From 61ad95ca712a374f6e58127fda738b67c57d743d Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 04 Jan 2017 21:19:52 +0000
Subject: [PATCH] Added many changes to trisurf.py. Mostly readability. Great fix in class Runner by introducing @property tag
---
python/trisurf/trisurf.py | 224 +++++++++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 191 insertions(+), 33 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index b1f99b6..01c3d0c 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
@@ -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):
@@ -142,7 +146,9 @@
'''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.'''
@@ -195,19 +201,67 @@
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;
@@ -228,8 +282,10 @@
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)
@@ -246,13 +302,23 @@
'''
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='', runArgs=[]):
+
+ @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
- if(tape!=''):
+ if(tape!=None):
self.initFromTape(tape)
- if(snapshot!=''):
+ if(snapshot!=None):
self.initFromSnapshot(snapshot)
return
@@ -260,6 +326,7 @@
def initFromTape(self, tape):
self.tape=Tape()
self.tape.readTape(tape)
+ self.tapeFile=tape
def initFromSnapshot(self, snapshotfile):
try:
@@ -276,8 +343,8 @@
self.tape.setTape(tapetxt.text)
def getPID(self):
- self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
- self.Dir.makeifnotexist()
+# 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:
@@ -286,14 +353,40 @@
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"))+int(self.tape.getValue("inititer"))==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
@@ -303,30 +396,70 @@
return TS_NONEXISTANT
def start(self):
- if(self.getStatus()==0):
- self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
- self.Dir.makeifnotexist()
+ 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()):
+ if(self.fromSnapshot==False):
+ try:
+ os.symlink(os.path.abspath(self.tapeFile), self.Dir.fullpath()+"/tape")
+ except:
+ print("Error while symlinking "+os.path.abspath(self.tapeFile)+" 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 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=""
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
@@ -338,30 +471,55 @@
return
def getStatistics(self, statfile="statistics.csv"):
- self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
- self.statistics=Statistics(self.Dir.fullpath(), statfile)
+# 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()]
+ 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\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):
+ 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.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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