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 | 42 +++++++++++++++++++++++++++---------------
1 files changed, 27 insertions(+), 15 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index 2f98e2c..310b4d3 100644
--- a/python/trisurf/trisurf.py
+++ b/python/trisurf/trisurf.py
@@ -199,13 +199,18 @@
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.
@@ -287,7 +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()
@@ -324,8 +329,15 @@
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
@@ -352,26 +364,26 @@
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 at localhost in "+self.Dir.fullpath()+"\n")
+ 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 localhost in "+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):
@@ -380,7 +392,7 @@
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):
--
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