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Package Details: deal-ii 9.6.0-1

Package Actions

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:	0.000464
First Submitted:	2013-09-11 11:11 (UTC)
Last Updated:	2024-08-23 22:02 (UTC)

Dependencies (28)

boost (boost-git^AUR)
kokkos^AUR (trilinos^AUR)
cmake (cmake-git^AUR) (make)
adol-c^AUR (adol-c-git^AUR, python-adolc^AUR) (optional) – automatic differentiation library
arpack (arpack-git^AUR) (optional) – Fortran77 subroutines designed to solve large scale eigenvalue problems
assimp (assimp-git^AUR) (optional) – Library to import various well-known 3D model formats in an uniform manner
cgal (cgal-git^AUR) (optional) – Computational Geometry Algorithms Library
gmsh^AUR (gmsh-git^AUR, gmsh-bin^AUR) (optional) – An automatic 3D finite element mesh generator with pre and post-processing facilities
gsl (gsl-git^AUR) (optional) – A modern numerical library for C and C++ programmers
hdf5-openmpi (optional) – General purpose library and file format for storing scientific data
intel-mkl (intel-oneapi-mkl) (optional) – Intel Math Kernel Library
lapack (aocl-libflame-aocc^AUR, lapack-git^AUR, atlas-lapack^AUR, blas-aocl-gcc^AUR, blas-aocl-aocc^AUR, openblas-lapack^AUR, blas-mkl^AUR, aocl-libflame^AUR, blas-openblas) (optional) – Linear Algebra PACKage
metis^AUR (metis-git^AUR) (optional) – partitioning graphs, finite element meshes, fill reducing orderings for sparse matrices.
muparser (optional) – A fast math parser library
opencascade (opencascade-git^AUR, opencascade-rc^AUR, opencascade-f3d^AUR) (optional) – Open CASCADE Technology, 3D modeling & numerical simulation
openmpi (openmpi-git^AUR) (optional) – High performance message passing library (MPI)
p4est-deal-ii^AUR (optional) – The parallel forest (p4est) library, built to work with deal.II
parmetis^AUR (parmetis-git^AUR) (optional) – A parallel graph partitioning library
petsc^AUR (petsc-git^AUR, petsc-complex^AUR) (optional) – Portable, extensible toolkit for scientific computation
scalapack^AUR (optional) – subset of scalable LAPACK routines redesigned for distributed memory MIMD parallel computers
Show 8 more dependencies...

Required by (0)

Sources (1)

https://github.com/dealii/dealii/releases/download/v9.6.0/dealii-9.6.0.tar.gz

Pinned Comments

drwells commented on 2024-06-19 03:16 (UTC)

I've updated to 9.5.2 and patched SUNDIALS.

9.6 should be out in the next month or two!

Latest Comments

« First ‹ Previous 1 2 3 4 5 6 7 Next › Last »

carlosal1015 commented on 2023-07-10 15:58 (UTC) (edited on 2023-07-10 23:39 (UTC) by carlosal1015)

Many thanks. In that case I see will not easy because last week with 9.4.2 I tried built with trilinos (appending cmake_configuration_flags+=" -DDEAL_II_WITH_TRILINOS=ON), but it has a problem with bundled kokkos library.

Also I see that kokkos will not a first option because will be in conflict with trilinos and prefer last one.

When finished building deal.II both with aur kokkos and with up to date aur trilinos I will edit and attach these logs in a few hours.

Edited: Successfully with standalone kokkos or trilinos suite, any case is building fine:

drwells commented on 2023-07-10 15:09 (UTC)

Thanks for the report - I need to make MPI and Trilinos required dependencies since deal.II now requires Kokkos. I'll fix this later today or tomorrow.

carlosal1015 commented on 2023-07-10 14:24 (UTC)

With the recent upgrade 9.5.0, fails in build() stage.

drwells commented on 2022-12-03 13:52 (UTC)

This is now up-to-date with the 9.4.1 patch release.

drwells commented on 2022-04-21 16:13 (UTC)

Hi @athulshaji,

I suspect that the quick tests failed to link correctly because of a problem with one of deal.II's dependencies. Can you attach the quicktests.log file from the build or any additional terminal output here if you have it?

athulshaji commented on 2022-04-21 02:56 (UTC)

I am installing deal.ii with the following packages

deal.II configuration:

CMAKE_BUILD_TYPE: DebugRelease

BUILD_SHARED_LIBS: ON

CMAKE_INSTALL_PREFIX: /usr

CMAKE_SOURCE_DIR: /var/tmp/pamac-build-workbook/deal-ii/src/dealii-9.3.3

(version 9.3.3)

CMAKE_BINARY_DIR: /var/tmp/pamac-build-workbook/deal-ii/src/build

CMAKE_CXX_COMPILER: GNU 11.2.0 on platform Linux x86_64

/usr/bin/c++

C++ language standard: C++17

Configured Features (DEAL_II_ALLOW_BUNDLED = OFF, DEAL_II_ALLOW_AUTODETECTION = ON):

( DEAL_II_WITH_64BIT_INDICES = OFF )

( DEAL_II_WITH_ADOLC = OFF )

( DEAL_II_WITH_ARBORX = OFF )

DEAL_II_WITH_ARPACK set up with external dependencies

DEAL_II_WITH_ASSIMP set up with external dependencies

DEAL_II_WITH_BOOST set up with external dependencies

DEAL_II_WITH_COMPLEX_VALUES = ON

( DEAL_II_WITH_CUDA = OFF )

( DEAL_II_WITH_GINKGO = OFF )

DEAL_II_WITH_GMSH set up with external dependencies

DEAL_II_WITH_GSL set up with external dependencies

DEAL_II_WITH_HDF5 set up with external dependencies

DEAL_II_WITH_KOKKOS set up with external dependencies

DEAL_II_WITH_LAPACK set up with external dependencies

DEAL_II_WITH_METIS set up with external dependencies

DEAL_II_WITH_MPI set up with external dependencies

DEAL_II_WITH_MUPARSER set up with external dependencies

DEAL_II_WITH_OPENCASCADE set up with external dependencies

DEAL_II_WITH_P4EST set up with external dependencies

DEAL_II_WITH_PETSC set up with external dependencies

DEAL_II_WITH_SCALAPACK set up with external dependencies

DEAL_II_WITH_SLEPC set up with external dependencies

( DEAL_II_WITH_SUNDIALS = OFF )

( DEAL_II_WITH_SYMENGINE = OFF )

DEAL_II_WITH_TBB set up with external dependencies

DEAL_II_WITH_TRILINOS set up with external dependencies

DEAL_II_WITH_UMFPACK set up with external dependencies

DEAL_II_WITH_ZLIB set up with external dependencies

Component configuration:

( DEAL_II_COMPONENT_DOCUMENTATION = OFF )

DEAL_II_COMPONENT_EXAMPLES

( DEAL_II_COMPONENT_PACKAGE = OFF )

( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )

I am getting the following error

0% tests passed, 19 tests failed out of 19

Total Test time (real) = 62.61 sec

The following tests FAILED: 1 - step.debug (Failed) 2 - step.release (Failed) 3 - affinity.debug (Failed) 4 - mpi.debug (Failed) 5 - tbb.debug (Failed) 6 - p4est.debug (Failed) 7 - step-petsc.debug (Failed) 8 - step-slepc.debug (Failed) 9 - step-trilinos.debug (Failed) 10 - step-metis.debug (Failed) 11 - lapack.debug (Failed) 12 - umfpack.debug (Failed) 13 - gsl.debug (Failed) 14 - hdf5.debug (Failed) 15 - arpack.debug (Failed) 16 - assimp.debug (Failed) 17 - scalapack.debug (Failed) 18 - boost_zlib.debug (Failed) 19 - gmsh.debug (Failed) Errors while running CTest

Error: Some of the quick tests failed.

Please scroll up or check the file tests/quick_tests/quicktests.log for the error messages. If you are unable to fix the problems, see the FAQ or write to the mailing list linked at http://www.dealii.org

The affinity test can fail when you are linking in a library like BLAS which uses OpenMP. Even without calling any BLAS functions, OpenMP messes with the thread affinity which causes TBB to run single-threaded only. You can fix this by exporting OMP_NUM_THREADS=1. Also see GOMP_CPU_AFFINITY and OMP_PROC_BIND.

The p4est test can fail if you are running an OpenMPI version before 1.5. This is a known problem and the only work around is to update to a more recent version or use a different MPI library like MPICH.

Additional information about PETSc issues is available at: http://www.dealii.org/developer/external-libs/petsc.html

CMake Error at /var/tmp/pamac-build-workbook/deal-ii/src/dealii-9.3.3/tests/quick_tests/run.cmake:90 (MESSAGE):

make[3]: [tests/quick_tests/CMakeFiles/test.dir/build.make:71: tests/quick_tests/CMakeFiles/test] Error 1 make[2]: [CMakeFiles/Makefile2:9230: tests/quick_tests/CMakeFiles/test.dir/all] Error 2 make[1]: [CMakeFiles/Makefile2:9237: tests/quick_tests/CMakeFiles/test.dir/rule] Error 2 make: [Makefile:4069: test] Error 2 ==> ERROR: A failure occurred in check(). Aborting...

Kindly help.

drwells commented on 2022-02-28 23:48 (UTC)

@Alad thanks for reporting this - I fixed the test upstream and added a band-aid to the PKGBUILD that fixes it here as well.

Alad commented on 2022-02-27 18:01 (UTC)

I'm getting an error on the tbb quicktest:

[163%] Building CXX object tests/quick_tests/CMakeFiles/tbb.debug.dir/tbb.cc.o


tbb.debug: ******    BUILD failed    *******

===============================    OUTPUT END   ===============================
Expected stage PASSED - aborting
CMake Error at /home/archie/.cache/aurutils/sync/deal-ii/src/dealii-9.3.3/cmake/scripts/run_test.cmake:140 (MESSAGE):
  *** abort



      Start  7: step-metis.debug
 2/13 Test  #3: affinity.debug ...................   Passed    9.19 sec
      Start  8: lapack.debug
 3/13 Test  #4: mpi.debug ........................   Passed    9.19 sec
      Start  9: umfpack.debug
 4/13 Test  #7: step-metis.debug .................   Passed   10.79 sec
      Start 10: hdf5.debug
 5/13 Test  #6: step-petsc.debug .................   Passed   16.54 sec
      Start 11: arpack.debug
 6/13 Test  #8: lapack.debug .....................   Passed    7.53 sec
      Start 12: boost_zlib.debug
 7/13 Test  #2: step.release .....................   Passed   18.12 sec
      Start 13: gmsh.debug
 8/13 Test #10: hdf5.debug .......................   Passed    4.31 sec
 9/13 Test  #1: step.debug .......................   Passed   23.74 sec
10/13 Test  #9: umfpack.debug ....................   Passed   14.77 sec
11/13 Test #12: boost_zlib.debug .................   Passed    7.74 sec
12/13 Test #13: gmsh.debug .......................   Passed    7.69 sec
13/13 Test #11: arpack.debug .....................   Passed   13.26 sec

92% tests passed, 1 tests failed out of 13

Total Test time (real) =  29.80 sec

The following tests FAILED:
          5 - tbb.debug (Failed)
Errors while running CTest

***************************************************************************
**                 Error: Some of the quick tests failed.                **
***************************************************************************

Please scroll up or check the file tests/quick_tests/quicktests.log for the
error messages. If you are unable to fix the problems, see the FAQ or write
to the mailing list linked at http://www.dealii.org

CMake Error at /home/archie/.cache/aurutils/sync/deal-ii/src/dealii-9.3.3/tests/quick_tests/run.cmake:90 (MESSAGE):


make[3]: *** [tests/quick_tests/CMakeFiles/test.dir/build.make:71: tests/quick_tests/CMakeFiles/test] Error 1
make[2]: *** [CMakeFiles/Makefile2:7636: tests/quick_tests/CMakeFiles/test.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:7643: tests/quick_tests/CMakeFiles/test.dir/rule] Error 2
make: *** [Makefile:3341: test] Error 2

TBB version:

pacman -Qi tbb
Name            : tbb
Version         : 2021.5.0-1
Description     : High level abstract threading library
Architecture    : x86_64
URL             : https://www.threadingbuildingblocks.org/
Licenses        : Apache
Groups          : None
Provides        : intel-tbb=2021.5.0
Depends On      : gcc-libs  hwloc
Optional Deps   : None
Required By     : opencascade  vtk
Optional For    : None
Conflicts With  : intel-tbb
Replaces        : intel-tbb
Installed Size  : 1923.15 KiB
Packager        : Felix Yan <felixonmars@archlinux.org>
Build Date      : Mon 20 Dec 2021 10:00:54 PM CET
Install Date    : Thu 27 Jan 2022 12:42:34 PM CET
Install Reason  : Installed as a dependency for another package
Install Script  : No
Validated By    : Signature

I'm building with all optdepends installed.

drwells commented on 2022-02-26 18:44 (UTC)

@archaeal I apologize for the delay in my response.

deal.II does not use netcdf. I suspect this problem comes from the following circumstance: 1. an AUR copy of Trilinos was compiled, linking against the older soname version of netcdf 2. the system copy of netcdf was updated 3. the AUR copy of Trilinos now links against a nonexistant library

Hence updating Trilinos should fix it - this is not a problem we can address with deal.II's PKGBUILD.

@adigitoleo You're welcome. I have seen that failure before - the best fix is to disable Adelus in the Trilinos PKGBUILD. See

https://groups.google.com/g/dealii/c/uTkQoj7NYcM/m/16ElDi33DAAJ

and the links to Trilinos bug reports. The problem is with Trilinos' build system

adigitoleo commented on 2022-02-26 03:43 (UTC)

Many thanks for the package. For me, tests are all failing with trilinos 13.2:

/home/admin/aurbuilds/deal-ii/src/build/tests/quick_tests/arpack.debug: symbol lookup error: /usr/lib/libzadelus.so.13: undefined symbol: _ZN6Adelus10nprocs_colE

I will try an older trilinos version.