Dear community
after having solved the Trilinos issue, deal.ii works just fine. However,
all examples that involve PETSc cannot run, of course,
since deal.ii was configured with the option DEAL_II_WITH_PETSC = OFF
I did attempt at installing PETSc through Candi, with the following outcome:
*
********************************************************************************
*candi tries now to download, configure, build and install:*
*Project: deal.II-toolchain*
*Platform: deal.II-toolchain/platforms/supported/macos.platform*
*Fetching petsc 3.16.4*
*Verifying petsc-lite-3.16.4.tar.gz*
*petsc-lite-3.16.4.tar.gz: OK(md5)*
*petsc-lite-3.16.4.tar.gz already downloaded and verified.*
*Unpacking petsc-lite-3.16.4.tar.gz*
*Building petsc 3.16.4*
*=============================================================================================*
* Configuring PETSc to compile on your system
*
*=============================================================================================*
*=============================================================================================
***** WARNING: CPPFLAGS (set to
-I/opt/homebrew/opt/openblas/include) found in environment variables -
ignoring
use ./configure CPPFLAGS=$CPPFLAGS if you really want to use that
value ******
=============================================================================================
=============================================================================================
***** WARNING: LDFLAGS (set to
-L/opt/homebrew/opt/openblas/lib) found in environment variables -
ignoring
use ./configure LDFLAGS=$LDFLAGS if you really want to use that
value ******
=============================================================================================
=============================================================================================
***** WARNING: You have a version of GNU make older
than 4.0. It will work,
but may not
support all the parallel testing options. You can install the
latest GNU make with your package manager, such as
brew or macports, or use
the
--download-make option to get the latest GNU make *****
=============================================================================================
TESTING: checklsame from
config.packages.BlasLapack(config/BuildSystem/config/packages/BlasLapack.py:662)
********************************************************************************
* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
details):*
*-------------------------------------------------------------------------------*
*The BLAS/LAPACK libraries
-Wl,-rpath,/opt/homebrew/Cellar/open-mpi/4.1.4_2/lib
-L/opt/homebrew/Cellar/open-mpi/4.1.4_2/lib
-Wl,-rpath,/opt/homebrew/opt/libevent/lib -L/opt/homebrew/opt/libevent/lib
-Wl,-rpath,/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/12
-L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/12
-Wl,-rpath,/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/current/gcc
-L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/current/gcc
-Wl,-rpath,/usr/local/lib -L/usr/local/lib
-Wl,-rpath,/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/current
-L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/current -llapack -lblas -llapack
-lblas -lc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
-lgfortran -lemutls_w -lquadmath*
*cannot be used with a shared library*
*Either run ./configure with --with-shared-libraries=0 or use a different
BLAS/LAPACK library*
*********************************************************************************
I could indeed figure out that home-brew openblas is present at
*/opt/homebrew/opt/openblas* and the error message suggests what should be
done
*./configure with --with-shared-libraries=0*
but I cannot see how and where I should use such a command. Any help
appreciated.
Erkin
24 Ocak 2023 Salı tarihinde saat 09:39:39 UTC+1 itibarıyla erkin yildiz
şunları yazdı:
> Dear Heister,
>
> Thank you for your reply. After I have applied second way that you
> recommended, deal.ii is working right now without any problem.
>
> Best regards,
> Erkin
>
> Timo Heister <hei...@clemson.edu>, 17 Oca 2023 Sal, 22:08 tarihinde şunu
> yazdı:
>
>> Erkin,
>> Please take a look at the conversation at
>> https://github.com/dealii/candi/issues/309#issuecomment-1295958250
>> that discusses the issue. You might be able to compile by going back
>> to the older version as mentioned in the comment.
>>
>> Alternatively, you could disable Trilinos explicit instantiations:
>>
>> https://github.com/dealii/candi/blob/beef9258162adcdc80ed0d8166600d5009640332/deal.II-toolchain/packages/trilinos.package#L211
>>
>> Please let us know your results by posting in that issue!
>>
>> On Tue, Jan 17, 2023 at 1:38 PM erkin yildiz <e.yi...@unibs.it> wrote:
>> >
>> > Dear community I have been trying to install deal. ii on my new
>> MacBookPRO M2 OSX 13. 1 (22C65) following the instructions at the webpage
>> https: //github. com/dealii/dealii/wiki/Apple-ARM-M1-OSX After brewing brew
>> install cmake open-mpi gcc@ 11
>> > ZjQcmQRYFpfptBannerStart
>> > This Message Is From an External Sender
>> > Use caution when opening links or attachments if you do not recognize
>> the sender.
>> >
>> > ZjQcmQRYFpfptBannerEnd
>> > Dear community
>> >
>> > I have been trying to install deal.ii on my new MacBookPRO M2 OSX 13.1
>> (22C65)
>> > following the instructions at the webpage
>> https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX
>> >
>> > After brewing
>> >
>> > brew install cmake open-mpi gcc@11
>> >
>> > (I tried also gcc@12, BTW) deal.ii has been installed according to
>> >
>> > git clone https://github.com/dealii/candi
>> > cd candi
>> > ./candi.sh -j 8 --packages="hdf5 p4est trilinos dealii"
>> >
>> > An error occurs in installing Trilinos, namely
>> >
>> > [ … ]
>> >
>> > [ 69%] Linking CXX shared library libstratimikosamesos2.dylib
>> >
>> > [ 69%] Linking CXX shared library libstratimikosbelos.dylib
>> >
>> > Undefined symbols for architecture arm64:
>> >
>> > "Amesos2::TachoSolver<Tpetra::CrsMatrix<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> >, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > >::TachoSolver(Teuchos::RCP<Tpetra::CrsMatrix<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const>, Teuchos::RCP<Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > >, Teuchos::RCP<Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const>)", referenced from:
>> >
>> > Amesos2::create_solver_with_supported_type<Amesos2::TachoSolver,
>> Tpetra::CrsMatrix<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> >, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > >::apply(Teuchos::RCP<Tpetra::CrsMatrix<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const>, Teuchos::RCP<Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > >, Teuchos::RCP<Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const>) in Thyra_Amesos2LinearOpWithSolveFactory.cpp.o
>> >
>> > "Amesos2::KLU2<Tpetra::CrsMatrix<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> >, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > >::KLU2(Teuchos::RCP<Tpetra::CrsMatrix<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const>, Teuchos::RCP<Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > >, Teuchos::RCP<Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const>)", referenced from:
>> >
>> > Amesos2::create_solver_with_supported_type<Amesos2::KLU2,
>> Tpetra::CrsMatrix<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> >, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > >::apply(Teuchos::RCP<Tpetra::CrsMatrix<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const>, Teuchos::RCP<Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > >, Teuchos::RCP<Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const>) in Thyra_Amesos2LinearOpWithSolveFactory.cpp.o
>> >
>> > ld: symbol(s) not found for architecture arm64
>> >
>> > clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>> >
>> > make[2]: ***
>> [packages/stratimikos/adapters/amesos2/src/libstratimikosamesos2.13.2.dylib]
>> Error 1
>> >
>> > make[1]: ***
>> [packages/stratimikos/adapters/amesos2/src/CMakeFiles/stratimikosamesos2.dir/all]
>>
>> Error 2
>> >
>> > make[1]: *** Waiting for unfinished jobs....
>> >
>> > Undefined symbols for architecture arm64:
>> >
>> > "Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> >::getNumVectors() const", referenced from:
>> >
>> > Tpetra::MatrixMarket::Writer<Tpetra::CrsMatrix<float, int, long
>> long, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial,
>> Kokkos::HostSpace> > >::writeDense(std::__1::basic_ostream<char,
>> std::__1::char_traits<char> >&, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const&, std::__1::basic_string<char, std::__1::char_traits<char>,
>> std::__1::allocator<char> > const&, std::__1::basic_string<char,
>> std::__1::char_traits<char>, std::__1::allocator<char> > const&,
>> Teuchos::RCP<Teuchos::basic_FancyOStream<char, std::__1::char_traits<char>
>> > > const&, Teuchos::RCP<Teuchos::basic_FancyOStream<char,
>> std::__1::char_traits<char> > > const&) in
>> Thyra_BelosLinearOpWithSolve.cpp.o
>> >
>> > Tpetra::MatrixMarket::Writer<Tpetra::CrsMatrix<float, int, long
>> long, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial,
>> Kokkos::HostSpace> > >::writeDenseHeader(std::__1::basic_ostream<char,
>> std::__1::char_traits<char> >&, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const&, std::__1::basic_string<char, std::__1::char_traits<char>,
>> std::__1::allocator<char> > const&, std::__1::basic_string<char,
>> std::__1::char_traits<char>, std::__1::allocator<char> > const&,
>> Teuchos::RCP<Teuchos::basic_FancyOStream<char, std::__1::char_traits<char>
>> > > const&, Teuchos::RCP<Teuchos::basic_FancyOStream<char,
>> std::__1::char_traits<char> > > const&) in
>> Thyra_BelosLinearOpWithSolve.cpp.o
>> >
>> > Tpetra::MatrixMarket::Writer<Tpetra::CrsMatrix<float, int, long
>> long, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial,
>> Kokkos::HostSpace> > >::writeDenseColumn(std::__1::basic_ostream<char,
>> std::__1::char_traits<char> >&, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const&, Teuchos::RCP<Teuchos::basic_FancyOStream<char,
>> std::__1::char_traits<char> > > const&,
>> Teuchos::RCP<Teuchos::basic_FancyOStream<char, std::__1::char_traits<char>
>> > > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>> >
>> > "Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> >::getLocalLength() const", referenced from:
>> >
>> > Tpetra::MatrixMarket::Writer<Tpetra::CrsMatrix<float, int, long
>> long, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial,
>> Kokkos::HostSpace> > >::writeDenseColumn(std::__1::basic_ostream<char,
>> std::__1::char_traits<char> >&, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const&, Teuchos::RCP<Teuchos::basic_FancyOStream<char,
>> std::__1::char_traits<char> > > const&,
>> Teuchos::RCP<Teuchos::basic_FancyOStream<char, std::__1::char_traits<char>
>> > > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>> >
>> > "Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> >::getGlobalLength() const", referenced from:
>> >
>> > Tpetra::MatrixMarket::Writer<Tpetra::CrsMatrix<float, int, long
>> long, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial,
>> Kokkos::HostSpace> > >::writeDenseHeader(std::__1::basic_ostream<char,
>> std::__1::char_traits<char> >&, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const&, std::__1::basic_string<char, std::__1::char_traits<char>,
>> std::__1::allocator<char> > const&, std::__1::basic_string<char,
>> std::__1::char_traits<char>, std::__1::allocator<char> > const&,
>> Teuchos::RCP<Teuchos::basic_FancyOStream<char, std::__1::char_traits<char>
>> > > const&, Teuchos::RCP<Teuchos::basic_FancyOStream<char,
>> std::__1::char_traits<char> > > const&) in
>> Thyra_BelosLinearOpWithSolve.cpp.o
>> >
>> > "Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> >::get1dCopy(Teuchos::ArrayView<float> const&, unsigned long) const",
>> referenced from:
>> >
>> > Tpetra::MatrixMarket::Writer<Tpetra::CrsMatrix<float, int, long
>> long, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial,
>> Kokkos::HostSpace> > >::writeDenseColumn(std::__1::basic_ostream<char,
>> std::__1::char_traits<char> >&, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const&, Teuchos::RCP<Teuchos::basic_FancyOStream<char,
>> std::__1::char_traits<char> > > const&,
>> Teuchos::RCP<Teuchos::basic_FancyOStream<char, std::__1::char_traits<char>
>> > > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>> >
>> > "Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> >::getVector(unsigned long) const", referenced from:
>> >
>> > Tpetra::MatrixMarket::Writer<Tpetra::CrsMatrix<float, int, long
>> long, Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial,
>> Kokkos::HostSpace> > >::writeDense(std::__1::basic_ostream<char,
>> std::__1::char_traits<char> >&, Tpetra::MultiVector<float, int, long long,
>> Kokkos::Compat::KokkosDeviceWrapperNode<Kokkos::Serial, Kokkos::HostSpace>
>> > const&, std::__1::basic_string<char, std::__1::char_traits<char>,
>> std::__1::allocator<char> > const&, std::__1::basic_string<char,
>> std::__1::char_traits<char>, std::__1::allocator<char> > const&,
>> Teuchos::RCP<Teuchos::basic_FancyOStream<char, std::__1::char_traits<char>
>> > > const&, Teuchos::RCP<Teuchos::basic_FancyOStream<char,
>> std::__1::char_traits<char> > > const&) in
>> Thyra_BelosLinearOpWithSolve.cpp.o
>> >
>> > ld: symbol(s) not found for architecture arm64
>> >
>> > clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>> >
>> > make[2]: ***
>> [packages/stratimikos/adapters/belos/src/libstratimikosbelos.13.2.dylib]
>> Error 1
>> >
>> > make[1]: ***
>> [packages/stratimikos/adapters/belos/src/CMakeFiles/stratimikosbelos.dir/all]
>>
>> Error 2
>> >
>> > make: *** [all] Error 2
>> >
>> > Failure with exit status: 2
>> >
>> > Exit message: There was a problem building trilinos 13-2-0.
>> >
>> >
>> >
>> >
>> > Can anyone provide me some way to address the issue? Is it perhaps
>> related to the version of Trilinos? Can I install a former version (and in
>> case, how to?)?
>> >
>> > Many thanks
>> >
>> > Erkin
>> >
>> >
>> >
>> >
>> >
>> > Informativa sulla Privacy: https://www.unibs.it/it/node/1452
>> >
>> > --
>> > The deal.II project is located at http://www.dealii.org/
>> > For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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>> .
>>
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>>
>> --
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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>>
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>> .
>>
>
>
> Informativa sulla Privacy: https://www.unibs.it/it/node/1452
>
--
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<https://www.unibs.it/it/node/1452>
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