AUR (en) - dolfin

Git Clone URL:	https://aur.archlinux.org/dolfin.git (read-only, click to copy)
Package Base:	dolfin
Description:	C++ interface of FEniCS
Upstream URL:	https://bitbucket.org/fenics-project/dolfin
Licenses:	LGPL-3.0-or-later
Submitter:	sigvald
Maintainer:	carlosal1015
Last Packager:	carlosal1015
Votes:	7
Popularity:	0.000000
First Submitted:	2018-01-08 14:06 (UTC)
Last Updated:	2024-02-29 20:54 (UTC)

Nice!

My full log is below:

$ makepkg -s
==> Making package: dolfin 2019.1.0.post0-5 (Sun 19 Feb 2023 05:07:30 PM GMT)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
  -> Found dolfin-2019.1.0.post0.tar.gz
  -> Found pkg-config.patch
  -> Found endian.patch
  -> Found catch.patch
==> Validating source files with sha512sums...
    dolfin-2019.1.0.post0.tar.gz ... Passed
    pkg-config.patch ... Passed
    endian.patch ... Passed
    catch.patch ... Passed
==> Extracting sources...
  -> Extracting dolfin-2019.1.0.post0.tar.gz with bsdtar
==> Starting prepare()...
patching file dolfin/io/VTKFile.cpp
patching file dolfin/io/VTKWriter.cpp
patching file cmake/modules/FindPETSc.cmake
patching file cmake/modules/FindSLEPc.cmake
patching file test/unit/cpp/catch/catch.hpp
==> Removing existing $pkgdir/ directory...
==> Starting build()...
-- Checking for one of the modules 'craypetsc_real;petsc;PETSc'
-- Test PETSC_TEST_RUNS with shared library linking - Failed
-- Test PETSC_TEST_RUNS static linking - Failed
-- PETSc could not be configured. (missing: PETSC_TEST_RUNS) (found suitable version "3.18.4", minimum required is "3.7")
-- ParMETIS could not be found/configured. (missing: PARMETIS_TEST_RUNS PARMETIS_INCLUDE_DIRS PARMETIS_VERSION PARMETIS_VERSION_OK) (Required is at least version "4.0.2")
-- Checking for package 'SCOTCH-PT'
-- Found SCOTCH (version 7)
-- Performing test SCOTCH_TEST_RUNS
-- Performing test SCOTCH_TEST_RUNS - Success
-- Checking for package 'AMD'
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Found BLAS: /usr/lib/libblas.so
-- Performing test CHOLMOD_TEST_RUNS - Success
-- Performing test UMFPACK_TEST_RUNS - Success
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Found BLAS: /usr/lib/libblas.so
-- Performing test CHOLMOD_TEST_RUNS - Success
-- The following features have been enabled:

 * BUILD_SHARED_LIBS, Build DOLFIN with shared libraries.
 * DOLFIN_AUTO_DETECT_MPI, Detect MPI automatically (turn this off to use the MPI compiler wrappers directly via setting CXX, CXX, FC).
 * DOLFIN_WITH_LIBRARY_VERSION, Build with library version information.
 * DOLFIN_ENABLE_DOCS, Enable generation of documentation.
 * CMAKE_INSTALL_RPATH_USE_LINK_PATH, Add paths to linker search and installed rpath.
 * DOLFIN_ENABLE_MPI, Compile with support for MPI.
 * DOLFIN_ENABLE_PETSC, Compile with support for PETSc.
 * DOLFIN_ENABLE_SLEPC, Compile with support for SLEPc.
 * DOLFIN_ENABLE_UMFPACK, Compile with support for UMFPACK.
 * DOLFIN_ENABLE_CHOLMOD, Compile with support for CHOLMOD.
 * DOLFIN_ENABLE_SCOTCH, Compile with support for SCOTCH.
 * DOLFIN_ENABLE_PARMETIS, Compile with support for ParMETIS.
 * DOLFIN_ENABLE_ZLIB, Compile with support for zlib.
 * DOLFIN_ENABLE_HDF5, Compile with support for HDF5.

-- The following OPTIONAL packages have been found:

 * MPI, Message Passing Interface (MPI)
   Enables DOLFIN to run in parallel with MPI
 * SCOTCH, Programs and libraries for graph, mesh and hypergraph partitioning, <https://www.labri.fr/perso/pelegrin/scotch>
   Enables parallel graph partitioning
 * UMFPACK, Sparse LU factorization library, <http://faculty.cse.tamu.edu/davis/suitesparse.html>
 * BLAS, Basic Linear Algebra Subprograms, <http://netlib.org/blas/>
 * Threads
 * CHOLMOD, Sparse Cholesky factorization library for sparse matrices, <http://faculty.cse.tamu.edu/davis/suitesparse.html>
 * HDF5, Hierarchical Data Format 5 (HDF5), <https://www.hdfgroup.org/HDF5>
 * ZLIB, Compression library, <http://www.zlib.net>

-- The following REQUIRED packages have been found:

 * Boost, Boost C++ libraries, <http://www.boost.org>
 * Eigen3 (required version >= 3.2.90), Lightweight C++ template library for linear algebra, <http://eigen.tuxfamily.org>
 * PythonInterp (required version >= 3), Interactive high-level object-oriented language, <http://www.python.org>
 * UFC (required version >= 2019.1), Unified language for form-compilers (part of FFC), <https://bitbucket.org/fenics-project/ffc>
 * PkgConfig

-- The following features have been disabled:

 * CMAKE_USE_RELATIVE_PATHS, Use relative paths in makefiles and projects.
 * DOLFIN_ENABLE_CODE_COVERAGE, Enable code coverage.
 * DOLFIN_ENABLE_BENCHMARKS, Enable benchmark programs.
 * DOLFIN_SKIP_BUILD_TESTS, Skip build tests for testing usability of dependency packages.
 * DOLFIN_DEPRECATION_ERROR, Turn deprecation warnings into errors.
 * DOLFIN_ENABLE_GEOMETRY_DEBUGGING, Enable geometry debugging.
 * DOLFIN_ENABLE_TRILINOS, Compile with support for Trilinos.
 * DOLFIN_ENABLE_SUNDIALS, Compile with support for SUNDIALS.

-- The following OPTIONAL packages have not been found:

 * PETSc (required version >= 3.7), Portable, Extensible Toolkit for Scientific Computation, <https://www.mcs.anl.gov/petsc/>
   Enables the PETSc linear algebra backend

-- 
-- Generating demo source files from reStructuredText
-- --------------------------------------------------
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/auto-adaptive-poisson/cpp/AdaptivePoisson.ufl
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/auto-adaptive-poisson/cpp/main.cpp
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/biharmonic/cpp/Biharmonic.ufl
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/biharmonic/cpp/main.cpp
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/built-in-meshes/cpp/main.cpp
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/eigenvalue/cpp/StiffnessMatrix.ufl
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/eigenvalue/cpp/main.cpp
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/hyperelasticity/cpp/HyperElasticity.ufl
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/hyperelasticity/cpp/main.cpp
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/mixed-poisson/cpp/MixedPoisson.ufl
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/mixed-poisson/cpp/main.cpp
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/nonmatching-interpolation/cpp/P1.ufl
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/nonmatching-interpolation/cpp/P3.ufl
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/nonmatching-interpolation/cpp/main.cpp
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/poisson/cpp/Poisson.ufl
extract written to /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/demo/documented/poisson/cpp/main.cpp
-- Configuring done
-- Generating done
-- Build files have been written to: /home/admin/abs/dolfin/src/build
[  0%] Built target compile_ale_forms
[  0%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/adapt.cpp.o
[  0%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/AdaptiveLinearVariationalSolver.cpp.o
[  0%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/AdaptiveNonlinearVariationalSolver.cpp.o
[  0%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/ErrorControl.cpp.o
[  0%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/Extrapolation.cpp.o
[  1%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/GenericAdaptiveVariationalSolver.cpp.o
[  1%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/marking.cpp.o
[  3%] Building CXX object dolfin/CMakeFiles/dolfin.dir/ale/ALE.cpp.o
[  3%] Building CXX object dolfin/CMakeFiles/dolfin.dir/ale/HarmonicSmoothing.cpp.o
[  3%] Building CXX object dolfin/CMakeFiles/dolfin.dir/ale/MeshDisplacement.cpp.o
[  3%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/assemble.cpp.o
[  3%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/assemble_local.cpp.o
[  4%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/AssemblerBase.cpp.o
[  4%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/Assembler.cpp.o
[  4%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/DirichletBC.cpp.o
[  6%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/DiscreteOperators.cpp.o
[  6%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/DofMapBuilder.cpp.o
[  6%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/DofMap.cpp.o
[  6%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/fem_utils.cpp.o
[  6%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/FiniteElement.cpp.o
[  6%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/Form.cpp.o
[  6%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/LinearVariationalProblem.cpp.o
[  7%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/LocalAssembler.cpp.o
[  7%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/LocalSolver.cpp.o
[  7%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/MultiMeshAssembler.cpp.o
[  9%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/MultiMeshDofMap.cpp.o
[  9%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/NonlinearVariationalProblem.cpp.o
[ 10%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/NonlinearVariationalSolver.cpp.o
[ 10%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/PointSource.cpp.o
[ 12%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/SparsityPatternBuilder.cpp.o
[ 12%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/SystemAssembler.cpp.o
[ 12%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/UFC.cpp.o
[ 14%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/assign.cpp.o
[ 14%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/Expression.cpp.o
[ 15%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/FunctionAssigner.cpp.o
[ 15%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/FunctionAXPY.cpp.o
[ 15%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/Function.cpp.o
[ 17%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/FunctionSpace.cpp.o
[ 17%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/LagrangeInterpolator.cpp.o
[ 18%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/MultiMeshFunction.cpp.o
[ 18%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/MultiMeshFunctionSpace.cpp.o
[ 18%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/MultiMeshSubSpace.cpp.o
[ 18%] Building CXX object dolfin/CMakeFiles/dolfin.dir/function/SpecialFunctions.cpp.o
[ 18%] Building CXX object dolfin/CMakeFiles/dolfin.dir/generation/SphericalShellMesh.cpp.o
[ 18%] Building CXX object dolfin/CMakeFiles/dolfin.dir/generation/UnitDiscMesh.cpp.o
[ 18%] Building CXX object dolfin/CMakeFiles/dolfin.dir/geometry/GenericBoundingBoxTree.cpp.o
[ 18%] Building CXX object dolfin/CMakeFiles/dolfin.dir/geometry/IntersectionConstruction.cpp.o
[ 20%] Building CXX object dolfin/CMakeFiles/dolfin.dir/geometry/MeshPointIntersection.cpp.o
[ 20%] Building CXX object dolfin/CMakeFiles/dolfin.dir/geometry/SimplexQuadrature.cpp.o
[ 20%] Building CXX object dolfin/CMakeFiles/dolfin.dir/graph/GraphBuilder.cpp.o
[ 21%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/HDF5File.cpp.o
[ 21%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/HDF5Interface.cpp.o
[ 21%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/HDF5Utility.cpp.o
[ 21%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/RAWFile.cpp.o
/home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5Interface.cpp: In static member function ‘static bool dolfin::HDF5Interface::has_group(hid_t, std::string)’:
/home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5Interface.cpp:285:22: error: too few arguments to function ‘herr_t H5Oget_info_by_name3(hid_t, const char*, H5O_info2_t*, unsigned int, hid_t)’
  285 |   H5Oget_info_by_name(hdf5_file_handle, group_name.c_str(), &object_info,
      |                      ^
In file included from /usr/include/H5Apublic.h:22,
                 from /usr/include/hdf5.h:23,
                 from /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5Interface.h:32,
                 from /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5Attribute.h:30,
                 from /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5File.h:32,
                 from /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5Interface.cpp:26:
/usr/include/H5Opublic.h:521:15: note: declared here
  521 | H5_DLL herr_t H5Oget_info_by_name3(hid_t loc_id, const char *name, H5O_info2_t *oinfo, unsigned fields,
      |               ^~~~~~~~~~~~~~~~~~~~
[ 21%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/SVGFile.cpp.o
make[2]: *** [dolfin/CMakeFiles/dolfin.dir/build.make:1434: dolfin/CMakeFiles/dolfin.dir/io/HDF5Interface.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5File.cpp: In member function ‘void dolfin::HDF5File::write(const dolfin::Function&, std::string)’:
/home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5File.cpp:918:30: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = plus<long unsigned int>; _Tp = long unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
  918 |                  std::bind2nd(std::plus<std::size_t>(), offset));
      |                  ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12.2.1/bits/stl_function.h:1438,
                 from /usr/include/c++/12.2.1/string:48,
                 from /usr/include/c++/12.2.1/bits/locale_classes.h:40,
                 from /usr/include/c++/12.2.1/bits/ios_base.h:41,
                 from /usr/include/c++/12.2.1/ios:42,
                 from /usr/include/c++/12.2.1/istream:38,
                 from /usr/include/c++/12.2.1/fstream:38,
                 from /home/admin/abs/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5File.cpp:23:
/usr/include/c++/12.2.1/backward/binders.h:172:5: note: declared here
  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
      |     ^~~~~~~
make[1]: *** [CMakeFiles/Makefile2:1495: dolfin/CMakeFiles/dolfin.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
==> ERROR: A failure occurred in build().
    Aborting...

carlosal1015 commented on 2023-02-19 17:03 (UTC)

Hi @CrocoDuck, let me check providing full log I will look a patch for HDF5Interface https://bitbucket.org/fenics-project/dolfin/issues/1110/hdf5interfacecpp-incompatible-with-recent

I will fix this afternoon.

CrocoDuck commented on 2023-02-19 16:55 (UTC)

Hi!

I am having this issue building the latest update. Any idea?

[ 45%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/pugixml.cpp.o
/home/admin/.cache/yay/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5Interface.cpp: In static member function ‘static bool dolfin::HDF5Interface::has_group(hid_t, std::string)’:
/home/admin/.cache/yay/dolfin/src/dolfin-2019.1.0.post0/dolfin/io/HDF5Interface.cpp:285:22: error: too few arguments to function ‘herr_t H5Oget_info_by_name3(hid_t, const char*, H5O_info2_t*, unsigned int, hid_t)’

evgenpog commented on 2022-10-13 16:30 (UTC) (edited on 2022-10-13 16:38 (UTC) by evgenpog)

(1) The error: "No such file or directory" can be fixed by modifying PKGBUILD file line 65, delete ${_base}-${pkgver}/ part of confusing path (because it is empty) (2) Line 29 is really not necessary, it much faster and still safe can be compiled at least on 8 cores (3) I hope it can support Trilinos somehow in future or fully drop support (I spent quite a while by building it) (4) Forgot to mention, now it (dolfin) is working fine for me (after installing python-dolfin and mshr, python-mshr)

carlosal1015 commented on 2022-06-30 03:19 (UTC)

This modified PKGBUILD is working from my side.

entshuld commented on 2022-06-20 17:42 (UTC)

@MartinDiehl let me know if disabling Trilinos and Sundials works :) .

entshuld commented on 2022-06-20 17:39 (UTC)

@carlosal1015 One month later, it's done. I hope I didn't break anything.

entshuld commented on 2022-05-27 12:25 (UTC)

@MartinDiehl: I don't actually have sundials nor trilinos, so I'll take your recommendation and add it to the PKGBUILD. Thanks.

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Package Details: dolfin 2019.1.0.post0-8

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CrocoDuck commented on 2023-02-19 17:08 (UTC)