From 354145cb4c260bdd7ef3dafcdae206e2d00d4d3a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Wed, 18 May 2016 06:51:10 +0000
Subject: [PATCH] snapshot symlinked to initial_snapshot.vtu. This eliminates possibility of overwriting the configuration snapshot file in cat it is named timestep_xxxxx.vtu during the simulation.
---
python/trisurf/trisurf.py | 134 ++++++++++++++++++++++++++++++++++++--------
1 files changed, 109 insertions(+), 25 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index b055f19..310b4d3 100644
--- a/python/trisurf/trisurf.py
+++ b/python/trisurf/trisurf.py
@@ -12,13 +12,15 @@
import psutil
import time
import datetime
-from subprocess import call, Popen
+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:
'''
@@ -142,7 +144,9 @@
'''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 +199,30 @@
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;
@@ -228,8 +243,10 @@
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 +263,13 @@
'''
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=[]):
+ 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 +277,7 @@
def initFromTape(self, tape):
self.tape=Tape()
self.tape.readTape(tape)
+ self.tapeFile=tape
def initFromSnapshot(self, snapshotfile):
try:
@@ -277,7 +295,7 @@
def getPID(self):
self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
- self.Dir.makeifnotexist()
+ #self.Dir.makeifnotexist()
try:
fp = open(os.path.join(self.Dir.fullpath(),'.lock'))
except IOError as e:
@@ -286,14 +304,40 @@
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
@@ -303,20 +347,52 @@
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)
- self.Dir.makeifnotexist()
+#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))
+ 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())
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
+ params=["trisurf", "--restore-from-vtk","initial_snapshot.vtu"]+self.runArgs
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
- Popen (params, stdout=False)
+ 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):
@@ -341,20 +417,28 @@
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)*1000), 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 writeComment(self, data, mode='w'):
--
Gitblit v1.9.3