[petsc-users] Problem in loading Matrix Market format

[Jed Brown]

We should make the (two line) functionality a command-line feature of
PetscBinaryIO.py.  Then a user could do

  python -m PetscBinaryIO matrix.mm matrix.petsc

Matthew Knepley via petsc-users <petsc-users at mcs.anl.gov> writes:

> It definitely should not be there under 'datafiles'. We should put it in an
> example, as Junchao graciously agreed to do.
>
>   Thanks,
>
>     Matt
>
> On Tue, Feb 12, 2019 at 11:15 AM Zhang, Hong <hzhang at mcs.anl.gov> wrote:
>
>> We have /home/petsc/datafiles/matrices/MtxMarket/mm2petsc.c
>> Hong
>>
>> On Tue, Feb 12, 2019 at 9:52 AM Zhang, Junchao via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>>
>>> Sure.
>>> --Junchao Zhang
>>>
>>>
>>> On Tue, Feb 12, 2019 at 9:47 AM Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> Hi Junchao,
>>>>
>>>> Could you fix the MM example in PETSc to have this full support? That
>>>> way we will always have it.
>>>>
>>>>  Thanks,
>>>>
>>>>     Matt
>>>>
>>>> On Tue, Feb 12, 2019 at 10:27 AM Zhang, Junchao via petsc-users <
>>>> petsc-users at mcs.anl.gov> wrote:
>>>>
>>>>> Eda,
>>>>>   I have a code that can read in Matrix Market and write out PETSc
>>>>> binary files.  Usage:  mpirun -n 1 ./mm2petsc -fin <infile> -fout
>>>>> <outfile>.  You can have a try.
>>>>> --Junchao Zhang
>>>>>
>>>>>
>>>>> On Tue, Feb 12, 2019 at 1:50 AM Eda Oktay via petsc-users <
>>>>> petsc-users at mcs.anl.gov> wrote:
>>>>>
>>>>>> 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
>>>>>>
>>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their
>>>> experiments is infinitely more interesting than any results to which their
>>>> experiments lead.
>>>> -- Norbert Wiener
>>>>
>>>> https://www.cse.buffalo.edu/~knepley/
>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>
>>>
>
> -- 
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>