From 3e4b62a5af1e71eb37474ab9f719e0b9a9cc66a0 Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Tue, 13 Jul 2021 21:29:51 -0400
Subject: [PATCH] gnu: dealii: Update to 9.3.1 and clean up.
The cleanup notably:
* Builds and installs the documentation into a separate doc output (in
the process moving around some files erroneously installed into the root
directory); and
* Removes unnecessary inputs and moves some inputs into
propagated-inputs (the candidates of which were determined with a search
for "include.*LIBNAME" in include/deal.II).
* gnu/packages/maths.scm (dealii): Reword comments.
[version]: Update to 9.3.1.
[outputs]: New field including doc output.
[native-inputs]: New field.
[inputs]: Sort them. Remove p4est (deal.II interfaces with it only when
MPI is enabled). Move boost, suitesparse and tbb to...
[propagated-inputs]: ...here. New field including hdf5, which is
actually supported in deal.II without MPI.
[arguments]<#:tests?>: New argument. The tests were not being run before
anyway.
<#:configure-flags>[-DDEAL_II_COMPONENT_DOCUMENTATION]: New flag.
[-DDEAL_II_DOCREADME_RELDIR]: New flag. Prevents the LICENSE.md,
README.md, detailed.log and summary.log files from being installed in
the root directory (though note that the logs are removed in the new
remove-build-logs phase).
[-DDEAL_II_DOCHTML_RELDIR]: New flag.
[-DDEAL_II_COMPILE_EXAMPLES]: New flag.
[-DDEAL_II_EXAMPLES_RELDIR]: New flag. Prevents the examples directory
from being installed in the root directory.
[-DCMAKE_POSITION_INDEPENDENT_CODE]: Remove flag. The issue has been
resolved.
<#:phases>{remove-build-logs}: New phase.
[home-page]: Add trailing slash.
(dealii-openmpi): Use package/inherit.
[inputs]: Sort them. Remove mumps-metis-openmpi (deal.II no longer
interfaces with MUMPS). Move hdf5-parallel-openmpi, openmpi,
p4est-openmpi, petsc-openmpi and slepc-openmpi to...
[propagated-inputs]: ...here. New field.
[arguments]<#:configure-flags>: Rename cf variable to flags.
<#:phases>{mpi-setup}: Remove phase which is unused because the tests
are disabled.
---
gnu/packages/maths.scm | 95 +++++++++++++++++++++++++++---------------
1 file changed, 62 insertions(+), 33 deletions(-)
@@ -4436,40 +4436,75 @@ revised simplex and the branch-and-bound methods.")
(define-public dealii
(package
(name "dealii")
- (version "9.2.0")
+ (version "9.3.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/dealii/dealii/releases/"
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
- (base32
- "0fm4xzrnb7dfn4415j24d8v3jkh0lssi86250x2f5wgi83xq4nnh"))
+ (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6"))
(modules '((guix build utils)))
(snippet
- ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
'(begin
+ ;; Remove bundled boost, muparser, TBB and UMFPACK.
(delete-file-recursively "bundled")
#t))))
(build-system cmake-build-system)
+ (outputs '("out" "doc"))
+ (native-inputs
+ ;; Required to build the documentation.
+ `(("dot" ,graphviz)
+ ("doxygen" ,doxygen)
+ ("perl" ,perl)))
(inputs
- `(("tbb" ,tbb)
- ("zlib" ,zlib)
- ("boost" ,boost)
- ("p4est" ,p4est)
+ `(("arpack" ,arpack-ng)
("blas" ,openblas)
+ ("gfortran" ,gfortran)
("lapack" ,lapack)
- ("arpack" ,arpack-ng)
("muparser" ,muparser)
- ("gfortran" ,gfortran)
- ("suitesparse" ,suitesparse))) ;for UMFPACK
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ ;; Some scripts are installed into share/deal.II/scripts that require
+ ;; perl and python, but they are not executable (and some are missing the
+ ;; shebang line) and therefore must be explicitly passed to the
+ ;; interpreter.
+ ;; Anyway, they are meant to be used at build time, so rather than adding
+ ;; the interpreters here, any package depending on them should just add
+ ;; the requisite interpreter to its native inputs.
+ `(("boost" ,boost)
+ ("hdf5" ,hdf5)
+ ("suitesparse" ,suitesparse) ; For UMFPACK.
+ ("tbb" ,tbb)))
(arguments
- `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
+ `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
+ ;; The tests take too long and must be explicitly enabled with "make
+ ;; setup_tests".
+ ;; See https://www.dealii.org/developer/developers/testsuite.html.
+ ;; (They can also be run for an already installed deal.II.)
+ #:tests? #f
#:configure-flags
- ;; Work around a bug in libsuitesparseconfig linking
- ;; see https://github.com/dealii/dealii/issues/4745
- '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
- (home-page "https://www.dealii.org")
+ (let ((doc (string-append (assoc-ref %outputs "doc")
+ "/share/doc/" ,name "-" ,version)))
+ `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
+ ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
+ ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
+ ;; Don't compile the examples because the source and CMakeLists.txt
+ ;; are installed anyway, allowing users to do so for themselves.
+ "-DDEAL_II_COMPILE_EXAMPLES=OFF"
+ ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'remove-build-logs
+ ;; These build logs leak the name of the build directory by storing
+ ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((doc (string-append (assoc-ref outputs "doc")
+ "/share/doc/" ,name "-" ,version)))
+ (for-each delete-file (map (lambda (f) (string-append doc "/" f))
+ '("detailed.log" "summary.log"))))
+ #t)))))
+ (home-page "https://www.dealii.org/")
(synopsis "Finite element library")
(description
"Deal.II is a C++ program library targeted at the computational solution
@@ -4480,30 +4515,24 @@ in finite element programs.")
(license license:lgpl2.1+)))
(define-public dealii-openmpi
- (package (inherit dealii)
+ (package/inherit dealii
(name "dealii-openmpi")
(inputs
- `(("mpi" ,openmpi)
- ;;Supported only with MPI:
- ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
+ `(("arpack" ,arpack-ng-openmpi)
+ ("metis" ,metis)
+ ("scalapack" ,scalapack)
+ ,@(alist-delete "arpack" (package-inputs dealii))))
+ (propagated-inputs
+ `(("hdf5" ,hdf5-parallel-openmpi)
+ ("mpi" ,openmpi)
("p4est" ,p4est-openmpi)
("petsc" ,petsc-openmpi)
("slepc" ,slepc-openmpi)
- ("metis" ,metis) ;for MUMPS
- ("scalapack" ,scalapack) ;for MUMPS
- ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
- ("arpack" ,arpack-ng-openmpi)
- ,@(fold alist-delete (package-inputs dealii)
- '("p4est" "arpack"))))
+ ,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
(arguments
(substitute-keyword-arguments (package-arguments dealii)
- ((#:configure-flags cf)
- `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
- ,cf))
- ((#:phases phases '%standard-phases)
- `(modify-phases ,phases
- (add-before 'check 'mpi-setup
- ,%openmpi-setup)))))
+ ((#:configure-flags flags)
+ `(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
(synopsis "Finite element library (with MPI support)")))
(define-public flann
--
2.32.0