Added many fixes for reruning the simulations, starting from tapes, added C...

Samo Penic

2016-05-13 3d0247677949505858b0b947fc3b216bb2a7bc80

Added many fixes for reruning the simulations, starting from tapes, added Completed status, etc.

 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)


 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"


 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);

 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);