Error building petsc

[PrasadBabarendaGamage]

Using instructions from:
http://staging.opencmiss.org/documentation/building/cmake/setup/docs/cli/gnulinux.html
with:
cmake -DOPENCMISS_CONFIG_BUILD_TYPE=Debug -DOPENCMISS_ROOT=../opencmiss ../setup

`[ 78%] Built target OC_SUPERLU_DIST
[ 80%] Performing build step for 'OC_PETSC'
CMake Error at extproj/stamp/OC_PETSC-build-Debug.cmake:16 (message):
Command failed: 2

'/usr/bin/cmake' '--build' '/home/psam012/opt/OpenCMISS/develop_new/opencmiss/build/dependencies/petsc/debug' '--' '-j8'

See also

/home/psam012/opt/OpenCMISS/develop_new/opencmiss/build/dependencies/petsc/debug/extproj/stamp/OC_PETSC-build-*.log

CMakeFiles/OC_PETSC.dir/build.make:120: recipe for target '/home/psam012/opt/OpenCMISS/develop_new/opencmiss/build/dependencies/petsc/debug/extproj/stamp/OC_PETSC-build' failed
make[9]: *** [/home/psam012/opt/OpenCMISS/develop_new/opencmiss/build/dependencies/petsc/debug/extproj/stamp/OC_PETSC-build] Error 1
CMakeFiles/Makefile2:2601: recipe for target 'CMakeFiles/OC_PETSC.dir/all' failed
make[8]: *** [CMakeFiles/OC_PETSC.dir/all] Error 2
`

OC_PETSC-build-*.log

^ /home/psam012/opt/OpenCMISS/develop_new/opencmiss/src/dependencies/petsc/src/vec/is/sf/impls/basic/sfbasic.c:56:36: error: static declaration of ‘MPI_Type_dup’ follows non-static declaration PETSC_STATIC_INLINE PetscErrorCode MPI_Type_dup(MPI_Datatype datatype,MPI_Datatype *newtype) ^ In file included from /home/psam012/opt/OpenCMISS/develop_new/opencmiss/src/dependencies/petsc/include/petscsys.h:108:0, from /home/psam012/opt/OpenCMISS/develop_new/opencmiss/src/dependencies/petsc/include/petscsf.h:6, from /home/psam012/opt/OpenCMISS/develop_new/opencmiss/src/dependencies/petsc/include/petsc/private/sfimpl.h:4, from /home/psam012/opt/OpenCMISS/develop_new/opencmiss/src/dependencies/petsc/src/vec/is/sf/impls/basic/sfbasic.c:2: /usr/include/mpich/mpi.h:1256:5: note: previous declaration of ‘MPI_Type_dup’ was here int MPI_Type_dup(MPI_Datatype oldtype, MPI_Datatype *newtype); ^ make[12]: *** [CMakeFiles/petsc.dir/src/vec/is/sf/impls/basic/sfbasic.c.o] Error 1 make[12]: *** Waiting for unfinished jobs.... make[11]: *** [CMakeFiles/petsc.dir/all] Error 2 make[10]: *** [all] Error 2

configbuildinfo.zip

[hsorby]

I have a fix for this pending I will submit it shortly.

[PrasadBabarendaGamage]

Hi @hsorby wondering if you had any luck with the fix for the petsc bug? Just wanted to check before recompiling as first need to delete my old version due to limited hdd space on my laptop. Thanks

[hsorby]

Yes I have fixed this up. The dependencies have been updated but I have a pull request pending onto Iron that is also part of the fix. I'm currently doing some more testing before I merge that in. I have some other changes that I would like to get in as well but these changes need more testing. You can start to rebuild with the latest but iron won't finish compiling until you merge in the changes from my pull request on iron.

[PrasadBabarendaGamage]

Ok thanks Hugh, I'll try merging in the pull request.​

…

On 9 October 2017 at 10:39, Hugh Sorby ***@***.***> wrote: Yes I have fixed this up. The dependencies have been updated but I have a pull request pending onto Iron that is also part of the fix. I'm currently doing some more testing before I merge that in. I have some other changes that I would like to get in as well but these changes need more testing. You can start to rebuild with the latest but iron won't finish compiling until you merge in the changes from my pull request on iron. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#14 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAyNHVWZokqQbKLqE-BNS-dC7UYrVk3sks5sqUEWgaJpZM4Pqk9M> .

-- Thiranja Prasad Babarenda Gamage, PhD Research Fellow Auckland Bioengineering Institute The University of Auckland New Zealand Phone: +64 (0) 93737599 ext 84651