[petsc-users] Problem in loading Matrix Market format

[Eda Oktay]

Dear Professor Roman,

Thank you for your answer. I used PetscBinaryWrite.m file and converted
matrices into binary format but I have a question:

When I look at Properties of the binary files Petsc have, their type is
stated as "Program (application/octet-stream)", however when I checked the
binary files I created their type is stated as "Binary
(application/octet-stream)". Can this cause a problem, why they are
different?

Eda

Jose E. Roman <jroman at dsic.upv.es>, 12 Şub 2019 Sal, 12:05 tarihinde şunu
yazdı:

> It is better to convert the matrices to PETSc binary format first. One
> easy way is to read them into Matlab with mmread.m and write with PETSc's
> PetscBinaryWrite.m. This can be done similarly in python.
> Jose
>
>
> > El 12 feb 2019, a las 8:50, Eda Oktay via petsc-users <
> petsc-users at mcs.anl.gov> escribió:
> >
> > Hello,
> >
> > I am trying to load matrix in Matrix Market format. I found an example
> on mat file  (ex78) whih can be tested by using .dat file. Since .dat file
> and .mtx file are similar  in structure (specially afiro_A.dat file is
> similar to amesos2_test_mat0.mtx since they both have 3 columns and the
> columns represent the same properties), I tried to run ex78 by using
> amesos2_test_mat0.mtx instead of afiro_A.dat. However, I got the error
> "Badly formatted input file". Here is the full error message:
> >
> > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > [0]PETSC ERROR: Badly formatted input file
> >
> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> > [0]PETSC ERROR: Petsc Release Version 3.10.3, Dec, 18, 2018
> > [0]PETSC ERROR: ./ex78 on a arch-linux2-c-debug named
> 7330.wls.metu.edu.tr by edaoktay Tue Feb 12 10:47:58 2019
> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --with-cxx-dialect=C++11 --download-openblas
> --download-metis --download-parmetis --download-superlu_dist
> --download-slepc --download-mpich
> > [0]PETSC ERROR: #1 main() line 73 in
> /home/edaoktay/petsc-3.10.3/src/mat/examples/tests/ex78.c
> > [0]PETSC ERROR: PETSc Option Table entries:
> > [0]PETSC ERROR: -Ain
> /home/edaoktay/petsc-3.10.3/share/petsc/datafiles/matrices/amesos2_test_mat0.mtx
> > [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
> > :
> > system msg for write_line failure : Bad file descriptor
> >
> > I know there is also an example (ex72) for Matrix Market format but in
> description, it is only proper for symmmetric and lower triangle, so I
> decided to use ex78.
> >
> > Best regards,
> >
> > Eda
>
>
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