[petsc-users] Rebuilding libmesh

[Fande Kong]

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
"

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,
> >
> >
> > On Wed, Mar 18, 2020 at 2:55 PM Lin <y7762516 at gmail.com> wrote:
> >
> >> Hi, all,
> >>
> >>  I met a problem with
> >>
> >> error: *** PETSc was not found, but --enable-petsc-required was
> specified.
> >>
> >> when I reinstalled MOOSE. However, I had been using MOOSE with no issues
> >> previously. Does someone know how to solve it? My system is Ubuntu
> 18.04.
> >>
> >> The error is listed as following:
> >>
> >> Found valid MPI installation...
> >>
> >> note: using /opt/moose/mpich-3.3/gcc-9.2.0/include/mpi.h
> >>
> >> checking mpi.h usability... yes
> >>
> >> checking mpi.h presence... yes
> >>
> >> checking for mpi.h... yes
> >>
> >> checking
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt//include/petscversion.h
> >> usability... yes
> >>
> >> checking
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt//include/petscversion.h
> >> presence... yes
> >>
> >> checking for
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt//include/petscversion.h...
> >> yes
> >>
> >> <<< Found PETSc 3.11.4 installation in /opt/moose/petsc-3.11.4/mpich-3.3
> >> _gcc-9.2.0-opt ... >>>
> >>
> >> checking whether we can compile a trivial PETSc program... no
> >>
> >> checking for TAO support via PETSc... no
> >>
> >> configure: error: *** PETSc was not found, but --enable-petsc-required
> >> was specified.
> >> make: *** No targets specified and no makefile found.  Stop.
> >>
> >>
> >>
> >> Besides, I attached my libMesh configure log file in the email.
> >>
> >> Regards,
> >> Lin
> >>
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> >>
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