[bug#66516] [PATCH 0/2] gnu: dealii: Update to 9.5.1.

[bug#66516] [PATCH 0/2] gnu: dealii: Update to 9.5.1.

[Paul A. Patience]

Hi,

The prerequisite-patch-id refers to the Trilinos build fix [1], which is not
strictly required (dealii-openmpi will just not build without it).

Unfortunately, I am flummoxed by the unset-cpath phase's fixing the build with
Kokkos.

[1]: https://bugs.gnu.org/66462

Paul A. Patience (2):
  gnu: Add kokkos.
  gnu: dealii: Update to 9.5.1.

 gnu/packages/maths.scm | 79 +++++++++++++++++++++++++++++++++++++++---
 1 file changed, 74 insertions(+), 5 deletions(-)


base-commit: f4e8baf3806e79d7111d2943859865ae4ee0b59d
prerequisite-patch-id: 15b686dd7cb363b42432fb9bc83701cd33bed641
-- 
2.41.0

[bug#66516] [PATCH 1/2] gnu: Add kokkos.

[Paul A. Patience]

* gnu/packages/maths.scm (kokkos): New variable.
---
 gnu/packages/maths.scm | 51 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 7a87fcb54e..2762e13a4f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -116,6 +116,7 @@ (define-module (gnu packages maths)
   #:use-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages datamash)
   #:use-module (gnu packages dbm)
+  #:use-module (gnu packages disk)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages emacs)
@@ -6403,6 +6404,56 @@ (define-public lpsolve
 revised simplex and the branch-and-bound methods.")
     (license license:lgpl2.1+)))
 
+(define-public kokkos
+  (package
+    (name "kokkos")
+    (version "4.1.00")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/kokkos/kokkos")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "15kjpa54ssrrbid9h2nr94nh85qna5c4vq2152i4iy7gaagigy3c"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Remove bundled googletest.
+        #~(delete-file-recursively "tpls/gtest"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:configure-flags
+           ;; deal.II uses only the serial backend, so do not enable the
+           ;; others yet.
+           #~(list "-DBUILD_SHARED_LIBS=ON"
+                   "-DKokkos_ENABLE_SERIAL=ON"
+                   "-DKokkos_ENABLE_TESTS=ON"
+                   "-DKokkos_ENABLE_EXAMPLES=ON"
+                   "-DKokkos_ENABLE_HWLOC=ON"
+                   "-DKokkos_ENABLE_MEMKIND=ON")
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'install-license-files 'remove-cruft
+                 (lambda _
+                   (delete-file
+                    (string-append #$output "/share/doc/"
+                                   #$name "-" #$version
+                                   "/LICENSE_FILE_HEADER")))))))
+    (native-inputs
+     (list googletest python))
+    (inputs
+     (list `(,hwloc "lib") memkind))
+    (home-page "https://github.com/kokkos/kokkos")
+    (synopsis "C++ abstractions for parallel execution and data management")
+    (description
+     "Kokkos Core implements a programming model in C++ for writing performance
+portable applications targeting all major HPC platforms.  For that purpose it
+provides abstractions for both parallel execution of code and data management.
+Kokkos is designed to target complex node architectures with N-level memory
+hierarchies and multiple types of execution resources.")
+    (license license:asl2.0))) ; With LLVM exception
+
 ;; Private Trilinos package for dealii-openmpi (similar to
 ;; trilinos-serial-xyce and trilinos-parallel-xyce).
 ;; This version is the latest known to be compatible with deal.II [1].
-- 
2.41.0

[bug#66516] [PATCH 2/2] gnu: dealii: Update to 9.5.1.

[Paul A. Patience]

* gnu/packages/maths.scm (dealii): Update to 9.5.1.
[propagated-inputs]: Add kokkos.
[arguments]<#:phases>: Add 'unset-cpath' phase.
(dealii-openmpi)[propagated-inputs]: Remove kokkos.
[arguments]<#:phases>: Delete 'unset-cpath' phase.
---
 gnu/packages/maths.scm | 28 +++++++++++++++++++++++-----
 1 file changed, 23 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2762e13a4f..e8d3cfed99 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6613,17 +6613,17 @@ (define trilinos-for-dealii-openmpi
 (define-public dealii
   (package
     (name "dealii")
-    (version "9.4.0")
+    (version "9.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/dealii/dealii/releases/"
                            "download/v" version "/dealii-" version ".tar.gz"))
        (sha256
-        (base32 "0v73q6f35f2yrjihaq6vh9lma07qc4cdv75nwmc3c5yrdh07g1i3"))
+        (base32 "0phgcfnil4rb41xipsdbm4lxrymlqxbiccakg3pkm3a8wqsva658"))
        (modules '((guix build utils)))
        (snippet
-        ;; Remove bundled boost, muparser, TBB and UMFPACK.
+        ;; Remove bundled boost, Kokkos, muparser, TBB and UMFPACK.
         #~(delete-file-recursively "bundled"))))
     (build-system cmake-build-system)
     (outputs '("out" "doc"))
@@ -6647,6 +6647,7 @@ (define-public dealii
      ;; the requisite interpreter to its native inputs.
      (list boost
            hdf5
+           kokkos
            suitesparse                  ; For UMFPACK.
            sundials
            tbb))
@@ -6671,6 +6672,18 @@ (define-public dealii
                                     "/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
@@ -6702,7 +6715,7 @@ (define-public dealii-openmpi
                 scalapack)))
     (propagated-inputs
      (modify-inputs (package-propagated-inputs dealii)
-       (delete "hdf5" "sundials")
+       (delete "hdf5" "kokkos" "sundials")
        (prepend hdf5-parallel-openmpi
                 openmpi
                 p4est-openmpi
@@ -6713,7 +6726,12 @@ (define-public dealii-openmpi
     (arguments
      (substitute-keyword-arguments (package-arguments dealii)
        ((#:configure-flags flags)
-        #~(cons "-DDEAL_II_WITH_MPI=ON" #$flags))))
+        #~(cons "-DDEAL_II_WITH_MPI=ON" #$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)")))
 
 (define-public flann
-- 
2.41.0

[bug#66516] [PATCH 1/2] gnu: Add kokkos.

[Paul A. Patience]

Hi,

Come to think of it, I placed kokkos in gnu/packages/maths.scm only so
that it would be right above trilinos-for-dealii-openmpi, because
Trilinos includes a version of Kokkos.

However, it seems that Kokkos is a project in its own right; perhaps it
should go into gnu/packages/cpp.scm, near where I placed Taskflow in
https://bugs.gnu.org/66521.

If you think this is a good idea, feel free to make the change or
request that I do so.

Best regards,
Paul

bug#66516: [PATCH 0/2] gnu: dealii: Update to 9.5.1.

[Ludovic Courtès]

"Paul A. Patience" <paul@apatience.com> skribis:

> The prerequisite-patch-id refers to the Trilinos build fix [1], which is not
> strictly required (dealii-openmpi will just not build without it).
>
> Unfortunately, I am flummoxed by the unset-cpath phase's fixing the build with
> Kokkos.

Yeah, #include_next is super sensitive to CPATH and duplicated entries
therein, so I’m unfortunately not surprised.

>   gnu: Add kokkos.
>   gnu: dealii: Update to 9.5.1.

Applied, and I moved Kokkos to cpp.scm as you suggested.

Thanks!

Ludo’.