Re: PETSc Problem with fgets

[Barry Smith <bsmith@xxxxxxxxxxx>]

  Stupid me, I don't know my own code.

  You can use PetscSynchronizedFGets() exactly for this purpose.

   Barry

  I have updated the manual page for PetscFOpen() to seealso:
PetscSynchronizedFGets()


On Fri, 12 May 2006, Barry Smith wrote:

>  Joshua,
>
>    PetscFOpen() only produces a valid fd on process 0. Thus fgets()
> can only be used on process 0. It is crashing on process 1 because
> fd is garbage there.
>
>    You need to MPI_Scatter the data to the other processes. There is
> no PetscFGets(), though come to think of it there should be! I will write
> one and send it to you.
>
>   Barry
>
>
>
> On Thu, 11 May 2006, Joshua Adelman wrote:
>
> > I am trying to read some parameters into my PETSc simulation using fgets, 
> > and am getting a strange error. It appears that fgets and sscanf are 
> > working since the proper values are read into the simulation, but it throws 
> > an error anyways. This problem only arises when I am using the parallel 
> > version of the code (i.e. setting -n in mpiexec to a value greater than 1). 
> > Basically if I comment everything out and then start uncommenting one line 
> > at a time, the error appears once I've uncommented the line with fgets. One 
> > strange thing to note is that the error happens after the program has 
> > already finished executing the function where the problem is. Here's a 
> > snippet of the code that seems to be causing the problem:
> >
> > PetscErrorCode DataReadParams(SimData *sdata) {
> > 	int 			rank, size;
> > 	PetscErrorCode	ierr;
> > 	int				i;
> > 	FILE			*fd;
> > 	char        	str[256];
> > 	char			line[100];
> > 	int				max = 100;
> > 		PetscFunctionBegin;
> >
> > 	ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size); CHKERRQ(ierr);
> > 	ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank); CHKERRQ(ierr);
> >
> > 		/* Read data from files	*/
> > 	sprintf(str,"%s%s",sdata->simname,".param");
> > 	ierr = PetscFOpen(PETSC_COMM_WORLD,str,"r",&fd); CHKERRQ(ierr);
> > 	if (!rank && !fd) {
> > 	    SETERRQ1(PETSC_ERR_FILE_OPEN,"Cannot open %s\n",str);
> > 	}
> > 	// PetscPrintf(PETSC_COMM_WORLD,"Opening file %s\n",str);
> > 	fgets(line,max,fd);
> >  	sscanf(line,"%d",&sdata->NP);
> >
> > The error that is kicked out is:
> >
> >
> > [1]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal 
> > memory access
> > [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> > [1]PETSC ERROR: or try http://valgrind.org on linux to find memory 
> > corruption errors
> > [1]PETSC ERROR: likely location of problem given in stack below
> > [1]PETSC ERROR: --------------- Stack Frames ---------------
> > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not 
> > available,
> > [1]PETSC ERROR:       INSTEAD the line number of the start of the function
> > [1]PETSC ERROR:       is given.
> > [1]PETSC ERROR: [1] DataReadParams line 23 datareadparams.c
> > [1]PETSC ERROR: [1] SimInit line 19 siminit.c
> > [1]PETSC ERROR: --------------------------------------------
> > [1]PETSC ERROR: User provided function() line 0 in unknown directory 
> > unknown file
> > [1]PETSC ERROR: Signal received!
> > [1]PETSC ERROR:  !
> >
> >
> > Any insight would be most appreciated.
> >
> > Josh
> >
> >
> > ------------------------------------------------------------------------------------------------------
> > Joshua L. Adelman
> > Biophysics Graduate Group              Lab: 510.643.2159
> > 218 Wellman Hall                                Fax: 510.642.7428
> > University of California, Berkeley 
> > http://www.ocf.berkeley.edu/~jadelman
> > Berkeley, CA 94720 USA                   jadelman@xxxxxxxxxxxxxxxx
> >
> > ------------------------------------------------------------------------------------------------------