Step-17 -PETSc () -- MPI -- Versions Conflict on Mac

[Ahmed Galal]

I tried to run Step-17 but I got the following error. Given I have two versions of PETSc. I use the other one for another software.

I googled and found that the issue is solved by commenting out the line "ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")" in "cmake/checks/check_01_compiler_features.cmake", make test, worked.
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https://groups.google.com/u/1/g/dealii/c/JxUOyd_4eFM?pli=1https://groups.google.com/u/1/g/dealii/c/JxUOyd_4eFM?pli=1

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Any suggestions for how to get around that in the new version of DealII.9.3 as I could not find a .cmake similar file to edit?

Thanks in advance!
Ahmed

Error:
------------------------

PETSc Error --- Application was linked against both OpenMPI and MPICH based MPI libraries and will not run correctly

[----] *** Process received signal ***

[----]  Signal: Segmentation fault: 11 (11)

[----]  Signal code: Address not mapped (1)

[----] Failing at address: 0x68

[----]  [ 0] 0   libsystem_platform.dylib            0x00007fff2041cd7d _sigtramp + 29

[----]  [ 1] 0   ???                                 0x0000000060b9d791 0x0 + 1622792081

[----]  [ 2] 0   libsystem_c.dylib                   0x00007fff202edfcc vfprintf_l + 28

[----]  [ 3] 0   libsystem_c.dylib                   0x00007fff202e69a2 fprintf + 160

[----]  [ 4] 0   libpetsc.3.15.dylib                 0x000000014c224f0d PetscVFPrintfDefault + 685

 [ 5] 0   libpetsc.3.15.dylib                 0x000000014c2280d6 PetscFPrintf + 726

 [ 6] 0   libpetsc.3.15.dylib                 0x000000014c21d537 PetscErrorPrintfDefault + 375

[ 7] 0   libpetsc.3.15.dylib                 0x000000014c21d66a PetscTraceBackErrorHandler + 154

 [ 8] 0   libpetsc.3.15.dylib                 0x000000014c21713c PetscError + 716

 [ 9] 0   libslepc.3.15.dylib                 0x000000014bc9cc8c SlepcInitialize + 428

 [10] 0   libdeal_II.g.9.3.0.dylib            0x00000001151ae627 _ZN6dealii9Utilities3MPI16MPI_InitFinalizeC2ERiRPPcj + 135

 [11] 0   libdeal_II.g.9.3.0.dylib            0x00000001151aece9 _ZN6dealii9Utilities3MPI16MPI_InitFinalizeC1ERiRPPcj + 9

[12] 0   step-17                             0x000000010f244892 main + 82

 [13] 0   libdyld.dylib                       0x00007fff203f2f3d start + 1

[14] 0   ???                                 0x0000000000000001 0x0 + 1

 *** End of error message ***

make[3]: *** [CMakeFiles/run] Segmentation fault: 11

make[2]: *** [CMakeFiles/run.dir/all] Error 2

make[1]: *** [CMakeFiles/run.dir/rule] Error 2

make: *** [run] Error 2

bash-3.2$ 

[Wolfgang Bangerth]

On 10/23/21 1:01 PM, Ahmed Galal wrote:
> PETSc Error --- Application was linked against both OpenMPI and MPICH based
> MPI libraries and will not run correctly

This is the error you need to address.

Best
W.



--
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Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

[Ahmed Galal]

Do you have a suggestion for how to address it?

Thanks!

[Wolfgang Bangerth]

On 10/25/21 5:11 AM, Ahmed Galal wrote:
> Do you have a suggestion for how to address it?

Ahmed,
the error says that you linked deal.II against one MPI implementation
and one of the other libraries you are using (PETSc, Trilinos, etc)
against another MPI implementation. That can't work.

It is generally a bad idea to have two MPI implementations on one
machine to begin with. I would remove one (typically either MPICH or
OpenMPI) and start the entire installation procedure from scratch.