[PATCH 00/41] Improve performance in lapack dependent packages.

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3 participants
  • Ludovic Courtès
  • Christopher Baines
  • Romain GARBAGE
Owner
unassigned
Submitted by
Romain GARBAGE
Severity
normal

Debbugs page

R
R
Romain GARBAGE wrote on 11 Mar 04:01 -0700
(address . guix-patches@gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110423.10785-1-romain.garbage@inria.fr
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
R
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Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 01/41] gnu: arpack-ng: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-2-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
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Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 02/41] gnu: armadillo: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-3-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
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Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 03/41] gnu: octave-cli: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-4-romain.garbage@inria.fr
* 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(-)

Toggle diff (18 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 04/41] gnu: scalapack: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-5-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 05/41] gnu: hypre: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-6-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 06/41] gnu: igraph: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-7-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
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Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 07/41] gnu: vosk-api: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-8-romain.garbage@inria.fr
* 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(-)

Toggle diff (35 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 08/41] gnu: jags: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-9-romain.garbage@inria.fr
* 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(-)

Toggle diff (21 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 09/41] gnu: sbcl-lla: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-10-romain.garbage@inria.fr
* 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(-)

Toggle diff (27 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 10/41] gnu: itpp: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-11-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 11/41] gnu: gmsh: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-12-romain.garbage@inria.fr
* 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(-)

Toggle diff (19 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 12/41] gnu: ghc-hmatrix: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-13-romain.garbage@inria.fr
* 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(-)

Toggle diff (28 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 13/41] gnu: fenics-dolfin: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-14-romain.garbage@inria.fr
* 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(-)

Toggle diff (23 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 16/41] gnu: sundials-julia: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-17-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 14/41] gnu: ipopt: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-15-romain.garbage@inria.fr
* 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(-)

Toggle diff (33 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 15/41] gnu: ceres: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-16-romain.garbage@inria.fr
* gnu/packages/maths.scm (ceres): Remove dependency to lapack.

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

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 18/41] gnu: p4est: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-19-romain.garbage@inria.fr
* gnu/packages/maths.scm (p4est): Remove dependency on lapack.

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

Toggle diff (24 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 19/41] gnu: plink-ng: Remove lapack dep.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-20-romain.garbage@inria.fr
* 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(-)

Toggle diff (24 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 21/41] gnu: elemental: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-22-romain.garbage@inria.fr
* gnu/packages/maths.scm (elemental): Remove dependency on lapack.

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

Toggle diff (14 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 20/41] gnu: dealii: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-21-romain.garbage@inria.fr
* gnu/packages/maths.scm (dealii): Remove dependency on lapack.

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

Toggle diff (14 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 25/41] gnu: meep: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-26-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 23/41] gnu: bonmin: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-24-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 26/41] gnu: casacore: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-27-romain.garbage@inria.fr
* gnu/packages/astronomy.scm (casacore): Remove dependency on lapack.

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

Toggle diff (14 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 27/41] gnu: aoflagger: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-28-romain.garbage@inria.fr
* gnu/packages/astronomy.scm (aoflagger): Remove dependency on lapack.

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

Toggle diff (14 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 29/41] gnu: eigensoft: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-30-romain.garbage@inria.fr
* gnu/packages/bioinformatics.scm (eigensoft): Remove dependency on lapack.

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

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 22/41] gnu: superlu-dist: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-23-romain.garbage@inria.fr
* 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(-)

Toggle diff (23 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 30/41] gnu: proteinortho: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-31-romain.garbage@inria.fr
* gnu/packages/bioinformatics.scm (proteinortho): Remove dependency on lapack.
---
gnu/packages/bioinformatics.scm | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)

Toggle diff (25 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 32/41] gnu: python-cvxopt: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-33-romain.garbage@inria.fr
* 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(-)

Toggle diff (22 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 33/41] gnu: dlib: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-34-romain.garbage@inria.fr
* gnu/packages/machine-learning.scm (dlib): Remove dependency on lapack.

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

Toggle diff (14 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 34/41] gnu: grass: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-35-romain.garbage@inria.fr
* 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(-)

Toggle diff (26 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 36/41] gnu: giac: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-37-romain.garbage@inria.fr
* 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(-)

Toggle diff (22 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 37/41] gnu: libflame: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-38-romain.garbage@inria.fr
* 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(-)

Toggle diff (27 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 38/41] gnu: lush2: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-39-romain.garbage@inria.fr
* gnu/packages/lisp.scm (lush2): Remove dependency on lapack.

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

Toggle diff (14 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 31/41] gnu: scilab: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-32-romain.garbage@inria.fr
* gnu/packages/maths.scm (scilab): Remove dependency on lapack.

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

Toggle diff (14 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 39/41] gnu: shogun: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-40-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 40/41] gnu: kaldi-for-vosk: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-41-romain.garbage@inria.fr
* 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(-)

Toggle diff (31 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:06 -0700
[PATCH 17/41] gnu: plink: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-18-romain.garbage@inria.fr
* 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(-)

Toggle diff (26 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 24/41] gnu: mpb: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-25-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 28/41] gnu: apl: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-29-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 35/41] gnu: harminv: Switch to openblas.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-36-romain.garbage@inria.fr
* 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(-)

Toggle diff (15 lines)
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
R
R
Romain GARBAGE wrote on 11 Mar 04:07 -0700
[PATCH 41/41] gnu: ocaml-lacaml: Remove dependency on lapack.
(address . 69729@debbugs.gnu.org)(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
20240311110750.16327-42-romain.garbage@inria.fr
* 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(-)

Toggle diff (23 lines)
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
L
L
Ludovic Courtès wrote on 28 Mar 03:40 -0700
Re: [bug#69729] [PATCH 00/41] Improve performance in lapack dependent packages.
(name . Romain GARBAGE)(address . romain.garbage@inria.fr)
878r22oczt.fsf@gnu.org
Hello,

Romain GARBAGE <romain.garbage@inria.fr> skribis:

Toggle quote (19 lines)
> 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

https://qa.guix.gnu.org/issue/69729 hasn’t processed it yet but it’s
already been more than two weeks. Given that you tested all the
dependents on guix.bordeaux.inria.fr, I’m willing to go ahead and push
the series within a few days even if qa.guix hasn’t caught up yet.

Thoughts?

Ludo’.
C
C
Christopher Baines wrote on 2 Apr 13:52 -0700
(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)
87y19vh4i4.fsf@cbaines.net
Ludovic Courtès <ludovic.courtes@inria.fr> writes:

Toggle quote (28 lines)
> Hello,
>
> Romain GARBAGE <romain.garbage@inria.fr> 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 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
>
> <https://qa.guix.gnu.org/issue/69729> hasn’t processed it yet but it’s
> already been more than two weeks. Given that you tested all the
> dependents on guix.bordeaux.inria.fr, I’m willing to go ahead and push
> the series within a few days even if qa.guix hasn’t 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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L
L
Ludovic Courtès wrote on 4 Apr 08:17 -0700
(name . Romain GARBAGE)(address . romain.garbage@inria.fr)(address . 69729-done@debbugs.gnu.org)
87plv5taww.fsf@gnu.org
Hello,

Romain GARBAGE <romain.garbage@inria.fr> skribis:

Toggle quote (42 lines)
> 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’.
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