epoch1=fields[0]
n1=fields[1]
@@ -234,61 +240,59 @@
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'))
+ dT=int(epoch2)-int(epoch1)
except:
- return(False)
- return(True)
+ return 0
+ return dT
+
+ def getLastIterationInStatistics(self):
+ try:
+ lines=self.tail()
+ except:
+ return 0
+
+ fields=shlex.split(lines[0])
+ epoch1=fields[0]
+ n1=fields[1]
+
+ fields=shlex.split(lines[1])
+ epoch2=fields[0]
+ return (fields[1])
+
+ def getColumn(self,n=0):
+ lines=self.readText().splitlines()
+ col=[]
+ name=lines[0].split()[n]
+ for line in lines:
+ col.append(line.split()[n])
+ return col[2:],name
+
+ def getTable(self):
+ lines=self.readText().splitlines()
+ keys=lines[0].split()
+ table={}
+ def num(s):
+ try:
+ return int(s)
+ except ValueError:
+ return float(s)
+ for key in keys:
+ table[key]=[]
+ for line in lines:
+ fields=line.split()
+ for i in range(0,len(keys)):
+ try:
+ value=num(fields[i])
+ table[keys[i]].append(value)
+ except:
+ pass
+ return table
+
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;
- for line in fin:
- if(i==1):
- #print (line)
- fields=shlex.split(line)
- epoch1=fields[0]
- n1=fields[1]
- if(i==nlines-1):
- fields=shlex.split(line)
- epoch2=fields[0]
- n2=fields[1]
- i=i+1
- except:
- #print("Cannot read statistics file in "+self.fullname+"\n")
- return(False)
- else:
- #print("File "+self.fullname+" does not exists.\n")
- return(False)
- 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):
'''
@@ -366,6 +370,13 @@
else:
return False
+
+ def getStartTime(self):
+ try:
+ return os.path.getmtime(os.path.join(self.Dir.fullpath(),'.lock'))
+ except:
+ return -1
+
def getStatus(self):
pid=self.getPID()
if(self.isCompleted()):
@@ -381,7 +392,7 @@
else:
procname=proc.name
procstat=proc.status
- if procname=="trisurf":
+ if procname=="tssystem":
if procstat=="stopped":
return TS_STOPPED
else:
@@ -394,7 +405,7 @@
def start(self):
if(self.getStatus()==0 or self.getStatus()==TS_COMPLETED):
#check if executable exists
- if(shutil.which('trisurf')==None):
+ if(shutil.which('tssystem')==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...
@@ -434,13 +445,13 @@
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
+ params=["tssystem", "--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
+ params=["tssystem"]+self.runArgs
subprocess.Popen (params, stdout=subprocess.DEVNULL)
cwd.goto()
else:
@@ -451,12 +462,12 @@
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]
+ #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=str(self.Tape.config[v])
maindir=maindir+p+tv
self.maindir=maindir
return
@@ -469,8 +480,8 @@
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.checkFileValidity()):
+ ETA=str(datetime.timedelta(microseconds=(int(self.Tape.config['iterations'])-int(self.Statistics.getLastIterationInStatistics()))*self.Statistics.getSimulationDeltaTime())*1000000)
if(status==TS_NONEXISTANT or status==TS_NOLOCK):
statustxt="Not running"
pid=""
@@ -485,8 +496,8 @@
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.checkFileValidity()):
+ report=[time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(self.getStartTime()))),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
@@ -505,12 +516,23 @@
self.Comment.writefile(data,mode=mode)
- def getLastVTU(self):
+ def getLastVTUold(self):
vtuidx=self.getLastIteration()-int(self.Tape.getValue("inititer"))
if vtuidx<0:
return None
else:
return 'timestep_{:06d}.vtu'.format(vtuidx)
+
+ def getLastVTU(self):
+ flist=[]
+ for file in os.listdir(self.Dir.fullpath()):
+ if file.endswith(".vtu"):
+ flist.append(file)
+ flist.sort()
+ if(len(flist)==0):
+ return -1
+ else:
+ return(flist[-1])
def __str__(self):
if(self.getStatus()==0):
@@ -519,4 +541,5 @@
str=" running."
return(self.Dir.fullpath()+str)
-
+ def __repr__(self):
+ return("Instance of trisurf in "+self.Dir.fullpath())
--
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