Toggle diff (354 lines)
diff --git a/gnu/local.mk b/gnu/local.mk
index 5429dc498c..dcedef5f99 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1682,6 +1682,8 @@ dist_patch_DATA = \
%D%/packages/patches/memtest86+-build-reproducibly.patch \
%D%/packages/patches/mercurial-hg-extension-path.patch \
%D%/packages/patches/mercurial-openssl-compat.patch \
+ %D%/packages/patches/mfem-fix-mk-file-export.patch \
+ %D%/packages/patches/mfem-remove-source-dir-refs.patch \
%D%/packages/patches/mhash-keygen-test-segfault.patch \
%D%/packages/patches/mia-fix-boost-headers.patch \
%D%/packages/patches/mia-vtk9.patch \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1b4d325649..1838b289e2 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -45,7 +45,7 @@
;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com>
;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr>
;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com>
-;;; Copyright © 2021, 2022 Paul A. Patience <paul@apatience.com>
+;;; Copyright © 2021-2024 Paul A. Patience <paul@apatience.com>
;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
;;; Copyright © 2021, 2023 Guillaume Le Vaillant <glv@posteo.net>
@@ -151,6 +151,7 @@ (define-module (gnu packages maths)
#:use-module (gnu packages xorg)
#:use-module (gnu packages gl)
#:use-module (gnu packages imagemagick)
+ #:use-module (gnu packages libunwind)
#:use-module (gnu packages m4)
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
@@ -6890,6 +6891,173 @@ (define-public dealii-openmpi
(delete 'unset-cpath)))))
(synopsis "Finite element library (with MPI support)")))
+(define-public mfem
+ (package
+ (name "mfem")
+ (version "4.6")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mfem/mfem")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0vr3s110bc42r81s1hi9brwwaz01d60l6mbdlsrfxxinpnzxq7ax"))
+ (patches (search-patches "mfem-remove-source-dir-refs.patch"
+ "mfem-fix-mk-file-export.patch"))))
+ (outputs '("out" "doc")) ; 338 MiB of documentation
+ (build-system cmake-build-system)
+ (arguments
+ (list #:configure-flags
+ ;; Follow order of config/defaults.mk, which has a more exhaustive
+ ;; list than config/defaults.cmake.
+ #~(list "-DBUILD_SHARED_LIBS=ON"
+ "-DMFEM_USE_MPI=OFF"
+ "-DMFEM_USE_METIS=OFF" ; MPI only
+ "-DMFEM_USE_METIS_5=OFF"
+ "-DMFEM_PRECISION=double" ; For versions beyond 4.6
+ "-DMFEM_DEBUG=OFF"
+ "-DMFEM_USE_EXCEPTIONS=ON"
+ "-DMFEM_USE_ZLIB=ON"
+ "-DMFEM_USE_LIBUNWIND=ON"
+ "-DMFEM_USE_LAPACK=ON"
+ "-DMFEM_THREAD_SAFE=OFF"
+ "-DMFEM_USE_OPENMP=ON"
+ "-DMFEM_USE_LEGACY_OPENMP=OFF"
+ "-DMFEM_USE_MEMALLOC=ON"
+ "-DMFEM_TIMER_TYPE=2"
+ "-DMFEM_USE_SUNDIALS=ON"
+ "-DMFEM_USE_SUITESPARSE=ON"
+ "-DMFEM_USE_SUPERLU=OFF" ; MPI only
+ "-DMFEM_USE_SUPERLU5=OFF"
+ "-DMFEM_USE_MUMPS=OFF" ; MPI only
+ "-DMFEM_USE_STRUMPACK=OFF" ; Missing dep, MPI only
+ "-DMFEM_USE_GINKGO=OFF" ; Missing dep
+ "-DMFEM_USE_AMGX=OFF" ; CUDA library
+ "-DMFEM_USE_GNUTLS=ON"
+ "-DMFEM_USE_NETCDF=ON"
+ "-DMFEM_USE_PETSC=OFF" ; MPI only
+ "-DMFEM_USE_SLEPC=OFF" ; MPI only
+ "-DMFEM_USE_MPFR=ON"
+ "-DMFEM_USE_SIDRE=OFF" ; Missing dep
+ "-DMFEM_USE_FMS=OFF" ; Missing dep
+ "-DMFEM_USE_CONDUIT=OFF" ; Missing dep
+ "-DMFEM_USE_PUMI=OFF" ; Missing dep, MPI only
+ "-DMFEM_USE_HIOP=OFF" ; Missing dep
+ "-DMFEM_USE_GSLIB=OFF" ; Missing dep
+ "-DMFEM_USE_CUDA=OFF"
+ "-DMFEM_USE_HIP=OFF" ; GPU library
+ "-DMFEM_USE_RAJA=OFF" ; Missing dep
+ "-DMFEM_USE_OCCA=OFF" ; Missing dep
+ "-DMFEM_USE_CEED=OFF" ; Missing dep
+ "-DMFEM_USE_CALIPER=OFF" ; Missing dep
+ "-DMFEM_USE_ALGOIM=OFF" ; Missing dep
+ "-DMFEM_USE_UMPIRE=OFF" ; Missing dep
+ "-DMFEM_USE_SIMD=ON"
+ "-DMFEM_USE_ADIOS2=OFF" ; Missing dep
+ "-DMFEM_USE_MKL_CPARDISO=OFF" ; Intel MKL
+ "-DMFEM_USE_MKL_PARDISO=OFF"
+ "-DMFEM_USE_MOONOLITH=OFF" ; Missing dep
+ "-DMFEM_USE_ADFORWARD=OFF"
+ "-DMFEM_USE_CODIPACK=OFF" ; Missing dep
+ "-DMFEM_USE_BENCHMARK=OFF" ; Only for benchmarks
+ "-DMFEM_USE_PARELAG=OFF" ; Missing dep, only for miniapps
+ "-DMFEM_USE_ENZYME=OFF" ; Missing dep, requires Clang
+ "-DMFEM_ENABLE_TESTING=ON"
+ "-DMFEM_ENABLE_EXAMPLES=ON"
+ "-DMFEM_ENABLE_MINIAPPS=ON" ; Used in some tests
+ "-DMFEM_ENABLE_GOOGLE_BENCHMARKS=OFF"
+ (string-append "-DHDF5_DIR=" #$(this-package-input "hdf5")))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'clean-mpi-references
+ (lambda _
+ (substitute* "config/config.mk.in"
+ (("(MFEM_MPIEXEC += ).*" _ prefix)
+ ;; Set to non-empty value, to avoid running unexpected
+ ;; commands.
+ (string-append prefix (which "false") "\n"))
+ (("(MFEM_MPIEXEC_NP +=).*" _ prefix)
+ (string-append prefix "\n"))
+ (("(MFEM_MPI_NP +=).*" _ prefix)
+ (string-append prefix "\n")))))
+ (add-after 'unpack 'clean-local-references
+ (lambda _
+ (substitute* "config/config.mk.in"
+ (("(MFEM_BUILD_TAG += ).*" _ prefix)
+ (string-append prefix "(none)\n")))))
+ (add-before 'check 'build-tests
+ (lambda _
+ (invoke "cmake" "--build" "." "--target" "tests")))
+ (add-after 'check 'build-doc
+ (lambda _
+ (setenv "HOME" "/tmp") ; Writable cache for fontconfig
+ (invoke "cmake" "--build" "." "--target" "doc")))
+ (add-after 'install 'remove-examples
+ (lambda _
+ (delete-file-recursively
+ (string-append #$output "/examples"))))
+ (add-after 'install 'install-doc
+ (lambda _
+ (let ((docdir (string-append #$output:doc "/share/doc/"
+ #$name "-" #$version)))
+ (install-file "doc/CodeDocumentation.html" docdir)
+ (copy-recursively
+ "doc/CodeDocumentation"
+ (string-append docdir "/CodeDocumentation")))))
+ (add-after 'install 'fix-library-paths
+ (let ((mpfr #$(this-package-input "mpfr"))
+ (libunwind #$(this-package-input "libunwind")))
+ (lambda _
+ (substitute* (string-append
+ #$output "/lib/cmake/mfem/MFEMTargets.cmake")
+ ((";mpfr;")
+ (string-append ";" mpfr "/lib/libmpfr.so;"))
+ ((";unwind;")
+ (string-append ";" libunwind "/lib/libunwind.so;")))
+ (substitute* (string-append #$output "/share/mfem/config.mk")
+ ((" mpfr ")
+ (string-append " -Wl,-rpath," mpfr "/lib"
+ " -L" mpfr "/lib"
+ " -lmpfr "))
+ ((" unwind ")
+ (string-append " -Wl,-rpath," libunwind "/lib"
+ " -L" libunwind "/lib"
+ " -lunwind ")))))))))
+ (native-inputs
+ (list doxygen graphviz perl)) ; For documentation
+ ;; No propagated inputs necessary because the installed CMake files and
+ ;; share/mfem/config.mk provide the full list of include directories.
+ (inputs
+ (list gnutls
+ hdf5 ; For NetCDF
+ lapack
+ libunwind
+ metis-suitesparse ; For SuiteSparse
+ mpfr
+ netcdf
+ suitesparse-amd
+ suitesparse-btf
+ suitesparse-camd
+ suitesparse-ccolamd
+ suitesparse-cholmod
+ suitesparse-colamd
+ suitesparse-config
+ suitesparse-klu
+ suitesparse-umfpack
+ sundials
+ zlib))
+ ;; TODO: Enable MFEM_USE_SIMD only if tuned?
+ (properties '((tunable? . #t)))
+ (home-page "https://mfem.org/")
+ (synopsis "Finite element library")
+ (description "MFEM is a modular parallel C++ library for finite element
+methods. Its goal is to enable high-performance scalable finite element
+discretization research and application development on a wide variety of
+platforms, ranging from laptops to supercomputers.")
+ (license license:bsd-3)))
+
(define-public flann
(package
(name "flann")
diff --git a/gnu/packages/patches/mfem-fix-mk-file-export.patch b/gnu/packages/patches/mfem-fix-mk-file-export.patch
new file mode 100644
index 0000000000..fbd35a029a
--- /dev/null
+++ b/gnu/packages/patches/mfem-fix-mk-file-export.patch
@@ -0,0 +1,29 @@
+From ccba86c0259c2ae56ad44a53d5d5a2a40822cbe3 Mon Sep 17 00:00:00 2001
+From: "Paul A. Patience" <paul@apatience.com>
+Date: Thu, 28 Mar 2024 13:28:49 -0400
+Subject: [PATCH 2/2] Add forgotten variable to mfem_export_mk_files
+
+MFEM_USE_MKL_PARDISO was missing.
+---
+ config/cmake/modules/MfemCmakeUtilities.cmake | 5 +++--
+ 1 file changed, 3 insertions(+), 2 deletions(-)
+
+diff --git a/config/cmake/modules/MfemCmakeUtilities.cmake b/config/cmake/modules/MfemCmakeUtilities.cmake
+index 204b7d87f..217f4eec7 100644
+--- a/config/cmake/modules/MfemCmakeUtilities.cmake
++++ b/config/cmake/modules/MfemCmakeUtilities.cmake
+@@ -851,8 +851,9 @@ function(mfem_export_mk_files)
+ MFEM_USE_CONDUIT MFEM_USE_PUMI MFEM_USE_HIOP MFEM_USE_GSLIB MFEM_USE_CUDA
+ MFEM_USE_HIP MFEM_USE_RAJA MFEM_USE_OCCA MFEM_USE_CEED MFEM_USE_CALIPER
+ MFEM_USE_UMPIRE MFEM_USE_SIMD MFEM_USE_ADIOS2 MFEM_USE_MKL_CPARDISO
+- MFEM_USE_ADFORWARD MFEM_USE_CODIPACK MFEM_USE_BENCHMARK MFEM_USE_PARELAG
+- MFEM_USE_MOONOLITH MFEM_USE_ALGOIM MFEM_USE_ENZYME)
++ MFEM_USE_MKL_PARDISO MFEM_USE_ADFORWARD MFEM_USE_CODIPACK
++ MFEM_USE_BENCHMARK MFEM_USE_PARELAG MFEM_USE_MOONOLITH MFEM_USE_ALGOIM
++ MFEM_USE_ENZYME)
+ foreach(var ${CONFIG_MK_BOOL_VARS})
+ if (${var})
+ set(${var} YES)
+--
+2.41.0
+
diff --git a/gnu/packages/patches/mfem-remove-source-dir-refs.patch b/gnu/packages/patches/mfem-remove-source-dir-refs.patch
new file mode 100644
index 0000000000..f9898748c7
--- /dev/null
+++ b/gnu/packages/patches/mfem-remove-source-dir-refs.patch
@@ -0,0 +1,101 @@
+From 0ad647e045e9cbe456ad0f5f3bdb6e015566e067 Mon Sep 17 00:00:00 2001
+From: "Paul A. Patience" <paul@apatience.com>
+Date: Thu, 28 Mar 2024 13:22:48 -0400
+Subject: [PATCH 1/2] Remove references to MFEM_SOURCE_DIR
+
+---
+ config/cmake/config.hpp.in | 3 ---
+ config/config.hpp.in | 3 ---
+ config/config.mk.in | 1 -
+ fem/ceed/interface/util.cpp | 8 +-------
+ general/device.cpp | 6 +-----
+ 5 files changed, 2 insertions(+), 19 deletions(-)
+
+diff --git a/config/cmake/config.hpp.in b/config/cmake/config.hpp.in
+index 7cb2a958d..13f13c48d 100644
+--- a/config/cmake/config.hpp.in
++++ b/config/cmake/config.hpp.in
+@@ -30,9 +30,6 @@
+ #define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100)
+ #define MFEM_VERSION_PATCH ((MFEM_VERSION)%100)
+
+-// MFEM source directory.
+-#define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@"
+-
+ // MFEM install directory.
+ #define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@"
+
+diff --git a/config/config.hpp.in b/config/config.hpp.in
+index 39d7737c7..dbee1f32f 100644
+--- a/config/config.hpp.in
++++ b/config/config.hpp.in
+@@ -30,9 +30,6 @@
+ #define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100)
+ #define MFEM_VERSION_PATCH ((MFEM_VERSION)%100)
+
+-// The absolute path of the MFEM source prefix.
+-// #define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@"
+-
+ // The absolute path of the MFEM installation prefix.
+ // #define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@"
+
+diff --git a/config/config.mk.in b/config/config.mk.in
+index 303750bf5..d2f538666 100644
+--- a/config/config.mk.in
++++ b/config/config.mk.in
+@@ -12,7 +12,6 @@
+ # Variables corresponding to defines in config.hpp (YES, NO, or value)
+ MFEM_VERSION = @MFEM_VERSION@
+ MFEM_VERSION_STRING = @MFEM_VERSION_STRING@
+-MFEM_SOURCE_DIR = @MFEM_SOURCE_DIR@
+ MFEM_INSTALL_DIR = @MFEM_INSTALL_DIR@
+ MFEM_GIT_STRING = @MFEM_GIT_STRING@
+ MFEM_USE_MPI = @MFEM_USE_MPI@
+diff --git a/fem/ceed/interface/util.cpp b/fem/ceed/interface/util.cpp
+index d122c2ab5..f2bc900a5 100644
+--- a/fem/ceed/interface/util.cpp
++++ b/fem/ceed/interface/util.cpp
+@@ -257,20 +257,14 @@ const std::string &GetCeedPath()
+ if (ceed_path.empty())
+ {
+ const char *install_dir = MFEM_INSTALL_DIR "/include/mfem/fem/ceed";
+- const char *source_dir = MFEM_SOURCE_DIR "/fem/ceed";
+ struct_stat m_stat;
+ if (stat(install_dir, &m_stat) == 0 && S_ISDIR(m_stat.st_mode))
+ {
+ ceed_path = install_dir;
+ }
+- else if (stat(source_dir, &m_stat) == 0 && S_ISDIR(m_stat.st_mode))
+- {
+- ceed_path = source_dir;
+- }
+ else
+ {
+- MFEM_ABORT("Cannot find libCEED kernels in MFEM_INSTALL_DIR or "
+- "MFEM_SOURCE_DIR");
++ MFEM_ABORT("Cannot find libCEED kernels in MFEM_INSTALL_DIR");
+ }
+ // Could be useful for debugging:
+ // out << "Using libCEED dir: " << ceed_path << std::endl;
+diff --git a/general/device.cpp b/general/device.cpp
+index ccee71cd7..a68ba7191 100644
+--- a/general/device.cpp
++++ b/general/device.cpp
+@@ -464,13 +464,9 @@ static void OccaDeviceSetup(const int dev)
+ {
+ mfemDir = MFEM_INSTALL_DIR "/include/mfem/";
+ }
+- else if (occa::io::exists(MFEM_SOURCE_DIR))
+- {
+- mfemDir = MFEM_SOURCE_DIR;
+- }
+ else
+ {
+- MFEM_ABORT("Cannot find OCCA kernels in MFEM_INSTALL_DIR or MFEM_SOURCE_DIR");
++ MFEM_ABORT("Cannot find OCCA kernels in MFEM_INSTALL_DIR");
+ }
+
+ occa::io::addLibraryPath("mfem", mfemDir);
+--
+2.41.0
+
base-commit: fb9549164520ad993c2fbbaedc899844d57baabc
--
2.41.0
