PETSc Problem with fgets

[Joshua L. Adelman]

Just to clarify, it appears from the documentation that this causes  
several processors to get the same line from a file. 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.

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?

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 at ocf.berkeley.edu
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