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>
View this message in rfc822 format
From: help-debbugs <at> gnu.org (GNU bug Tracking System) To: Andreas Enge <andreas <at> enge.fr> Cc: tracker <at> debbugs.gnu.org Subject: bug#78878: closed ([PATCH] gnu:fenics-dolfin: Fix build with hdf5 <at> 1.14.) Date: Sat, 28 Jun 2025 14:39:02 +0000
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Your message dated Sat, 28 Jun 2025 16:38:24 +0200 with message-id <aF_-YCwUwr4nv9q2 <at> jurong> and subject line Re: [PATCH] gnu:fenics-dolfin: Fix build with hdf5 <at> 1.14. has caused the debbugs.gnu.org bug report #78878, regarding [PATCH] gnu:fenics-dolfin: Fix build with hdf5 <at> 1.14. to be marked as done. (If you believe you have received this mail in error, please contact help-debbugs <at> gnu.org.) -- 78878: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=78878 GNU Bug Tracking System Contact help-debbugs <at> gnu.org with problems
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From: Paul Garlick <pgarlick <at> tourbillion-technology.com> To: guix-patches <at> gnu.org Cc: Paul Garlick <pgarlick <at> tourbillion-technology.com> Subject: [PATCH] gnu:fenics-dolfin: Fix build with hdf5 <at> 1.14. Date: Mon, 23 Jun 2025 17:58:49 +0100* gnu/packages/patches/fenics-dolfin-hdf5-version-check.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/simulation.scm (fenics-dolfin)[source]: Use it. --- gnu/local.mk | 1 + .../fenics-dolfin-hdf5-version-check.patch | 26 ++ gnu/packages/simulation.scm | 270 +++++++++--------- 3 files changed, 158 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..451e305fc8 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -744,143 +744,137 @@ (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. 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"))))))) (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 +890,15 @@ (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
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From: Andreas Enge <andreas <at> enge.fr> To: Paul Garlick <pgarlick <at> tourbillion-technology.com> Cc: 78878-done <at> debbugs.gnu.org Subject: Re: [PATCH] gnu:fenics-dolfin: Fix build with hdf5 <at> 1.14. Date: Sat, 28 Jun 2025 16:38:24 +0200Hello Paul, Am Fri, Jun 27, 2025 at 07:18:15PM +0100 schrieb Paul Garlick: > Thanks, I have been able to repeat this failure. > It seems to be intermittent, possibly related to the so-called "static > initialization order fiasco". Something to investigate on another day, > perhaps. > In the meantime, I have added this test to the list of skipped tests > and re-submitted the patch. that sounds very reasonable, I could build and have pushed the commit. Thank you for all that work! Andreas
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