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Re: PETSc Problem with fgets
On Fri, 12 May 2006, Joshua L. Adelman wrote:
Just to clarify, it appears from the documentation that this causes several
processors to get the same line from a file.
Yes
If I just want to have a single
processor get a line and then parse that to some variables within a struct,
it would seem like I don't need all of my processors reading the line.
Yes, you don't need
Would I just use PETSC_WORLD_SELF in the PetscFOpen() command to have a
single processor open the file, and then use _SELF again in the synchronized
fgets to have a single processor take care of retrieving the line?
Yes, you can just use SELF, but you need to put all of this stuff INSIDE
the test of if (!rank) { In fact, if you are only having process 0 open the
file, read the data and parse it then you don't need to use PetscFOpen(), etc
AT ALL, you can just use plan old fopen(), fgets() inside the if (!rank).
On the other hand if you want all the information from the file on all
the processes you can just use the PetscFOpen(), PetscFGets(), PetscFClose()
with NO if (!rank) { code needed.
Barry
Thanks again for your help.
Josh
On May 12, 2006, at 11:23 AM, Barry Smith wrote:
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
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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
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