03/10: gnu: sundials: Fix various issues.

[guix-commits]

civodul pushed a commit to branch master
in repository guix.

commit 0d3c2c954393d0344e11ba0532e276cecb9ef2fb
Author: Paul A. Patience <paul@apatience.com>
AuthorDate: Mon May 2 13:28:39 2022 +0000

    gnu: sundials: Fix various issues.
    
    This commit fixes various issues. First, some of SUNDIALS's CMake
    variables were renamed at some point between 5.2.0 and 5.7.0, in
    particular KLU_ENABLE, which was changed to ENABLE_KLU. Since
    sundials-julia is essentially SUNDIALS 5.2.0, its configure flags need
    to be different from those of the sundials package. Second, commit
    61bcd648ca215e3d8e75b3a3f49bfb94d66f7c79, which updated SUNDIALS to
    6.1.1, accidentally completely disabled PETSc support for
    sundials-openmpi (PETSc is supported only with MPI) by removing the
    relevant configure flags. Third, SUNDIALS's default index size is
    64 bits, but PETSc's is 32 bits, and they need to be the same; this
    issue is discussed in the next three paragraphs.
    
    The default index size in SUNDIALS 3.1.1 (which was the sundials
    package's version previous to the aforementioned commit) 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
    SUNDIALS's configure script didn't warn of any incompatibility with
    PETSc's 32-bit indices. I don't know if 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)[source]: Reuse version in URL.
    [native-inputs]: Capitalize and punctuate comment.
    [inputs]: Remove petsc, now unnecessary gfortran, and obsolete
    comment. Move TODO item to sundials-openmpi.
    [arguments]<#:configure-flags>: Add -DSUNDIALS_INDEX_SIZE=32 to match
    PETSc's 32-bit indices. Remove obsolete -DEXAMPLES_ENABLE_F77,
    -DEXAMPLES_ENABLE_F90 and -DFCMIX_ENABLE. Mention new but currently
    unusable -DBUILD_FORTRAN_MODULE_INTERFACE and
    -DEXAMPLES_ENABLE_F2003. Rename KLU_ENABLE to ENABLE_KLU.
    (sundials-openmpi): Use package/inherit.
    [inputs]: Move openmpi and petsc-openmpi from here...
    [propagated-inputs]: ...to here. Clarify comment.
    [arguments]<#:configure-flags>: Add -DENABLE_PETSC and -DPETSC_DIR, the
    equivalents of which were accidentally removed in commit
    61bcd648ca215e3d8e75b3a3f49bfb94d66f7c79.
    <#:phases>: Replace a tab with spaces.
    [synopsis]: Replace OpenMPI with MPI to conform to other package
    synopses.
    (sundials-julia)[inputs]: Add gfortran.
    [arguments]<#:configure-flags>: Set only, and manually, -DCMAKE_C_FLAGS,
    -DSUNDIALS_INDEX_SIZE, -DKLU_ENABLE, -DKLU_INCLUDE_DIR,
    -DKLU_LIBRARY_DIR and -DLAPACK_ENABLE instead of inheriting from the
    sundials package, because some of SUNDIALS's CMake variables have
    changed name.
    [synopsis]: Capitalize “LAPACK”.
    
    Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/maths.scm | 64 ++++++++++++++++++++++++++++++--------------------
 1 file changed, 38 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2922d95a70..5d4778da83 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6129,28 +6129,30 @@ and comparisons are supported.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append 
"https://github.com/LLNL/sundials/releases/download/v6.1.1/";
-                           "sundials-" version ".tar.gz"))
+       (uri (string-append 
"https://github.com/LLNL/sundials/releases/download/v";
+                           version "/sundials-" version ".tar.gz"))
        (sha256
         (base32
          "0327a1fy8rilwc4brsqqb71jd1ymb7mqgxsylab06crcg5xn7byg"))))
     (build-system cmake-build-system)
     (native-inputs
-     (list python-2))    ;for tests; syntax incompatible with python 3
+     (list python-2))          ; For tests; syntax incompatible with Python 3.
     (inputs
-     (list gfortran                               ;for fcmix
-           openblas petsc suitesparse))           ;TODO: Add hypre
+     (list openblas suitesparse))
     (arguments
-     `(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon"
+     '(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon"
+
+                           "-DSUNDIALS_INDEX_SIZE=32"
+                           ;; Incompatible with 32-bit indices.
+                           ;;"-DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON"
+
                            "-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"
-
-                           "-DKLU_ENABLE:BOOL=ON"
+                           "-DENABLE_KLU:BOOL=ON"
                            ,(string-append "-DKLU_INCLUDE_DIR="
                                            (assoc-ref %build-inputs 
"suitesparse")
                                            "/include")
@@ -6168,22 +6170,26 @@ easily be incorporated into existing simulation codes.")
     (license license:bsd-3)))
 
 (define-public sundials-openmpi
-  (package
-    (inherit sundials)
+  (package/inherit sundials
     (name "sundials-openmpi")
-    (inputs
-     (modify-inputs (package-inputs sundials)
-       (delete "petsc")
-       (prepend openmpi petsc-openmpi)))     ;support in SUNDIALS requires MPI
+    (propagated-inputs
+     (list openmpi
+           ;; Support for the below requires MPI.
+           ;; TODO: Add HYPRE.
+           petsc-openmpi))
     (arguments
      (substitute-keyword-arguments (package-arguments sundials)
        ((#:configure-flags flags '())
-        `(cons* "-DENABLE_MPI:BOOL=ON" ,flags))
+        `(cons* "-DENABLE_MPI:BOOL=ON"
+                "-DENABLE_PETSC:BOOL=ON"
+                (string-append "-DPETSC_DIR="
+                               (assoc-ref %build-inputs "petsc-openmpi"))
+                ,flags))
        ((#:phases phases '%standard-phases)
         `(modify-phases ,phases
            (add-before 'check 'mpi-setup
-            ,%openmpi-setup)))))
-    (synopsis "SUNDIALS with OpenMPI support")))
+             ,%openmpi-setup)))))
+    (synopsis "SUNDIALS with MPI support")))
 
 (define-public sundials-julia
   (package
@@ -6202,13 +6208,19 @@ easily be incorporated into existing simulation codes.")
          "0nx4sqhmi126m14myzm7syv2053harav9snl0a247wnkcgs5rxrv"))))
     (inputs
      (modify-inputs (package-inputs sundials)
-       (prepend lapack)))
+       (prepend gfortran lapack)))
     (arguments
-     (substitute-keyword-arguments (package-arguments sundials)
-       ((#:configure-flags flags '())
-        `(cons* "-DLAPACK_ENABLE:BOOL=ON"
-                ,flags))))
-    (synopsis "SUNDIALS with lapack support as required by 
julia-sundials-jll")))
+     '(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon"
+                           "-DSUNDIALS_INDEX_SIZE=32"
+                           "-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")
+                           "-DLAPACK_ENABLE:BOOL=ON")))
+    (synopsis "SUNDIALS with LAPACK support as required by 
julia-sundials-jll")))
 
 (define-public combinatorial-blas
   (package