[petsc-users] Reading in a matrix from ASCII file
Jed Brown
jed at jedbrown.org
Thu Oct 5 17:21:17 CDT 2017
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Storm Weiner <stormweiner at berkeley.edu> writes:
> Thanks,
>
> I decided to use one of the example matrices provided on the ftp to start
> with but now I have another issue.
> I tried to port /mat/ex1.c to f90 but when I do
>
> CALL PetscViewerBinaryOpen(PETSC_COMM_WORLD,DataFile,fd,ierr)
>
> I get a bad file descriptor error.
>
> A simple open() close() check immediately before PetscViewerBinaryOpen()
> passes, so I know I'm using an appropriate file path.
>
> Furthermore, the unaltered ex1.c works fine with the file I'm attempting.
> Is there something special about petsc+f90 file descriptors, or did I mess
> up somewhere along the way?
No, but Fortran doesn't warn when you pass the wrong number of
parameters. You need this.
diff --git i/ex1.F90 w/ex1.F90
index 049e6ae..311d6f0 100644
--- i/ex1.F90
+++ w/ex1.F90
@@ -25,7 +25,7 @@
close(10)
write(*,*) "before viewer create"
- CALL PetscViewerBinaryOpen(PETSC_COMM_WORLD,DataFile,fd,ierr);CHKERRA(ierr)
+ CALL PetscViewerBinaryOpen(PETSC_COMM_WORLD,DataFile,FILE_MODE_READ,fd,ierr);CHKERRA(ierr)
!! Load the matrix; then destroy the viewer.
> The complete error message is:
>
>
> $ ./ex1 -f $PWD/testmat
> before initialize
> DataFile=
> /usr/workspace/wsa/weiner6/MPI_sandbox/Minimal/testmat
>
>
> before test open/close
> before viewer create
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X
> to find memory corruption errors
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> [0]PETSC ERROR: INSTEAD the line number of the start of the function
> [0]PETSC ERROR: is given.
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
> trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.8.0, unknown
> [0]PETSC ERROR: ./ex1 on a arch-linux2-c-debug named borax2 by weiner6 Thu
> Oct 5 14:48:33 2017
> [0]PETSC ERROR: Configure options --with-scalar-type=complex
> --with-valgrind-dir=/usr/bin/
> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59
> :
> system msg for write_line failure : Bad file descriptor
>
> -Storm
>
> P.S. Should I be using reply-all to in these email threads?
>
> On Thu, Oct 5, 2017 at 2:10 PM, Jed Brown <jed at jedbrown.org> wrote:
>
>> http://www.mcs.anl.gov/petsc/documentation/faq.html#sparse-
>> matrix-ascii-format
>>
>> Better, read it using Python on MATLAB and write it (using the provided
>> PETSc scripts) in PETSc binary format. Parallel IO with ASCII files is
>> a dead end.
>>
>> Storm Weiner <stormweiner at berkeley.edu> writes:
>>
>> > Hey there,
>> >
>> > I'm working through some basic examples, and I want to read in a test
>> > matrix I have stored in a (row, column, value) ASCII file. How can I
>> read
>> > this in using PETSc?
>> >
>> >
>> > I found the routine PetscViewerASCIIOpen and PetscViewerASCIIRead but
>> I'm
>> > not sure how to tell it that what I have is actually a matrix. In this
>> > example, I know the matrix, so I can specify how many entries to read,
>> but
>> > is there a way to just read "the whole file"?
>> >
>> > What's the preferred PETSc way to do this?
>> >
>> > I'm using F90 by the way.
>> >
>> >
>> > -Storm
>>
> Program Main
> use PETSCMAT
> implicit NONE
> #include <petsc/finclude/petscmat.h>
>
>
> Mat :: A
> PetscViewer :: fd
> character(100) :: DataFile ! input file name
> IS :: isrow,iscol ! row and column permutations
> PetscErrorCode :: ierr
> MatOrderingType :: rtype = MATORDERINGRCM
> PetscBool :: flg,PetscPreLoad = PETSC_FALSE
>
> write(*,*) "before initialize"
> call PETSCinitialize(PETSC_NULL_CHARACTER,ierr)
>
> call PetscOptionsGetString(petsc_NULL_OPTIONS,PETSC_NULL_CHARACTER,"-f",DataFile,flg,ierr)
> CHKERRA(ierr)
> write(*,*) "DataFile=",DataFile
> !!Open ascii file. Note that we use FILE_MODE_READ to indicate
> !!reading from this file.
> write(*,*) "before test open/close"
> open(10, FILE=DataFile)
> close(10)
>
> write(*,*) "before viewer create"
> CALL PetscViewerBinaryOpen(PETSC_COMM_WORLD,DataFile,fd,ierr);CHKERRA(ierr)
>
>
> !! Load the matrix; then destroy the viewer.
> write(*,*) "before matcreate"
> call MatCreate(PETSC_COMM_WORLD,A,ierr);CHKERRA(ierr);
> write(*,*) "before matsettype"
> call MatSetType(A,MATSEQAIJ,ierr);CHKERRA(ierr);
> write(*,*) "before matload"
> call MatLoad(A,fd,ierr);CHKERRA(ierr);
> write(*,*) "before destroyviewer"
> call PetscViewerDestroy(fd,ierr);CHKERRA(ierr);
>
>
>
> call MatGetOrdering(A,rtype,isrow,iscol,ierr);CHKERRA(ierr);
>
>
> !! All PETSc objects should be destroyed when they are no longer needed.
> call MatDestroy(A,ierr);CHKERRA(ierr);
> call ISDestroy(isrow,ierr);CHKERRA(ierr);
> call ISDestroy(iscol,ierr);CHKERRA(ierr);
> write(*,*) isrow,iscol
> call PetscFinalize(ierr)
> stop
> end program Main
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