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Package Details: deal-ii 9.6.2-1
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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: | 0.000205 |
First Submitted: | 2013-09-11 11:11 (UTC) |
Last Updated: | 2024-12-24 03:10 (UTC) |
Dependencies (28)
- boost (boost-gitAUR)
- kokkosAUR (trilinosAUR)
- cmake (cmake-gitAUR) (make)
- adol-cAUR (adol-c-gitAUR, python-adolcAUR) (optional) – automatic differentiation library
- arpack (arpack-gitAUR) (optional) – Fortran77 subroutines designed to solve large scale eigenvalue problems
- assimp (assimp-gitAUR) (optional) – Library to import various well-known 3D model formats in an uniform manner
- cgal (cgal-gitAUR) (optional) – Computational Geometry Algorithms Library
- gmshAUR (gmsh-gitAUR, gmsh-binAUR) (optional) – An automatic 3D finite element mesh generator with pre and post-processing facilities
- gsl (gsl-gitAUR) (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-aoccAUR, lapack-gitAUR, atlas-lapackAUR, blas-aocl-gccAUR, blas-aocl-aoccAUR, openblas-lapackAUR, blas-mklAUR, aocl-libflameAUR, blas-openblas) (optional) – Linear Algebra PACKage
- metisAUR (metis-gitAUR) (optional) – partitioning graphs, finite element meshes, fill reducing orderings for sparse matrices.
- muparser (optional) – A fast math parser library
- opencascade (opencascade-gitAUR, opencascade-rcAUR, opencascade-f3dAUR) (optional) – Open CASCADE Technology, 3D modeling & numerical simulation
- openmpi (openmpi-gitAUR) (optional) – High performance message passing library (MPI)
- p4est-deal-iiAUR (optional) – The parallel forest (p4est) library, built to work with deal.II
- parmetisAUR (parmetis-gitAUR) (optional) – A parallel graph partitioning library
- petscAUR (petsc-gitAUR, petsc-complexAUR) (optional) – Portable, extensible toolkit for scientific computation
- scalapackAUR (optional) – subset of scalable LAPACK routines redesigned for distributed memory MIMD parallel computers
- slepcAUR (slepc-gitAUR) (optional) – Scalable library for Eigenvalue problem computations
- suitesparse (optional) – A collection of sparse matrix libraries
- sundials (sundials-seqAUR) (optional) – Suite of nonlinear differential/algebraic equation solvers
- symengine (symengine-gitAUR) (optional) – Fast symbolic manipulation library
- tbb (onetbb-gitAUR, onetbb) (optional) – High level abstract threading library
- trilinosAUR (trilinos-gitAUR) (optional) – algorithms for the solution of large-scale scientific problems
- vtk (vtk-gitAUR, vtk93AUR) (optional) – Software system for 3D computer graphics, image processing, and visualization
- zlib (zlib-ng-compat-gitAUR, zlib-gitAUR, zlib-ng-compat) (optional) – Compression library implementing the deflate compression method found in gzip and PKZIP
Latest Comments
« First ‹ Previous 1 2 3 4 5 6 7 Next › Last »
drwells commented on 2023-07-11 11:09 (UTC)
I wanted to get this done by now but I'm heading on vacation so it will have to wait until Saturday. We need to put out a 9.5.1 release due to some obscure Trilinos problems so this will need to be updated at that point anyway.
Thanks for investigating - I didn't realize the AUR had its own Kokkos package. To the best of my knowledge, Trilinos cannot be configured with an external Kokkos (they're working on it) so that's going to conflict with deal.II (though deal.II - Trilinos + external Kokkos should be OK).
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 withtrilinos
(appendingcmake_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 withtrilinos
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
ortrilinos
suite, any case is building fine:PKGBUILD patched
deal-ii-9.5.0-trilinos-14-2-0.txt
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 inbuild()
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:TBB version:
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
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