GNU bug report logs - #69729
[PATCH 00/41] Improve performance in lapack dependent packages.

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Package: guix-patches; Reported by: Romain GARBAGE <romain.garbage@HIDDEN>; Keywords: patch; Done: Ludovic Courtès <ludovic.courtes@HIDDEN>; Maintainer for guix-patches is guix-patches@HIDDEN.

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From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludovic.courtes@HIDDEN>
To: Romain GARBAGE <romain.garbage@HIDDEN>
Subject: Re: [bug#69729] [PATCH 00/41] Improve performance in lapack
 dependent packages.
In-Reply-To: <20240311110423.10785-1-romain.garbage@HIDDEN> (Romain
 GARBAGE's message of "Mon, 11 Mar 2024 12:01:55 +0100")
References: <20240311110423.10785-1-romain.garbage@HIDDEN>
Date: Thu, 04 Apr 2024 17:17:19 +0200
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Hello,

Romain GARBAGE <romain.garbage@HIDDEN> skribis:

>   gnu: arpack-ng: Switch to openblas.
>   gnu: armadillo: Switch to openblas.
>   gnu: octave-cli: Switch to openblas.
>   gnu: scalapack: Switch to openblas.
>   gnu: hypre: Switch to openblas.
>   gnu: igraph: Switch to openblas.
>   gnu: vosk-api: Remove dependency on lapack.
>   gnu: jags: Switch to openblas.
>   gnu: sbcl-lla: Switch to openblas.
>   gnu: itpp: Switch to openblas.
>   gnu: gmsh: Switch to openblas.
>   gnu: ghc-hmatrix: Switch to openblas.
>   gnu: fenics-dolfin: Remove dependency on lapack.
>   gnu: ipopt: Switch to openblas.
>   gnu: ceres: Remove dependency on lapack.
>   gnu: sundials-julia: Switch to openblas.
>   gnu: plink: Switch to openblas.
>   gnu: p4est: Remove dependency on lapack.
>   gnu: plink-ng: Remove lapack dep.
>   gnu: dealii: Remove dependency on lapack.
>   gnu: elemental: Remove dependency on lapack.
>   gnu: superlu-dist: Remove dependency on lapack.
>   gnu: bonmin: Switch to openblas.
>   gnu: mpb: Switch to openblas.
>   gnu: meep: Switch to openblas.
>   gnu: casacore: Remove dependency on lapack.
>   gnu: aoflagger: Remove dependency on lapack.
>   gnu: apl: Switch to openblas.
>   gnu: eigensoft: Remove dependency on lapack.
>   gnu: proteinortho: Remove dependency on lapack.
>   gnu: scilab: Remove dependency on lapack.
>   gnu: python-cvxopt: Remove dependency on lapack.
>   gnu: dlib: Remove dependency on lapack.
>   gnu: grass: Remove dependency on lapack.
>   gnu: harminv: Switch to openblas.
>   gnu: giac: Switch to openblas.
>   gnu: libflame: Switch to openblas.
>   gnu: lush2: Remove dependency on lapack.
>   gnu: shogun: Switch to openblas.
>   gnu: kaldi-for-vosk: Remove dependency on lapack.
>   gnu: ocaml-lacaml: Remove dependency on lapack.

Pushed as e6df74d2b1afb71121228330fce9b5020d00220a.

Thanks!

Ludo=E2=80=99.




Notification sent to Romain GARBAGE <romain.garbage@HIDDEN>:
bug acknowledged by developer. Full text available.
Reply sent to Ludovic Courtès <ludovic.courtes@HIDDEN>:
You have taken responsibility. Full text available.

Message received at 69729 <at> debbugs.gnu.org:


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From: Christopher Baines <mail@HIDDEN>
To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludovic.courtes@HIDDEN>
Subject: Re: [bug#69729] [PATCH 00/41] Improve performance in lapack
 dependent packages.
In-Reply-To: <878r22oczt.fsf@HIDDEN> ("Ludovic =?utf-8?Q?Court=C3=A8s=22'?=
 =?utf-8?Q?s?= message of "Thu, 28 Mar 2024 11:40:54 +0100")
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--=-=-=
Content-Type: text/plain; charset=utf-8
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Ludovic Court=C3=A8s <ludovic.courtes@HIDDEN> writes:

> Hello,
>
> Romain GARBAGE <romain.garbage@HIDDEN> skribis:
>
>> This patch series aims at improving the performance of several packages =
by changing the LAPACK library they depend on.
>>
>> The package `lapack` is the reference implementation from netlib.org of =
a numerical linear algebra library, written in FORTRAN.
>>
>> The package `openblas` is a optimized implementation of the LAPACK and B=
LAS APIs.
>>
>> Among the modified packages affected by the change, the following don't =
build:
>>  * shogun: atlas dependency doesn't build (pre-existing error)
>>  * lush2: preexisting error
>>  * proteinortho: preexisting error (tests 2 and 3 fail)
>>  * superlu-dist: dependency failure (combinatorial-blas)
>>
>>
>> Also, the following packages have not been modified as it breaks the pac=
kage:
>>  * xyce-serial
>>  * xyce-parallel
>>  * gnss-sdr
>>  * julia
>
> <https://qa.guix.gnu.org/issue/69729> hasn=E2=80=99t processed it yet but=
 it=E2=80=99s
> already been more than two weeks.  Given that you tested all the
> dependents on guix.bordeaux.inria.fr, I=E2=80=99m willing to go ahead and=
 push
> the series within a few days even if qa.guix hasn=E2=80=99t caught up yet.

QA shouldn't block things, especially at the moment when it's not
keeping up. So yeah, please push.

--=-=-=
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Information forwarded to guix-patches@HIDDEN:
bug#69729; Package guix-patches. Full text available.

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From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludovic.courtes@HIDDEN>
To: Romain GARBAGE <romain.garbage@HIDDEN>
Subject: Re: [bug#69729] [PATCH 00/41] Improve performance in lapack
 dependent packages.
In-Reply-To: <20240311110423.10785-1-romain.garbage@HIDDEN> (Romain
 GARBAGE's message of "Mon, 11 Mar 2024 12:01:55 +0100")
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Hello,

Romain GARBAGE <romain.garbage@HIDDEN> skribis:

> This patch series aims at improving the performance of several packages b=
y changing the LAPACK library they depend on.
>
> The package `lapack` is the reference implementation from netlib.org of a=
 numerical linear algebra library, written in FORTRAN.
>
> The package `openblas` is a optimized implementation of the LAPACK and BL=
AS APIs.
>
> Among the modified packages affected by the change, the following don't b=
uild:
>  * shogun: atlas dependency doesn't build (pre-existing error)
>  * lush2: preexisting error
>  * proteinortho: preexisting error (tests 2 and 3 fail)
>  * superlu-dist: dependency failure (combinatorial-blas)
>
>
> Also, the following packages have not been modified as it breaks the pack=
age:
>  * xyce-serial
>  * xyce-parallel
>  * gnss-sdr
>  * julia

<https://qa.guix.gnu.org/issue/69729> hasn=E2=80=99t processed it yet but i=
t=E2=80=99s
already been more than two weeks.  Given that you tested all the
dependents on guix.bordeaux.inria.fr, I=E2=80=99m willing to go ahead and p=
ush
the series within a few days even if qa.guix hasn=E2=80=99t caught up yet.

Thoughts?

Ludo=E2=80=99.




Information forwarded to guix-patches@HIDDEN:
bug#69729; Package guix-patches. Full text available.

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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 41/41] gnu: ocaml-lacaml: Remove dependency on lapack.
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* gnu/packages/ocaml.scm (ocaml-lacaml): Remove dependency on lapack.

Change-Id: If3100fc29088110705e13e9be97abb7739f2fcab
---
 gnu/packages/ocaml.scm | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 0f4c351141..a45b2d3592 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -8344,9 +8344,14 @@ (define-public ocaml-lacaml
     (properties '((tunable? . #t)))
     (build-system dune-build-system)
     (arguments
-     `(#:tests? #f)) ; No test target.
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'find-openblas
+                 (lambda* _
+                   (setenv "LACAML_LIBS" "-lopenblas"))))
+           #:tests? #f))                ; No test target.
     (native-inputs
-     (list openblas lapack ocaml-base ocaml-stdio))
+     (list openblas ocaml-base ocaml-stdio))
     (home-page "https://mmottl.github.io/lacaml/")
     (synopsis
      "OCaml-bindings to BLAS and LAPACK")
-- 
2.41.0





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Subject: [PATCH 35/41] gnu: harminv: Switch to openblas.
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* gnu/packages/engineering.scm (harminv): Switch input dependency from
lapack to openblas.

Change-Id: Id6e85550f3559afde6732346e299486b3255cebe
---
 gnu/packages/engineering.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index d6552739c6..2eddc40f50 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -1616,7 +1616,7 @@ (define-public harminv
     (native-inputs
      `(("fortran" ,gfortran)))
     (inputs
-     (list lapack))
+     (list openblas))
     (home-page "https://github.com/stevengj/harminv")
     (synopsis "Harmonic inversion solver")
     (description
-- 
2.41.0





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bug#69729; Package guix-patches. Full text available.

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Subject: [PATCH 28/41] gnu: apl: Switch to openblas.
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* gnu/packages/apl.scm (apl): Switch input dependency from
lapack to openblas.

Change-Id: I29f27ee4c9277cf21fa34d718e56291427293cdf
---
 gnu/packages/apl.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/apl.scm b/gnu/packages/apl.scm
index afe02736ad..0b56c8b088 100644
--- a/gnu/packages/apl.scm
+++ b/gnu/packages/apl.scm
@@ -56,7 +56,7 @@ (define-public apl
       (home-page "https://www.gnu.org/software/apl/")
       (inputs
        (list gettext-minimal
-             lapack
+             openblas
              pcre2
              readline
              sqlite))
-- 
2.41.0





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* gnu/packages/engineering.scm (mpb): Switch input dependency from
lapack to openblas.

Change-Id: Ie5920a0014942642360660f7022f887af4eab721
---
 gnu/packages/engineering.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index ae287cf51b..0b6f1f14f3 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -1682,7 +1682,7 @@ (define-public mpb
        ("gsl" ,gsl)
        ("guile" ,guile-2.2)
        ("hdf5" ,hdf5)
-       ("lapack" ,lapack)
+       ("openblas" ,openblas)
        ("libctl" ,guile-libctl)
        ("readline" ,readline)
        ("zlib" ,zlib)))
-- 
2.41.0





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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 17/41] gnu: plink: Switch to openblas.
Date: Mon, 11 Mar 2024 12:06:58 +0100
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* gnu/packages/bioinformatics.scm (plink): Switch input dependency from
lapack to openblas.

Change-Id: I8066a50c880b72a77ba00c2bc39403e212605b9d
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b8ecea013c..8b2fe2d017 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9599,8 +9599,8 @@ (define-public plink
     (arguments
      `(#:tests? #f ;no "check" target
        #:make-flags ,#~(list (string-append "LIB_LAPACK="
-                                            #$(this-package-input "lapack")
-                                            "/lib/liblapack.so")
+                                            #$(this-package-input "openblas")
+                                            "/lib/libopenblas.so")
                              "WITH_LAPACK=1"
                              "FORCE_DYNAMIC=1"
                              ;; disable phoning home
@@ -9615,7 +9615,7 @@ (define-public plink
                                        "/bin/")))
                (install-file "plink" bin)))))))
     (inputs
-     (list zlib lapack))
+     (list zlib openblas))
     (native-inputs
      (list unzip gcc-8))
     (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
-- 
2.41.0





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From: Romain GARBAGE <romain.garbage@HIDDEN>
To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 40/41] gnu: kaldi-for-vosk: Remove dependency on lapack.
Date: Mon, 11 Mar 2024 12:07:21 +0100
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* gnu/packages/machine-learning.scm (kaldi-for-vosk): Remove dependency
to lapack.

Change-Id: I0f5f508288ccb2e7fd086aabeffb5b0b4d3f96b2
---
 gnu/packages/machine-learning.scm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 005ae0a8d5..aa375b0c34 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -2517,7 +2517,6 @@ (define kaldi-for-vosk
           (base32 "16w90za8narkfi590cxj4p7vc1f5sdxc927g5hk6kh4l3mf6iisl"))))
       (inputs
        (list alsa-lib
-             lapack ;compared to base kaldi, replacing `(,gfortran "lib")
              glib
              gstreamer
              jack-2
@@ -2536,7 +2535,6 @@ (define kaldi-for-vosk
             (replace 'configure
               (lambda _
                 (let ((portaudio #$(this-package-input "portaudio"))
-                      (lapack    #$(this-package-input "lapack"))
                       (openfst   #$(this-package-input "openfst"))
                       (openblas  #$(this-package-input "openblas")))
                   #$@(if (target-x86?)
@@ -2570,7 +2568,7 @@ (define kaldi-for-vosk
                      (string-append "OPENBLASROOT=\"" openblas "\""))
                     (("-L\\$OPENBLASLIBDIR -l:libopenblas.a -l:libblas.a -l:liblapack.a -l:libf2c.a")
                      (string-append "-L$OPENBLASLIBDIR -lopenblas "
-                                    "-L" lapack "/lib -lblas -llapack")))
+                                    "-L" openblas "/lib -lopenblas")))
                   (mkdir-p #$output) ; must exist
                   (setenv "CONFIG_SHELL" (which "bash"))
                   (setenv "OPENFST_VER" #$(package-version openfst))
-- 
2.41.0





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Subject: [PATCH 39/41] gnu: shogun: Switch to openblas.
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* gnu/packages/machine-learning.scm (shogun): Switch from lapack to
openblas dependency.

Change-Id: Ib8dde7d9ed9df4bda0eab945f3098a28d0e5927b
---
 gnu/packages/machine-learning.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 4315d0d5b9..005ae0a8d5 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1255,7 +1255,7 @@ (define (delete-ifdefs file)
        ("hdf5" ,hdf5)
        ("atlas" ,atlas)
        ("arpack" ,arpack-ng)
-       ("lapack" ,lapack)
+       ("openblas" ,openblas)
        ("glpk" ,glpk)
        ("libxml2" ,libxml2)
        ("lzo" ,lzo)
-- 
2.41.0





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Subject: [PATCH 31/41] gnu: scilab: Remove dependency on lapack.
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* gnu/packages/maths.scm (scilab): Remove dependency on lapack.

Change-Id: I5c825c9e6eee6f7fbde078c67d3208fcadf100b6
---
 gnu/packages/maths.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index a544aa12af..5aa3c50fd2 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -9776,7 +9776,6 @@ (define-public scilab
                   fftw
                   gettext-minimal
                   hdf5-1.10
-                  lapack
                   libarchive
                   libx11
                   libxml2
-- 
2.41.0





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Subject: [PATCH 38/41] gnu: lush2: Remove dependency on lapack.
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* gnu/packages/lisp.scm (lush2): Remove dependency on lapack.

Change-Id: Idb7734e93021d6be9f65a5a0f9c4da4581786aee
---
 gnu/packages/lisp.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index c58e56b7a7..ecc22107aa 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -874,7 +874,6 @@ (define-public lush2
        ("sdl-mixer" ,sdl-mixer)
        ("sdl-net" ,sdl-net)
        ("sdl-ttf" ,sdl-ttf)
-       ("lapack" ,lapack)
        ("libxft" ,libxft)
        ("fontconfig" ,fontconfig)
        ("gsl" ,gsl)
-- 
2.41.0





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bug#69729; Package guix-patches. Full text available.

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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 37/41] gnu: libflame: Switch to openblas.
Date: Mon, 11 Mar 2024 12:07:18 +0100
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* gnu/packages/maths.scm (libflame): Switch input dependency from
lapack to openblas.

Change-Id: I7abdb8d126856488b0722b73c336309bf5c2234d
---
 gnu/packages/maths.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index c6d67a1bcb..3d955e7e18 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2763,9 +2763,9 @@ (define-public libflame
                    (lambda* (#:key tests? #:allow-other-keys)
                      (substitute* "test/Makefile"
                        (("LIBBLAS .*")
-                        "LIBBLAS = -lblas\n")
+                        "LIBBLAS = -lopenblas\n")
                        (("LIBLAPACK .*")
-                        "LIBLAPACK = -llapack\n"))
+                        "LIBLAPACK = -lopenblas\n"))
                      (when tests?
                        (with-directory-excursion "test"
                          (mkdir "obj")
@@ -2784,7 +2784,7 @@ (define-public libflame
                                                     "/include/FLAME.h")
                                      (string-append static "/include"))))))))
       (inputs (list gfortran))
-      (native-inputs (list lapack perl python-wrapper))
+      (native-inputs (list openblas perl python-wrapper))
       (synopsis "High-performance library for @acronym{DLA, dense linear algebra} computations")
       (description "@code{libflame} is a portable library for dense matrix
 computations, providing much of the functionality present in LAPACK, developed
-- 
2.41.0





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bug#69729; Package guix-patches. Full text available.

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* gnu/packages/algebra.scm (giac): Switch input dependency from
lapack to openblas.

Change-Id: I1ba95b5b606baf3192fdd3f651c9a74ab6e820c1
---
 gnu/packages/algebra.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 90507ebd90..5ec47428fc 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -413,7 +413,6 @@ (define-public giac
            glpk-4
            gmp
            gsl
-           lapack
            libjpeg-turbo
            libpng
            libsamplerate
@@ -425,6 +424,7 @@ (define-public giac
            mpfi
            mpfr
            ntl
+           openblas
            pari-gp
            perl
            tcsh))
-- 
2.41.0





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bug#69729; Package guix-patches. Full text available.

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Subject: [PATCH 34/41] gnu: grass: Remove dependency on lapack.
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* gnu/packages/geo.scm (grass): Remove dependency on lapack.
Add 'fix-lapack build phase.

Change-Id: I758a9b2434f0ad9f8b85a5c5cde6d0a80e6defb2
---
 gnu/packages/geo.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 687effcace..6d3162b10d 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -2610,7 +2610,6 @@ (define-public grass
          ("gdal" ,gdal)
          ("geos" ,geos)
          ("glu" ,glu)
-         ("lapack" ,lapack)
          ("libpng" ,libpng)
          ("libtiff" ,libtiff)
          ("mesa" ,mesa)
@@ -2644,6 +2643,11 @@ (define-public grass
                              (guix build python-build-system))
          #:phases
          (modify-phases %standard-phases
+           (add-after 'unpack 'fix-lapack
+             (lambda _
+               (substitute* "./configure"
+                 (("-lblas") "-lopenblas")
+                 (("-llapack") "-lopenblas"))))
            (replace 'configure
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let ((shell (search-input-file inputs "/bin/bash")))
-- 
2.41.0





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bug#69729; Package guix-patches. Full text available.

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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 33/41] gnu: dlib: Remove dependency on lapack.
Date: Mon, 11 Mar 2024 12:07:14 +0100
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* gnu/packages/machine-learning.scm (dlib): Remove dependency on lapack.

Change-Id: I1e230cef64f1a847bb44845ebf3f59e7f4704b7b
---
 gnu/packages/machine-learning.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e51877411d..4315d0d5b9 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1650,7 +1650,6 @@ (define-public dlib
            libnsl))
     (inputs
      `(("giflib" ,giflib)
-       ("lapack" ,lapack)
        ("libjpeg" ,libjpeg-turbo)
        ("libpng" ,libpng)
        ("libx11" ,libx11)
-- 
2.41.0





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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 32/41] gnu: python-cvxopt: Remove dependency on lapack.
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* gnu/packages/maths.scm (python-cvxopt): Remove dependency on lapack.

Change-Id: I2a28ecf1ab5ea7683d6b8adf72054d3f86892771
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5aa3c50fd2..c6d67a1bcb 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -401,6 +401,7 @@ (define-public python-cvxopt
          (add-after 'unpack 'find-libraries
            (lambda* (#:key inputs #:allow-other-keys)
              (setenv "CVXOPT_BLAS_LIB" "openblas")
+             (setenv "CVXOPT_LAPACK_LIB" "openblas")
              (setenv "CVXOPT_BUILD_FFTW" "1")
              (setenv "CVXOPT_BUILD_GLPK" "1")
              (setenv "CVXOPT_BUILD_GSL" "1")
@@ -409,7 +410,6 @@ (define-public python-cvxopt
      (list fftw
            glpk
            gsl
-           lapack
            openblas
            suitesparse))
     (home-page "https://www.cvxopt.org")
-- 
2.41.0





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Subject: [PATCH 30/41] gnu: proteinortho: Remove dependency on lapack.
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* gnu/packages/bioinformatics.scm (proteinortho): Remove dependency on lapack.
---
 gnu/packages/bioinformatics.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ac2f7c1ade..98bc05d154 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8673,7 +8673,9 @@ (define-public proteinortho
              (substitute* "Makefile"
                (("INSTALLDIR=.*")
                 (string-append
-                 "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")))
+                 "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n"))
+               (("-llapack -lblas")
+                "-lopenblas"))
              #t))
          (add-before 'install 'make-install-directory
            ;; The install directory is not created during 'make install'.
@@ -8697,7 +8699,6 @@ (define-public proteinortho
        ("perl" ,perl)
        ("python" ,python-wrapper)
        ("blast+" ,blast+)
-       ("lapack" ,lapack)
        ("openblas" ,openblas)))
     (native-inputs
      (list which))
-- 
2.41.0





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* gnu/packages/maths.scm (superlu-dist): Remove dependency on lapack.

Change-Id: I5893e16f7ef6fd688fd6b53eba6d3005b832f0ef
---
 gnu/packages/maths.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index c14dede5e0..2b2252746e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4443,7 +4443,6 @@ (define-public superlu-dist
     (inputs
      `(("gfortran" ,gfortran)
        ("blas" ,openblas)
-       ("lapack" ,lapack)
        ("combblas" ,combinatorial-blas)))
     (propagated-inputs
      `(("mpi" ,openmpi)                 ;headers include MPI heades
@@ -4454,7 +4453,7 @@ (define-public superlu-dist
        #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
                                "-DTPL_ENABLE_COMBBLASLIB=YES"
                                "-DTPL_BLAS_LIBRARIES=-lopenblas"
-                               "-DTPL_LAPACK_LIBRARIES=-llapack"
+                               "-DTPL_LAPACK_LIBRARIES=-lopenblas"
                                (string-append "-DTPL_PARMETIS_LIBRARIES="
                                               (string-join
                                                '("ptscotchparmetis" "ptscotch" "ptscotcherr"
-- 
2.41.0





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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 29/41] gnu: eigensoft: Remove dependency on lapack.
Date: Mon, 11 Mar 2024 12:07:10 +0100
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* gnu/packages/bioinformatics.scm (eigensoft): Remove dependency on lapack.

Change-Id: I9d4adfd64a32333a0d605d4ce1aa998035decf2a
---
 gnu/packages/bioinformatics.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6c2dc95fa6..ac2f7c1ade 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5834,7 +5834,7 @@ (define-public eigensoft
                          (find-files "../bin" ".*"))
                #t))))))
     (inputs
-     (list gsl lapack openblas perl
+     (list gsl openblas perl
            `(,gfortran "lib")))
     (home-page "https://github.com/DReichLab/EIG")
     (synopsis "Tools for population genetics")
-- 
2.41.0





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Subject: [PATCH 27/41] gnu: aoflagger: Remove dependency on lapack.
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* gnu/packages/astronomy.scm (aoflagger): Remove dependency on lapack.

Change-Id: I9a8d56364c1989cca23e826bc984831a2c93b776
---
 gnu/packages/astronomy.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 3fce881386..da10308ef3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -323,7 +323,6 @@ (define-public aoflagger
            gsl
            gtkmm-3
            hdf5
-           lapack
            libpng
            libsigc++
            libxml2
-- 
2.41.0





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Subject: [PATCH 26/41] gnu: casacore: Remove dependency on lapack.
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* gnu/packages/astronomy.scm (casacore): Remove dependency on lapack.

Change-Id: I83776d9d780715fc4fe40daad9e1724a94f6910d
---
 gnu/packages/astronomy.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d7747f051d..3fce881386 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -411,7 +411,6 @@ (define-public casacore
            fftwf
            gfortran
            hdf5
-           lapack
            ncurses
            openblas
            python
-- 
2.41.0





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* gnu/packages/maths.scm (bonmin): Switch input dependency from
lapack to openblas.

Change-Id: I3f1ef50827873fdc1eddcd152a74ffbbbf02ee44
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2b2252746e..a544aa12af 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1433,7 +1433,7 @@ (define-public bonmin
                 "153kj4wx386609g21hw3cv5yxps62qqrc64zwb9ryd2xad1w1a4y"))))
     (build-system gnu-build-system)
     (native-inputs (list gfortran pkg-config))
-    (inputs (list cbc ipopt lapack))
+    (inputs (list cbc ipopt openblas))
     (home-page "https://coin-or.github.io/Bonmin/")
     (synopsis "Basic Open-source Nonlinear Mixed INteger programming")
     (description "Bonmin is a code for solving general MINLP (Mixed Integer
-- 
2.41.0





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bug#69729; Package guix-patches. Full text available.

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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 25/41] gnu: meep: Switch to openblas.
Date: Mon, 11 Mar 2024 12:07:06 +0100
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* gnu/packages/engineering.scm (meep): Switch input dependency from
lapack to openblas.

Change-Id: I0d7e3281b588472abd7a9b9c33249d52c925fe35
---
 gnu/packages/engineering.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 0b6f1f14f3..d6552739c6 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -1724,7 +1724,7 @@ (define-public meep
        ("guile" ,guile-2.2)
        ("harminv" ,harminv)
        ("hdf5" ,hdf5)
-       ("lapack" ,lapack)
+       ("openblas" ,openblas)
        ("libctl" ,guile-libctl)
        ("mpb" ,mpb)
        ("zlib" ,zlib)))
-- 
2.41.0





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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 20/41] gnu: dealii: Remove dependency on lapack.
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* gnu/packages/maths.scm (dealii): Remove dependency on lapack.

Change-Id: I6f3439c886a574b8a8d2d91a4afa04ed09daba7f
---
 gnu/packages/maths.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index efe2387742..115eb8e5f0 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6789,7 +6789,6 @@ (define-public dealii
      (list arpack-ng
            openblas
            gfortran
-           lapack
            muparser
            zlib))
     (propagated-inputs
-- 
2.41.0





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Subject: [PATCH 21/41] gnu: elemental: Remove dependency on lapack.
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* gnu/packages/maths.scm (elemental): Remove dependency on lapack.

Change-Id: Iad28ceb70b87a26de75feec631b40aeedf977b53
---
 gnu/packages/maths.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 115eb8e5f0..c14dede5e0 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7801,7 +7801,6 @@ (define-public elemental
       (inputs
        (list `(,gfortran "lib")
              gmp
-             lapack
              metis
              mpc
              mpfr
-- 
2.41.0





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* gnu/packages/bioinformatics.scm (plink-ng): Remove dependency to lapack.

Change-Id: I4d14789c42dc216244872d70120efeeb97127a62
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8b2fe2d017..6c2dc95fa6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9650,7 +9650,7 @@ (define-public plink-ng
      (list
       #:tests? #false ;TEST_EXTRACT_CHR doesn't produce expected files
       #:make-flags
-      #~(list "BLASFLAGS=-llapack -lopenblas"
+      #~(list "BLASFLAGS=-lopenblas"
               "NO_SSE42=1"
               "NO_AVX2=1"
               "STATIC_ZSTD="
@@ -9677,7 +9677,7 @@ (define-public plink-ng
                            (string-append
                             (assoc-ref outputs "out") "/bin")))))))
     (inputs
-     (list lapack openblas zlib `(,zstd "lib")))
+     (list openblas zlib `(,zstd "lib")))
     (native-inputs
      (list diffutils plink python simde)) ; for tests
     (home-page "https://www.cog-genomics.org/plink/")
-- 
2.41.0





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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 18/41] gnu: p4est: Remove dependency on lapack.
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* gnu/packages/maths.scm (p4est): Remove dependency on lapack.

Change-Id: I9c76f8b9ba3fc7d5feabfb059505f66ac50972c3
---
 gnu/packages/maths.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 980fa89d82..efe2387742 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4730,15 +4730,14 @@ (define-public p4est
     (inputs
      `(("fortran" ,gfortran)
        ("blas" ,openblas)
-       ("lapack" ,lapack)
        ("zlib" ,zlib)))
     (arguments
      `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
                                            (assoc-ref %build-inputs "blas")
                                            " -lopenblas")
                            ,(string-append "LAPACK_LIBS=-L"
-                                           (assoc-ref %build-inputs "lapack")
-                                           " -llapack"))
+                                           (assoc-ref %build-inputs "blas")
+                                           " -lopenblas"))
        #:phases (modify-phases %standard-phases
                   (add-before 'check 'mpi-setup
 		    ,%openmpi-setup))))
-- 
2.41.0





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Subject: [PATCH 15/41] gnu: ceres: Remove dependency on lapack.
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* gnu/packages/maths.scm (ceres): Remove dependency to lapack.

Change-Id: Iac55faf30a83bbbe3693cac73a9996af8ddcbde7
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 916dcde2c1..4990c80dd3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2858,7 +2858,7 @@ (define-public ceres
     (native-inputs (list pkg-config))
     ;; These inputs need to be propagated to satisfy dependent packages.
     (propagated-inputs (list eigen gflags glog))
-    (inputs (list openblas lapack suitesparse))
+    (inputs (list openblas suitesparse))
     (synopsis "C++ library for solving large optimization problems")
     (description
      "Ceres Solver is a C++ library for modeling and solving large,
-- 
2.41.0





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Subject: [PATCH 14/41] gnu: ipopt: Switch to openblas.
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* gnu/packages/maths.scm (ipopt): Switch input dependency from
lapack to openblas and add required configure flags.

Change-Id: I58b84f0741a973adf81da1716e2e2659af1c50c4
---
 gnu/packages/maths.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d38dac267f..916dcde2c1 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2399,7 +2399,8 @@ (define-public ipopt
                 "08gznhwhqv1x4baksz350ih8q16r5rd0k8vals6078m3h94khr4b"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
+     '(#:configure-flags (list "--with-lapack=-lopenblas")
+       #:phases (modify-phases %standard-phases
                   (add-after 'install 'add--L-flags-in-ipopt.pc
                     (lambda* (#:key inputs outputs #:allow-other-keys)
                       ;; The '.pc' file lists '-llapack -lblas' in "Libs";
@@ -2412,14 +2413,14 @@ (define-public ipopt
                           (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
                            (string-append "Libs: " before " " after "\n"
                                           "Libs.private: " before
-                                          "-L" lapack "/lib -llapack -lblas "
+                                          "-L" openblas "/lib -lopenblas"
                                           after "\n")))
                         #t))))))
     (native-inputs
      (list gfortran pkg-config))
     (inputs
      ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
-     (list lapack))                    ;for both libblas and liblapack
+     (list openblas))                    ;for both libblas and liblapack
     (home-page "https://www.coin-or.org")
     (synopsis "Large-scale nonlinear optimizer")
     (description
-- 
2.41.0





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Subject: [PATCH 16/41] gnu: sundials-julia: Switch to openblas.
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* gnu/packages/maths.scm (sundials-julia): Switch input dependency from
lapack to openblas.

Change-Id: I7c5990b09f3a006600bab73ef998b081cbaa8935
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 4990c80dd3..980fa89d82 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8041,7 +8041,7 @@ (define-public sundials-julia
          "0nx4sqhmi126m14myzm7syv2053harav9snl0a247wnkcgs5rxrv"))))
     (inputs
      (modify-inputs (package-inputs sundials)
-       (prepend gfortran lapack)))
+       (prepend gfortran openblas)))
     (arguments
      '(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon"
                            "-DSUNDIALS_INDEX_SIZE=32"
-- 
2.41.0





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bug#69729; Package guix-patches. Full text available.

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To: 69729 <at> debbugs.gnu.org
Subject: [PATCH 13/41] gnu: fenics-dolfin: Remove dependency on lapack.
Date: Mon, 11 Mar 2024 12:06:54 +0100
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* gnu/packages/simulation.scm (fenics-dolfin): Remove input dependency
from to lapack.

Change-Id: Ie60437e365c45e92f03ac3f147ec41eba40e2963
---
 gnu/packages/simulation.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index b2fb123815..8cbf9be22a 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -773,7 +773,6 @@ (define-public fenics-dolfin
            boost
            eigen
            hdf5-parallel-openmpi
-           lapack
            libxml2
            openmpi
            python-3
@@ -805,7 +804,7 @@ (define-public fenics-dolfin
                    (setenv "CATCH_DIR"
                            #$(this-package-input "catch"))
                    (setenv "LAPACK_DIR"
-                           #$(this-package-input "lapack"))
+                           #$(this-package-input "openblas"))
                    (setenv "PETSC_DIR"
                            #$(this-package-input "petsc"))
                    (setenv "SLEPC_DIR"
-- 
2.41.0





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bug#69729; Package guix-patches. Full text available.

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Subject: [PATCH 12/41] gnu: ghc-hmatrix: Switch to openblas.
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* gnu/packages/haskell-xyz.scm (ghc-hmatrix): Switch input dependency from
lapack to openblas. Add configure flags.

Change-Id: Ic8924b1fb9fa61af16abd1ac2a22c82a352a8e1b
---
 gnu/packages/haskell-xyz.scm | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm
index 5d9e5757a0..b5943f2f47 100644
--- a/gnu/packages/haskell-xyz.scm
+++ b/gnu/packages/haskell-xyz.scm
@@ -5325,18 +5325,15 @@ (define-public ghc-hmatrix
     (build-system haskell-build-system)
     (properties '((upstream-name . "hmatrix")))
     (arguments
-     `(#:extra-directories ("lapack")))
+     `(#:configure-flags '("--flags=openblas")
+       #:extra-directories ("openblas")))
     (inputs
      (list ghc-random
            ghc-split
            ghc-storable-complex
            ghc-semigroups
            ghc-vector
-           ;;("openblas" ,openblas)
-           lapack))
-    ;; Guix's OpenBLAS is built with the flag "NO_LAPACK=1" which
-    ;; disables inclusion of the LAPACK functions.
-    ;; (arguments `(#:configure-flags '("--flags=openblas")))
+           openblas))
     (home-page "https://github.com/albertoruiz/hmatrix")
     (synopsis "Haskell numeric linear algebra library")
     (description "The HMatrix package provices a Haskell library for
-- 
2.41.0





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* gnu/packages/maths.scm (gmsh): Switch input dependency from
lapack to openblas.

Change-Id: Ib04c07a51f3af65d259b9970073ec1f68603aed4
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 29b6bbf76f..d38dac267f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3262,11 +3262,11 @@ (define-public gmsh
            glu
            gmp
            hdf5
-           lapack
            libx11
            libxext
            mesa
            metis
+           openblas
            opencascade-occt))
     (inputs
      (list fontconfig
-- 
2.41.0





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bug#69729; Package guix-patches. Full text available.

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Subject: [PATCH 10/41] gnu: itpp: Switch to openblas.
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* gnu/packages/maths.scm (itpp): Switch input dependency from
lapack to openblas.

Change-Id: I42606d5ed379093a076790d2b300dfa96f18d2ea
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index e80b7df0e2..29b6bbf76f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2151,7 +2151,7 @@ (define-public itpp
                      ;; SOURCE_DATE_EPOCH
                      (lambda _
                        (setenv "FORCE_SOURCE_DATE" "1"))))))
-    (inputs (list lapack fftw))
+    (inputs (list openblas fftw))
     ;; FIXME: Even though the fonts are available dvips complains:
     ;; "Font cmmi10 not found; characters will be left blank."
     (native-inputs
-- 
2.41.0





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Subject: [PATCH 09/41] gnu: sbcl-lla: Switch to openblas.
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* gnu/packages/lisp-xyz.scm (sbcl-lla): Switch input dependency from
lapack to openblas and fixup.

Change-Id: I1d17ed3299a9e62f15b6e52e5ae2c9b9134646d1
---
 gnu/packages/lisp-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 6ee8ef22d2..e5a943e32c 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -25021,17 +25021,17 @@ (define-public sbcl-lla
                (substitute* "src/configuration.lisp"
                  (("\"libblas.so.3gf\"")
                   (string-append "\"" (assoc-ref inputs "lapack")
-                                 "/lib/libblas.so\""))
+                                 "/lib/libopenblas.so\""))
                  (("\"liblapack.so.3gf\"")
                   (string-append "\"" (assoc-ref inputs "lapack")
-                                 "/lib/liblapack.so\""))))))))
+                                 "/lib/libopenblas.so\""))))))))
       (inputs
        `(("anaphora" ,sbcl-anaphora)
          ("alexandria" ,sbcl-alexandria)
          ("cffi" ,sbcl-cffi)
          ("cl-num-utils" ,sbcl-cl-num-utils)
          ("cl-slice" ,sbcl-cl-slice)
-         ("lapack" ,lapack)
+         ("lapack" ,openblas)
          ("let-plus" ,sbcl-let-plus)))
       (native-inputs
        (list sbcl-clunit))
-- 
2.41.0





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* gnu/packages/statistics.scm (jags) [inputs]: Switch input
dependency from lapack to openblas.
[arguments]: Add configure flags.

Change-Id: Iea0efef5c70a5284f6859c1424fd4523edcf2bac
---
 gnu/packages/statistics.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0d9f593614..3a70f5f997 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -180,9 +180,13 @@ (define-public jags
                (base32
                 "0aa2w4g5057vn1qjp954s2kwxfmy1h7p5yn56fyi7sz9nmaq69gr"))))
     (build-system gnu-build-system)
+    (arguments
+     (list #:configure-flags
+           #~(list "--with-lapack=-lopenblas"
+              "--with-blas=-lopenblas")))
     (home-page "https://mcmc-jags.sourceforge.net/")
     (native-inputs
-     (list gfortran lapack))
+     (list gfortran openblas))
     (synopsis "Gibbs sampler")
     (description "JAGS is Just Another Gibbs Sampler.  It is a program for
 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
-- 
2.41.0





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* gnu/packages/machine-learning.scm (vosk-api): Remove input
dependency on lapack.

Change-Id: Id46b37f06bffde5f8a198c1ac913a3dff8ce63e6
---
 gnu/packages/machine-learning.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 5c18a2e9d5..e51877411d 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5105,8 +5105,7 @@ (define-public vosk-api
               (lambda _ (chdir "src")))
             (replace 'configure
               (lambda _
-                (let* ((lapack   #$(this-package-input "lapack"))
-                       (openfst  #$(this-package-input "openfst"))
+                (let* ((openfst  #$(this-package-input "openfst"))
                        (openblas #$(this-package-input "openblas"))
                        (kaldi    #$(this-package-input "kaldi")))
                   (substitute* "./Makefile"
@@ -5116,8 +5115,7 @@ (define-public vosk-api
                      "")
                     (("-lopenblas -llapack -lblas -lf2c")
                      (string-append
-                      "-L" openblas "/lib " "-lopenblas "
-                      "-L" lapack "/lib " "-llapack -lblas "))
+                      "-L" openblas "/lib " "-lopenblas "))
                     (("-lfst -lfstngram")
                      (string-append
                       "-L" openfst "/lib " "-lfst -lfstngram "))
@@ -5139,7 +5137,7 @@ (define-public vosk-api
                   (for-each
                    (lambda (x) (install-file x src))
                    (find-files "." "\\.h$"))))))))
-      (inputs (list kaldi openfst lapack openblas))
+      (inputs (list kaldi openfst openblas))
       (home-page "https://alphacephei.com/vosk")
       (synopsis "Speech recognition toolkit based on @code{kaldi}")
       (description "\
-- 
2.41.0





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Subject: [PATCH 06/41] gnu: igraph: Switch to openblas.
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* gnu/packages/graph.scm (igraph): Switch input dependency from
lapack to openblas.

Change-Id: Idcaada16496d2854cce7375b4d9fa647430206eb
---
 gnu/packages/graph.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index a3607689a3..437f744451 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -195,7 +195,7 @@ (define-public igraph
      (list arpack-ng
            bliss
            glpk
-           lapack
+           ;lapack
            openblas
            plfit
            suitesparse-cxsparse))
-- 
2.41.0





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* gnu/packages/maths.scm (hypre): Switch input dependency from
lapack to openblas.

Change-Id: I8bc2c3abf0d3ead52c9616e1a23bf4ac6113ac3b
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 7deb652e77..e80b7df0e2 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7106,7 +7106,7 @@ (define-public hypre
                   texlive-xcolor
                   texlive-xypic))))
     (inputs
-     (list openblas lapack))
+     (list openblas))
     (arguments
      `(#:modules ((srfi srfi-1)
                   ,@%gnu-build-system-modules)
-- 
2.41.0





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* gnu/packages/maths.scm (scalapack): Switch input dependency from
lapack to openblas.

Change-Id: Ie025e6ced66c75755314b53989547ffe26fbcd11
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index c42626ffca..7deb652e77 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1197,7 +1197,7 @@ (define-public scalapack
     (inputs
      `(("mpi" ,openmpi)
        ("fortran" ,gfortran)
-       ("lapack" ,lapack)))             ;for testing only
+       ("lapack" ,openblas)))             ;for testing only
     (arguments
      `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
        #:phases (modify-phases %standard-phases
-- 
2.41.0





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Subject: [PATCH 03/41] gnu: octave-cli: Switch to openblas.
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* gnu/packages/maths.scm (octave-cli): Switch input dependency from
lapack to openblas.

Change-Id: I3a624a44c1c9bc6be7360cfecbb61c955fa0d209
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0c3216d0f0..c42626ffca 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2955,10 +2955,10 @@ (define-public octave-cli
            libjpeg-turbo
 
            hdf5
-           lapack
            libsndfile
            libxft
            mesa
+           openblas
            pcre
            portaudio
            qhull
-- 
2.41.0





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Subject: [PATCH 02/41] gnu: armadillo: Switch to openblas.
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* gnu/packages/maths.scm (armadillo): Switch inputs from lapack to openblas.

Change-Id: I718371f2e95fafc31e5dccddccbc223c111f594d
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index e9deef60f4..0c3216d0f0 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4987,7 +4987,7 @@ (define-public armadillo
     (build-system cmake-build-system)
     (arguments `(#:tests? #f))          ; no test target
     (inputs
-     (list openblas lapack arpack-ng))
+     (list openblas arpack-ng))
     (home-page "https://arma.sourceforge.net/")
     (synopsis "C++ linear algebra library")
     (description
-- 
2.41.0





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* gnu/packages/maths.scm (arpack-ng): Switch inputs from lapack to openblas.

Change-Id: I0d825373f0f267cc97748a9c2c7de1d73698354e
---
 gnu/packages/maths.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 47070ded15..e9deef60f4 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1070,7 +1070,7 @@ (define-public arpack-ng
     (native-inputs
      (list pkg-config))
     (inputs
-     (list eigen lapack gfortran))
+     (list eigen openblas gfortran))
     (synopsis "Fortran subroutines for solving eigenvalue problems")
     (description
      "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
-- 
2.41.0





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From: Romain GARBAGE <romain.garbage@HIDDEN>
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Subject: [PATCH 00/41] Improve performance in lapack dependent packages.
Date: Mon, 11 Mar 2024 12:01:55 +0100
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This patch series aims at improving the performance of several packages by changing the LAPACK library they depend on.

The package `lapack` is the reference implementation from netlib.org of a numerical linear algebra library, written in FORTRAN.

The package `openblas` is a optimized implementation of the LAPACK and BLAS APIs.

Among the modified packages affected by the change, the following don't build:
 * shogun: atlas dependency doesn't build (pre-existing error)
 * lush2: preexisting error
 * proteinortho: preexisting error (tests 2 and 3 fail)
 * superlu-dist: dependency failure (combinatorial-blas)


Also, the following packages have not been modified as it breaks the package:
 * xyce-serial
 * xyce-parallel
 * gnss-sdr
 * julia

Romain GARBAGE (41):
  gnu: arpack-ng: Switch to openblas.
  gnu: armadillo: Switch to openblas.
  gnu: octave-cli: Switch to openblas.
  gnu: scalapack: Switch to openblas.
  gnu: hypre: Switch to openblas.
  gnu: igraph: Switch to openblas.
  gnu: vosk-api: Remove dependency on lapack.
  gnu: jags: Switch to openblas.
  gnu: sbcl-lla: Switch to openblas.
  gnu: itpp: Switch to openblas.
  gnu: gmsh: Switch to openblas.
  gnu: ghc-hmatrix: Switch to openblas.
  gnu: fenics-dolfin: Remove dependency on lapack.
  gnu: ipopt: Switch to openblas.
  gnu: ceres: Remove dependency on lapack.
  gnu: sundials-julia: Switch to openblas.
  gnu: plink: Switch to openblas.
  gnu: p4est: Remove dependency on lapack.
  gnu: plink-ng: Remove lapack dep.
  gnu: dealii: Remove dependency on lapack.
  gnu: elemental: Remove dependency on lapack.
  gnu: superlu-dist: Remove dependency on lapack.
  gnu: bonmin: Switch to openblas.
  gnu: mpb: Switch to openblas.
  gnu: meep: Switch to openblas.
  gnu: casacore: Remove dependency on lapack.
  gnu: aoflagger: Remove dependency on lapack.
  gnu: apl: Switch to openblas.
  gnu: eigensoft: Remove dependency on lapack.
  gnu: proteinortho: Remove dependency on lapack.
  gnu: scilab: Remove dependency on lapack.
  gnu: python-cvxopt: Remove dependency on lapack.
  gnu: dlib: Remove dependency on lapack.
  gnu: grass: Remove dependency on lapack.
  gnu: harminv: Switch to openblas.
  gnu: giac: Switch to openblas.
  gnu: libflame: Switch to openblas.
  gnu: lush2: Remove dependency on lapack.
  gnu: shogun: Switch to openblas.
  gnu: kaldi-for-vosk: Remove dependency on lapack.
  gnu: ocaml-lacaml: Remove dependency on lapack.

 gnu/packages/algebra.scm          |  2 +-
 gnu/packages/apl.scm              |  2 +-
 gnu/packages/astronomy.scm        |  2 --
 gnu/packages/bioinformatics.scm   | 17 ++++++------
 gnu/packages/engineering.scm      |  6 ++--
 gnu/packages/geo.scm              |  6 +++-
 gnu/packages/graph.scm            |  2 +-
 gnu/packages/haskell-xyz.scm      |  9 ++----
 gnu/packages/lisp-xyz.scm         |  6 ++--
 gnu/packages/lisp.scm             |  1 -
 gnu/packages/machine-learning.scm | 15 ++++------
 gnu/packages/maths.scm            | 46 ++++++++++++++-----------------
 gnu/packages/ocaml.scm            |  9 ++++--
 gnu/packages/simulation.scm       |  3 +-
 gnu/packages/statistics.scm       |  6 +++-
 15 files changed, 65 insertions(+), 67 deletions(-)

-- 
2.41.0





Acknowledgement sent to Romain GARBAGE <romain.garbage@HIDDEN>:
New bug report received and forwarded. Copy sent to guix-patches@HIDDEN. Full text available.
Report forwarded to guix-patches@HIDDEN:
bug#69729; Package guix-patches. Full text available.
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