Package: guix-patches;
Reported by: Paul Garlick <pgarlick <at> tourbillion-technology.com>
Date: Mon, 23 Jun 2025 17:01:01 UTC
Severity: normal
Tags: patch
Done: Andreas Enge <andreas <at> enge.fr>
Message #11 received at 78878 <at> debbugs.gnu.org (full text, mbox):
From: Paul Garlick <pgarlick <at> tourbillion-technology.com> To: andreas <at> enge.fr, 78878 <at> debbugs.gnu.org Cc: Paul Garlick <pgarlick <at> tourbillion-technology.com> Subject: [PATCH v2] gnu:fenics-dolfin: Fix build with hdf5 <at> 1.14. Date: Fri, 27 Jun 2025 19:04:29 +0100
* gnu/packages/patches/fenics-dolfin-hdf5-version-check.patch: New
patch.
* gnu/local.mk (dist_patch_DATA): Register new patch.
* gnu/packages/simulation.scm (fenics-dolfin): Run guix style.
[source]: Use new patch. [arguments] <phases>: Update 'pre-check' comment.
Add 'demo_stokes-iterative_mpi' test to list of skipped tests.
---
gnu/local.mk | 1 +
.../fenics-dolfin-hdf5-version-check.patch | 26 ++
gnu/packages/simulation.scm | 271 +++++++++---------
3 files changed, 159 insertions(+), 139 deletions(-)
create mode 100644 gnu/packages/patches/fenics-dolfin-hdf5-version-check.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index c569c327a9..d3a2c81bd7 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1288,6 +1288,7 @@ dist_patch_DATA = \
%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/fenics-dolfin-hdf5-version-check.patch \
%D%/packages/patches/ffmpeg-jami-change-RTCP-ratio.patch \
%D%/packages/patches/ffmpeg-jami-rtp_ext_abs_send_time.patch \
%D%/packages/patches/ffmpeg-jami-libopusdec-enable-FEC.patch \
diff --git a/gnu/packages/patches/fenics-dolfin-hdf5-version-check.patch b/gnu/packages/patches/fenics-dolfin-hdf5-version-check.patch
new file mode 100644
index 0000000000..6128ed5b3c
--- /dev/null
+++ b/gnu/packages/patches/fenics-dolfin-hdf5-version-check.patch
@@ -0,0 +1,26 @@
+This patch checks the HDF5 API version before selecting the appropriate H5O
+function. A new function name and an extra argument are required for v1.12
+and above.
+
+See <https://support.hdfgroup.org/documentation/hdf5/latest/api-compat-macros.html> for the Technical Notes.
+
+See <https://bitbucket.org/fenics-project/dolfin/commits/4201e172c88dc51eb8846cb350acbbe23c95246d> for the upstream fix.
+
+--- a/dolfin/io/HDF5Interface.cpp
++++ b/dolfin/io/HDF5Interface.cpp
+@@ -282,8 +282,13 @@
+ }
+
+ H5O_info_t object_info;
+- H5Oget_info_by_name(hdf5_file_handle, group_name.c_str(), &object_info,
+- lapl_id);
++ #if H5_VERSION_GE(1, 12, 0)
++ H5Oget_info_by_name3(hdf5_file_handle, group_name.c_str(), &object_info,
++ H5O_INFO_BASIC, lapl_id);
++ #else
++ H5Oget_info_by_name(hdf5_file_handle, group_name.c_str(), &object_info,
++ lapl_id);
++ #endif
+
+ // Close link access properties
+ status = H5Pclose(lapl_id);
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index ebfe477265..e6f86fb736 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -744,143 +744,138 @@ (define-public fenics-dolfin
(name "fenics-dolfin")
(version "2019.1.0.post0")
(source
- (origin
- (method url-fetch)
- (uri (string-append
- "https://bitbucket.org/fenics-project/dolfin/get/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (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
- ;; Make sure we don't use the bundled test framework.
- (delete-file-recursively "test/unit/cpp/catch")
- (substitute* "test/unit/cpp/main.cpp"
- ;; Use standard search paths for 'catch' header file.
- (("#include.*")
- "#include <catch.hpp>\n"))
- (substitute* "test/unit/cpp/CMakeLists.txt"
- ;; Specify directory to find the header file.
- (("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
- (string-append front
- "$ENV{CATCH_DIR}/include" back "\n")))))))
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://bitbucket.org/fenics-project/dolfin/get/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1m91hwcq5gfj4qqswp8l8kj58nia48f0n4kq13w0xqj4biq7rla0"))
+ (patches (search-patches "fenics-dolfin-algorithm.patch"
+ "fenics-dolfin-demo-init.patch"
+ "fenics-dolfin-boost.patch"
+ "fenics-dolfin-config-slepc.patch"
+ "fenics-dolfin-hdf5-version-check.patch"))
+ (modules '((guix build utils)))
+ (snippet '(begin
+ ;; Make sure we don't use the bundled test framework.
+ (delete-file-recursively "test/unit/cpp/catch")
+ (substitute* "test/unit/cpp/main.cpp"
+ ;; Use standard search paths for 'catch' header file.
+ (("#include.*")
+ "#include <catch.hpp>\n"))
+ (substitute* "test/unit/cpp/CMakeLists.txt"
+ ;; Specify directory to find the header file.
+ (("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
+ (string-append front "$ENV{CATCH_DIR}/include" back "\n")))))))
(build-system cmake-build-system)
- (inputs
- (list openblas
- boost
- eigen
- hdf5-parallel-openmpi
- libxml2
- openmpi
- python-3
- pt-scotch32
- suitesparse
- sundials-openmpi
- zlib))
- (native-inputs
- (list catch-framework pkg-config))
- (propagated-inputs
- (list python-fenics-ffc petsc-openmpi slepc-openmpi))
+ (inputs (list openblas
+ boost
+ eigen
+ hdf5-parallel-openmpi
+ libxml2
+ openmpi
+ python-3
+ pt-scotch32
+ suitesparse
+ sundials-openmpi
+ zlib))
+ (native-inputs (list catch-framework pkg-config))
+ (propagated-inputs (list python-fenics-ffc petsc-openmpi slepc-openmpi))
(arguments
- (list #:configure-flags #~`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
- "-DDOLFIN_ENABLE_HDF5:BOOL=ON"
- "-DDOLFIN_ENABLE_MPI:BOOL=ON"
- "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
- "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
- "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
- "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'patch-usr-bin-file 'mpi-setup
- #$%openmpi-setup)
- (add-after 'patch-source-shebangs 'set-paths
- (lambda _
- ;; Define paths to store locations.
- (setenv "BLAS_DIR"
- #$(this-package-input "openblas"))
- (setenv "CATCH_DIR"
- #$(this-package-input "catch"))
- (setenv "LAPACK_DIR"
- #$(this-package-input "openblas"))
- (setenv "PETSC_DIR"
- #$(this-package-input "petsc"))
- (setenv "SLEPC_DIR"
- #$(this-package-input "slepc"))
- (setenv "SCOTCH_DIR"
- #$(this-package-input "scotch"))
- (setenv "SUNDIALS_DIR"
- #$(this-package-input "sundials"))
- (setenv "UMFPACK_DIR"
- #$(this-package-input "suitesparse"))))
- (add-before 'check 'pre-check
- (lambda _
- ;; The Dolfin repository uses git-lfs, whereby web links are
- ;; substituted for large files. Guix does not currently support
- ;; git-lfs, so only the links are downloaded. The tests that
- ;; require the absent meshes cannot run and are skipped.
- ;;
- ;; One serial test fails and is skipped.
- ;; i) demo_multimesh-stokes_serial:
- ;; Warning: Found no facets matching domain for boundary
- ;; condition.
- ;;
- ;; One mpi test fails and is skipped.
- ;; i) demo_stokes-iterative_mpi:
- ;; The MPI_Comm_rank() function was called before MPI_INIT was
- ;; invoked
- (call-with-output-file "CTestCustom.cmake"
- (lambda (port)
- (display (string-append
- "set(CTEST_CUSTOM_TESTS_IGNORE "
- "demo_bcs_serial "
- "demo_bcs_mpi "
- "demo_eigenvalue_serial "
- "demo_eigenvalue_mpi "
- "demo_navier-stokes_serial "
- "demo_navier-stokes_mpi "
- "demo_stokes-taylor-hood_serial "
- "demo_stokes-taylor-hood_mpi "
- "demo_subdomains_serial "
- "demo_advection-diffusion_serial "
- "demo_advection-diffusion_mpi "
- "demo_auto-adaptive-navier-stokes_serial "
- "demo_contact-vi-snes_serial "
- "demo_contact-vi-snes_mpi "
- "demo_contact-vi-tao_serial "
- "demo_contact-vi-tao_mpi "
- "demo_curl-curl_serial "
- "demo_curl-curl_mpi "
- "demo_dg-advection-diffusion_serial "
- "demo_dg-advection-diffusion_mpi "
- "demo_elasticity_serial "
- "demo_elasticity_mpi "
- "demo_elastodynamics_serial "
- "demo_elastodynamics_mpi "
- "demo_lift-drag_serial "
- "demo_lift-drag_mpi "
- "demo_mesh-quality_serial "
- "demo_mesh-quality_mpi "
- "demo_multimesh-stokes_serial "
- ")\n") port)))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "make" "unittests")
- (invoke "make" "demos")
- (invoke "ctest" "-R" "unittests")
- (invoke "ctest" "-R" "demo" "-R" "serial")
- (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
+ (list
+ #:configure-flags
+ #~`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF" "-DDOLFIN_ENABLE_HDF5:BOOL=ON"
+ "-DDOLFIN_ENABLE_MPI:BOOL=ON"
+ "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
+ "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
+ "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
+ "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'patch-usr-bin-file 'mpi-setup
+ #$%openmpi-setup)
+ (add-after 'patch-source-shebangs 'set-paths
+ (lambda _
+ ;; Define paths to store locations.
+ (setenv "BLAS_DIR"
+ #$(this-package-input "openblas"))
+ (setenv "CATCH_DIR"
+ #$(this-package-input "catch"))
+ (setenv "LAPACK_DIR"
+ #$(this-package-input "openblas"))
+ (setenv "PETSC_DIR"
+ #$(this-package-input "petsc"))
+ (setenv "SLEPC_DIR"
+ #$(this-package-input "slepc"))
+ (setenv "SCOTCH_DIR"
+ #$(this-package-input "scotch"))
+ (setenv "SUNDIALS_DIR"
+ #$(this-package-input "sundials"))
+ (setenv "UMFPACK_DIR"
+ #$(this-package-input "suitesparse"))))
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; The Dolfin repository uses git-lfs, whereby web links are
+ ;; substituted for large files. Only the links are downloaded.
+ ;; The tests that require the absent meshes cannot run and are
+ ;; skipped.
+ ;;
+ ;; One serial test fails and is skipped.
+ ;; i) demo_multimesh-stokes_serial:
+ ;; Warning: Found no facets matching domain for boundary
+ ;; condition.
+ ;;
+ ;; One mpi test fails and is skipped.
+ ;; i) demo_stokes-iterative_mpi:
+ ;; The MPI_Comm_rank() function was called before MPI_INIT was
+ ;; invoked.
+ (call-with-output-file "CTestCustom.cmake"
+ (lambda (port)
+ (display (string-append "set(CTEST_CUSTOM_TESTS_IGNORE "
+ "demo_bcs_serial "
+ "demo_bcs_mpi "
+ "demo_eigenvalue_serial "
+ "demo_eigenvalue_mpi "
+ "demo_navier-stokes_serial "
+ "demo_navier-stokes_mpi "
+ "demo_stokes-taylor-hood_serial "
+ "demo_stokes-taylor-hood_mpi "
+ "demo_subdomains_serial "
+ "demo_advection-diffusion_serial "
+ "demo_advection-diffusion_mpi "
+ "demo_auto-adaptive-navier-stokes_serial "
+ "demo_contact-vi-snes_serial "
+ "demo_contact-vi-snes_mpi "
+ "demo_contact-vi-tao_serial "
+ "demo_contact-vi-tao_mpi "
+ "demo_curl-curl_serial "
+ "demo_curl-curl_mpi "
+ "demo_dg-advection-diffusion_serial "
+ "demo_dg-advection-diffusion_mpi "
+ "demo_elasticity_serial "
+ "demo_elasticity_mpi "
+ "demo_elastodynamics_serial "
+ "demo_elastodynamics_mpi "
+ "demo_lift-drag_serial "
+ "demo_lift-drag_mpi "
+ "demo_mesh-quality_serial "
+ "demo_mesh-quality_mpi "
+ "demo_multimesh-stokes_serial "
+ "demo_stokes-iterative_mpi"
+ ")\n") port)))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "make" "unittests")
+ (invoke "make" "demos")
+ (invoke "ctest" "-R" "unittests")
+ (invoke "ctest" "-R" "demo" "-R" "serial")
+ (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
(home-page "https://bitbucket.org/fenics-project/dolfin/")
(synopsis "Problem solving environment for differential equations")
(description
- "DOLFIN is a computational framework for finding numerical
+ "DOLFIN is a computational framework for finding numerical
solutions to problems described by differential equations. Numerical
models in DOLFIN are constructed using general families of finite
elements. Data structures are provided for discretizing the governing
@@ -896,17 +891,15 @@ (define-public fenics-dolfin
;; following exceptions:
;;
;; public-domain: dolfin/geometry/predicates.cpp
- ;; dolfin/geometry/predicates.h
+ ;; dolfin/geometry/predicates.h
;;
;; zlib: dolfin/io/base64.cpp
- ;; dolfin/io/base64.h
+ ;; dolfin/io/base64.h
;;
;; expat: dolfin/io/pugiconfig.hpp
- ;; dolfin/io/pugixml.cpp
- ;; dolfin/io/pugixml.hpp
- (license (list license:public-domain
- license:zlib
- license:expat
+ ;; dolfin/io/pugixml.cpp
+ ;; dolfin/io/pugixml.hpp
+ (license (list license:public-domain license:zlib license:expat
license:lgpl3+))))
(define-public fenics
--
2.39.5
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.