[bug#50080] [PATCH] gnu: sundials, dealii: Update sundials to 5.7.0 and add to dealii inputs.

["Paul A. Patience" <paul@apatience.com>]

[-- Attachment #1: Type: text/plain, Size: 13 bytes --]

Empty Message

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-sundials-openmpi-Fix-compilation-with-PETSc.patch --]
[-- Type: text/x-patch; name=0001-gnu-sundials-openmpi-Fix-compilation-with-PETSc.patch, Size: 1520 bytes --]

From f40bc7354c0534febcec0cb7496b575e4e75acc5 Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Wed, 11 Aug 2021 20:41:53 -0400
Subject: [PATCH 1/6] gnu: sundials-openmpi: Fix compilation with PETSc.

Without HDF5 in PETSc's propagated inputs, SUNDIALS's configure script
disables PETSc support (even though it is requested in the configure
flags) because it fails to compile a test program which includes a PETSc
header which itself includes an HDF5 header.

* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Move
hdf5-parallel-openmpi to...
[propagated-inputs]: ...here.
---
 gnu/packages/maths.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index ce9515fb35..29a4aa4c07 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2724,14 +2724,15 @@ scientific applications modeled by partial differential equations.")
   (package (inherit petsc)
     (name "petsc-openmpi")
     (inputs
-     `(("hdf5" ,hdf5-parallel-openmpi)
-       ("hypre" ,hypre-openmpi)
+     `(("hypre" ,hypre-openmpi)
        ("metis" ,metis)
        ("mumps" ,mumps-openmpi)
        ("openmpi" ,openmpi)
        ("scalapack" ,scalapack)
        ("scotch" ,pt-scotch32)
        ,@(package-inputs petsc)))
+    (propagated-inputs
+     `(("hdf5" ,hdf5-parallel-openmpi))) ; petscis.h includes H5Ipublic.h.
     (arguments
      (substitute-keyword-arguments (package-arguments petsc)
        ((#:configure-flags cf)
-- 
2.32.0


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: 0005-gnu-sundials-Update-to-5.7.0.patch --]
[-- Type: text/x-patch; name=0005-gnu-sundials-Update-to-5.7.0.patch, Size: 5869 bytes --]

From 61278697659c4368f3f4806337f77f8695644204 Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Wed, 11 Aug 2021 22:34:22 -0400
Subject: [PATCH 5/6] gnu: sundials: Update to 5.7.0.

This commit notably changes SUNDIALS's index size to 32 bits rather than
64 bits, because it is otherwise incompatible with PETSc's 32-bit
indices.

The default index size in SUNDIALS 3.1.1 was also 64 bits (though it was
configured through the SUNDIALS_INDEX_TYPE CMake variable, which could
take the values INT64_T or INT32_T), but the configure script didn't
warn of any incompatibility with PETSc's 32-bit indices.
It is unclear whether this was an accidental omission from the configure
script or if SUNDIALS's index size didn't have to correspond to PETSc's
at the time.

Keeping 64-bit indices in SUNDIALS would require adding a package for
PETSc with 64-bit indices (using the --with-64-bit-indices configure
flag), possibly named petsc64-openmpi (to follow the style of the SCOTCH
packages, i.e., scotch, scotch32, etc., though there the unadorned
package name represents the 64-bit version, unlike the unadorned petsc),
which would in turn require a package for METIS with 64-bit
indices (using IDXTYPEWIDTH=64).
However, SUNDIALS is an optional dependency of deal.II, both of which
have PETSc as an optional dependency, and deal.II's index size (which
defaults to 32 bits) must match PETSc's.
In other words, the current deal.II package can build with SUNDIALS only
if SUNDIALS has 32-bit indices.

Furthermore, users needing 64-bit indices in SUNDIALS probably also need
them in PETSc and other libraries.
If and when 64-bit indices are deemed necessary, we can add all the
package variations at once (for SUNDIALS, PETSc, METIS, deal.II and any
others).

* gnu/packages/maths.scm (sundials)[version]: Update to 5.7.0.
[source]<origin>{uri}: Update to that linked from SUNDIALS's home page.
[native-inputs]: Replace python-2 with python-wrapper.
[arguments]<#:configure-flags>: Add -DSUNDIALS_INDEX_SIZE=32 to match
PETSc's 32-bit indices. Replace -DFCMIX_ENABLE with
-DBUILD_FORTRAN77_INTERFACE. Rename KLU_ENABLE to ENABLE_KLU.
(sundials-openmpi)[arguments]<#:configure-flags>: Rename MPI_ENABLE,
HYPRE_ENABLE and PETSC_ENABLE to ENABLE_MPI, ENABLE_HYPRE and
ENABLE_PETSC, respectively. Replace -DPETSC_INCLUDE_DIR and
-DPETSC_LIBRARY_DIR with -DPETSC_DIR.
---
 gnu/packages/maths.scm | 35 +++++++++++++++++++----------------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 8ca9505985..980460fa85 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5679,33 +5679,39 @@ and comparisons are supported.")
 (define-public sundials
   (package
     (name "sundials")
-    (version "3.1.1")
+    (version "5.7.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
-                           "sundials-" version ".tar.gz"))
+       (uri (string-append "https://github.com/LLNL/sundials/releases/download/v"
+                           version "/sundials-" version ".tar.gz"))
        (sha256
-        (base32 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
+        (base32 "0hqa20x3180s04s7dxmc4bmbykxv3lnxh0hvxlmb5pajh6m7pnj8"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("python" ,python-2)))    ; For tests; syntax incompatible with Python 3.
+     `(("python" ,python-wrapper))) ; For tests.
     (inputs
      `(("blas" ,openblas)
-       ("gfortran" ,gfortran)           ; For FCMIX.
+       ("gfortran" ,gfortran)
        ("suitesparse" ,suitesparse)))
     (arguments
      `(#:configure-flags
        (let ((suitesparse (assoc-ref %build-inputs "suitesparse")))
-         `("-DEXAMPLES_ENABLE_C:BOOL=ON"
+         `("-DSUNDIALS_INDEX_SIZE=32"
+
+           "-DEXAMPLES_ENABLE_C:BOOL=ON"
            "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
            "-DEXAMPLES_ENABLE_F77:BOOL=ON"
            "-DEXAMPLES_ENABLE_F90:BOOL=ON"
+           ;; Requires -DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON.
+           ;;"-DEXAMPLES_ENABLE_F2003:BOOL=ON"
            "-DEXAMPLES_INSTALL:BOOL=OFF"
 
-           "-DFCMIX_ENABLE:BOOL=ON"
+           "-DBUILD_FORTRAN77_INTERFACE:BOOL=ON"
+           ;; Incompatible with 32-bit indices.
+           ;;"-DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON"
 
-           "-DKLU_ENABLE:BOOL=ON"
+           "-DENABLE_KLU:BOOL=ON"
            ,(string-append "-DKLU_INCLUDE_DIR=" suitesparse "/include")
            ,(string-append "-DKLU_LIBRARY_DIR=" suitesparse "/lib")))))
     (home-page "https://computation.llnl.gov/projects/sundials")
@@ -5727,17 +5733,14 @@ easily be incorporated into existing simulation codes.")
     (arguments
      (substitute-keyword-arguments (package-arguments sundials)
        ((#:configure-flags flags '())
-        `(cons* "-DMPI_ENABLE:BOOL=ON"
-                "-DHYPRE_ENABLE:BOOL=ON"
+        `(cons* "-DENABLE_MPI:BOOL=ON"
+                "-DENABLE_HYPRE:BOOL=ON"
                 (string-append "-DHYPRE_INCLUDE_DIR="
                                (assoc-ref %build-inputs "hypre") "/include")
                 (string-append "-DHYPRE_LIBRARY_DIR="
                                (assoc-ref %build-inputs "hypre") "/lib")
-                "-DPETSC_ENABLE:BOOL=ON"
-                (string-append "-DPETSC_INCLUDE_DIR="
-                               (assoc-ref %build-inputs "petsc") "/include")
-                (string-append "-DPETSC_LIBRARY_DIR="
-                               (assoc-ref %build-inputs "petsc") "/lib")
+                "-DENABLE_PETSC:BOOL=ON"
+                (string-append "-DPETSC_DIR=" (assoc-ref %build-inputs "petsc"))
                 ,flags))
        ((#:phases phases '%standard-phases)
         `(modify-phases ,phases
-- 
2.32.0


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #4: 0004-gnu-sundials-Clean-up.patch --]
[-- Type: text/x-patch; name=0004-gnu-sundials-Clean-up.patch, Size: 5384 bytes --]

From 6cc4907550b33af4432caf21489c89247f9e9ac7 Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Wed, 11 Aug 2021 21:37:28 -0400
Subject: [PATCH 4/6] gnu: sundials: Clean up.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/maths.scm (sundials): Capitalize and punctuate comments.
[source]<origin>{sha256}: Join base32 line.
[inputs]: Rename gfortran label from “fortran” to “gfortran”. Sort the
inputs.
[arguments]<#:configure-flags>: Extract assoc-ref form into a let.
(sundials-openmpi): Use package/inherit. Replace tab with spaces.
[arguments]<#:configure-flags>: Join some lines.
[synopsis]: Reuse sundials's synopsis and mention MPI support in
parentheses (thus conforming to the usual style followed by other
package definitions).
---
 gnu/packages/maths.scm | 56 +++++++++++++++++++-----------------------
 1 file changed, 25 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5195dd6180..8ca9505985 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5686,31 +5686,28 @@ and comparisons are supported.")
        (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
                            "sundials-" version ".tar.gz"))
        (sha256
-        (base32
-         "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
+        (base32 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("python" ,python-2)))    ;for tests; syntax incompatible with python 3
+     `(("python" ,python-2)))    ; For tests; syntax incompatible with Python 3.
     (inputs
-     `(("fortran" ,gfortran)            ;for fcmix
-       ("blas" ,openblas)
+     `(("blas" ,openblas)
+       ("gfortran" ,gfortran)           ; For FCMIX.
        ("suitesparse" ,suitesparse)))
     (arguments
-     `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
-                           "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
-                           "-DEXAMPLES_ENABLE_F77:BOOL=ON"
-                           "-DEXAMPLES_ENABLE_F90:BOOL=ON"
-                           "-DEXAMPLES_INSTALL:BOOL=OFF"
-
-                           "-DFCMIX_ENABLE:BOOL=ON"
-
-                           "-DKLU_ENABLE:BOOL=ON"
-                           ,(string-append "-DKLU_INCLUDE_DIR="
-                                           (assoc-ref %build-inputs "suitesparse")
-                                           "/include")
-                           ,(string-append "-DKLU_LIBRARY_DIR="
-                                           (assoc-ref %build-inputs "suitesparse")
-                                           "/lib"))))
+     `(#:configure-flags
+       (let ((suitesparse (assoc-ref %build-inputs "suitesparse")))
+         `("-DEXAMPLES_ENABLE_C:BOOL=ON"
+           "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
+           "-DEXAMPLES_ENABLE_F77:BOOL=ON"
+           "-DEXAMPLES_ENABLE_F90:BOOL=ON"
+           "-DEXAMPLES_INSTALL:BOOL=OFF"
+
+           "-DFCMIX_ENABLE:BOOL=ON"
+
+           "-DKLU_ENABLE:BOOL=ON"
+           ,(string-append "-DKLU_INCLUDE_DIR=" suitesparse "/include")
+           ,(string-append "-DKLU_LIBRARY_DIR=" suitesparse "/lib")))))
     (home-page "https://computation.llnl.gov/projects/sundials")
     (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
     (description "SUNDIALS is a family of software packages implemented with
@@ -5719,7 +5716,7 @@ easily be incorporated into existing simulation codes.")
     (license license:bsd-3)))
 
 (define-public sundials-openmpi
-  (package (inherit sundials)
+  (package/inherit sundials
     (name "sundials-openmpi")
     (propagated-inputs
      `(("mpi" ,openmpi)
@@ -5733,24 +5730,21 @@ easily be incorporated into existing simulation codes.")
         `(cons* "-DMPI_ENABLE:BOOL=ON"
                 "-DHYPRE_ENABLE:BOOL=ON"
                 (string-append "-DHYPRE_INCLUDE_DIR="
-                               (assoc-ref %build-inputs "hypre")
-                               "/include")
+                               (assoc-ref %build-inputs "hypre") "/include")
                 (string-append "-DHYPRE_LIBRARY_DIR="
-                               (assoc-ref %build-inputs "hypre")
-                               "/lib")
+                               (assoc-ref %build-inputs "hypre") "/lib")
                 "-DPETSC_ENABLE:BOOL=ON"
                 (string-append "-DPETSC_INCLUDE_DIR="
-                               (assoc-ref %build-inputs "petsc")
-                               "/include")
+                               (assoc-ref %build-inputs "petsc") "/include")
                 (string-append "-DPETSC_LIBRARY_DIR="
-                               (assoc-ref %build-inputs "petsc")
-                               "/lib")
+                               (assoc-ref %build-inputs "petsc") "/lib")
                 ,flags))
        ((#:phases phases '%standard-phases)
         `(modify-phases ,phases
            (add-before 'check 'mpi-setup
-	     ,%openmpi-setup)))))
-    (synopsis "SUNDIALS with OpenMPI support")))
+             ,%openmpi-setup)))))
+    (synopsis "Suite of nonlinear and differential/algebraic equation solvers
+(with MPI support)")))
 
 (define-public combinatorial-blas
   (package
-- 
2.32.0


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #5: 0006-gnu-dealii-Add-SUNDIALS-dependency.patch --]
[-- Type: text/x-patch; name=0006-gnu-dealii-Add-SUNDIALS-dependency.patch, Size: 1469 bytes --]

From 99be21c21b0d7793af6bcf5aa0f214f026037fe0 Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Thu, 12 Aug 2021 16:01:02 -0400
Subject: [PATCH 6/6] gnu: dealii: Add SUNDIALS dependency.

* gnu/packages/maths.scm (dealii)[propagated-inputs]: Add sundials.
(dealii-openmpi)[propagated-inputs]: Add sundials-openmpi.
---
 gnu/packages/maths.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 980460fa85..49624c0f52 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4837,6 +4837,7 @@ A unique design feature of Trilinos is its focus on packages.")
      `(("boost" ,boost)
        ("hdf5" ,hdf5)
        ("suitesparse" ,suitesparse)     ; For UMFPACK.
+       ("sundials" ,sundials)
        ("tbb" ,tbb)))
     (arguments
      `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
@@ -4890,8 +4891,10 @@ in finite element programs.")
        ("p4est" ,p4est-openmpi)
        ("petsc" ,petsc-openmpi)
        ("slepc" ,slepc-openmpi)
+       ("sundials" ,sundials-openmpi)
        ("trilinos" ,trilinos-for-dealii-openmpi)
-       ,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
+       ,@(fold alist-delete (package-propagated-inputs dealii)
+               '("hdf5" "sundials"))))
     (arguments
      (substitute-keyword-arguments (package-arguments dealii)
        ((#:configure-flags flags)
-- 
2.32.0


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #6: 0003-gnu-sundials-openmpi-Add-HYPRE-dependency.patch --]
[-- Type: text/x-patch; name=0003-gnu-sundials-openmpi-Add-HYPRE-dependency.patch, Size: 2189 bytes --]

From 18bce77a9baa50bbe485ce4a74e5b281aa7dcc8a Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Wed, 11 Aug 2021 21:00:33 -0400
Subject: [PATCH 3/6] gnu: sundials-openmpi: Add HYPRE dependency.

* gnu/packages/maths.scm (sundials): Remove TODO item obsoleted by this
commit.
(sundials-openmpi)[propagated-inputs]: Add hypre-openmpi.
[arguments]<#:configure-flags>: Add -DHYPRE_ENABLE, -DHYPRE_INCLUDE_DIR
and -DHYPRE_LIBRARY_DIR.
---
 gnu/packages/maths.scm | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d90cc94156..5195dd6180 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5694,7 +5694,7 @@ and comparisons are supported.")
     (inputs
      `(("fortran" ,gfortran)            ;for fcmix
        ("blas" ,openblas)
-       ("suitesparse" ,suitesparse)))   ;TODO: Add hypre
+       ("suitesparse" ,suitesparse)))
     (arguments
      `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
                            "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
@@ -5723,12 +5723,21 @@ easily be incorporated into existing simulation codes.")
     (name "sundials-openmpi")
     (propagated-inputs
      `(("mpi" ,openmpi)
-       ("petsc" ,petsc-openmpi)         ;support in SUNDIALS requires MPI
+       ;; Support for the below requires MPI.
+       ("hypre" ,hypre-openmpi)
+       ("petsc" ,petsc-openmpi)
        ,@(package-propagated-inputs sundials)))
     (arguments
      (substitute-keyword-arguments (package-arguments sundials)
        ((#:configure-flags flags '())
         `(cons* "-DMPI_ENABLE:BOOL=ON"
+                "-DHYPRE_ENABLE:BOOL=ON"
+                (string-append "-DHYPRE_INCLUDE_DIR="
+                               (assoc-ref %build-inputs "hypre")
+                               "/include")
+                (string-append "-DHYPRE_LIBRARY_DIR="
+                               (assoc-ref %build-inputs "hypre")
+                               "/lib")
                 "-DPETSC_ENABLE:BOOL=ON"
                 (string-append "-DPETSC_INCLUDE_DIR="
                                (assoc-ref %build-inputs "petsc")
-- 
2.32.0


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #7: 0002-gnu-sundials-openmpi-Propagate-all-inputs.patch --]
[-- Type: text/x-patch; name=0002-gnu-sundials-openmpi-Propagate-all-inputs.patch, Size: 1116 bytes --]

From 6d8efb16b8e3919a58d7d7bbef939802824a168d Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Wed, 11 Aug 2021 21:04:42 -0400
Subject: [PATCH 2/6] gnu: sundials-openmpi: Propagate all inputs.

* gnu/packages/maths.scm (sundials-openmpi)[inputs]: Move openmpi and
petsc-openmpi to...
[propagated-inputs]: ...here.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 29a4aa4c07..d90cc94156 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5721,10 +5721,10 @@ easily be incorporated into existing simulation codes.")
 (define-public sundials-openmpi
   (package (inherit sundials)
     (name "sundials-openmpi")
-    (inputs
+    (propagated-inputs
      `(("mpi" ,openmpi)
        ("petsc" ,petsc-openmpi)         ;support in SUNDIALS requires MPI
-       ,@(package-inputs sundials)))
+       ,@(package-propagated-inputs sundials)))
     (arguments
      (substitute-keyword-arguments (package-arguments sundials)
        ((#:configure-flags flags '())
-- 
2.32.0