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

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3 participants
  • Eric Bavier
  • Ludovic Courtès
  • Ludovic Courtès
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Ludovic Courtès
Severity
normal
L
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Ludovic Courtès wrote on 29 Aug 17:38 +0200
(address . guix-patches@gnu.org)(name . Ludovic Courtès)(address . ludo@gnu.org)
cover.1724945557.git.ludo@gnu.org
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:

Toggle snippet (26 lines)
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
**************************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
********************************************************************
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


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
L
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Ludovic Courtès wrote on 29 Aug 17:39 +0200
[PATCH 1/8] gnu: petsc: Update to 3.21.4.
(address . 72877@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)
7c1e3b92955a4133ffae9bc277f0b8a2d89df6d4.1724945557.git.ludo@gnu.org
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(-)

Toggle diff (51 lines)
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
L
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Ludovic Courtès wrote on 29 Aug 17:39 +0200
[PATCH 2/8] gnu: python-petsc4py: Update to 3.21.4.
(address . 72877@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)
77468fe53b0ea23abc1e544d71c0c31dcf49a078.1724945557.git.ludo@gnu.org
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(-)

Toggle diff (65 lines)
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
L
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Ludovic Courtès wrote on 29 Aug 17:39 +0200
[PATCH 3/8] gnu: slepc: Update to 3.21.1.
(address . 72877@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)
32d909e4f934e6bf116cbe62e90ffa355bed1caa.1724945557.git.ludo@gnu.org
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(-)

Toggle diff (24 lines)
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
L
L
Ludovic Courtès wrote on 29 Aug 17:39 +0200
[PATCH 4/8] gnu: python-slepc4py: Update to 3.21.1.
(address . 72877@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)
52bd9a22889bd47f077bc6b8240a748ce2cb30e7.1724945557.git.ludo@gnu.org
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(-)

Toggle diff (56 lines)
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
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Ludovic Courtès wrote on 29 Aug 17:39 +0200
[PATCH 5/8] gnu: petsc: Make ‘petscvariab les’ reproducible.
(address . 72877@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludo@gnu.org)
4785fd2599682973b16ea0bdab44c909568b0292.1724945557.git.ludo@gnu.org
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(-)

Toggle diff (19 lines)
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
L
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Ludovic Courtès wrote on 29 Aug 17:39 +0200
[PATCH 6/8] gnu: sundials: Upgrade to 7.1.1.
(address . 72877@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)
fb46aa0073483ab25016d1b2133b8048cd8b26cc.1724945557.git.ludo@gnu.org
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(-)

Toggle diff (40 lines)
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
L
L
Ludovic Courtès wrote on 29 Aug 17:39 +0200
[PATCH 7/8] gnu: sundials, sundials-openmpi: Use gexps.
(address . 72877@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludo@gnu.org)
b06f41ec84c2e9315827a450cb090c2a48443ad4.1724945557.git.ludo@gnu.org
* 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(-)

Toggle diff (97 lines)
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
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Ludovic Courtès wrote on 29 Aug 17:39 +0200
[PATCH 8/8] gnu: dealii: Update to 9.6.0.
(address . 72877@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)
66aa3e6c1221344b4129d2c4f82ced06a082a94a.1724945557.git.ludo@gnu.org
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(-)

Toggle diff (23 lines)
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
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Ludovic Courtès wrote on 5 Sep 10:17 +0200
Re: [bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII
(address . 72877-done@debbugs.gnu.org)
87seue8qg8.fsf@gnu.org
Hi,

Ludovic Courtès <ludo@gnu.org> skribis:

Toggle quote (9 lines)
> 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’.
Closed
E
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Eric Bavier wrote on 5 Sep 15:07 +0200
(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)
692205d6c164d7e3e339068c65a43db4@posteo.net
On 05.09.2024 03:17, Ludovic Courtès wrote:
Toggle quote (16 lines)
> 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
Closed
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Ludovic Courtès wrote on 5 Sep 16:40 +0200
(name . Eric Bavier)(address . bavier@posteo.net)
87a5gm6u4z.fsf@inria.fr
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:

Toggle quote (20 lines)
> 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:


Ludo’.
Closed
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