[petsc-dev] reading gmsh into DMPlex

[Adrian Croucher]

hi

On 16/05/19 7:37 PM, Stefano Zampini wrote:
> Can you try with this PR 
> https://bitbucket.org/petsc/petsc/pull-requests/1660/binary-i-o-and-gmsh-dmplex-reader/diff?


Yes, I just tried using PETSc 3.11.2 which has this PR merged in, and it 
does work again now. Thanks!

Cheers, Adrian

>
>> On May 16, 2019, at 5:59 AM, Adrian Croucher via petsc-dev 
>> <petsc-dev at mcs.anl.gov <mailto:petsc-dev at mcs.anl.gov>> wrote:
>>
>> hi
>>
>> A couple of years ago (see below) I was having problems reading in 
>> GMSH files using DMPlexCreateFromFile(), if the MSH file didn't have 
>> a newline on the end.
>>
>> It was fixed at the time, but the problem seems to be happening again 
>> with PETSc 3.11.1.
>>
>> I've attached an example mesh which no longer works (unless you add a 
>> newline on the end of it). The error message is below.
>>
>> - Adrian
>>
>> [0]PETSC ERROR: Invalid argument
>> [0]PETSC ERROR: File is not a valid Gmsh file, expecting $EndElements
>> [0]PETSC ERROR: See 
>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>> [0]PETSC ERROR: Petsc Development GIT revision: 
>> v3.11.1-701-g5065da2f63  GIT Date: 2019-05-13 01:43:35 -0
>> 500
>> [0]PETSC ERROR: ./plexview on a linux-gnu-c-opt named en-354401 by 
>> acro018 Thu May 16 14:54:13 2019
>> [0]PETSC ERROR: Configure options --with-x --download-hdf5 
>> --download-zlib --download-pnetcdf --download-
>> netcdf --download-exodusii --download-triangle --download-ptscotch 
>> --download-chaco --download-hypre --wi
>> th-debugging=0 COPTFLAGS="-O3 -march=native -mtune=native" 
>> CXXOPTFLAGS="-O3 -march=native -mtune=native"
>> FOPTFLAGS="-O3 -march=native -mtune=native"
>> [0]PETSC ERROR: #1 GmshExpect() line 80 in 
>> /home/acro018/software/PETSc/code/src/dm/impls/plex/plexgmsh.c
>> [0]PETSC ERROR: #2 GmshReadEndSection() line 108 in 
>> /home/acro018/software/PETSc/code/src/dm/impls/plex/p
>> lexgmsh.c
>> [0]PETSC ERROR: #3 DMPlexCreateGmsh() line 1107 in 
>> /home/acro018/software/PETSc/code/src/dm/impls/plex/pl
>> exgmsh.c
>> [0]PETSC ERROR: #4 DMPlexCreateGmshFromFile() line 989 in 
>> /home/acro018/software/PETSc/code/src/dm/impls/
>> plex/plexgmsh.c
>> [0]PETSC ERROR: #5 DMPlexCreateFromFile() line 3268 in 
>> /home/acro018/software/PETSc/code/src/dm/impls/ple
>> x/plexcreate.c
>> [0]PETSC ERROR: #6 User provided function() line 0 in User file
>>
>
-- 
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
University of Auckland, New Zealand
email: a.croucher at auckland.ac.nz
tel: +64 (0)9 923 4611

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