Add glicid-dealii and glicid-dealii-openmpi to guix/packages/maths.scm

glicid/packages/maths.scm

@@ -10,8 +10,112 @@
   #:use-module (gnu packages compression)
   #:use-module (guix build-system cmake)
   #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (glicid utils))
+  #:use-module (glicid utils)
-
+  #:use-module (ice-9 regex)
+  #:use-module (ice-9 match)
+  #:use-module (guix gexp)
+  #:use-module ((guix build utils) #:select (alist-replace))
+  #:use-module (guix build-system ant)
+  #:use-module (guix build-system copy)
+  #:use-module (guix build-system dune)
+  #:use-module (guix build-system glib-or-gtk)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system meson)
+  #:use-module (guix build-system ocaml)
+  #:use-module (guix build-system perl)
+  #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
+  #:use-module (guix build-system ruby)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages audio)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages backup)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages bash)
+  #:use-module (gnu packages bison)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages calendar)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages cmake)
+  #:use-module (gnu packages coq)
+  #:use-module (gnu packages curl)
+  #:use-module (gnu packages cyrus-sasl)
+  #:use-module (gnu packages cpp)
+  #:use-module (gnu packages datamash)
+  #:use-module (gnu packages dbm)
+  #:use-module (gnu packages documentation)
+  #:use-module (gnu packages elf)
+  #:use-module (gnu packages emacs)
+  #:use-module (gnu packages file)
+  #:use-module (gnu packages flex)
+  #:use-module (gnu packages fltk)
+  #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages gd)
+  #:use-module (gnu packages ghostscript)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gperf)
+  #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages groff)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages icu4c)
+  #:use-module (gnu packages image)
+  #:use-module (gnu packages image-processing)
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages less)
+  #:use-module (gnu packages lisp)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages llvm)
+  #:use-module (gnu packages logging)
+  #:use-module (gnu packages lua)
+  #:use-module (gnu packages gnome)
+  #:use-module (gnu packages guile)
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages gl)
+  #:use-module (gnu packages imagemagick)
+  #:use-module (gnu packages m4)
+  #:use-module (gnu packages mpi)
+  #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages netpbm)
+  #:use-module (gnu packages ocaml)
+  #:use-module (gnu packages onc-rpc)
+  #:use-module (gnu packages parallel)
+  #:use-module (gnu packages pcre)
+  #:use-module (gnu packages popt)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages prolog)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages pulseaudio)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-science)
+  #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages qt)
+  #:use-module (gnu packages readline)
+  #:use-module (gnu packages ruby)
+  #:use-module (gnu packages tbb)
+  #:use-module (gnu packages scheme)
+  #:use-module (gnu packages serialization)
+  #:use-module (gnu packages shells)
+  #:use-module (gnu packages simulation)
+  #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages swig)
+  #:use-module (gnu packages tcl)
+  #:use-module (gnu packages texinfo)
+  #:use-module (gnu packages tex)
+  #:use-module (gnu packages time)
+  #:use-module (gnu packages tls)
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages wxwidgets)
+  #:use-module (gnu packages xdisorg)
+  #:use-module (gnu packages xml)
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-26))
 (define-public scalapack-upstream
   (package
     (inherit gnu:scalapack)
@@ -103,3 +207,89 @@
     (license license:bsd-3))
 )
 
+(define-public glicid-dealii
+  (package
+    (inherit dealii)
+    (version "9.6.0")
+    (name "glicid-dealii")
+    (arguments
+     (list #:build-type "Release"  ; Only Debug, Release or 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
+           #~(let ((doc (string-append #$output:doc "/share/doc/"
+                                       #$name "-" #$version)))
+               (list "-DDEAL_II_COMPONENT_DOCUMENTATION=OFF"
+                     (string-append "-DCMAKE_CXX_FLAGS='-march=znver3'")
+                     (string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
+                     (string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
+                     ;; Don't compile the examples because the source and
+                     ;; CMakeLists.txt are installed anyway, allowing users to
+                     ;; do so for themselves.
+                     "-DDEAL_II_COMPILE_EXAMPLES=OFF"
+                     (string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc
+                                    "/examples")))
+           #:phases
+           #~(modify-phases %standard-phases
+               ;; Without unsetting CPATH, the build fails with the following
+               ;; error (similar to <https://bugs.gnu.org/30756>):
+               ;;
+               ;;   /gnu/store/…-gcc-11.3.0/include/c++/math.h:30:16: fatal error: math.h: No such file or directory
+               ;;      30 | # include_next <math.h>
+               ;;         |                ^~~~~~~~
+               ;;
+               ;; Why does unsetting CPATH magically fix the error?
+               ;; TODO: Properly fix this issue.
+               (add-after 'set-paths 'unset-cpath
+                 (lambda _
+                   (unsetenv "CPATH")))
+               (add-after 'install 'remove-build-logs
+                 ;; These build logs leak the name of the build directory by
+                 ;; storing the values of CMAKE_SOURCE_DIR and
+                 ;; CMAKE_BINARY_DIR.
+                 (lambda _
+                   (let ((doc (string-append #$output:doc "/share/doc/"
+                                             #$name "-" #$version)))
+                     (for-each delete-file
+                               (map (lambda (f) (string-append doc "/" f))
+                                    '("detailed.log" "summary.log")))))))))
+    ))
+
+
+(define trilinos-for-dealii-openmpi
+  (@@ (gnu packages maths) trilinos-for-dealii-openmpi))
+
+
+(define-public glicid-dealii-openmpi
+  (package
+    (inherit glicid-dealii)
+    (name "glicid-dealii-openmpi")
+    (inputs
+     (modify-inputs (package-inputs glicid-dealii)
+       (delete "arpack")
+       (prepend arpack-ng-openmpi
+                metis
+                scalapack)))
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs glicid-dealii)
+       (delete "hdf5" "kokkos" "sundials")
+       (prepend hdf5-parallel-openmpi
+                openmpi
+                p4est-openmpi
+                petsc-openmpi
+                slepc-openmpi
+                sundials-openmpi
+                trilinos-for-dealii-openmpi)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments glicid-dealii)
+       ((#:configure-flags flags)
+        #~(cons "-DDEAL_II_WITH_MPI=ON" #$flags))
+       ((#:phases phases #~%standard-phases)
+        #~(modify-phases #$phases
+            ;; The build failure fixed by this phase does not manifest when
+            ;; Kokkos is included via Trilinos.
+            (delete 'unset-cpath)))))
+    (synopsis "Finite element library (with MPI support)")))