"PETSc installation does not include a copy of the hypre package" while running the step-40 program

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Ihar Suvorau

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Jan 25, 2020, 3:29:32 PM1/25/20
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Software:
  • macOS Catalina 10.15.2
  • deal.ii 9.1.1
  • PETSc 3.12
Question:

Hey, does somebody know a potential reason for this message while running a well-compiled step-40 program:

ihar@husky build3 % ./step-40


Running with PETSc on 1 MPI rank(s)...

Cycle 0:

  Number of active cells:       1024

  Number of degrees of freedom: 4225


-------------------------------------------------------


An error occurred in line <543> of file </Users/ihar/lib/dealii-9.1.1/source/lac/petsc_precondition.cc> in function

   void dealii::PETScWrappers::PreconditionBoomerAMG::initialize(const dealii::PETScWrappers::MatrixBase &, const dealii::PETScWrappers::PreconditionBoomerAMG::AdditionalData &)

The violated condition was:

   false

Additional information:

   Your PETSc installation does not include a copy of the hypre package necessary for this preconditioner.


Stacktrace:

-----------

#0  2   libdeal_II.g.9.1.1.dylib            0x000000011188b86f _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE + 95: 2   libdeal_II.g.9.1.1.dylib            0x000000011188b86f _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE

#1  3   step-40                             0x000000010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266: 3   step-40                             0x000000010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv

#2  4   step-40                             0x000000010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv + 451: 4   step-40                             0x000000010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv

#3  5   step-40                             0x000000010642e23a main + 106: 5   step-40                             0x000000010642e23a main

#4  6   libdyld.dylib                       0x00007fff6350f7fd start + 1: 6   libdyld.dylib                       0x00007fff6350f7fd start

--------------------------------------------------------


[husky:92536] *** Process received signal ***

[husky:92536] Signal: Abort trap: 6 (6)

[husky:92536] Signal code:  (0)

[husky:92536] [ 0] 0   libsystem_platform.dylib            0x00007fff6370842d _sigtramp + 29

[husky:92536] [ 1] 0   ???                                 0x00007ffee97d8838 0x0 + 140732815738936

[husky:92536] [ 2] 0   libsystem_c.dylib                   0x00007fff635dda1c abort + 120

[husky:92536] [ 3] 0   libdeal_II.g.9.1.1.dylib            0x00000001119ec74d _ZN6dealii18deal_II_exceptions9internals5abortERKNS_13ExceptionBaseE + 205

[husky:92536] [ 4] 0   libdeal_II.g.9.1.1.dylib            0x000000010de0f63f _ZN6dealii18deal_II_exceptions9internals20issue_error_noreturnINS_18StandardExceptions10ExcMessageEEEvNS1_17ExceptionHandlingEPKciS7_S7_S7_T_ + 223

[husky:92536] [ 5] 0   libdeal_II.g.9.1.1.dylib            0x000000011188b86f _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE + 95

[husky:92536] [ 6] 0   step-40                             0x000000010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266

[husky:92536] [ 7] 0   step-40                             0x000000010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv + 451

[husky:92536] [ 8] 0   step-40                             0x000000010642e23a main + 106

[husky:92536] [ 9] 0   libdyld.dylib                       0x00007fff6350f7fd start + 1

[husky:92536] *** End of error message ***



The thing is that I've compiled PETSC with the "--download-hypre=1" option and there is a compiled library with the name "libHYPRE-2.18.2.dylib" alongside "libpetsc.3.12.3.dylib" and others in the folder for my architecture "arch-darwin-c-debug". Environment variables "PETSC_DIR" and "PETSC_ARCH" all point to the correct folder like in the instruction at https://www.dealii.org/developer/external-libs/petsc.html. 

Did I miss something?

I'm trying to install all the packages with "dealii/candi", but PETSc compilation fails there also, but for a different reason though (https://github.com/dealii/candi/issues/133).

luca.heltai

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Jan 26, 2020, 4:48:21 AM1/26/20
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Did you try the pre-compiled deal.II package?

Both

dealii-9.1.1-clang-9.0.0.dmg

and

dealii-9.1.1-catalina-haswell-ro.dmg.zip


from https://github.com/dealii/dealii/releases/tag/v9.1.1

should work.

Luca.
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Ihar Suvorau

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Jan 26, 2020, 6:59:05 AM1/26/20
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Not yet, I have a running version via docker images though. I'll try the bundle also, thank you, before I was thinking that it shouldn't support parallel programming, but now I see it is configured with "DEAL_II_WITH_MPI set up with external dependencies" and "DEAL_II_WITH_PETSC set up with external dependencies" and has all packages installed.

But I'm still interested in solving the issue with "Your PETSc installation does not include a copy of the hypre package necessary for this preconditioner" when I do have the hypre package installed via the option "--download-hypre=1" while configuring PETSc. 

On Sunday, January 26, 2020 at 11:48:21 AM UTC+2, luca.heltai wrote:
Did you try the pre-compiled deal.II package?

Both

dealii-9.1.1-clang-9.0.0.dmg

and

dealii-9.1.1-catalina-haswell-ro.dmg.zip


from https://github.com/dealii/dealii/releases/tag/v9.1.1

should work.

Luca.

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David Wells

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Jan 27, 2020, 10:42:39 AM1/27/20
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Hi Ihar,

This sounds like something has gone wrong inside either PETSc's or
deal.II's build process. Would you please show us a copy of PETSc's
configure.log?

Thanks,
David
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Ihar Suvorau

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Jan 27, 2020, 5:59:18 PM1/27/20
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Sure, attaching a file, please.


On Monday, January 27, 2020 at 5:42:39 PM UTC+2, David Wells wrote:
Hi Ihar,

This sounds like something has gone wrong inside either PETSc's or
deal.II's build process. Would you please show us a copy of PETSc's
configure.log?

Thanks,
David

configure.log

David Wells

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Jan 28, 2020, 9:18:44 AM1/28/20
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Hi Ihar,

It looks like nothing went wrong with PETsc. Would you please also
send a copy of deal.II's detailed.log and, if available,
CMakeCache.txt from the build directory?

Thanks,
David
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Ihar Suvorau

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Jan 28, 2020, 10:14:43 AM1/28/20
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Hi, David,

okay, please, attaching these files also.

On Tuesday, January 28, 2020 at 4:18:44 PM UTC+2, David Wells wrote:
Hi Ihar,

It looks like nothing went wrong with PETsc. Would you please also
send a copy of deal.II's detailed.log and, if available,
CMakeCache.txt from the build directory?

Thanks,
David

detailed.log
CMakeCache.txt

David Wells

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Jan 30, 2020, 11:02:56 AM1/30/20
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Hi Ihar,

I'm not sure what went wrong - everything looks right except that
deal.II did not find hypre.

Could you also send

/Users/ihar/lib/petsc-3.12.3/arch-darwin-c-debug/include/petscconf.h

to check something else?
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Ihar Suvorau

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Jan 30, 2020, 11:05:11 AM1/30/20
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Hi, David,

yes, here it is.


On Thursday, January 30, 2020 at 6:02:56 PM UTC+2, David Wells wrote:
Hi Ihar,

I'm not sure what went wrong - everything looks right except that
deal.II did not find hypre.

Could you also send

/Users/ihar/lib/petsc-3.12.3/arch-darwin-c-debug/include/petscconf.h

to check something else?


petscconf.h

David Wells

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Jan 30, 2020, 11:23:11 AM1/30/20
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OK, that also looks right. Could you also send me, from deal.II's
build directory,

cmake/config/deal.IIConfig.cmake

?
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Ihar Suvorau

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Jan 30, 2020, 11:29:21 AM1/30/20
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I believe this is the correct file. I see the line "SET(DEAL_II_PETSC_WITH_HYPRE FALSE)” in the file.

deal.IIConfig.cmake

David Wells

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Jan 30, 2020, 11:49:24 AM1/30/20
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Yup - deal.II did not pick up HYPRE or MUMPS even though you
configured PETSc with both (which can be seen by checking the end of
PETSc's configure log).

I can only think of one more thing to check - try deleting
CMakeCache.txt in deal.II's build directory and rerun CMake to see if
the cache got stuck in a wrong state. Could you try that?



On Thu, Jan 30, 2020 at 11:29 AM Ihar Suvorau <ihar.s...@gmail.com> wrote:
>
> I believe this is the correct file. I see the line "SET(DEAL_II_PETSC_WITH_HYPRE FALSE)” in the file.
>
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>
>
> Best,
> Ihar Suvorau
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