[petsc-users] Rebuilding libmesh

[Jed Brown]

Fande Kong <fdkong.jd at gmail.com> writes:

> HI Lin,
>
> Do you have a home-brew installed MPI?
>
> "
> configure:6076: mpif90 -v >&5
> mpifort for MPICH version 3.3
> Reading specs from
> /home/lin/.linuxbrew/Cellar/gcc/5.5.0_7/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.5.0/specs

So "mpich-3.3_gcc-9.2.0" uses gcc-5.5.0?  Was it also like that when you
configured PETSc, or is this a result of changing environment variables?

As usual, configure.log would have helped answer these sorts of questions.

> "
>
> MOOSE environment package should carry everything you need: compiler, mpi,
> and petsc.
>
> You could home-brew uninstall your mpi, and retry.
>
> Thanks,
>
> Fande,
>
> On Wed, Mar 18, 2020 at 5:57 PM Jed Brown <jed at jedbrown.org> wrote:
>
>> Alexander Lindsay <alexlindsay239 at gmail.com> writes:
>>
>> > Does anyone have a suggestion for this compilation error from
>> petscconf.h?
>> > Sorry this is with a somewhat old PETSc version:
>> >
>> > configure:34535: checking whether we can compile a trivial PETSc program
>> > configure:34564: mpicxx -c  -std=gnu++11
>>
>> What do you get with `mpicxx --version`?
>>
>> This is usually a result of configuring PETSc with a different compiler
>> version than you use to run.
>>
>> > -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include
>> > -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt//include
>> > -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include
>> > -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include  conftest.cpp
>> >&5
>> > In file included from
>> > /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscsys.h:14:0,
>> >                  from
>> > /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscbag.h:4,
>> >                  from
>> > /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petsc.h:5,
>> >                  from conftest.cpp:144:
>> >
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscconf.h:85:36:
>> > error: expected '}' before '__attribute'
>> >  #define PETSC_DEPRECATED_ENUM(why) __attribute((deprecated))
>> >                                     ^
>> >
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:430:76:
>> > note: in expansion of macro 'PETSC_DEPRECATED_ENUM'
>> >  #define KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED
>> KSP_DIVERGED_PCSETUP_FAILED
>> > PETSC_DEPRECATED_ENUM("Use KSP_DIVERGED_PC_FAILED (since v3.11)")
>> >
>> > ^
>> >
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:452:15:
>> > note: in expansion of macro 'KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED'
>> >                KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED  = -11,