diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/local.mk | 4 | ||||
| -rw-r--r-- | gnu/packages/patches/fenics-dolfin-algorithm.patch | 37 | ||||
| -rw-r--r-- | gnu/packages/patches/fenics-dolfin-boost.patch | 45 | ||||
| -rw-r--r-- | gnu/packages/patches/fenics-dolfin-config-slepc.patch | 48 | ||||
| -rw-r--r-- | gnu/packages/patches/fenics-dolfin-demo-init.patch | 39 | ||||
| -rw-r--r-- | gnu/packages/simulation.scm | 14 |
6 files changed, 180 insertions, 7 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index b906d234fc..3ae66803f2 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1053,6 +1053,10 @@ dist_patch_DATA = \ %D%/packages/patches/fasthenry-spSolve.patch \ %D%/packages/patches/fasthenry-spFactor.patch \ %D%/packages/patches/fbreader-curl-7.62.patch \ + %D%/packages/patches/fenics-dolfin-algorithm.patch \ + %D%/packages/patches/fenics-dolfin-demo-init.patch \ + %D%/packages/patches/fenics-dolfin-boost.patch \ + %D%/packages/patches/fenics-dolfin-config-slepc.patch \ %D%/packages/patches/fifengine-boost-compat.patch \ %D%/packages/patches/fifengine-swig-compat.patch \ %D%/packages/patches/fifo-map-fix-flags-for-gcc.patch \ diff --git a/gnu/packages/patches/fenics-dolfin-algorithm.patch b/gnu/packages/patches/fenics-dolfin-algorithm.patch new file mode 100644 index 0000000000..e2a3148a64 --- /dev/null +++ b/gnu/packages/patches/fenics-dolfin-algorithm.patch @@ -0,0 +1,37 @@ +Fix compilation errors: + + dolfin/geometry/IntersectionConstruction.cpp: In static member function ‘static std::vector<dolfin::Point> dolfin::IntersectionConstruction::intersection_segment_segment_2d(const dolfin::Point&, const dolfin::Point&, const dolfin::Point&, const dolfin::Point&)’: + dolfin/geometry/IntersectionConstruction.cpp:442:24: error: ‘min_element’ is not a member of ‘std’; did you mean ‘tuple_element’? + 442 | const auto it = std::min_element(oo.begin(), oo.end()); + | ^~~~~~~~~~~ + | tuple_element + + dolfin/mesh/MeshFunction.h: In member function ‘std::vector<long unsigned int> dolfin::MeshFunction<T>::where_equal(T)’: + dolfin/mesh/MeshFunction.h:652:26: error: ‘count’ is not a member of ‘std’; did you mean ‘cout’? + 652 | std::size_t n = std::count(_values.get(), _values.get() + _size, value); + | ^~~~~ + | cout + +Submitted upstream at https://bitbucket.org/fenics-project/dolfin/issues/1128 + +--- a/dolfin/geometry/IntersectionConstruction.cpp ++++ b/dolfin/geometry/IntersectionConstruction.cpp +@@ -18,7 +18,8 @@ + // First added: 2014-02-03 + // Last changed: 2017-12-12 + ++#include <algorithm> + #include <iomanip> + #include <dolfin/mesh/MeshEntity.h> + #include "predicates.h" + +--- a/dolfin/mesh/MeshFunction.h ++++ b/dolfin/mesh/MeshFunction.h +@@ -24,6 +24,7 @@ + #ifndef __MESH_FUNCTION_H + #define __MESH_FUNCTION_H + ++#include <algorithm> + #include <map> + #include <vector> + diff --git a/gnu/packages/patches/fenics-dolfin-boost.patch b/gnu/packages/patches/fenics-dolfin-boost.patch new file mode 100644 index 0000000000..de56ebb9b3 --- /dev/null +++ b/gnu/packages/patches/fenics-dolfin-boost.patch @@ -0,0 +1,45 @@ +The `BOOST_LITTLE_ENDIAN` and `BOOST_BIG_ENDIAN` macros, along with the +"boost/detail/endian.hpp" header, were deprecated in boost 1.69.0 and finally +removed in boost 1.73.0. They are superseded by the BOOST_ENDIAN_LITTLE_BYTE +and BOOST_ENDIAN_BIG_BYTE macros and "boost/predef/other/endian.h" header. + +Deprecated: https://github.com/boostorg/predef/commit/32d4581c1689370444f2e565cfbb8421d5071807 +Removed: https://github.com/boostorg/predef/commit/aa6e232bf170ad8b856aff9e7c70334f77441c7f + +Adaptation of patch from https://bitbucket.org/fenics-project/dolfin/issues/1116 + +--- a/dolfin/io/VTKFile.cpp ++++ b/dolfin/io/VTKFile.cpp +@@ -20,7 +20,7 @@ + #include <vector> + #include <iomanip> + #include <boost/cstdint.hpp> +-#include <boost/detail/endian.hpp> ++#include <boost/predef/other/endian.h> + + #include "pugixml.hpp" + +@@ -614,9 +614,9 @@ + std::string endianness = ""; + if (encode_string == "binary") + { +- #if defined BOOST_LITTLE_ENDIAN ++ #if defined BOOST_ENDIAN_LITTLE_BYTE + endianness = "byte_order=\"LittleEndian\""; +- #elif defined BOOST_BIG_ENDIAN ++ #elif defined BOOST_ENDIAN_BIG_BYTE + endianness = "byte_order=\"BigEndian\"";; + #else + dolfin_error("VTKFile.cpp", + +--- a/dolfin/io/VTKWriter.cpp ++++ b/dolfin/io/VTKWriter.cpp +@@ -24,7 +24,6 @@ + #include <sstream> + #include <vector> + #include <iomanip> +-#include <boost/detail/endian.hpp> + + #include <dolfin/fem/GenericDofMap.h> + #include <dolfin/fem/FiniteElement.h> + \ No newline at end of file diff --git a/gnu/packages/patches/fenics-dolfin-config-slepc.patch b/gnu/packages/patches/fenics-dolfin-config-slepc.patch new file mode 100644 index 0000000000..fa06179285 --- /dev/null +++ b/gnu/packages/patches/fenics-dolfin-config-slepc.patch @@ -0,0 +1,48 @@ +From https://bitbucket.org/fenics-project/dolfin/issues/1120 + +From f627a442350560e50dbbb11f7828b6d807369533 Mon Sep 17 00:00:00 2001 +From: Alexei Colin <acolin@isi.edu> +Date: Sun, 11 Apr 2021 20:40:00 -0400 +Subject: [PATCH] cmake: PETSc,SLEPc: match lowercase .pc pkg-config files + +Upstream has moved to lowercase. PETSc has kept the mixed-case file for +compatibility, but SLEPc hasn't. + +pkg_search_module takes multiple patterns and succeeds on first match, +so this commit is backward-compatible with older installations of PETSc, +SLEPc. + +--- + cmake/modules/FindPETSc.cmake | 2 +- + cmake/modules/FindSLEPc.cmake | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/cmake/modules/FindPETSc.cmake b/cmake/modules/FindPETSc.cmake +index 80faffdad..728a6ec30 100644 +--- a/cmake/modules/FindPETSc.cmake ++++ b/cmake/modules/FindPETSc.cmake +@@ -51,7 +51,7 @@ find_package(PkgConfig REQUIRED) + + # Find PETSc pkg-config file. Note: craypetsc_real is on Cray systems + set(ENV{PKG_CONFIG_PATH} "$ENV{CRAY_PETSC_PREFIX_DIR}/lib/pkgconfig:$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{PETSC_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}") +-pkg_search_module(PETSC craypetsc_real PETSc) ++pkg_search_module(PETSC craypetsc_real petsc PETSc) + + # Extract major, minor, etc from version string + if (PETSC_VERSION) +diff --git a/cmake/modules/FindSLEPc.cmake b/cmake/modules/FindSLEPc.cmake +index 327cffc23..dec26fcc4 100644 +--- a/cmake/modules/FindSLEPc.cmake ++++ b/cmake/modules/FindSLEPc.cmake +@@ -48,7 +48,7 @@ find_package(PkgConfig REQUIRED) + set(ENV{PKG_CONFIG_PATH} "$ENV{SLEPC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{SLEPC_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}") + set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{PETSC_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}") + set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}:$ENV{PETSC_DIR}:$ENV{PKG_CONFIG_PATH}") +-pkg_search_module(SLEPC crayslepc_real SLEPc) ++pkg_search_module(SLEPC crayslepc_real slepc SLEPc) + + # Extract major, minor, etc from version string + if (SLEPC_VERSION) +-- +2.30.0 + diff --git a/gnu/packages/patches/fenics-dolfin-demo-init.patch b/gnu/packages/patches/fenics-dolfin-demo-init.patch new file mode 100644 index 0000000000..5a01320147 --- /dev/null +++ b/gnu/packages/patches/fenics-dolfin-demo-init.patch @@ -0,0 +1,39 @@ +Ensure MPI is initialized before getting rank, which may be called early by +Logger::write() via dolfin::info(). + +Fixes "MPI_Comm_rank called before MPI_INIT" error from +`demo_stokes-iterative_serial` and `demo_waveguide_serial` tests. + +Submitted upstream at https://bitbucket.org/fenics-project/dolfin/issues/1127 + +--- a/dolfin/common/MPI.cpp ++++ b/dolfin/common/MPI.cpp +@@ -143,6 +143,7 @@ MPI_Info& dolfin::MPIInfo::operator*() + unsigned int dolfin::MPI::rank(const MPI_Comm comm) + { + #ifdef HAS_MPI ++ SubSystemsManager::init_mpi(); + int rank; + MPI_Comm_rank(comm, &rank); + return rank; +diff --git a/dolfin/common/MPI.h b/dolfin/common/MPI.h +index b93f6df30..854114a3f 100644 +--- a/dolfin/common/MPI.h ++++ b/dolfin/common/MPI.h +@@ -102,12 +102,13 @@ namespace dolfin + /// communicator + void reset(MPI_Comm comm); + +- /// Return process rank for the communicator ++ /// Return process rank for the communicator. This function will ++ /// also initialize MPI if it hasn't already been initialised. + unsigned int rank() const; + + /// Return size of the group (number of processes) associated +- /// with the communicator. This function will also intialise MPI +- /// if it hasn't already been intialised. ++ /// with the communicator. This function will also initialise MPI ++ /// if it hasn't already been initialised. + unsigned int size() const; + + /// Set a barrier (synchronization point) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 240549be47..3f2d8e136d 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2022 Eric Bavier <bavier@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -430,6 +431,10 @@ FFC is part of the FEniCS Project.") (sha256 (base32 "1m91hwcq5gfj4qqswp8l8kj58nia48f0n4kq13w0xqj4biq7rla0")) + (patches (search-patches "fenics-dolfin-algorithm.patch" + "fenics-dolfin-demo-init.patch" + "fenics-dolfin-boost.patch" + "fenics-dolfin-config-slepc.patch")) (modules '((guix build utils))) (snippet '(begin @@ -498,11 +503,8 @@ FFC is part of the FEniCS Project.") ;; git-lfs, so only the links are downloaded. The tests that ;; require the absent meshes cannot run and are skipped. ;; - ;; Two other serial tests fail and are skipped. - ;; i) demo_stokes-iterative_serial, - ;; The MPI_Comm_rank() function was called before MPI_INIT was - ;; invoked - ;; ii) demo_multimesh-stokes_serial: + ;; One serial test fails and is skipped. + ;; i) demo_multimesh-stokes_serial: ;; Warning: Found no facets matching domain for boundary ;; condition. ;; @@ -544,8 +546,6 @@ FFC is part of the FEniCS Project.") "demo_mesh-quality_serial " "demo_mesh-quality_mpi " "demo_multimesh-stokes_serial " - "demo_stokes-iterative_serial " - "demo_stokes-iterative_mpi " ")\n") port))) #t)) (replace 'check |