[PATCH 14/14] gnu: Add deal.II.

[ericbavier]

From: Eric Bavier <address@hidden>

* gnu/packages/maths.scm (deal.II, deal.II-openmpi): New variables.
* gnu/packages/patches/deal.II-p4est-interface.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
---
 gnu-system.am                                      |  1 +
 gnu/packages/maths.scm                             | 84 +++++++++++++++++++++-
 gnu/packages/patches/deal.II-p4est-interface.patch | 62 ++++++++++++++++
 3 files changed, 146 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/deal.II-p4est-interface.patch

diff --git a/gnu-system.am b/gnu-system.am
index 16b71e9..3eb9f54 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -412,6 +412,7 @@ dist_patch_DATA =                                           
\
   gnu/packages/patches/clucene-contribs-lib.patch               \
   gnu/packages/patches/cursynth-wave-rand.patch                        \
   gnu/packages/patches/dbus-localstatedir.patch                        \
+  gnu/packages/patches/deal.II-p4est-interface.patch           \
   gnu/packages/patches/diffutils-gets-undeclared.patch         \
   gnu/packages/patches/dfu-programmer-fix-libusb.patch         \
   gnu/packages/patches/doxygen-test.patch                      \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index ff3a048..e2c7d89 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -37,6 +37,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
@@ -72,7 +73,8 @@
   #:use-module (gnu packages texlive)
   #:use-module (gnu packages wxwidgets)
   #:use-module (gnu packages xml)
-  #:use-module (gnu packages zip))
+  #:use-module (gnu packages zip)
+  #:use-module (srfi srfi-1))
 
 (define-public units
   (package
@@ -1842,3 +1844,83 @@ specifications.")
      "lp_solve is a mixed integer linear programming solver based on the
 revised simplex and the branch-and-bound methods.")
     (license license:lgpl2.1+)))
+
+(define-public deal.II
+  (package
+    (name "deal.II")
+    (version "8.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/dealii/dealii/releases/";
+                           "download/v" version "/dealii-" version ".tar.gz"))
+       (sha256
+        (base32
+         "185jych0gdnpkjwxni7pd0dda149492zwq2457xdjg76bzj78mnp"))
+       (patches (list (search-patch "deal.II-p4est-interface.patch")))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
+        '(delete-file-recursively "bundled"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("tbb" ,tbb)
+       ("zlib" ,zlib)
+       ("boost" ,boost)
+       ("p4est" ,p4est)
+       ("blas" ,openblas)
+       ("lapack" ,lapack)
+       ("arpack" ,arpack-ng)
+       ("muparser" ,muparser)
+       ("gfortran" ,gfortran)
+       ("suitesparse" ,suitesparse)))   ;for UMFPACK
+    (arguments
+     `(#:build-type "DebugRelease" ;only supports Release, Debug, or 
DebugRelease
+       #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory 
structure
+       #:phases (modify-phases %standard-phases
+                  (add-after
+                   'install 'hint-example-prefix
+                   ;; Set Cmake hints in examples so that they can find this
+                   ;; deal.II when configuring.
+                   (lambda* (#:key outputs #:allow-other-keys)
+                     (let* ((out (assoc-ref %outputs "out"))
+                            (exmpl (string-append out "/share/doc"
+                                                  "/deal.II/examples")))
+                       (substitute* (find-files exmpl "CMakeLists.txt")
+                         (("([[:space:]]*HINTS.*)\n" _ line)
+                          (string-append line " $ENV{HOME}/.guix-profile "
+                                         out "\n")))
+                       #t))))))
+    (home-page "https://www.dealii.org";)
+    (synopsis "Finite element library")
+    (description
+     "Deal.II is a C++ program library targeted at the computational solution
+of partial differential equations using adaptive finite elements.  The main
+aim of deal.II is to enable rapid development of modern finite element codes,
+using among other aspects adaptive meshes and a wide array of tools often used
+in finite element programs.")
+    (license license:lgpl2.1+)))
+
+(define-public deal.II-openmpi
+  (package (inherit deal.II)
+    (name "deal.II-openmpi")
+    (inputs
+     `(("mpi" ,openmpi)
+       ;;Supported only with MPI:
+       ("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 deal.II)
+               '("p4est" "arpack"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments deal.II)
+       ((#:configure-flags cf)
+        ``("-DMPI_C_COMPILER=mpicc"
+           "-DMPI_CXX_COMPILER=mpicxx"
+           "-DMPI_Fortran_COMPILER=mpifort"
+           ,@,cf))))
+    (synopsis "Finite element library (with MPI support)")))
diff --git a/gnu/packages/patches/deal.II-p4est-interface.patch 
b/gnu/packages/patches/deal.II-p4est-interface.patch
new file mode 100644
index 0000000..4c4125d
--- /dev/null
+++ b/gnu/packages/patches/deal.II-p4est-interface.patch
@@ -0,0 +1,62 @@
+From upstream commit f764598c.
+
+The p4est_connectivity_load function used to take an unsigned long as argument,
+but this has been changed to size_t in p4est 1.0. This makes no difference on
+64 bit systems, but leads to compiler errors on 32 bit systems. Fix this.
+
+--- a/source/distributed/tria.cc
++++ b/source/distributed/tria.cc
+@@ -204,7 +204,11 @@ namespace internal
+       static
+       int (&connectivity_is_valid) (types<2>::connectivity *connectivity);
+ 
+-#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
++#if DEAL_II_P4EST_VERSION_GTE(1,0,0,0)
++      static
++      types<2>::connectivity *(&connectivity_load) (const char *filename,
++                                                    size_t *length);
++#elif DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
+       static
+       types<2>::connectivity *(&connectivity_load) (const char *filename,
+                                                     long unsigned *length);
+@@ -384,7 +388,12 @@ namespace internal
+                                                 *connectivity)
+       = p4est_connectivity_is_valid;
+ 
+-#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
++#if DEAL_II_P4EST_VERSION_GTE(1,0,0,0)
++    types<2>::connectivity *
++    (&functions<2>::connectivity_load) (const char *filename,
++                                        size_t *length)
++      = p4est_connectivity_load;
++#elif DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
+     types<2>::connectivity *
+     (&functions<2>::connectivity_load) (const char *filename,
+                                         long unsigned *length)
+@@ -564,7 +573,11 @@ namespace internal
+       static
+       int (&connectivity_is_valid) (types<3>::connectivity *connectivity);
+ 
+-#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
++#if DEAL_II_P4EST_VERSION_GTE(1,0,0,0)
++      static
++      types<3>::connectivity *(&connectivity_load) (const char *filename,
++                                                    size_t *length);
++#elif DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
+       static
+       types<3>::connectivity *(&connectivity_load) (const char *filename,
+                                                     long unsigned *length);
+@@ -747,7 +760,12 @@ namespace internal
+                                                 *connectivity)
+       = p8est_connectivity_is_valid;
+ 
+-#if DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
++#if DEAL_II_P4EST_VERSION_GTE(1,0,0,0)
++    types<3>::connectivity *
++    (&functions<3>::connectivity_load) (const char *filename,
++                                        size_t *length)
++      = p8est_connectivity_load;
++#elif DEAL_II_P4EST_VERSION_GTE(0,3,4,3)
+     types<3>::connectivity *
+     (&functions<3>::connectivity_load) (const char *filename,
+                                         long unsigned *length)
-- 
2.2.1