From 3d0247677949505858b0b947fc3b216bb2a7bc80 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 13 May 2016 19:09:59 +0000
Subject: [PATCH] Added many fixes for reruning the simulations, starting from tapes, added Completed status, etc.
---
src/main.c | 6 +++
src/timestep.c | 8 +++
python/myTestConfig.py | 15 ++++++-
python/trisurf/trisurf.py | 48 +++++++++++++++++++++--
4 files changed, 69 insertions(+), 8 deletions(-)
diff --git a/python/myTestConfig.py b/python/myTestConfig.py
index 23f9342..79c4f51 100644
--- a/python/myTestConfig.py
+++ b/python/myTestConfig.py
@@ -1,17 +1,28 @@
from trisurf import tsmgr
from trisurf import trisurf
+
+#Simple example how to start simulation from a previos snapshot
run1=trisurf.Runner(snapshot='snapshot.vtu')
run1.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
run1.setSubdir("run0")
+#Example how to start simulation from tape. Extra argument in runArgs will be passed to trisurf executable (meaning that simulation will always start from the beginning (bipyramid) ignoring the fact that some states may have been calculated already)
run2=trisurf.Runner(tape='tape', runArgs=['--force-from-tape'])
run2.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
run2.setSubdir("run1")
+#Example of programatical setup of 4 runs
+pRun=[]
+for i in range(0,4): #0,1,2,3
+ tpRun=trisurf.Runner(tape='tape')
+ tpRun.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
+ tpRun.setSubdir("programatical_"+str(i))
+ pRun.append(tpRun)
-#obligatory: combine all runs
-Runs=[run1,run2]
+#obligatory final configuration step: combine all runs
+Runs=[run1,run2]+pRun
+#start manager with configured runs
tsmgr.start(Runs)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index 9018555..c57de3e 100644
--- a/python/trisurf/trisurf.py
+++ b/python/trisurf/trisurf.py
@@ -19,6 +19,7 @@
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:
'''
@@ -209,7 +210,13 @@
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 +237,10 @@
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)
@@ -289,8 +298,27 @@
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))):
@@ -306,7 +334,7 @@
return TS_NONEXISTANT
def start(self):
- if(self.getStatus()==0):
+ if(self.getStatus()==0 or self.getStatus()==TS_COMPLETED):
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()):
@@ -328,13 +356,21 @@
os.symlink(os.path.abspath(self.snapshotFile), os.path.join(self.Dir.fullpath(),self.snapshotFile))
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")
+ return
+
cwd=Directory(maindir=os.getcwd())
self.Dir.goto()
- print("Starting trisurf-ng executable at "+self.Dir.fullpath()+"\n")
+ print("Starting trisurf-ng executable at localhost in "+self.Dir.fullpath()+"\n")
if(self.fromSnapshot==True):
params=["trisurf", "--restore-from-vtk",self.snapshotFile]+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()
@@ -371,6 +407,8 @@
pid=""
elif status==TS_STOPPED:
statustxt="Stopped"
+ elif status==TS_COMPLETED:
+ statustxt="Completed"
else:
statustxt="Running"
diff --git a/src/main.c b/src/main.c
index df7d6fa..36da13a 100644
--- a/src/main.c
+++ b/src/main.c
@@ -46,6 +46,12 @@
ts_fprintf(stdout,"************************************************\n\n");
vesicle = parseDump(command_line_args.dump_from_vtk);
tape = vesicle->tape;
+ FILE *fd=fopen(".status","r");
+ if(fd!=NULL){
+ fscanf(fd,"%u", &start_iteration);
+ fclose(fd);
+ start_iteration++;
+ }
/* Here you should read new tape file, reassign some values in vertex from the tape and assign read tape to vesicle->tape */
// tape=parsetape(command_line_args.tape_fullfilename);
// vesicle=vtk2vesicle(command_line_args.dump_from_vtk,tape);
diff --git a/src/timestep.c b/src/timestep.c
index 9f30dda..a8c0b32 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -22,7 +22,7 @@
ts_double r0,kc1=0,kc2=0,kc3=0,kc4=0;
ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
ts_ulong epochtime;
- FILE *fd1,*fd2=NULL;
+ FILE *fd1,*fd2=NULL,*fd3=NULL;
char filename[10000];
strcpy(filename,command_line_args.path);
strcat(filename,"statistics.csv");
@@ -76,6 +76,12 @@
cell_occupation(vesicle);
ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
dump_state(vesicle,i);
+ fd3=fopen(".status","w");
+ if(fd3==NULL){
+ fatal("Cannot open .status file for writing",1);
+ }
+ fprintf(fd3,"%d",i);
+ fclose(fd3);
if(i>=inititer){
write_vertex_xml_file(vesicle,i-inititer);
write_master_xml_file(command_line_args.output_fullfilename);
--
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