[bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII

[bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII

[Ludovic Courtès]

Hello Guix!

The impetus for this patch series is that PETSc fails to build on
‘core-updates’ (soon to be merged) and it’s pretty critical in
applied maths and HPC:

--8<---------------cut here---------------start------------->8---
Using MAKE: /gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/bin/make
Using MAKEFLAGS: -j16 -l96.0 w -- PETSC_DIR=/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1 PETSC_ARCH=arch-linux-c-opt MAKE_NP=16
==========================================
make[3]: Entering directory '/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1'
/gnu/store/nvpcidxh4wqp5prdlyfsbcymg67xqqn9-python-3.10.7/bin/python3 ./config/gmakegen.py --petsc-arch=arch-linux-c-opt
/gnu/store/nvpcidxh4wqp5prdlyfsbcymg67xqqn9-python-3.10.7/bin/python3 /tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1/config/gmakegentest.py --petsc-dir=/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1 --petsc-arch=arch-linux-c-opt --testdir=./arch-linux-c-opt/tests
make[3]: *** No rule to make target 'w'.  Stop.
make[3]: Leaving directory '/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1'
make[2]: *** [/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1/lib/petsc/conf/rules:50: libs] Error 2
make[2]: Leaving directory '/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1'
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
^[[1;31m**************************ERROR*************************************
  Error during compile, check arch-linux-c-opt/lib/petsc/conf/make.log
  Send it and arch-linux-c-opt/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov
********************************************************************^[[0;39m^[[0;49m
make[1]: *** [makefile:40: all] Error 1
make: *** [GNUmakefile:9: all] Error 2
error: in phase 'build': uncaught exception:
%exception #<&invoke-error program: "make" arguments: ("MAKE_NP=16") exit-status: 2 term-signal: #f stop-signal: #f> 
phase `build' failed after 9.7 seconds
command "make" "MAKE_NP=16" failed with status 2
build process 18 exited with status 256
builder for `/gnu/store/wxzwzjlcq10grqrjl9w144fv3myr0kf9-petsc-3.16.1.drv' failed with exit code 1
--8<---------------cut here---------------end--------------->8---

(From <https://ci.guix.gnu.org/log/4pncdcw7lmls9fi0978fabypv7ili7wb-petsc-3.16.1>.)

Ironically I tested this on top of today’s ‘master’ but I’m hopeful that it’ll
work on ‘core-updates’ (because of this, I think we should get this series
merged shortly once ‘core-updates’ is merged).

I rebuilt all dependents, but ‘fenics’ and its dependents remain broken:
fenics, python-vedo, and python-dolfin-adjoint.

Thanks,
Ludo’.

Ludovic Courtès (8):
  gnu: petsc: Update to 3.21.4.
  gnu: python-petsc4py: Update to 3.21.4.
  gnu: slepc: Update to 3.21.1.
  gnu: python-slepc4py: Update to 3.21.1.
  gnu: petsc: Make ‘petscvariables’ reproducible.
  gnu: sundials: Upgrade to 7.1.1.
  gnu: sundials, sundials-openmpi: Use gexps.
  gnu: dealii: Update to 9.6.0.

 gnu/packages/maths.scm | 190 ++++++++++++++++++++++-------------------
 1 file changed, 100 insertions(+), 90 deletions(-)


base-commit: d5312370b46ace47e138d84e1bb28e5651cee94b
-- 
2.45.2

[bug#72877] [PATCH 1/8] gnu: petsc: Update to 3.21.4.

[Ludovic Courtès]

From: Ludovic Courtès <ludovic.courtes@inria.fr>

* gnu/packages/maths.scm (petsc): Update to 3.21.4.  Update source URL.
[arguments]: Move ‘check’ phase after ‘install’.
[home-page]: Update.

Change-Id: I8e7244ad4f8566119bc259f1dccec9589760a491
---
 gnu/packages/maths.scm | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 557d9acc48..4be9ad9d7e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3510,15 +3510,15 @@ (define-public maxflow
 (define-public petsc
   (package
     (name "petsc")
-    (version "3.16.1")
+    (version "3.21.4")
     (source
      (origin
       (method url-fetch)
       ;; The *-lite-* tarball does not contain the *large* documentation
-      (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
+      (uri (string-append "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/"
                           "petsc-lite-" version ".tar.gz"))
       (sha256
-       (base32 "0sm03vpg010q9icidiq587n325m0598cj6hab2rdv85nwyygg74h"))))
+       (base32 "1394ybnchawb2kghx4xk36gw26930aa73lxyw96diiqp8rnhgbm9"))))
     (outputs '("out"                    ; libraries and headers
                "examples"))             ; ~30MiB of examples
     (build-system gnu-build-system)
@@ -3614,6 +3614,16 @@ (define-public petsc
                 (("([[:graph:]]+)/bin/diff") "diff")
                 (("([[:graph:]]+)/bin/sed") "sed")
                 (("([[:graph:]]+)/bin/gfortran") "gfortran")))))
+
+          ;; Some of the tests get linked with '-L$prefix/lib -lpetsc' (even
+          ;; though that's unnecessary because they also explicitly link
+          ;; against 'libpetsc.so' from the build directory).  To work around
+          ;; it, run tests after installation.  See
+          ;; <https://gitlab.com/petsc/petsc/-/issues/1634>.
+          (delete 'check)
+          (add-after 'install 'check
+            (assoc-ref %standard-phases 'check))
+
           (add-after 'install 'move-examples
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))
@@ -3622,7 +3632,7 @@ (define-public petsc
                      (exdir' (string-append examples "/share/petsc/examples")))
                 (copy-recursively exdir exdir')
                 (delete-file-recursively exdir)))))))
-    (home-page "https://www.mcs.anl.gov/petsc")
+    (home-page "https://petsc.org")
     (synopsis "Library to solve PDEs")
     (description "PETSc, pronounced PET-see (the S is silent), is a suite of
 data structures and routines for the scalable (parallel) solution of
-- 
2.45.2

[bug#72877] [PATCH 2/8] gnu: python-petsc4py: Update to 3.21.4.

[Ludovic Courtès]

From: Ludovic Courtès <ludovic.courtes@inria.fr>

* gnu/packages/maths.scm (python-petsc4py): Update to 3.21.4.
[source](modules, snippet): Remove.
[arguments]: Switch to gexps.  Rename ‘pre-build’ phase to
‘set-PETSC_DIR’.  Replace ‘check’ phase.
[native-inputs]: Switch to ‘python-cython-3’.
[inputs]: Remove labels.

Change-Id: I2d8ef3519f6ffe93ff761ef99c4b8951b6107e1c
---
 gnu/packages/maths.scm | 44 ++++++++++++++++--------------------------
 1 file changed, 17 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 4be9ad9d7e..c6a40a2652 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3727,41 +3727,31 @@ (define-public petsc-complex-openmpi
 (define-public python-petsc4py
   (package
     (name "python-petsc4py")
-    (version "3.16.1")
+    (version "3.21.4")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "petsc4py" version))
         (sha256
           (base32
-           "0pxr6qa7p0pmpq0av29lx8lzlrdcfdzj87ynixzr8dn42y13a662"))
-        (modules '((guix build utils)))
-        (snippet
-         '(begin
-            ;; Ensure source file is regenerated in the build phase.
-            (delete-file "src/petsc4py.PETSc.c")
-            ;; Remove legacy GC code.  See
-            ;; https://bitbucket.org/petsc/petsc4py/issues/125.
-            (substitute* "src/PETSc/cyclicgc.pxi"
-                         ((".*gc_refs.*") "" )
-                         ((".*PyGC_Head.*") ""))
-            #t))))
+           "1kffxhcwkx6283n2p83ymanz6m8j2xmz5kpa5s8qc4f9iiah59sb"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'pre-build
-           (lambda _
-             ;; Define path to PETSc installation.
-             (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
-             #t))
-         (add-before 'check 'mpi-setup
-           ,%openmpi-setup))))
-    (native-inputs
-     (list python-cython))
-    (inputs
-     `(("petsc" ,petsc-openmpi)
-       ("python-numpy" ,python-numpy)))
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'build 'set-PETSC_DIR
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   ;; Define path to PETSc installation.
+                   (setenv "PETSC_DIR"
+                           (assoc-ref inputs "petsc-openmpi"))))
+               (add-before 'check 'mpi-setup
+                 #$%openmpi-setup)
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python" "test/runtests.py")))))))
+    (native-inputs (list python-cython-3))
+    (inputs (list petsc-openmpi python-numpy))
     (home-page "https://bitbucket.org/petsc/petsc4py/")
     (synopsis "Python bindings for PETSc")
     (description "PETSc, the Portable, Extensible Toolkit for
-- 
2.45.2

[bug#72877] [PATCH 3/8] gnu: slepc: Update to 3.21.1.

[Ludovic Courtès]

From: Ludovic Courtès <ludovic.courtes@inria.fr>

* gnu/packages/maths.scm (slepc): Update to 3.21.1.

Change-Id: Ib82754c351100de94b57c650a3688747bf706713
---
 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 c6a40a2652..22e7fc5804 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3928,7 +3928,7 @@ (define-public python-quadpy
 (define-public slepc
   (package
     (name "slepc")
-    (version "3.16.1")
+    (version "3.21.1")
     (source
      (origin
        (method url-fetch)
@@ -3936,7 +3936,7 @@ (define-public slepc
                            version ".tar.gz"))
        (sha256
         (base32
-         "1ysfm77s5fcissv3q0k5d65mlp93zi4anqg62q3cd25dn66sva5i"))))
+         "12kdgnw9lm5q6bq5wp27ygdp1bjdz3fhkb8m9ds83kn32l53zcxy"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python)
-- 
2.45.2

[bug#72877] [PATCH 4/8] gnu: python-slepc4py: Update to 3.21.1.

[Ludovic Courtès]

From: Ludovic Courtès <ludovic.courtes@inria.fr>

* gnu/packages/maths.scm (python-slepc4py): Update to 3.21.1.
[arguments]: Switch to gexps.  Replace ‘check’ phase.
[native-inputs]: New field.
[inputs]: Remove labels.  Add ‘petsc-openmpi’.

Change-Id: Ib6f1480415ac5128399c32c1974779b67edb5550
---
 gnu/packages/maths.scm | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 22e7fc5804..7249eb68da 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4042,31 +4042,32 @@ (define-public slepc-complex-openmpi
 (define-public python-slepc4py
   (package
     (name "python-slepc4py")
-    (version "3.16.1")
+    (version "3.21.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "slepc4py" version))
         (sha256
           (base32
-            "0fq997y73ymvcvdrxycp450pxwdgnqaw62gv9rwncfgsfplkvs9w"))))
+            "01vvpl8g73knkwnh6mbxd45vwcs4zsw814147fvgkvj30qkhx3mw"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'pre-build
-           (lambda _
-             ;; Define path to PETSc installation.
-             (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
-             ;; Define path to SLEPc installation.
-             (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
-             #t))
-         (add-before 'check 'mpi-setup
-           ,%openmpi-setup))))
-    (inputs
-     `(("python-numpy" ,python-numpy)
-       ("python-petsc4py" ,python-petsc4py)
-       ("slepc" ,slepc-openmpi)))
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'build 'pre-build
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   ;; Define path to PETSc installation.
+                   (setenv "PETSC_DIR" (assoc-ref inputs "petsc-openmpi"))
+                   ;; Define path to SLEPc installation.
+                   (setenv "SLEPC_DIR" (assoc-ref inputs "slepc-openmpi"))))
+               (add-before 'check 'mpi-setup
+                 #$%openmpi-setup)
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python" "test/runtests.py")))))))
+    (native-inputs (list python-cython-3))
+    (inputs (list python-numpy python-petsc4py petsc-openmpi slepc-openmpi))
     (home-page "https://bitbucket.org/slepc/slepc4py/")
     (synopsis "Python bindings for SLEPc")
     (description "SLEPc, the Scalable Library for Eigenvalue Problem
-- 
2.45.2

[bug#72877] [PATCH 5/8] gnu: petsc: Make ‘petscvariables’ reproducible.

[Ludovic Courtès]

This is a followup to 31fe177a97bacec643180cc5bcf8805a6cb07481.

* gnu/packages/maths.scm (petsc)[arguments]: In
‘clean-local-references’, fix typo in ‘MAKE_NP’ and ‘NPMAX’ regexps.
Substitute ‘MAKE_TEST_NP’ and ‘MAKE_LOAD’ as well.

Change-Id: I41b4279a3cdc4b077fab21f0f99273d0d50ed8e1
---
 gnu/packages/maths.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 7249eb68da..ff1be6d35a 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3578,8 +3578,10 @@ (define-public petsc
                     "Machine characteristics: Linux-x.x.x"))
                 (substitute* (find-files "." "petscvariables")
                   ;; Do not expose build machine characteristics, set to defaults.
-                  (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
-                  (("NPMAX = [:digit:]+") "NPMAX = 2")))))
+                  (("MAKE_NP = [[:digit:]]+") "MAKE_NP = 2")
+                  (("MAKE_TEST_NP = [[:digit:]]+") "MAKE_TEST_NP = 2")
+                  (("MAKE_LOAD = .*") "MAKE_LOAD = 256.0\n")
+                  (("NPMAX = [[:digit:]]+") "NPMAX = 2")))))
           (add-after 'install 'clean-install
             ;; Try to keep installed files from leaking build directory names.
             (lambda* (#:key inputs outputs #:allow-other-keys)
-- 
2.45.2

[bug#72877] [PATCH 6/8] gnu: sundials: Upgrade to 7.1.1.

[Ludovic Courtès]

From: Ludovic Courtès <ludovic.courtes@inria.fr>

* gnu/packages/maths.scm (sundials): Update to 7.1.1.
[native-inputs]: Add PKG-CONFIG.
(sundials-openmpi)[arguments]: Pass ‘-DPETSC_INCLUDE_DIRS’ instead of
‘-DPETSC_DIR’.

Change-Id: I750415109d69b53afbcf461dc98b2028af03c35a
---
 gnu/packages/maths.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index ff1be6d35a..4dc67ea313 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8036,7 +8036,7 @@ (define-public tiny-bignum
 (define-public sundials
   (package
     (name "sundials")
-    (version "6.2.0")
+    (version "7.1.1")
     (source
      (origin
        (method url-fetch)
@@ -8044,10 +8044,10 @@ (define-public sundials
                            version "/sundials-" version ".tar.gz"))
        (sha256
         (base32
-         "07gk9060xk3bzfqf8v4fqlp0rcxswiwlsy887zv87i1gfy9map8r"))))
+         "1fwlgbcdxz30dzsqw3y1b6ic1rhzfadghj7cq7yxsj14npgnwzga"))))
     (build-system cmake-build-system)
     (native-inputs
-     (list python-2))          ; For tests; syntax incompatible with Python 3.
+     (list pkg-config python-2)) ;for tests; syntax incompatible with Python 3
     (inputs
      (list openblas suitesparse))
     (arguments
@@ -8100,8 +8100,9 @@ (define-public sundials-openmpi
                                (assoc-ref %build-inputs "hypre-openmpi")
                                "/lib")
                 "-DENABLE_PETSC:BOOL=ON"
-                (string-append "-DPETSC_DIR="
-                               (assoc-ref %build-inputs "petsc-openmpi"))
+                (string-append "-DPETSC_INCLUDE_DIRS="
+                               (assoc-ref %build-inputs "petsc-openmpi")
+                               "/include")
                 ,flags))
        ((#:phases phases '%standard-phases)
         `(modify-phases ,phases
-- 
2.45.2

[bug#72877] [PATCH 7/8] gnu: sundials, sundials-openmpi: Use gexps.

[Ludovic Courtès]

* gnu/packages/maths.scm (sundials)[arguments]: Use gexps and use
‘search-input-file’ rather than ‘assoc-ref’.
(sundials-openmpi)[arguments]: Likewise.

Change-Id: Ife0c2ae3604cf66c90ec4a13fe9242f7fe7d550f
---
 gnu/packages/maths.scm | 74 +++++++++++++++++++++++-------------------
 1 file changed, 40 insertions(+), 34 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 4dc67ea313..194e4ea399 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8051,25 +8051,28 @@ (define-public sundials
     (inputs
      (list openblas suitesparse))
     (arguments
-     '(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon"
+     (list #:configure-flags
+           #~(list "-DCMAKE_C_FLAGS=-O2 -g -fcommon"
 
-                           "-DSUNDIALS_INDEX_SIZE=32"
-                           ;; Incompatible with 32-bit indices.
-                           ;;"-DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON"
+                   "-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"
-                           ;; Requires -DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON.
-                           ;;"-DEXAMPLES_ENABLE_F2003:BOOL=ON"
-                           "-DEXAMPLES_INSTALL:BOOL=OFF"
+                   "-DEXAMPLES_ENABLE_C:BOOL=ON"
+                   "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
+                   ;; Requires -DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON.
+                   ;;"-DEXAMPLES_ENABLE_F2003:BOOL=ON"
+                   "-DEXAMPLES_INSTALL:BOOL=OFF"
 
-                           "-DENABLE_KLU:BOOL=ON"
-                           ,(string-append "-DKLU_INCLUDE_DIR="
-                                           (assoc-ref %build-inputs "suitesparse")
-                                           "/include")
-                           ,(string-append "-DKLU_LIBRARY_DIR="
-                                           (assoc-ref %build-inputs "suitesparse")
-                                           "/lib"))))
+                   "-DENABLE_KLU:BOOL=ON"
+                   (string-append "-DKLU_INCLUDE_DIR="
+                                  (dirname
+                                   (search-input-file %build-inputs
+                                                      "include/klu.h")))
+                   (string-append "-DKLU_LIBRARY_DIR="
+                                  (dirname
+                                   (search-input-file %build-inputs
+                                                      "lib/libklu.so"))))))
     (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
@@ -8090,24 +8093,27 @@ (define-public sundials-openmpi
            petsc-openmpi))
     (arguments
      (substitute-keyword-arguments (package-arguments sundials)
-       ((#:configure-flags flags '())
-        `(cons* "-DENABLE_MPI:BOOL=ON"
-                "-DENABLE_HYPRE:BOOL=ON"
-                (string-append "-DHYPRE_INCLUDE_DIR="
-                               (assoc-ref %build-inputs "hypre-openmpi")
-                               "/include")
-                (string-append "-DHYPRE_LIBRARY_DIR="
-                               (assoc-ref %build-inputs "hypre-openmpi")
-                               "/lib")
-                "-DENABLE_PETSC:BOOL=ON"
-                (string-append "-DPETSC_INCLUDE_DIRS="
-                               (assoc-ref %build-inputs "petsc-openmpi")
-                               "/include")
-                ,flags))
-       ((#:phases phases '%standard-phases)
-        `(modify-phases ,phases
-           (add-before 'check 'mpi-setup
-             ,%openmpi-setup)))))
+       ((#:configure-flags flags #~())
+        #~(cons* "-DENABLE_MPI:BOOL=ON"
+                 "-DENABLE_HYPRE:BOOL=ON"
+                 (string-append "-DHYPRE_INCLUDE_DIR="
+                                (dirname
+                                 (search-input-file %build-inputs
+                                                    "include/HYPRE.h")))
+                 (string-append "-DHYPRE_LIBRARY_DIR="
+                                (dirname
+                                 (search-input-file %build-inputs
+                                                    "lib/libHYPRE.so")))
+                 "-DENABLE_PETSC:BOOL=ON"
+                 (string-append "-DPETSC_INCLUDE_DIRS="
+                                (dirname
+                                 (search-input-file %build-inputs
+                                                    "include/petsc.h")))
+                 #$flags))
+       ((#:phases phases #~%standard-phases)
+        #~(modify-phases #$phases
+            (add-before 'check 'mpi-setup
+              #$%openmpi-setup)))))
     (synopsis "SUNDIALS with MPI support")))
 
 (define-public sundials-5
-- 
2.45.2

[bug#72877] [PATCH 8/8] gnu: dealii: Update to 9.6.0.

[Ludovic Courtès]

From: Ludovic Courtès <ludovic.courtes@inria.fr>

* gnu/packages/maths.scm (dealii): Update to 9.6.0.

Change-Id: I197511908d9ac27dd4ba1356515f1fbf7bafd218
---
 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 194e4ea399..7d0d4127cf 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6874,14 +6874,14 @@ (define trilinos-for-dealii-openmpi
 (define-public dealii
   (package
     (name "dealii")
-    (version "9.5.1")
+    (version "9.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/dealii/dealii/releases/"
                            "download/v" version "/dealii-" version ".tar.gz"))
        (sha256
-        (base32 "0phgcfnil4rb41xipsdbm4lxrymlqxbiccakg3pkm3a8wqsva658"))
+        (base32 "1vbvw76xv8h1diwfgybgarm7qwn51rxd1kp2jgy2rvcfxgq26lv7"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled boost, Kokkos, muparser, TBB and UMFPACK.
-- 
2.45.2

bug#72877: [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII

[Ludovic Courtès]

Hi,

Ludovic Courtès <ludo@gnu.org> skribis:

>   gnu: petsc: Update to 3.21.4.
>   gnu: python-petsc4py: Update to 3.21.4.
>   gnu: slepc: Update to 3.21.1.
>   gnu: python-slepc4py: Update to 3.21.1.
>   gnu: petsc: Make ‘petscvariables’ reproducible.
>   gnu: sundials: Upgrade to 7.1.1.
>   gnu: sundials, sundials-openmpi: Use gexps.
>   gnu: dealii: Update to 9.6.0.

Pushed as 993d6d2e7be4dac738629c76a51058f4dc5bc449 after re-testing
locally.

I had to fix ‘hypre’ as well in 6bf70cf9a60464701ca0741d9f63f5ace9810fc9
since it broke on ‘core-updates’ due to a missing TeX Live dependency.

Ludo’.

[bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII

[Eric Bavier]

On 05.09.2024 03:17, Ludovic Courtès wrote:
> Hi,
> 
> Ludovic Courtès <ludo@gnu.org> skribis:
> 
>>   gnu: petsc: Update to 3.21.4.
>>   gnu: python-petsc4py: Update to 3.21.4.
>>   gnu: slepc: Update to 3.21.1.
>>   gnu: python-slepc4py: Update to 3.21.1.
>>   gnu: petsc: Make ‘petscvariables’ reproducible.
>>   gnu: sundials: Upgrade to 7.1.1.
>>   gnu: sundials, sundials-openmpi: Use gexps.
>>   gnu: dealii: Update to 9.6.0.
> 
> Pushed as 993d6d2e7be4dac738629c76a51058f4dc5bc449 after re-testing
> locally.

Thank you for this series, it looks great!

I finally got a chance to look through it just before you pushed. My 
only
note is that I noticed this in the output of petsc's "check" phase:

# -------------
#   Summary
# -------------
# FAILED vec_pf_impls_string_tests-ex1_1 diff-snes_tutorials-ex78_2
# success 5721/10154 tests (56.3%)
# failed 2/10154 tests (0.0%)
# todo 240/10154 tests (2.4%)
# skip 4191/10154 tests (41.3%)

but the 'check' phase doesn't fail.  I wonder if the `make check`
invocation does not return a failure code when the tests fail.  These 
test failures
in particular look mostly harmless, but maybe other more catastrophic 
failures
might not be caught if `check` is not detecting failures.

-- 
`~Eric

[bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII

[Ludovic Courtès]

Hi Eric,

Thanks for taking the time to look into it.  (I rushed the patch series
more than usual because the whole stack was broken since the
‘core-updates’ merge.)

Eric Bavier <bavier@posteo.net> skribis:

> I finally got a chance to look through it just before you pushed. My
> only
> note is that I noticed this in the output of petsc's "check" phase:
>
> # -------------
> #   Summary
> # -------------
> # FAILED vec_pf_impls_string_tests-ex1_1 diff-snes_tutorials-ex78_2
> # success 5721/10154 tests (56.3%)
> # failed 2/10154 tests (0.0%)
> # todo 240/10154 tests (2.4%)
> # skip 4191/10154 tests (41.3%)
>
> but the 'check' phase doesn't fail.  I wonder if the `make check`
> invocation does not return a failure code when the tests fail.  These
> test failures
> in particular look mostly harmless, but maybe other more catastrophic
> failures
> might not be caught if `check` is not detecting failures.

Oh.  I was told in the meantime that we might want to use ‘make test’
instead, so perhaps we should followup on this update with a switch to
‘make test’ and see if problems as shown above still appear:

  https://gitlab.com/petsc/petsc/-/issues/1634#note_2070200322

Ludo’.