GNU bug report logs - #77195
fenics-dolfin@2019.1.0.post0: Fails to build, deprecated upstream.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: <bug-guix <at> gnu.org>
Cc: ludo <at> gnu.org, pgarlick <at> tourbillion-technology.com, efraim <at> flashner.co.il
Subject: fenics-dolfin <at> 2019.1.0.post0: Fails to build, deprecated upstream.
Date: Sun, 23 Mar 2025 00:04:58 +0000

[Message part 1 (text/plain, inline)]

Hi,

While checking the full python-science collection build state I've faced
with fenics-dolfin not building for a long time; upstream introduced a
fresh fork: <https://bitbucket.org/fenics-project/dolfin> ->
<https://github.com/FEniCS/dolfinx> which might need some packaging
efforts to bring it in.

I've fixed the build of python-fenics-fiat, but fenics-dolfin still
failes to build.
--8<---------------cut here---------------start------------->8---
 Generation 86   Mar 20 2025 08:00:04    (current)
  guix 77ff73a
    repository URL: https://git.savannah.gnu.org/git/guix.git
    branch: master
    commit: 77ff73a920759437639e8eb77601e51409fefefa

guix refresh --list-dependent fenics-dolfin

Building the following 2 packages would ensure 3 dependent packages are
rebuilt: python-vedo <at> 2022.2.0 python-dolfin-adjoint <at> 2019.1.0
--8<---------------cut here---------------end--------------->8---

CC everytone paticipated in <https://issues.guix.gnu.org/33059>

--
Oleg

[signature.asc (application/pgp-signature, inline)]

Message #8 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: Andreas Enge <andreas <at> enge.fr>, pgarlick <at> tourbillion-technology.com,
 77195 <at> debbugs.gnu.org, efraim <at> flashner.co.il
Subject: Re: bug#77195: fenics-dolfin <at> 2019.1.0.post0: Fails to build,
 deprecated upstream.
Date: Mon, 31 Mar 2025 22:31:36 +0200

Hi Oleg,

Sharlatan Hellseher <sharlatanus <at> gmail.com> skribis:

> While checking the full python-science collection build state I've faced
> with fenics-dolfin not building for a long time; upstream introduced a
> fresh fork: <https://bitbucket.org/fenics-project/dolfin> ->
> <https://github.com/FEniCS/dolfinx> which might need some packaging
> efforts to bring it in.
>
> I've fixed the build of python-fenics-fiat, but fenics-dolfin still
> failes to build.

(Cc: Andreas, who stumbled upon this build failure today.)

I think we can remove ‘fenics-dolfin’ in accordance with the deprecation
policy.

Ludo’.

Message #11 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77195 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 Andreas Enge <andreas <at> enge.fr>, efraim <at> flashner.co.il
Subject: [PATCH 0/7] Remove fenics
Date: Mon, 31 Mar 2025 23:52:49 +0200

Indeed, comments in our source code say that the fenics project has been
dormant for three years now. I think fenics-dolfin has not built for
months, probably years. So I suppose that nobody actually uses the
fenics packages in Guix, and I would suggest to remove them all on or
after May 1st. Patch series following.

PS: Indeed, years ago. See here:
    https://issues.guix.gnu.org/57143

Andreas Enge (7):
  gnu: Remove python-dolfin-adjoint.
  gnu: Remove fenics.
  gnu: Remove fenics-dolfin.
  gnu: Remove python-fenics-ffc.
  gnu: Remove python-fenics-dijitso.
  gnu: Remove python-fenics-ufl.
  gnu: Remove python-fenics-fiat.

 gnu/packages/simulation.scm | 576 ------------------------------------
 1 file changed, 576 deletions(-)


base-commit: 5ef3295c8fd8af9beda6f1f30a899044951cda0c
-- 
2.49.0

Message #14 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77195 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 Andreas Enge <andreas <at> enge.fr>, efraim <at> flashner.co.il
Subject: [PATCH 1/7] gnu: Remove python-dolfin-adjoint.
Date: Mon, 31 Mar 2025 23:52:50 +0200

* gnu/packages/simulation.scm (python-dolfin-adjoint): Delete variable.

Change-Id: Ia2bec142747a44a74cf35145838c9c5d440a8a4b
---
 gnu/packages/simulation.scm | 92 -------------------------------------
 1 file changed, 92 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index ebfe477265..161e6a85d4 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1187,98 +1187,6 @@ (define-public python-pygmsh
 command-line utility for mesh optimisation.")
     (license license:gpl3+)))
 
-(define-public python-dolfin-adjoint
-  (package
-    (name "python-dolfin-adjoint")
-    (version "2019.1.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/dolfin-adjoint/pyadjoint")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; One of the migration tests attempts to call openmpi
-           ;; recursively and fails.  See
-           ;; https://bitbucket.org/mpi4py/mpi4py/issues/95.  Run the
-           ;; test sequentially instead.
-           (with-directory-excursion "tests/migration/optimal_control_mms"
-             (substitute* "test_optimal_control_mms.py"
-               (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") "")))
-           ;; Result files are regenerated in the check phase.
-           (delete-file-recursively
-            "tests/migration/viscoelasticity/test-results")))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      #~(list
-         ;; Ignore tests which require missing packages and/or failed during
-         ;; tests collection.
-         "--ignore=tests/firedrake_adjoint/test_assignment.py"
-         "--ignore=tests/firedrake_adjoint/test_burgers_newton.py"
-         "--ignore=tests/firedrake_adjoint/test_dynamic_meshes.py"
-         "--ignore=tests/firedrake_adjoint/test_hessian.py"
-         "--ignore=tests/firedrake_adjoint/test_reduced_functional.py"
-         "--ignore=tests/firedrake_adjoint/test_shape_derivatives.py"
-         "--ignore=tests/firedrake_adjoint/test_solving.py"
-         "--ignore=tests/firedrake_adjoint/test_tlm.py"
-         "--ignore=tests/migration/burgers_newton/test_burgers_newton.py"
-         "--ignore=tests/migration/linear_solver/test_linear_solver.py"
-         "--ignore=tests/migration/optimization_scipy/test_optimization_scipy.py"
-         "--ignore=tests/migration/projection/test_projection.py"
-         "--ignore=tests/migration/reduced_functional/test_reduced_functional.py"
-         "--ignore=tests/migration/split/test_split.py"
-         "-k" (string-append "not test_read_checkpoint"
-                             " and not test_krylov_solver_preconditioner_function_ctrl"))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'build 'mpi-setup #$%openmpi-setup)
-          (add-before 'check 'set-environment-variables
-            (lambda _
-              (setenv "HOME" (getcwd))))
-          (add-after 'install 'install-doc
-            (lambda _
-              (let* ((doc (string-append #$output "/share/doc/" #$name "-" #$version))
-                     (examples (string-append doc "/examples")))
-                (mkdir-p examples)
-                (copy-recursively "examples" examples))))
-          ;; Remove 'sanity-check, because it tries to import
-          ;; firedrake_adjoint after importing fenics_adjoint.
-          ;; Both load a module named 'backend' and firedrake_adjoint
-          ;; fails with an ImportError if it sees that the backend module
-          ;; has already been loaded.
-          (delete 'sanity-check))))
-    (inputs
-     (list fenics openmpi pybind11))
-    (native-inputs
-     (list pkg-config
-           python-coverage
-           python-decorator
-           python-flake8
-           python-pkgconfig
-           python-pytest))
-    (propagated-inputs
-     (list python-scipy))
-    (home-page "https://www.dolfin-adjoint.org")
-    (synopsis "Automatic differentiation library")
-    (description
-     "@code{python-dolfin-adjoint} is a solver of differential equations
-associated with a governing system and a functional of interest.  Working from
-the forward model the solver automatically derives the discrete adjoint and
-tangent linear models.  These additional models are key ingredients in many
-algorithms such as data assimilation, optimal control, sensitivity analysis,
-design optimisation and error estimation.  The dolfin-adjoint project provides
-the necessary tools and data structures for cases where the forward model is
-implemented in @code{fenics} or
-@url{https://firedrakeproject.org,firedrake}.")
-    (license license:lgpl3)))
-
 (define %commonroad-dont-install-license-at-root
   #~(substitute* "setup.py"
       (("data_files=\\[\\('.', \\['LICENSE.txt'\\]\\)\\],")
-- 
2.49.0

Message #17 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77195 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 Andreas Enge <andreas <at> enge.fr>, efraim <at> flashner.co.il
Subject: [PATCH 3/7] gnu: Remove fenics-dolfin.
Date: Mon, 31 Mar 2025 23:52:52 +0200

* gnu/packages/simulation.scm (fenics-dolfin): Delete variable.

Change-Id: If3eed285af25544a2369afecd6c525b160804d78
---
 gnu/packages/simulation.scm | 170 ------------------------------------
 1 file changed, 170 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 102cbf8977..c5345c934f 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -739,176 +739,6 @@ (define-public python-fenics-ffc
     ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'.
     (license (list license:public-domain license:lgpl3+))))
 
-(define-public fenics-dolfin
-  (package
-    (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
-                              "$ENV{CATCH_DIR}/include" back "\n")))))))
-    (build-system cmake-build-system)
-    (inputs
-     (list openblas
-           boost
-           eigen
-           hdf5-parallel-openmpi
-           libxml2
-           openmpi
-           python-3
-           pt-scotch32
-           suitesparse
-           sundials-openmpi
-           zlib))
-    (native-inputs
-     (list catch-framework pkg-config))
-    (propagated-inputs
-     (list python-fenics-ffc petsc-openmpi slepc-openmpi))
-    (arguments
-     (list #:configure-flags #~`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
-                                 "-DDOLFIN_ENABLE_HDF5:BOOL=ON"
-                                 "-DDOLFIN_ENABLE_MPI:BOOL=ON"
-                                 "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
-                                 "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
-                                 "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
-                                 "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'patch-usr-bin-file 'mpi-setup
-                 #$%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")))))))
-    (home-page "https://bitbucket.org/fenics-project/dolfin/")
-    (synopsis "Problem solving environment for differential equations")
-    (description
-      "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
-system on a computational mesh.  A compact syntax, similar to
-mathematical notation, is made available for defining function spaces
-and expressing variational forms.  Interfaces to specialized matrix
-solvers are provided for solving the resultant linear systems.
-
-@code{fenics-dolfin} is part of the FEniCS project.  It is the C++
-user interface to the FEniCS core components and external libraries.")
-    ;; The source code for the DOLFIN C++ library is licensed under the
-    ;; GNU Lesser General Public License, version 3 or later, with the
-    ;; following exceptions:
-    ;;
-    ;; public-domain: dolfin/geometry/predicates.cpp
-    ;;                dolfin/geometry/predicates.h
-    ;;
-    ;; zlib:          dolfin/io/base64.cpp
-    ;;                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
-                   license:lgpl3+))))
-
 (define-public fullswof-2d
   (let ((revision 505)
         (release "1.09.01"))
-- 
2.49.0

Message #20 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77195 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 Andreas Enge <andreas <at> enge.fr>, efraim <at> flashner.co.il
Subject: [PATCH 5/7] gnu: Remove python-fenics-dijitso.
Date: Mon, 31 Mar 2025 23:52:54 +0200

* gnu/packages/simulation.scm (python-fenics-dijitso): Delete variable.

Change-Id: Ie0b071dd08b7185d37044a1d4941c71793e16b8c
---
 gnu/packages/simulation.scm | 50 -------------------------------------
 1 file changed, 50 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 5aef3da133..b32bf997df 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -554,56 +554,6 @@ (define-public esmini
 some support for generating and analysing traffic scenarios..")
     (license license:mpl2.0)))
 
-(define-public python-fenics-dijitso
-  (package
-    (name "python-fenics-dijitso")
-    (version "2019.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "fenics-dijitso" version))
-       (sha256
-        (base32 "0lhqsq8ypdak0ahr2jnyvg07yrqp6wicjxi6k56zx24wp3qg60sc"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'build 'mpi-setup
-            #$%openmpi-setup)
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (setenv "HOME" "/tmp")
-                (with-directory-excursion "test"
-                  ;; Disable parallel tests to avoid race condition.  See
-                  ;; https://github.com/pytest-dev/pytest-cov/issues/237.
-                  (substitute* "runtests.sh"
-                    (("for p in 1 4 8 16; do") "for p in 1; do"))
-                  (invoke "./runtests.sh"))))))))
-    (native-inputs
-     (list python-pytest
-           python-pytest-cov
-           python-setuptools
-           python-wheel))
-    (inputs
-     (list openmpi python-numpy))
-    (propagated-inputs
-     (list python-mpi4py))
-    (home-page "https://bitbucket.org/fenics-project/dijitso/")
-    (synopsis "Distributed just-in-time building of shared libraries")
-    (description
-     "Dijitso provides a core component of the @code{FEniCS} framework,
-namely the just-in-time compilation of C++ code that is generated from
-Python modules.  It is called from within a C++ library, using ctypes
-to import the dynamic shared library directly.
-
-As long as the compiled code can provide a simple factory function to
-a class implementing a predefined C++ interface, there is no limit to
-the complexity of that interface.  Parallel support depends on the
-@code{mpi4py} interface.")
-    (license license:lgpl3+)))
-
 (define-public python-fenics-ufl
   (package
     (name "python-fenics-ufl")
-- 
2.49.0

Message #23 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77195 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 Andreas Enge <andreas <at> enge.fr>, efraim <at> flashner.co.il
Subject: [PATCH 2/7] gnu: Remove fenics.
Date: Mon, 31 Mar 2025 23:52:51 +0200

* gnu/packages/simulation.scm (fenics): Delete variable.

Change-Id: I3d34832d935c2a6ebcd6ec71e6e9a7167a0a59f6
---
 gnu/packages/simulation.scm | 129 ------------------------------------
 1 file changed, 129 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 161e6a85d4..102cbf8977 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -909,135 +909,6 @@ (define-public fenics-dolfin
                    license:expat
                    license:lgpl3+))))
 
-(define-public fenics
-  (package/inherit fenics-dolfin
-    (name "fenics")
-    (build-system python-build-system)
-    (inputs
-     (modify-inputs (package-inputs fenics-dolfin)
-       (delete "python")
-       (prepend pybind11 python-matplotlib)))
-    (native-inputs
-     (modify-inputs (package-native-inputs fenics-dolfin)
-       (prepend cmake-minimal python-ply python-pytest python-decorator)))
-    (propagated-inputs
-     (list fenics-dolfin
-           python-petsc4py
-           python-slepc4py
-
-           ;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at run time.
-           python-pkgconfig))
-    (arguments
-     (list #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'unpack 'relax-requirements
-                 (lambda _
-                   (substitute* "python/setup.py"
-                     (("pybind11==")
-                      "pybind11>="))))
-               (add-after 'unpack 'set-dolfin-pc-file-name
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   ;; Instead of cluttering the user's 'PKG_CONFIG_PATH' environment
-                   ;; variable, hard-code the 'dolfin.pc' absolute file name.
-                   (let ((pc-file (search-input-file inputs
-                                                     "/lib/pkgconfig/dolfin.pc")))
-                     (substitute* "python/dolfin/jit/jit.py"
-                       (("pkgconfig\\.parse\\(\"dolfin\"\\)")
-                        (string-append "pkgconfig.parse(\"" pc-file
-                                       "\")"))))))
-               (add-after 'patch-source-shebangs 'set-paths
-                 (lambda _
-                   ;; Define paths to store locations.
-                   (setenv "PYBIND11_DIR" #$(this-package-input "pybind11"))
-                   ;; Move to python sub-directory.
-                   (chdir "python")))
-               (add-after 'build 'mpi-setup
-                 #$%openmpi-setup)
-               (add-before 'check 'pre-check
-                 (lambda _
-                   ;; Exclude three tests that generate
-                   ;; 'NotImplementedError' in matplotlib version 3.1.2.
-                   ;; See
-                   ;; <https://github.com/matplotlib/matplotlib/issues/15382>.
-                   ;; Also exclude tests that require meshes supplied by
-                   ;; git-lfs.
-                   (substitute* "demo/test.py"
-                     (("(.*stem !.*)" line)
-                      (string-append line
-                                     "\n"
-                                     "excludeList = [\n"
-                                     "'built-in-meshes', \n"
-                                     "'hyperelasticity', \n"
-                                     "'elasticity', \n"
-                                     "'multimesh-quadrature', \n"
-                                     "'multimesh-marking', \n"
-                                     "'mixed-poisson-sphere', \n"
-                                     "'mesh-quality', \n"
-                                     "'lift-drag', \n"
-                                     "'elastodynamics', \n"
-                                     "'dg-advection-diffusion', \n"
-                                     "'curl-curl', \n"
-                                     "'contact-vi-tao', \n"
-                                     "'contact-vi-snes', \n"
-                                     "'collision-detection', \n"
-                                     "'buckling-tao', \n"
-                                     "'auto-adaptive-navier-stokes', \n"
-                                     "'advection-diffusion', \n"
-                                     "'subdomains', \n"
-                                     "'stokes-taylor-hood', \n"
-                                     "'stokes-mini', \n"
-                                     "'navier-stokes', \n"
-                                     "'eigenvalue']\n"
-                                     "demos = ["
-                                     "d for d in demos if d[0].stem not in "
-                                     "excludeList]\n")))
-                   (setenv "HOME"
-                           (getcwd))
-                   ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
-                   (setenv "OPENBLAS_NUM_THREADS" "1")))
-               (replace 'check
-                 (lambda* (#:key tests? #:allow-other-keys)
-                   (when tests?
-                     (with-directory-excursion "test"
-                       (invoke "pytest"
-                               "unit"
-                               ;; The test test_snes_set_from_options() in the file
-                               ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
-                               "--ignore"
-                               "unit/nls/test_PETScSNES_solver.py"
-                               ;; Fails with a segfault.
-                               "--ignore"
-                               "unit/io/test_XDMF.py")))))
-               (add-after 'install 'install-demo-files
-                 (lambda* (#:key outputs #:allow-other-keys)
-                   (let* ((demos (string-append (assoc-ref outputs "out")
-                                                "/share/python-dolfin/demo")))
-                     (mkdir-p demos)
-                     (with-directory-excursion "demo"
-                       (for-each (lambda (file)
-                                   (let* ((dir (dirname file))
-                                          (tgt-dir (string-append
-                                                    demos "/" dir)))
-                                     (unless (equal? "." dir)
-                                       (mkdir-p tgt-dir)
-                                       (install-file file tgt-dir))))
-                                 (find-files "." ".*\\.(py|gz|xdmf)$")))))))))
-    (home-page "https://fenicsproject.org/")
-    (synopsis "High-level environment for solving differential equations")
-    (description
-      "@code{fenics} is a computing platform for solving general classes of
-problems that involve differential equations.  @code{fenics} facilitates
-access to efficient methods for dealing with ordinary differential
-equations (ODEs) and partial differential equations (PDEs).  Systems of
-equations such as these are commonly encountered in areas of engineering,
-mathematics and the physical sciences.  It is particularly well-suited to
-problems that can be solved using the Finite Element Method (FEM).
-
-@code{fenics} is the top level of the set of packages that are developed
-within the FEniCS project.  It provides the python user interface to the
-FEniCS core components and external libraries.")
-    (license license:lgpl3+)))
-
 (define-public fullswof-2d
   (let ((revision 505)
         (release "1.09.01"))
-- 
2.49.0

Message #26 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77195 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 Andreas Enge <andreas <at> enge.fr>, efraim <at> flashner.co.il
Subject: [PATCH 4/7] gnu: Remove python-fenics-ffc.
Date: Mon, 31 Mar 2025 23:52:53 +0200

* gnu/packages/simulation.scm (python-fenics-ffc): Delete variable.

Change-Id: I4308e0e9a7232e320988962bd7a908f7c9d01a47
---
 gnu/packages/simulation.scm | 48 -------------------------------------
 1 file changed, 48 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index c5345c934f..5aef3da133 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -691,54 +691,6 @@ (define-public python-fenics-fiat
 FIAT is part of the FEniCS Project.")
     (license license:lgpl3+)))
 
-(define-public python-fenics-ffc
-  (package
-    (name "python-fenics-ffc")
-    (version "2019.1.0.post0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "fenics-ffc" version))
-        (sha256
-          (base32
-            "1f2a44ha65fg3a1prrbrsz4dgvibsv0j5c3pi2m52zi93bhwwgg9"))))
-    (build-system python-build-system)
-    (native-inputs
-     (list python-pytest))
-    (propagated-inputs
-     (list python-fenics-dijitso python-fenics-fiat python-fenics-ufl))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (setenv "HOME" (getcwd))
-             (with-directory-excursion "test"
-               ;; FIXME: the tests in subdirectory
-               ;; 'unit/ufc/finite_element' require the ffc_factory
-               ;; extension module.  This module, located in the 'libs'
-               ;; subdirectory, needs to be built and made accessible
-               ;; prior to running the tests.
-               (invoke "py.test" "unit/" "--ignore=unit/ufc/")
-               (with-directory-excursion "uflacs"
-                 (invoke "py.test" "unit/")))
-             #t)))))
-    (home-page "https://bitbucket.org/fenics-project/ffc/")
-    (synopsis "Compiler for finite element variational forms")
-    (description "The FEniCS Form Compiler (FFC) is a compiler for
-finite element variational forms.  From a high-level description of
-the form, it generates efficient low-level C++ code that can be used
-to assemble the corresponding discrete operator (tensor).  In
-particular, a bilinear form may be assembled into a matrix and a
-linear form may be assembled into a vector.  FFC may be used either
-from the command line (by invoking the @code{ffc} command) or as a
-Python module (@code{import ffc}).
-
-FFC is part of the FEniCS Project.")
-    ;; There are two files released with a public domain licence;
-    ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'.
-    (license (list license:public-domain license:lgpl3+))))
-
 (define-public fullswof-2d
   (let ((revision 505)
         (release "1.09.01"))
-- 
2.49.0

Message #29 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77195 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 Andreas Enge <andreas <at> enge.fr>, efraim <at> flashner.co.il
Subject: [PATCH 6/7] gnu: Remove python-fenics-ufl.
Date: Mon, 31 Mar 2025 23:52:55 +0200

* gnu/packages/simulation.scm (python-fenics-ufl): Delete variable.

Change-Id: Ib80ed4ef5789e5815537731b828c492919bff697
---
 gnu/packages/simulation.scm | 34 ----------------------------------
 1 file changed, 34 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index b32bf997df..ce38f30c04 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -554,40 +554,6 @@ (define-public esmini
 some support for generating and analysing traffic scenarios..")
     (license license:mpl2.0)))
 
-(define-public python-fenics-ufl
-  (package
-    (name "python-fenics-ufl")
-    (version "2019.1.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "fenics-ufl" version))
-        (sha256
-          (base32
-            "10dz8x3lm68x2w3kkqcjask38h0zkhhak26jdbkppr8g9y8wny7p"))))
-    (build-system python-build-system)
-    (inputs
-     (list python-numpy))
-    (native-inputs
-     (list python-pytest))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (invoke "py.test" "test"))))))
-    (home-page "https://bitbucket.org/fenics-project/ufl/")
-    (synopsis "Unified language for form-compilers")
-    (description "The Unified Form Language (UFL) is a domain specific
-language for declaration of finite element discretizations of
-variational forms.  More precisely, it defines a flexible interface
-for choosing finite element spaces and defining expressions for weak
-forms in a notation close to mathematical notation.
-
-UFL is part of the FEniCS Project.")
-    (license license:lgpl3+)))
-
-
 ;; XXX: This package is quite dated and upstream no longer maintains it: "This
 ;; repository was archived by the owner on Feb 21, 2022. It is now read-only."
 ;; <https://bitbucket.org/fenics-project/fiat> ->
-- 
2.49.0

Message #32 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77195 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 Andreas Enge <andreas <at> enge.fr>, efraim <at> flashner.co.il
Subject: [PATCH 7/7] gnu: Remove python-fenics-fiat.
Date: Mon, 31 Mar 2025 23:52:56 +0200

* gnu/packages/simulation.scm (python-fenics-fiat): Delete variable.

Change-Id: I7f2d5b11aeff850718327112e206b54c973e9d4e
---
 gnu/packages/simulation.scm | 53 -------------------------------------
 1 file changed, 53 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index ce38f30c04..b540ee1919 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -554,59 +554,6 @@ (define-public esmini
 some support for generating and analysing traffic scenarios..")
     (license license:mpl2.0)))
 
-;; XXX: This package is quite dated and upstream no longer maintains it: "This
-;; repository was archived by the owner on Feb 21, 2022. It is now read-only."
-;; <https://bitbucket.org/fenics-project/fiat> ->
-;; <https://github.com/FEniCS/fiat> while providing a new refactored fork
-;; <https://github.com/firedrakeproject/fiat>.
-(define-public python-fenics-fiat
-  (package
-    (name "python-fenics-fiat")
-    (version "2019.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "fenics-fiat" version))
-       (sha256
-        (base32 "13sc7lma3d2mh43an7i4kkdbbk4cmvxjk45wi43xnjd7qc38zg4b"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      #~(list
-         ;; FIXME: three FIAT test modules are known to fail with recent
-         ;; versions of pytest (>= 4).  These are skipped for FIAT version
-         ;; 2019.1.0 pending an upstream pull request. For details see request
-         ;; #59 at https://bitbucket.org/fenics-project/fiat/.
-         "--ignore=test/regression/"
-         "--ignore=test/unit/test_quadrature.py"
-         "--ignore=test/unit/test_reference_element.py"
-         "-k" (string-join
-               (list "not test_nodality"
-                     "test_basis_values")
-               " and not "))))
-    (native-inputs
-     (list python-pytest
-           python-setuptools
-           python-wheel))
-    (propagated-inputs
-     (list python-numpy
-           python-sympy))
-    (home-page "https://bitbucket.org/fenics-project/fiat/")
-    (synopsis "Tabulation of finite element function spaces")
-    (description
-     "The FInite element Automatic Tabulator (FIAT) supports generation of
-arbitrary order instances of the Lagrange elements on lines, triangles, and
-tetrahedra.  It is also capable of generating arbitrary order instances of
-Jacobi-type quadrature rules on the same element shapes.  Further, H(div) and
-H(curl) conforming finite element spaces such as the families of
-Raviart-Thomas, Brezzi-Douglas-Marini and Nedelec are supported on triangles
-and tetrahedra.  Upcoming versions will also support Hermite and nonconforming
-elements.
-
-FIAT is part of the FEniCS Project.")
-    (license license:lgpl3+)))
-
 (define-public fullswof-2d
   (let ((revision 505)
         (release "1.09.01"))
-- 
2.49.0

Message #35 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Andreas Enge <andreas <at> enge.fr>
Cc: sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 77195 <at> debbugs.gnu.org, efraim <at> flashner.co.il
Subject: Re: [PATCH 0/7] Remove fenics
Date: Tue, 01 Apr 2025 14:33:24 +0200

Hi,

Andreas Enge <andreas <at> enge.fr> skribis:

> Indeed, comments in our source code say that the fenics project has been
> dormant for three years now. I think fenics-dolfin has not built for
> months, probably years. So I suppose that nobody actually uses the
> fenics packages in Guix, and I would suggest to remove them all on or
> after May 1st. Patch series following.

My understanding of <https://issues.guix.gnu.org/77195> is that only
‘fenics-dolfin’ fails to build, so perhaps we could limit to this one
package?

No strong opinion though.

Ludo’.

Message #38 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: Andreas Enge <andreas <at> enge.fr>, pgarlick <at> tourbillion-technology.com,
 77195 <at> debbugs.gnu.org, Efraim Flashner <efraim <at> flashner.co.il>
Subject: Re: [PATCH 0/7] Remove fenics
Date: Tue, 1 Apr 2025 13:48:26 +0100

[Message part 1 (text/plain, inline)]

The project is still alive but distracted from other sources now
 (listed above), I think we may sacrifice deprecated variant and will
 check how to bring a maintained version. No strong opinion to
keep still working ones or delete them.

VCS: https://github.incerto.xyz/; https://git.sr.ht/~hellseher/
GPG: 9847 81DE 689C 21C2 6418 0867 76D7 27BF F62C D2B5

… наш разум - превосходная объяснительная машина которая способна найти
смысл почти в чем угодно, истолковать любой феномен, но совершенно не в
состоянии принять мысль о непредсказуемости.

On Tue, 1 Apr 2025, 13:34 Ludovic Courtès, <ludo <at> gnu.org> wrote:

> Hi,
>
> Andreas Enge <andreas <at> enge.fr> skribis:
>
> > Indeed, comments in our source code say that the fenics project has been
> > dormant for three years now. I think fenics-dolfin has not built for
> > months, probably years. So I suppose that nobody actually uses the
> > fenics packages in Guix, and I would suggest to remove them all on or
> > after May 1st. Patch series following.
>
> My understanding of <https://issues.guix.gnu.org/77195> is that only
> ‘fenics-dolfin’ fails to build, so perhaps we could limit to this one
> package?
>
> No strong opinion though.
>
> Ludo’.
>

[Message part 2 (text/html, inline)]

Message #41 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: sharlatanus <at> gmail.com, pgarlick <at> tourbillion-technology.com,
 77195 <at> debbugs.gnu.org, efraim <at> flashner.co.il
Subject: Re: [PATCH 0/7] Remove fenics
Date: Tue, 1 Apr 2025 15:54:23 +0200

Am Tue, Apr 01, 2025 at 02:33:24PM +0200 schrieb Ludovic Courtès:
> My understanding of <https://issues.guix.gnu.org/77195> is that only
> ‘fenics-dolfin’ fails to build, so perhaps we could limit to this one
> package?
> No strong opinion though.

Me neither. I tend to rather the other side, why should we keep a
package that is outdated and that probably nobody uses anymore, but
that uses project resources (builds; people trying to fix it when it
potentially stops building, which is bound to happen with unmaintained
software)?

So I would drop them all unless someone speaks up who uses any of them
(or knows someone else who does).

Andreas

Message #44 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Paul Garlick <pgarlick <at> tourbillion-technology.com>
To: Andreas Enge <andreas <at> enge.fr>, Ludovic Courtès
 <ludo <at> gnu.org>
Cc: sharlatanus <at> gmail.com, efraim <at> flashner.co.il, 77195 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/7] Remove fenics
Date: Wed, 02 Apr 2025 15:31:29 +0100

Hi Guix,

Thank you for the notification that fenics-dolfin is not currently
building.

It has been a while :-) but I plan to resume maintaining the fenics
packages in Guix by the end of this month.

A quick look at the build log for fenics-dolfin suggests that the
problem is VTK-related; possibly a new VTK version containing an
updated function.

In terms of the upstream project, fenicsx will replace fenics.  It has
currently reached version 0.9; the production version may be released
later this year.

I intend to package fenicsx for Guix, including its new dependencies. 
Ideally, the fenicsx and fenics packages would co-exist for a period,

Best regards,

Paul.


On Tue, 2025-04-01 at 15:54 +0200, Andreas Enge wrote:
> Am Tue, Apr 01, 2025 at 02:33:24PM +0200 schrieb Ludovic Courtès:
> > My understanding of <https://issues.guix.gnu.org/77195> is that
> > only
> > ‘fenics-dolfin’ fails to build, so perhaps we could limit to this
> > one
> > package?
> > No strong opinion though.
> 
> Me neither. I tend to rather the other side, why should we keep a
> package that is outdated and that probably nobody uses anymore, but
> that uses project resources (builds; people trying to fix it when it
> potentially stops building, which is bound to happen with
> unmaintained
> software)?
> 
> So I would drop them all unless someone speaks up who uses any of
> them
> (or knows someone else who does).
> 
> Andreas
> 

Message #47 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Paul Garlick <pgarlick <at> tourbillion-technology.com>
Cc: Ludovic Courtès <ludo <at> gnu.org>, sharlatanus <at> gmail.com,
 efraim <at> flashner.co.il, 77195 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/7] Remove fenics
Date: Wed, 7 May 2025 10:30:12 +0200

Hello Paul,

just a quick reminder concerning the fenics-dolfin and related packages;
do you think you will have the time to repair it/them (I am not sure
which packages exactly are concerned, this seems to be a little complex
of several related ones)? Or should we drop them and wait for fenicsx?

Thanks,

Andreas

Message #50 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Paul Garlick <pgarlick <at> tourbillion-technology.com>
To: Andreas Enge <andreas <at> enge.fr>
Cc: Ludovic Courtès <ludo <at> gnu.org>, sharlatanus <at> gmail.com,
 efraim <at> flashner.co.il, 77195 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/7] Remove fenics
Date: Fri, 09 May 2025 18:28:39 +0100

Hello Andreas,

Thank you for the reminder.

I am planning to look at this next week.  My feeling is that the fix is
likely to a simple
one, so it is worth doing now (as opposed to waiting for fenicsx).

Best regards,

Paul.


On Wed, 2025-05-07 at 10:30 +0200, Andreas Enge wrote:
> Hello Paul,
> 
> just a quick reminder concerning the fenics-dolfin and related
> packages;
> do you think you will have the time to repair it/them (I am not sure
> which packages exactly are concerned, this seems to be a little
> complex
> of several related ones)? Or should we drop them and wait for
> fenicsx?
> 
> Thanks,
> 
> Andreas
> 

Message #53 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Paul Garlick <pgarlick <at> tourbillion-technology.com>
Cc: Ludovic Courtès <ludo <at> gnu.org>, sharlatanus <at> gmail.com,
 efraim <at> flashner.co.il, 77195 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/7] Remove fenics
Date: Fri, 9 May 2025 20:56:03 +0200

Am Fri, May 09, 2025 at 06:28:39PM +0100 schrieb Paul Garlick:
> I am planning to look at this next week.  My feeling is that the fix is
> likely to a simple
> one, so it is worth doing now (as opposed to waiting for fenicsx).

Okay, that would be great and much appreciated! Since the package looks
complicated, I was discouraged to try it myself, so it is good to have
a specialist look at it.

Thanks,

Andreas

Message #56 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Paul Garlick <pgarlick <at> tourbillion-technology.com>
To: Andreas Enge <andreas <at> enge.fr>
Cc: Ludovic Courtès <ludo <at> gnu.org>, sharlatanus <at> gmail.com,
 efraim <at> flashner.co.il, 77195 <at> debbugs.gnu.org
Subject: Re: [PATCH 0/7] Remove fenics
Date: Thu, 15 May 2025 18:35:40 +0100

Hi Andreas,

On Fri, 2025-05-09 at 20:56 +0200, Andreas Enge wrote:
> I was discouraged to try it myself, so it is good to have
> a specialist look at it.

Aha! 

I have checked the build logs on ci.guix.gnu.org and I can see that
some of the fenics dependencies are failing to build,  Specifically,
hdf5-parallel-openmpi:

https://ci.guix.gnu.org/build/10583084/details

Three tests are now failing.  This seems to be related to a recent
commit, that re-enables Fortran support:

https://codeberg.org/guix/guix-mirror/commit/ca3be0964af171721123f97e0850b3e734a575f5

Do you know whether the commit author, Romain Garbage, is already
working on a fix?

Best regards,

Paul.

Message #59 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Romain Garbage <romain.garbage <at> inria.fr>
To: Paul Garlick <pgarlick <at> tourbillion-technology.com>
Cc: Andreas Enge <andreas <at> enge.fr>, sharlatanus <at> gmail.com,
 Ludovic Courtès <ludo <at> gnu.org>, 77195 <at> debbugs.gnu.org,
 efraim <at> flashner.co.il
Subject: Re: bug#77195: [PATCH 0/7] Remove fenics
Date: Tue, 20 May 2025 11:23:45 +0200

Hi Paul,

Paul Garlick <pgarlick <at> tourbillion-technology.com> writes:

> Three tests are now failing.  This seems to be related to a recent
> commit, that re-enables Fortran support:
>
> https://codeberg.org/guix/guix-mirror/commit/ca3be0964af171721123f97e0850b3e734a575f5

To my understanding, these tests fail in a non-reproducible way since I
managed to build 'hdf5-parallel-openmpi' on my machine.

> Do you know whether the commit author, Romain Garbage, is already
> working on a fix?

I will not have time to have a look at the issue for at least the next 2
weeks, feel free to have a look at it in the meantime and keep me
posted.

In any case, I'll keep you posted about any work I do regarding this
issue.

Best regards,
Romain

Message #62 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Romain Garbage <romain.garbage <at> inria.fr>
Cc: Ludovic Courtès <ludo <at> gnu.org>, sharlatanus <at> gmail.com,
 Paul Garlick <pgarlick <at> tourbillion-technology.com>, 77195 <at> debbugs.gnu.org,
 efraim <at> flashner.co.il
Subject: Re: bug#77195: [PATCH 0/7] Remove fenics
Date: Mon, 2 Jun 2025 10:28:31 +0200

Am Tue, May 20, 2025 at 11:23:45AM +0200 schrieb Romain Garbage:
> Paul Garlick <pgarlick <at> tourbillion-technology.com> writes:
> > Three tests are now failing.  This seems to be related to a recent
> > commit, that re-enables Fortran support:
> > https://codeberg.org/guix/guix-mirror/commit/ca3be0964af171721123f97e0850b3e734a575f5
> To my understanding, these tests fail in a non-reproducible way since I
> managed to build 'hdf5-parallel-openmpi' on my machine.

So did I before merging the patch by Romain. And now there is a
substitute on the bordeaux server, so you may give repairing/updating
fenics a try.

Andreas

Message #65 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Paul Garlick <pgarlick <at> tourbillion-technology.com>
To: Andreas Enge <andreas <at> enge.fr>, Romain Garbage <romain.garbage <at> inria.fr>
Cc: 77195 <at> debbugs.gnu.org
Subject: Re: bug#77195: [PATCH 0/7] Remove fenics
Date: Wed, 04 Jun 2025 13:14:59 +0100

Hi,

On Mon, 2025-06-02 at 10:28 +0200, Andreas Enge wrote:
> Am Tue, May 20, 2025 at 11:23:45AM +0200 schrieb Romain Garbage:
> > Paul Garlick <pgarlick <at> tourbillion-technology.com> writes:
> > > Three tests are now failing.  This seems to be related to a
> > > recent
> > > commit, that re-enables Fortran support:
> > > https://codeberg.org/guix/guix-mirror/commit/ca3be0964af171721123f97e0850b3e734a575f5
> > To my understanding, these tests fail in a non-reproducible way
> > since I
> > managed to build 'hdf5-parallel-openmpi' on my machine.
> 
> So did I before merging the patch by Romain. And now there is a
> substitute on the bordeaux server, so you may give repairing/updating
> fenics a try.

The package builds successfully on my machine too.  

Interestingly, the ci build is still failing
(https://ci.guix.gnu.org/build/10915547/details), which could be worth
a look.  However, I will attempt to fix the fenics packages next.

Best regards,

Paul.

Message #68 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Paul Garlick <pgarlick <at> tourbillion-technology.com>
To: Andreas Enge <andreas <at> enge.fr>, Romain Garbage <romain.garbage <at> inria.fr>
Cc: Ludovic Courtès <ludo <at> gnu.org>, 77195 <at> debbugs.gnu.org
Subject: Re: bug#77195: [PATCH 0/7] Remove fenics
Date: Wed, 11 Jun 2025 14:16:18 +0100

Hi Guix,

I have made some progress on the fenics packages.

First up is an update of the scalapack package, which is a dependency
of petsc-openmpi.  The current package has been failing to build, with
new test failures, for ten days or so.

I have submitted a patch that updates scalapack to version 2.2.2, the
latest release.  This is bug #78755 [0].

Best regards,

Paul.


[0]:
https://lists.gnu.org/archive/html/guix-patches/2025-06/msg00253.html

Message #71 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Paul Garlick <pgarlick <at> tourbillion-technology.com>
Cc: Ludovic Courtès <ludo <at> gnu.org>,
 Romain Garbage <romain.garbage <at> inria.fr>, 77195 <at> debbugs.gnu.org
Subject: Re: bug#77195: [PATCH 0/7] Remove fenics
Date: Wed, 11 Jun 2025 20:14:04 +0200

Am Wed, Jun 11, 2025 at 02:16:18PM +0100 schrieb Paul Garlick:
> First up is an update of the scalapack package, which is a dependency
> of petsc-openmpi.  The current package has been failing to build, with
> new test failures, for ten days or so.
> I have submitted a patch that updates scalapack to version 2.2.2, the
> latest release.  This is bug #78755 [0].

Great, this is pushed.
If you can keep me updated, I will continue following your progress and
try to push as soon as possible.

Andreas

Message #74 received at 77195 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: Romain Garbage <romain.garbage <at> inria.fr>, Paul Garlick
 <pgarlick <at> tourbillion-technology.com>
Cc: Andreas Enge <andreas <at> enge.fr>, sharlatanus <at> gmail.com,
 Ludovic Courtès <ludo <at> gnu.org>, 77195 <at> debbugs.gnu.org,
 efraim <at> flashner.co.il
Subject: hdf5-parallel-openmpi failure (was Re: bug#77195: [PATCH 0/7]
 Remove fenics)
Date: Mon, 16 Jun 2025 14:05:46 +0200

Hi,

On Tue, 20 May 2025 at 11:23, Romain Garbage <romain.garbage <at> inria.fr> wrote:

>> Three tests are now failing.  This seems to be related to a recent
>> commit, that re-enables Fortran support:
>>
>> https://codeberg.org/guix/guix-mirror/commit/ca3be0964af171721123f97e0850b3e734a575f5
>
> To my understanding, these tests fail in a non-reproducible way since I
> managed to build 'hdf5-parallel-openmpi' on my machine.

Please note that the substitute is available on

    https://guix.bordeaux.inria.fr

Well, the failure is probably hardware dependants.

Since it’s only 3 tests, maybe we could just drop them for now and make
it on ci.guix.gnu.org.

--8<---------------cut here---------------start------------->8---
99% tests passed, 3 tests failed out of 2729

Total Test time (real) = 4770.77 sec

The following tests FAILED:
	135 - MPI_TEST_t_pmulti_dset (Timeout)
	137 - MPI_TEST_t_shapesame (Timeout)
	138 - MPI_TEST_t_filters_parallel (Failed)
Errors while running CTest
--8<---------------cut here---------------end--------------->8---

Somehow, it’s only 14 packages that depends on hdf5-parallel-openmpi
which is not much but still annoying when you depends on them. :-)

Cheers,
simon

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