[bug#78878] gnu:fenics-dolfin: Fix build with hdf5@1.14.
Commit Message
* 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
Comments
Hello Paul,
thanks a lot for this patch! It looks generally good, but I get one test
failure on my own machine:
Start 26: demo_stokes-iterative_mpi
13/38 Test #26: demo_stokes-iterative_mpi ..............***Failed 142.07 sec
...
97% tests passed, 1 tests failed out of 38
Total Test time (real) = 1215.38 sec
The following tests FAILED:
26 - demo_stokes-iterative_mpi (Failed)
Errors while running CTest
It has not yet been built on QA.
Andreas
@@ -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 \
new file mode 100644
@@ -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);
@@ -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