Package Details: deal-ii 9.6.2-1

Git Clone URL: https://aur.archlinux.org/deal-ii.git (read-only, click to copy)
Package Base: deal-ii
Description: An Open Source Finite Element Differential Equations Analysis Library
Upstream URL: https://www.dealii.org/
Keywords: fem pde science
Licenses: LGPL-2.1-or-later
Submitter: coincoin
Maintainer: coincoin (drwells)
Last Packager: drwells
Votes: 15
Popularity: 0.000023
First Submitted: 2013-09-11 11:11 (UTC)
Last Updated: 2024-12-24 03:10 (UTC)

Dependencies (28)

Required by (0)

Sources (1)

Latest Comments

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juliandoerner commented on 2021-12-11 12:35 (UTC) (edited on 2021-12-11 12:56 (UTC) by juliandoerner)

By the recent update of tbb from version 2021.3.0 to 2021.4.0 deal-ii no longer builds software using for example mesh-worker, which relies on deprecated interfaces. This is caused by the revamp of tbb and already know to the authors of deal-ii, see here.

Downgrading tbb helps at the moment. Let me know if I can help in any other way.

carlosal1015 commented on 2021-08-06 20:31 (UTC) (edited on 2021-08-06 22:55 (UTC) by carlosal1015)

Thanks for add optional dependency intel-mkl, I do not report any errors but I canceled in 75% because filled my memory (because I was BUILDDIR=/tmp/makepkg in /etc/makepkg.conf). Now, we have:

-- Found LAPACK: /opt/intel/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/mkl/lib/intel64_lin/libmkl_core.so;/usr/lib/libgomp.so;-lpthread;-lm;-ldl;-lpthread;-lm;-ldl  
--   LAPACK_LIBRARIES: /opt/intel/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/mkl/lib/intel64_lin/libmkl_core.so;/usr/lib/libgomp.so;-lpthread;-lm;-ldl;-lpthread;-lm;-ldl;/opt/intel/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/mkl/lib/intel64_lin/libmkl_core.so;/usr/lib/libgomp.so;-lpthread;-lm;-ldl
--   LAPACK_LINKER_FLAGS: 
--   LAPACK_INCLUDE_DIRS: /opt/intel/mkl/include
--   LAPACK_USER_INCLUDE_DIRS: /opt/intel/mkl/include

First attempt is here. Second attempt is here. In the second attempt I log in tty2 and enable in /etc/makepkgconf #BUILDDIR=/tmp/makepkg, MAKEFLAGS="-j$(nproc)" (disabled build on ram and use all cores) but it stopped in 30% with cpu full, showed some 20 lines of messages (no related with cmake or deal-ii installation) about address errors and kernel modules, I do not saved this messages, and force reboot. For now, that was my attempt, do not worry because is due a limit resources.

drwells commented on 2021-08-06 17:48 (UTC)

@carlosal1015 This should now work with MKL - I followed the workaround I mentioned in issue 12435.

carlosal1015 commented on 2021-08-04 23:25 (UTC)

Thanks a lot :-), when I type pacman -Ql intel-mkl shows me /opt/intel/mkl/include/mkl.h.

drwells commented on 2021-08-04 20:32 (UTC)

You're welcome. That gist is very helpful.

  1. I think you figured it out but PETSc does not support compiling with one MPI version and linking against another so that should work.
  2. This is a known bug in deal.II's configuration script: see

https://github.com/dealii/dealii/issues/12435

In particular, we expect CMake to set LAPACK_INCLUDE_DIRS but it does not.

I can try to help but I am not that familiar with MKL. Do you know where the mkl.h header is installed? The test fails because it is not on the default search path.

carlosal1015 commented on 2021-08-04 19:24 (UTC) (edited on 2021-08-04 19:26 (UTC) by carlosal1015)

Thank you very much for the quick answer. I am sharing the log installation here. Since it is an unsupported (yet) package, I removed intel-openmpi. Then, I run yay -Syu deal-ii --noconfirm 2>&1 | tee error1.txt and I looked an error: #error "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version" in the line 1301 of error1.txt. After I uninstall pets-complex from arch4edu repository and I run again yay -Syu deal-ii --noconfirm 2>&1 | tee error2.txt. I looked in the line 348 of error2.txt: Use other than Intel MKL implementation of BLAS/LAPACK (consult CMakeFiles/CMakeError.log for further information). I looked also that LAPACK_LIBRARIES are pointing to intel-mkl and finally finish with:

 74%] Linking CXX shared library ../lib/libdeal_II.g.so
collect2: fatal error: ld terminated with signal 9 [Killed]
compilation terminated.
make[2]: *** [source/CMakeFiles/deal_II.g.dir/build.make:1031: lib/libdeal_II.g.so.9.3.1] Error 1
make[1]: *** [CMakeFiles/Makefile2:1684: source/CMakeFiles/deal_II.g.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 74%] Building CXX object source/matrix_free/CMakeFiles/obj_matrix_free_release.dir/shape_info.cc.o
[ 74%] Building CXX object source/non_matching/CMakeFiles/obj_non_matching_release.dir/immersed_surface_quadrature.cc.o
[ 74%] Building CXX object source/matrix_free/CMakeFiles/obj_matrix_free_release.dir/task_info.cc.o
[ 74%] Built target obj_non_matching_release
[ 75%] Building CXX object source/matrix_free/CMakeFiles/obj_matrix_free_release.dir/vector_data_exchange.cc.o
[ 75%] Built target obj_matrix_free_release

Finally I append the file /tmp/makepkg/deal-ii/src/build/detailed.log, /tmp/makepkg/deal-ii/src/build/CMakeFiles/CMakeError.log. If after I will try to remove the intel residue with lapack, etc, I'm sure it would build, surely someone else could confirm the successful compilation.

drwells commented on 2021-08-04 17:26 (UTC)

Thanks - I missed the intel-tbb -> tbb rename.

Issues with intel's MPI may be outside the scope of this PKGBUILD but if you have a bug report we can always send it upstream.

carlosal1015 commented on 2021-08-04 17:01 (UTC)

Thank you very much @drwells, @bartus for your valuable time on the update, I am having some error related to some MPI redefinitions using intel-mpi (orphan aur package). If this next attempt fails, I will remove intel-mpi.

intel-tbb was replaced by tbb a few months ago. I'm limiting my cpus cores and writing the log with tee command to post here in a few hours.

drwells commented on 2021-08-04 15:19 (UTC)

9.3.1 is now officially out so I have updated the AUR script.

Please post if you have problems - I will try to be more available for resolving issues. Special thanks to @bartus for the help (fortunately we no longer require patches so SRCDEST should work automatically).

archaeal commented on 2021-01-27 19:24 (UTC)

I was able to build deal.ii, but had two of the tests failed, one with p4est and the other with scalapack:

The following tests FAILED:
     6 - p4est.debug (Failed)
    16 - scalapack.debug (Failed)

The output from p4est:

./p4est.debug: symbol lookup error: ./p4est.debug: undefined symbol: _ZN6dealii8parallel11distributed13TriangulationILi2ELi2EEC1EP19ompi_communicator_tNS_13TriangulationILi2ELi2EE13MeshSmoothingENS3_8SettingsE

The output from scalapack:

./scalapack.debug: symbol lookup error: ./scalapack.debug: undefined symbol: _ZN6dealii15ScaLAPACKMatrixIdEC1EjRKSt10shared_ptrIKNS_9Utilities3MPI11ProcessGridEEjNS_13LAPACKSupport8PropertyE

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