Rebuilding libmesh

[Lin]

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

[Alexander Lindsay]

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 -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,

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[Jed Brown]

Alexander Lindsay <alexlin...@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.

>> <https://groups.google.com/d/msgid/moose-users/db12322c-eae6-4ed4-b54f-3ab5e118f466%40googlegroups.com?utm_medium=email&utm_source=footer>
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[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,

To view this discussion on the web visit https://groups.google.com/d/msgid/moose-users/87r1xpw71l.fsf%40jedbrown.org.

[Jed Brown]

Fande Kong <fdko...@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.

[Lin]

Hi, Fande,

Thank you so much, it works when I uninstall the GCC in Linux-brew.

Regards,

Lin

Fande Kong wrote：

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