From 37791bf67add4094040a9b8706450695805bf88f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 20 May 2016 18:35:21 +0000
Subject: [PATCH] Minimal changes to trisurf core to permit the trout rbc simulations with eliptical nucleus (optional parameters in tape R_nucleusX, R_nucleusY and R_nucleusZ) were added
---
python/trisurf/trisurf.py | 103 +++++++++++++++++++++++++++++++++++++++++----------
1 files changed, 82 insertions(+), 21 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index 9018555..310b4d3 100644
--- a/python/trisurf/trisurf.py
+++ b/python/trisurf/trisurf.py
@@ -13,12 +13,14 @@
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:
'''
@@ -197,19 +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;
@@ -230,8 +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)
@@ -277,7 +292,7 @@
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 +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
@@ -306,7 +347,11 @@
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()):
@@ -319,27 +364,35 @@
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("#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(),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())
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
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):
@@ -364,20 +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)*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 writeComment(self, data, mode='w'):
--
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