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Date: Wed, 06 Mar 2024 12:54:49 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: Re: [PATCH v4] gnu: petsc: scrub build machine specifics
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v4 should (hopefully) fix all issues regarding reprocuibility of petsc:
I have tested v4 on multiple machines with exact identical output (ran `g=
uix hash -S nar ...` on the packages) and also tested on one machine with=
`guix build --check`
On 6 Mar 2024, at 12:51, Lars Bilke wrote:
> 'Libraries compiled on' does not have to be removed since PETSc 3.9:
>
> https: //gitlab.com/petsc/petsc/-/commit/a970bd748978a4e12790be7c36b10e=
832ec0149f
>
> Also merged all add-after 'install phases into `clean-install.
>
> Change-Id: I41d82339e43187d7dc7e3fc189a338784c363c68
>
> sort source files in generated makefiles for reproducibility
>
> Change-Id: I86e5b9cd0d7184019617bd8ae9a23eaf459891d7
> ---
> gnu/packages/maths.scm | 56 ++++++++++++++++++------------------------=
> 1 file changed, 24 insertions(+), 32 deletions(-)
>
> diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
> index 1f61ee0583..1ea5ccee74 100644
> --- a/gnu/packages/maths.scm
> +++ b/gnu/packages/maths.scm
> @@ -3447,38 +3447,41 @@ (define-public petsc
> (let* ((prefix (assoc-ref outputs "out"))
> (flags `(,(string-append "--prefix=3D" prefix)
> ,@configure-flags)))
> + ;; sort source files in configure (for reproducibility=
)
> + (substitute* "config/gmakegen.py"
> + (("join\\(srcs\\[lang\\]\\)") "join(sorted(srcs[lan=
g]))"))
> (format #t "build directory: ~s~%" (getcwd))
> (format #t "configure flags: ~s~%" flags)
> (apply invoke "./configure" flags)
> -
> + ;; Prevent build directory Linux version from leaking =
into
> + ;; compiled code
> + (substitute* (find-files "." "petscmachineinfo.h")
> + (((getcwd)) out)
> + ;; Scrub build machine characteristic
> + (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.=
[0-9]+")
> + "Machine characteristics: Linux-x.x.x"))
> ;; Generate test scripts with the right shebang.
> (substitute* "config/example_template.py"
> (("#!/usr/bin/env bash")
> (string-append "#!" (which "bash")))))))
> - (add-after 'configure 'clean-local-references
> - (lambda* (#:key outputs #:allow-other-keys)
> - (let ((out (assoc-ref outputs "out")))
> - (substitute* (find-files "." "^petsc(conf|machineinfo)=
=2Eh$")
> - ;; Prevent build directory from leaking into compile=
d code
> - (((getcwd)) out)
> - ;; Scrub timestamp for reproducibility
> - ((".*Libraries compiled on.*") ""))
> - (substitute* (find-files "." "petscvariables")
> - ;; Do not expose build machine characteristics, set =
to defaults.
> - (("MAKE_NP =3D [:digit:]+") "MAKE_NP =3D 2")
> - (("NPMAX =3D [:digit:]+") "NPMAX =3D 2")))))
> (add-after 'install 'clean-install
> - ;; Try to keep installed files from leaking build director=
y names.
> (lambda* (#:key inputs outputs #:allow-other-keys)
> (let ((out (assoc-ref outputs "out")))
> - (substitute* (map (lambda (file)
> - (string-append out "/lib/petsc/con=
f/" file))
> - '("petscvariables"))
> - (((getcwd)) out))
> - ;; Make compiler references point to the store
> (substitute* (string-append out "/lib/petsc/conf/petsc=
variables")
> - (("=3D (gcc|g\\+\\+|gfortran)" _ compiler)
> - (string-append "=3D " (which compiler))))
> + ;; Try to keep installed files from leaking build di=
rectory names.
> + (((getcwd)) out)
> + ;; Do not expose build machine characteristics, set =
to defaults.
> + (("MAKE_NP =3D [[:digit:]]+") "MAKE_NP =3D 2")
> + (("MAKE_TEST_NP =3D [[:digit:]]+") "MAKE_TEST_NP =3D=
2")
> + (("MAKE_LOAD =3D [[:digit:]]+\\.[[:digit:]]+") "MAKE=
_LOAD =3D 2.0")
> + (("NPMAX =3D [[:digit:]]+") "NPMAX =3D 2")
> + ;; Do not retain a reference to GCC and other build =
only inputs.
> + (("([[:graph:]]+)/bin/gcc") "gcc")
> + (("([[:graph:]]+)/bin/g\\+\\+") "g++")
> + (("([[:graph:]]+)/bin/make") "make")
> + (("([[:graph:]]+)/bin/diff") "diff")
> + (("([[:graph:]]+)/bin/sed") "sed")
> + (("([[:graph:]]+)/bin/gfortran") "gfortran"))
> ;; PETSc installs some build logs, which aren't necess=
ary.
> (for-each (lambda (file)
> (let ((f (string-append out "/lib/petsc/co=
nf/" file)))
> @@ -3490,17 +3493,6 @@ (define-public petsc
> "configure-hash"
> ;; Once installed, should uninstall with G=
uix
> "uninstall.py")))))
> - (add-after 'clean-install 'clear-reference-to-compiler
> - (lambda* (#:key inputs outputs #:allow-other-keys)
> - ;; Do not retain a reference to GCC and other build only=
inputs.
> - (let ((out (assoc-ref outputs "out")))
> - (substitute* (string-append out "/lib/petsc/conf/petscva=
riables")
> - (("([[:graph:]]+)/bin/gcc") "gcc")
> - (("([[:graph:]]+)/bin/g\\+\\+") "g++")
> - (("([[:graph:]]+)/bin/make") "make")
> - (("([[:graph:]]+)/bin/diff") "diff")
> - (("([[:graph:]]+)/bin/sed") "sed")
> - (("([[:graph:]]+)/bin/gfortran") "gfortran")))))
> (add-after 'install 'move-examples
> (lambda* (#:key outputs #:allow-other-keys)
> (let* ((out (assoc-ref outputs "out"))
>
> base-commit: 75bad75367fcf2c289fae3b40dbcc850f92177be
> -- =
> 2.43.0
--=_MailMate_65FDE64D-0B39-4C62-BFE2-D4B6A89FD0A6_=
Content-Type: text/html
Content-Transfer-Encoding: quoted-printable
<!DOCTYPE html>
<html>
<head>
<meta http-equiv=3D"Content-Type" content=3D"text/xhtml; charset=3Dutf-8"=
>
</head>
<body><div style=3D"font-family: sans-serif;"><div class=3D"markdown" sty=
le=3D"white-space: normal;">
<p dir=3D"auto">v4 should (hopefully) fix all issues regarding reprocuibi=
lity of petsc:</p>
<p dir=3D"auto">I have tested v4 on multiple machines with exact identica=
l output (ran <code style=3D"margin: 0 0; padding: 0 0.25em; border-radiu=
s: 3px; background-color: #F7F7F7;">guix hash -S nar ...</code> on the pa=
ckages) and also tested on one machine with <code style=3D"margin: 0 0; p=
adding: 0 0.25em; border-radius: 3px; background-color: #F7F7F7;">guix bu=
ild --check</code></p>
<p dir=3D"auto">On 6 Mar 2024, at 12:51, Lars Bilke wrote:</p>
</div><div class=3D"plaintext" style=3D"white-space: normal;"><blockquote=
style=3D"margin: 0 0 5px; padding-left: 5px; border-left: 2px solid #777=
777; color: #777777;"><p dir=3D"auto">'Libraries compiled on' does not ha=
ve to be removed since PETSc 3.9:</p>
<p dir=3D"auto">https: //gitlab.com/petsc/petsc/-/commit/a970bd748978a4e1=
2790be7c36b10e832ec0149f</p>
<p dir=3D"auto">Also merged all add-after 'install phases into `clean-ins=
tall.</p>
<p dir=3D"auto">Change-Id: I41d82339e43187d7dc7e3fc189a338784c363c68</p>
<p dir=3D"auto">sort source files in generated makefiles for reproducibil=
ity</p>
<p dir=3D"auto">Change-Id: I86e5b9cd0d7184019617bd8ae9a23eaf459891d7
<br>
---
<br>
gnu/packages/maths.scm | 56 ++++++++++++++++++------------------------
<br>
1 file changed, 24 insertions(+), 32 deletions(-)</p>
<p dir=3D"auto">diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.=
scm
<br>
index 1f61ee0583..1ea5ccee74 100644
<br>
--- a/gnu/packages/maths.scm
<br>
+++ b/gnu/packages/maths.scm
<br>
@@ -3447,38 +3447,41 @@ (define-public petsc
<br>
(let* ((prefix (assoc-ref outputs "out"))
<br>
(flags `(,(string-append "--prefix=3D" prefix)
<br>
,@configure-flags)))
<br>
+ ;; sort source files in configure (for reproducibility)
<br>
+ (substitute* "config/gmakegen.py"
<br>
+ (("join\\(srcs\\[lang\\]\\)") "join(sorted(srcs[lang]=
))"))
<br>
(format #t "build directory: ~s~%" (getcwd))
<br>
(format #t "configure flags: ~s~%" flags)
<br>
(apply invoke "./configure" flags)
<br>
-
<br>
+ ;; Prevent build directory Linux version from leaking in=
to
<br>
+ ;; compiled code
<br>
+ (substitute* (find-files "." "petscmachineinfo.h")
<br>
+ (((getcwd)) out)
<br>
+ ;; Scrub build machine characteristic
<br>
+ (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.[0=
-9]+")
<br>
+ "Machine characteristics: Linux-x.x.x"))
<br>
;; Generate test scripts with the right shebang.
<br>
(substitute* "config/example_template.py"
<br>
(("#!/usr/bin/env bash")
<br>
(string-append "#!" (which "bash")))))))
<br>
- (add-after 'configure 'clean-local-references
<br>
- (lambda* (#:key outputs #:allow-other-keys)
<br>
- (let ((out (assoc-ref outputs "out")))
<br>
- (substitute* (find-files "." "^petsc(conf|machineinfo).h=
$")
<br>
- ;; Prevent build directory from leaking into compiled =
code
<br>
- (((getcwd)) out)
<br>
- ;; Scrub timestamp for reproducibility
<br>
- ((".*Libraries compiled on.*") ""))
<br>
- (substitute* (find-files "." "petscvariables")
<br>
- ;; Do not expose build machine characteristics, set to=
defaults.
<br>
- (("MAKE_NP =3D [:digit:]+") "MAKE_NP =3D 2")
<br>
- (("NPMAX =3D [:digit:]+") "NPMAX =3D 2")))))
<br>
(add-after 'install 'clean-install
<br>
- ;; Try to keep installed files from leaking build directory =
names.
<br>
(lambda* (#:key inputs outputs #:allow-other-keys)
<br>
(let ((out (assoc-ref outputs "out")))
<br>
- (substitute* (map (lambda (file)
<br>
- (string-append out "/lib/petsc/conf/=
" file))
<br>
- '("petscvariables"))
<br>
- (((getcwd)) out))
<br>
- ;; Make compiler references point to the store
<br>
(substitute* (string-append out "/lib/petsc/conf/petscva=
riables")
<br>
- (("=3D (gcc|g\\+\\+|gfortran)" _ compiler)
<br>
- (string-append "=3D " (which compiler))))
<br>
+ ;; Try to keep installed files from leaking build dire=
ctory names.
<br>
+ (((getcwd)) out)
<br>
+ ;; Do not expose build machine characteristics, set to=
defaults.
<br>
+ (("MAKE_NP =3D [[:digit:]]+") "MAKE_NP =3D 2")
<br>
+ (("MAKE_TEST_NP =3D [[:digit:]]+") "MAKE_TEST_NP =3D 2=
")
<br>
+ (("MAKE_LOAD =3D [[:digit:]]+\\.[[:digit:]]+") "MAKE_L=
OAD =3D 2.0")
<br>
+ (("NPMAX =3D [[:digit:]]+") "NPMAX =3D 2")
<br>
+ ;; Do not retain a reference to GCC and other build on=
ly inputs.
<br>
+ (("([[:graph:]]+)/bin/gcc") "gcc")
<br>
+ (("([[:graph:]]+)/bin/g\\+\\+") "g++")
<br>
+ (("([[:graph:]]+)/bin/make") "make")
<br>
+ (("([[:graph:]]+)/bin/diff") "diff")
<br>
+ (("([[:graph:]]+)/bin/sed") "sed")
<br>
+ (("([[:graph:]]+)/bin/gfortran") "gfortran"))
<br>
;; PETSc installs some build logs, which aren't necessar=
y.
<br>
(for-each (lambda (file)
<br>
(let ((f (string-append out "/lib/petsc/conf=
/" file)))
<br>
@@ -3490,17 +3493,6 @@ (define-public petsc
<br>
"configure-hash"
<br>
;; Once installed, should uninstall with Gui=
x
<br>
"uninstall.py")))))
<br>
- (add-after 'clean-install 'clear-reference-to-compiler
<br>
- (lambda* (#:key inputs outputs #:allow-other-keys)
<br>
- ;; Do not retain a reference to GCC and other build only i=
nputs.
<br>
- (let ((out (assoc-ref outputs "out")))
<br>
- (substitute* (string-append out "/lib/petsc/conf/petscvari=
ables")
<br>
- (("([[:graph:]]+)/bin/gcc") "gcc")
<br>
- (("([[:graph:]]+)/bin/g\\+\\+") "g++")
<br>
- (("([[:graph:]]+)/bin/make") "make")
<br>
- (("([[:graph:]]+)/bin/diff") "diff")
<br>
- (("([[:graph:]]+)/bin/sed") "sed")
<br>
- (("([[:graph:]]+)/bin/gfortran") "gfortran")))))
<br>
(add-after 'install 'move-examples
<br>
(lambda* (#:key outputs #:allow-other-keys)
<br>
(let* ((out (assoc-ref outputs "out"))</p>
<p dir=3D"auto">base-commit: 75bad75367fcf2c289fae3b40dbcc850f92177be
<br>
-- </p>
</blockquote></div>
<div class=3D"markdown" style=3D"white-space: normal;">
<blockquote style=3D"margin: 0 0 5px; padding-left: 5px; border-left: 2px=
solid #777777; color: #777777;">
<p dir=3D"auto">2.43.0</p>
</blockquote>
</div>
</div>
</body>
</html>
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bug-guix@HIDDEN:bug#57005; Package guix.
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Date: Wed, 06 Mar 2024 12:51:14 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH v4] gnu: petsc: scrub build machine specifics
To: 57005 <at> debbugs.gnu.org
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'Libraries compiled on' does not have to be removed since PETSc 3.9:
https: //gitlab.com/petsc/petsc/-/commit/a970bd748978a4e12790be7c36b10e832ec0149f
Also merged all add-after 'install phases into `clean-install.
Change-Id: I41d82339e43187d7dc7e3fc189a338784c363c68
sort source files in generated makefiles for reproducibility
Change-Id: I86e5b9cd0d7184019617bd8ae9a23eaf459891d7
---
gnu/packages/maths.scm | 56 ++++++++++++++++++------------------------
1 file changed, 24 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1f61ee0583..1ea5ccee74 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3447,38 +3447,41 @@ (define-public petsc
(let* ((prefix (assoc-ref outputs "out"))
(flags `(,(string-append "--prefix=" prefix)
,@configure-flags)))
+ ;; sort source files in configure (for reproducibility)
+ (substitute* "config/gmakegen.py"
+ (("join\\(srcs\\[lang\\]\\)") "join(sorted(srcs[lang]))"))
(format #t "build directory: ~s~%" (getcwd))
(format #t "configure flags: ~s~%" flags)
(apply invoke "./configure" flags)
-
+ ;; Prevent build directory Linux version from leaking into
+ ;; compiled code
+ (substitute* (find-files "." "petscmachineinfo.h")
+ (((getcwd)) out)
+ ;; Scrub build machine characteristic
+ (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.[0-9]+")
+ "Machine characteristics: Linux-x.x.x"))
;; Generate test scripts with the right shebang.
(substitute* "config/example_template.py"
(("#!/usr/bin/env bash")
(string-append "#!" (which "bash")))))))
- (add-after 'configure 'clean-local-references
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
- ;; Prevent build directory from leaking into compiled code
- (((getcwd)) out)
- ;; Scrub timestamp for reproducibility
- ((".*Libraries compiled on.*") ""))
- (substitute* (find-files "." "petscvariables")
- ;; Do not expose build machine characteristics, set to defaults.
- (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
- (("NPMAX = [:digit:]+") "NPMAX = 2")))))
(add-after 'install 'clean-install
- ;; Try to keep installed files from leaking build directory names.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- (substitute* (map (lambda (file)
- (string-append out "/lib/petsc/conf/" file))
- '("petscvariables"))
- (((getcwd)) out))
- ;; Make compiler references point to the store
(substitute* (string-append out "/lib/petsc/conf/petscvariables")
- (("= (gcc|g\\+\\+|gfortran)" _ compiler)
- (string-append "= " (which compiler))))
+ ;; Try to keep installed files from leaking build directory names.
+ (((getcwd)) out)
+ ;; Do not expose build machine characteristics, set to defaults.
+ (("MAKE_NP = [[:digit:]]+") "MAKE_NP = 2")
+ (("MAKE_TEST_NP = [[:digit:]]+") "MAKE_TEST_NP = 2")
+ (("MAKE_LOAD = [[:digit:]]+\\.[[:digit:]]+") "MAKE_LOAD = 2.0")
+ (("NPMAX = [[:digit:]]+") "NPMAX = 2")
+ ;; Do not retain a reference to GCC and other build only inputs.
+ (("([[:graph:]]+)/bin/gcc") "gcc")
+ (("([[:graph:]]+)/bin/g\\+\\+") "g++")
+ (("([[:graph:]]+)/bin/make") "make")
+ (("([[:graph:]]+)/bin/diff") "diff")
+ (("([[:graph:]]+)/bin/sed") "sed")
+ (("([[:graph:]]+)/bin/gfortran") "gfortran"))
;; PETSc installs some build logs, which aren't necessary.
(for-each (lambda (file)
(let ((f (string-append out "/lib/petsc/conf/" file)))
@@ -3490,17 +3493,6 @@ (define-public petsc
"configure-hash"
;; Once installed, should uninstall with Guix
"uninstall.py")))))
- (add-after 'clean-install 'clear-reference-to-compiler
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Do not retain a reference to GCC and other build only inputs.
- (let ((out (assoc-ref outputs "out")))
- (substitute* (string-append out "/lib/petsc/conf/petscvariables")
- (("([[:graph:]]+)/bin/gcc") "gcc")
- (("([[:graph:]]+)/bin/g\\+\\+") "g++")
- (("([[:graph:]]+)/bin/make") "make")
- (("([[:graph:]]+)/bin/diff") "diff")
- (("([[:graph:]]+)/bin/sed") "sed")
- (("([[:graph:]]+)/bin/gfortran") "gfortran")))))
(add-after 'install 'move-examples
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
base-commit: 75bad75367fcf2c289fae3b40dbcc850f92177be
--
2.43.0
andreas@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, bug-guix@HIDDEN:bug#57005; Package guix.
Full text available.
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Date: Tue, 05 Mar 2024 16:01:27 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: Re: [PATCH v3] gnu: petsc: scrub build machine specifics
In-reply-to: <65e5bfc8e0e0580eb9c86e1cc0dc8bb89b286a7a.1709650693.git.lars.bilke@HIDDEN>
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v3 of this patch finally makes PETSc fully reproducible!
On 5 Mar 2024, at 15:58, Lars Bilke wrote:
> 'Libraries compiled on' does not have to be removed since PETSc 3.9:
>
> https: //gitlab.com/petsc/petsc/-/commit/a970bd748978a4e12790be7c36b10e=
832ec0149f
>
> Also merged all add-after 'install phases into `clean-install.
>
> Change-Id: I41d82339e43187d7dc7e3fc189a338784c363c68
>
> sort source files in generated makefiles for reproducibility
>
> Change-Id: I86e5b9cd0d7184019617bd8ae9a23eaf459891d7
> ---
> gnu/packages/maths.scm | 46 +++++++++++++++++++-----------------------=
> 1 file changed, 21 insertions(+), 25 deletions(-)
>
> diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
> index 1f61ee0583..b828d5d5cb 100644
> --- a/gnu/packages/maths.scm
> +++ b/gnu/packages/maths.scm
> @@ -3447,6 +3447,9 @@ (define-public petsc
> (let* ((prefix (assoc-ref outputs "out"))
> (flags `(,(string-append "--prefix=3D" prefix)
> ,@configure-flags)))
> + ;; sort source files in configure (for reproducibility=
)
> + (substitute* "config/gmakegen.py"
> + (("join\\(srcs\\[lang\\]\\)") "join(sorted(srcs[lan=
g]))"))
> (format #t "build directory: ~s~%" (getcwd))
> (format #t "configure flags: ~s~%" flags)
> (apply invoke "./configure" flags)
> @@ -3455,30 +3458,34 @@ (define-public petsc
> (substitute* "config/example_template.py"
> (("#!/usr/bin/env bash")
> (string-append "#!" (which "bash")))))))
> - (add-after 'configure 'clean-local-references
> - (lambda* (#:key outputs #:allow-other-keys)
> + (add-after 'install 'clean-install
> + ;; Try to keep installed files from leaking build director=
y names.
> + (lambda* (#:key inputs outputs #:allow-other-keys)
> (let ((out (assoc-ref outputs "out")))
> - (substitute* (find-files "." "^petsc(conf|machineinfo)=
=2Eh$")
> + (substitute* (find-files "." "petscmachineinfo.h")
> ;; Prevent build directory from leaking into compile=
d code
> (((getcwd)) out)
> - ;; Scrub timestamp for reproducibility
> - ((".*Libraries compiled on.*") ""))
> + ;; Scrub build machine characteristic
> + (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.=
[0-9]+")
> + "Machine characteristics: Linux-x.x.x"))
> (substitute* (find-files "." "petscvariables")
> ;; Do not expose build machine characteristics, set =
to defaults.
> - (("MAKE_NP =3D [:digit:]+") "MAKE_NP =3D 2")
> - (("NPMAX =3D [:digit:]+") "NPMAX =3D 2")))))
> - (add-after 'install 'clean-install
> - ;; Try to keep installed files from leaking build director=
y names.
> - (lambda* (#:key inputs outputs #:allow-other-keys)
> - (let ((out (assoc-ref outputs "out")))
> + (("MAKE_NP =3D [[:digit:]]+") "MAKE_NP =3D 2")
> + (("MAKE_TEST_NP =3D [[:digit:]]+") "MAKE_TEST_NP =3D=
2")
> + (("MAKE_LOAD =3D [[:digit:]]+\\.[[:digit:]]+") "MAKE=
_LOAD =3D 2.0")
> + (("NPMAX =3D [[:digit:]]+") "NPMAX =3D 2"))
> (substitute* (map (lambda (file)
> (string-append out "/lib/petsc/con=
f/" file))
> '("petscvariables"))
> (((getcwd)) out))
> - ;; Make compiler references point to the store
> (substitute* (string-append out "/lib/petsc/conf/petsc=
variables")
> - (("=3D (gcc|g\\+\\+|gfortran)" _ compiler)
> - (string-append "=3D " (which compiler))))
> + ;; Do not retain a reference to GCC and other build =
only inputs.
> + (("([[:graph:]]+)/bin/gcc") "gcc")
> + (("([[:graph:]]+)/bin/g\\+\\+") "g++")
> + (("([[:graph:]]+)/bin/make") "make")
> + (("([[:graph:]]+)/bin/diff") "diff")
> + (("([[:graph:]]+)/bin/sed") "sed")
> + (("([[:graph:]]+)/bin/gfortran") "gfortran"))
> ;; PETSc installs some build logs, which aren't necess=
ary.
> (for-each (lambda (file)
> (let ((f (string-append out "/lib/petsc/co=
nf/" file)))
> @@ -3490,17 +3497,6 @@ (define-public petsc
> "configure-hash"
> ;; Once installed, should uninstall with G=
uix
> "uninstall.py")))))
> - (add-after 'clean-install 'clear-reference-to-compiler
> - (lambda* (#:key inputs outputs #:allow-other-keys)
> - ;; Do not retain a reference to GCC and other build only=
inputs.
> - (let ((out (assoc-ref outputs "out")))
> - (substitute* (string-append out "/lib/petsc/conf/petscva=
riables")
> - (("([[:graph:]]+)/bin/gcc") "gcc")
> - (("([[:graph:]]+)/bin/g\\+\\+") "g++")
> - (("([[:graph:]]+)/bin/make") "make")
> - (("([[:graph:]]+)/bin/diff") "diff")
> - (("([[:graph:]]+)/bin/sed") "sed")
> - (("([[:graph:]]+)/bin/gfortran") "gfortran")))))
> (add-after 'install 'move-examples
> (lambda* (#:key outputs #:allow-other-keys)
> (let* ((out (assoc-ref outputs "out"))
>
> base-commit: 75bad75367fcf2c289fae3b40dbcc850f92177be
> -- =
> 2.43.0
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bug-guix@HIDDEN:bug#57005; Package guix.
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Date: Tue, 05 Mar 2024 15:58:13 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH v3] gnu: petsc: scrub build machine specifics
To: 57005 <at> debbugs.gnu.org
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'Libraries compiled on' does not have to be removed since PETSc 3.9:
https: //gitlab.com/petsc/petsc/-/commit/a970bd748978a4e12790be7c36b10e832ec0149f
Also merged all add-after 'install phases into `clean-install.
Change-Id: I41d82339e43187d7dc7e3fc189a338784c363c68
sort source files in generated makefiles for reproducibility
Change-Id: I86e5b9cd0d7184019617bd8ae9a23eaf459891d7
---
gnu/packages/maths.scm | 46 +++++++++++++++++++-----------------------
1 file changed, 21 insertions(+), 25 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1f61ee0583..b828d5d5cb 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3447,6 +3447,9 @@ (define-public petsc
(let* ((prefix (assoc-ref outputs "out"))
(flags `(,(string-append "--prefix=" prefix)
,@configure-flags)))
+ ;; sort source files in configure (for reproducibility)
+ (substitute* "config/gmakegen.py"
+ (("join\\(srcs\\[lang\\]\\)") "join(sorted(srcs[lang]))"))
(format #t "build directory: ~s~%" (getcwd))
(format #t "configure flags: ~s~%" flags)
(apply invoke "./configure" flags)
@@ -3455,30 +3458,34 @@ (define-public petsc
(substitute* "config/example_template.py"
(("#!/usr/bin/env bash")
(string-append "#!" (which "bash")))))))
- (add-after 'configure 'clean-local-references
- (lambda* (#:key outputs #:allow-other-keys)
+ (add-after 'install 'clean-install
+ ;; Try to keep installed files from leaking build directory names.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
+ (substitute* (find-files "." "petscmachineinfo.h")
;; Prevent build directory from leaking into compiled code
(((getcwd)) out)
- ;; Scrub timestamp for reproducibility
- ((".*Libraries compiled on.*") ""))
+ ;; Scrub build machine characteristic
+ (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.[0-9]+")
+ "Machine characteristics: Linux-x.x.x"))
(substitute* (find-files "." "petscvariables")
;; Do not expose build machine characteristics, set to defaults.
- (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
- (("NPMAX = [:digit:]+") "NPMAX = 2")))))
- (add-after 'install 'clean-install
- ;; Try to keep installed files from leaking build directory names.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
+ (("MAKE_NP = [[:digit:]]+") "MAKE_NP = 2")
+ (("MAKE_TEST_NP = [[:digit:]]+") "MAKE_TEST_NP = 2")
+ (("MAKE_LOAD = [[:digit:]]+\\.[[:digit:]]+") "MAKE_LOAD = 2.0")
+ (("NPMAX = [[:digit:]]+") "NPMAX = 2"))
(substitute* (map (lambda (file)
(string-append out "/lib/petsc/conf/" file))
'("petscvariables"))
(((getcwd)) out))
- ;; Make compiler references point to the store
(substitute* (string-append out "/lib/petsc/conf/petscvariables")
- (("= (gcc|g\\+\\+|gfortran)" _ compiler)
- (string-append "= " (which compiler))))
+ ;; Do not retain a reference to GCC and other build only inputs.
+ (("([[:graph:]]+)/bin/gcc") "gcc")
+ (("([[:graph:]]+)/bin/g\\+\\+") "g++")
+ (("([[:graph:]]+)/bin/make") "make")
+ (("([[:graph:]]+)/bin/diff") "diff")
+ (("([[:graph:]]+)/bin/sed") "sed")
+ (("([[:graph:]]+)/bin/gfortran") "gfortran"))
;; PETSc installs some build logs, which aren't necessary.
(for-each (lambda (file)
(let ((f (string-append out "/lib/petsc/conf/" file)))
@@ -3490,17 +3497,6 @@ (define-public petsc
"configure-hash"
;; Once installed, should uninstall with Guix
"uninstall.py")))))
- (add-after 'clean-install 'clear-reference-to-compiler
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Do not retain a reference to GCC and other build only inputs.
- (let ((out (assoc-ref outputs "out")))
- (substitute* (string-append out "/lib/petsc/conf/petscvariables")
- (("([[:graph:]]+)/bin/gcc") "gcc")
- (("([[:graph:]]+)/bin/g\\+\\+") "g++")
- (("([[:graph:]]+)/bin/make") "make")
- (("([[:graph:]]+)/bin/diff") "diff")
- (("([[:graph:]]+)/bin/sed") "sed")
- (("([[:graph:]]+)/bin/gfortran") "gfortran")))))
(add-after 'install 'move-examples
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
base-commit: 75bad75367fcf2c289fae3b40dbcc850f92177be
--
2.43.0
andreas@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, bug-guix@HIDDEN:bug#57005; Package guix.
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Date: Fri, 01 Mar 2024 09:27:02 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH v2] gnu: petsc: scrub build machine specifics
To: 57005 <at> debbugs.gnu.org
Message-id: <18f29b40d908e9c965f49bc124a505a6278b2a50.1709281622.git.lars.bilke@HIDDEN>
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'Libraries compiled on' does not have to be removed since PETSc 3.9:
https: //gitlab.com/petsc/petsc/-/commit/a970bd748978a4e12790be7c36b10e832ec0149f
Also merged all add-after 'install phases into `clean-install.
Change-Id: I41d82339e43187d7dc7e3fc189a338784c363c68
---
gnu/packages/maths.scm | 43 ++++++++++++++++++------------------------
1 file changed, 18 insertions(+), 25 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1f61ee0583..4b4d033506 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3455,30 +3455,34 @@ (define-public petsc
(substitute* "config/example_template.py"
(("#!/usr/bin/env bash")
(string-append "#!" (which "bash")))))))
- (add-after 'configure 'clean-local-references
- (lambda* (#:key outputs #:allow-other-keys)
+ (add-after 'install 'clean-install
+ ;; Try to keep installed files from leaking build directory names.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
+ (substitute* (find-files "." "petscmachineinfo.h")
;; Prevent build directory from leaking into compiled code
(((getcwd)) out)
- ;; Scrub timestamp for reproducibility
- ((".*Libraries compiled on.*") ""))
+ ;; Scrub build machine characteristic
+ (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.[0-9]+")
+ "Machine characteristics: Linux-x.x.x"))
(substitute* (find-files "." "petscvariables")
;; Do not expose build machine characteristics, set to defaults.
- (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
- (("NPMAX = [:digit:]+") "NPMAX = 2")))))
- (add-after 'install 'clean-install
- ;; Try to keep installed files from leaking build directory names.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
+ (("MAKE_NP = [[:digit:]]+") "MAKE_NP = 2")
+ (("MAKE_TEST_NP = [[:digit:]]+") "MAKE_TEST_NP = 2")
+ (("MAKE_LOAD = [[:digit:]]+\\.[[:digit:]]+") "MAKE_LOAD = 2.0")
+ (("NPMAX = [[:digit:]]+") "NPMAX = 2"))
(substitute* (map (lambda (file)
(string-append out "/lib/petsc/conf/" file))
'("petscvariables"))
(((getcwd)) out))
- ;; Make compiler references point to the store
(substitute* (string-append out "/lib/petsc/conf/petscvariables")
- (("= (gcc|g\\+\\+|gfortran)" _ compiler)
- (string-append "= " (which compiler))))
+ ;; Do not retain a reference to GCC and other build only inputs.
+ (("([[:graph:]]+)/bin/gcc") "gcc")
+ (("([[:graph:]]+)/bin/g\\+\\+") "g++")
+ (("([[:graph:]]+)/bin/make") "make")
+ (("([[:graph:]]+)/bin/diff") "diff")
+ (("([[:graph:]]+)/bin/sed") "sed")
+ (("([[:graph:]]+)/bin/gfortran") "gfortran"))
;; PETSc installs some build logs, which aren't necessary.
(for-each (lambda (file)
(let ((f (string-append out "/lib/petsc/conf/" file)))
@@ -3490,17 +3494,6 @@ (define-public petsc
"configure-hash"
;; Once installed, should uninstall with Guix
"uninstall.py")))))
- (add-after 'clean-install 'clear-reference-to-compiler
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Do not retain a reference to GCC and other build only inputs.
- (let ((out (assoc-ref outputs "out")))
- (substitute* (string-append out "/lib/petsc/conf/petscvariables")
- (("([[:graph:]]+)/bin/gcc") "gcc")
- (("([[:graph:]]+)/bin/g\\+\\+") "g++")
- (("([[:graph:]]+)/bin/make") "make")
- (("([[:graph:]]+)/bin/diff") "diff")
- (("([[:graph:]]+)/bin/sed") "sed")
- (("([[:graph:]]+)/bin/gfortran") "gfortran")))))
(add-after 'install 'move-examples
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
base-commit: 75bad75367fcf2c289fae3b40dbcc850f92177be
--
2.43.0
andreas@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, bug-guix@HIDDEN:bug#57005; Package guix.
Full text available.Received: (at 57005) by debbugs.gnu.org; 29 Feb 2024 17:49:52 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Feb 29 12:49:52 2024 Received: from localhost ([127.0.0.1]:35287 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rfkXX-0003DR-N4 for submit <at> debbugs.gnu.org; Thu, 29 Feb 2024 12:49:51 -0500 Received: from hera.aquilenet.fr ([185.233.100.1]:40886) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <andreas@HIDDEN>) id 1rfkXT-0003DD-ID for 57005 <at> debbugs.gnu.org; Thu, 29 Feb 2024 12:49:50 -0500 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 10ACE1264; Thu, 29 Feb 2024 18:48:44 +0100 (CET) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id MzubfQLf-8FZ; Thu, 29 Feb 2024 18:48:43 +0100 (CET) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 1CC0D287; Thu, 29 Feb 2024 18:48:42 +0100 (CET) Date: Thu, 29 Feb 2024 18:48:40 +0100 From: Andreas Enge <andreas@HIDDEN> To: 57005 <at> debbugs.gnu.org Subject: Suggestion Message-ID: <ZeDDeFwO98E7pi1g@jurong> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 57005 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hello Lars, thanks for the patch! Concerning "Machine characteristics", I see it only in petscmachineinfo.h, so we can probably drop looking for petscconf.h in find-files. There is already the cleaning phase 'clean-install after 'install. So I would either suggest to keep the phase 'clean-local-references where it is, or to merge its content with 'clean-install (I do not see why one should be preferred over the other). Andreas
bug-guix@HIDDEN:bug#57005; Package guix.
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Date: Thu, 29 Feb 2024 11:00:19 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: Re: [PATCH v1] gnu: petsc: scrub build machine specifics
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boundary="=_MailMate_C07CF1BE-6717-41EE-8772-7248BCEDD4A7_="
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This patch makes these files deterministic:
- petscmachineinfo.h
- petscvariables
Unfortunately libpetsc.so.3.16.1 still differs between builds, see e.g. t=
his diffoscope output:
https://jsfiddle.net/dLx15obp/show (click on run)
Maybe someone has an idea how to also fix the library?
Sincerely,
Lars
On 29 Feb 2024, at 10:46, Lars Bilke wrote:
> 'Libraries compiled on' does not have to be removed since PETSc 3.9:
>
> https: //gitlab.com/petsc/petsc/-/commit/a970bd748978a4e12790be7c36b10e=
832ec0149f
>
> Change-Id: I41d82339e43187d7dc7e3fc189a338784c363c68
>
> ---
> gnu/packages/maths.scm | 13 ++++++++-----
> 1 file changed, 8 insertions(+), 5 deletions(-)
>
> diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
> index 1f61ee0583..f09cbee48b 100644
> --- a/gnu/packages/maths.scm
> +++ b/gnu/packages/maths.scm
> @@ -3455,18 +3455,21 @@ (define-public petsc
> (substitute* "config/example_template.py"
> (("#!/usr/bin/env bash")
> (string-append "#!" (which "bash")))))))
> - (add-after 'configure 'clean-local-references
> + (add-after 'install 'clean-local-references
> (lambda* (#:key outputs #:allow-other-keys)
> (let ((out (assoc-ref outputs "out")))
> (substitute* (find-files "." "^petsc(conf|machineinfo)=
=2Eh$")
> ;; Prevent build directory from leaking into compile=
d code
> (((getcwd)) out)
> - ;; Scrub timestamp for reproducibility
> - ((".*Libraries compiled on.*") ""))
> + ;; Scrub build machine characteristic
> + (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.=
[0-9]+")
> + "Machine characteristics: Linux-x.x.x"))
> (substitute* (find-files "." "petscvariables")
> ;; Do not expose build machine characteristics, set =
to defaults.
> - (("MAKE_NP =3D [:digit:]+") "MAKE_NP =3D 2")
> - (("NPMAX =3D [:digit:]+") "NPMAX =3D 2")))))
> + (("MAKE_NP =3D [[:digit:]]+") "MAKE_NP =3D 2")
> + (("MAKE_TEST_NP =3D [[:digit:]]+") "MAKE_TEST_NP =3D=
2")
> + (("MAKE_LOAD =3D [[:digit:]]+\\.[[:digit:]]+") "MAKE=
_LOAD =3D 2.0")
> + (("NPMAX =3D [[:digit:]]+") "NPMAX =3D 2")))))
> (add-after 'install 'clean-install
> ;; Try to keep installed files from leaking build director=
y names.
> (lambda* (#:key inputs outputs #:allow-other-keys)
>
> base-commit: 75bad75367fcf2c289fae3b40dbcc850f92177be
> -- =
> 2.43.0
--=_MailMate_C07CF1BE-6717-41EE-8772-7248BCEDD4A7_=
Content-Type: text/html
Content-Transfer-Encoding: quoted-printable
<!DOCTYPE html>
<html>
<head>
<meta http-equiv=3D"Content-Type" content=3D"text/xhtml; charset=3Dutf-8"=
>
</head>
<body><div style=3D"font-family: sans-serif;"><div class=3D"markdown" sty=
le=3D"white-space: normal;">
<p dir=3D"auto">This patch makes these files deterministic:</p>
<ul>
<li>petscmachineinfo.h</li>
<li>petscvariables</li>
</ul>
<p dir=3D"auto">Unfortunately libpetsc.so.3.16.1 still differs between bu=
ilds, see e.g. this diffoscope output:</p>
<p dir=3D"auto"><a href=3D"https://jsfiddle.net/dLx15obp/show" style=3D"c=
olor: #3983C4;">https://jsfiddle.net/dLx15obp/show</a> (click on run)</p>=
<p dir=3D"auto">Maybe someone has an idea how to also fix the library?</p=
>
<p dir=3D"auto">Sincerely,<br>
Lars</p>
<p dir=3D"auto">On 29 Feb 2024, at 10:46, Lars Bilke wrote:</p>
</div><div class=3D"plaintext" style=3D"white-space: normal;"><blockquote=
style=3D"margin: 0 0 5px; padding-left: 5px; border-left: 2px solid #777=
777; color: #777777;"><p dir=3D"auto">'Libraries compiled on' does not ha=
ve to be removed since PETSc 3.9:</p>
<p dir=3D"auto">https: //gitlab.com/petsc/petsc/-/commit/a970bd748978a4e1=
2790be7c36b10e832ec0149f</p>
<p dir=3D"auto">Change-Id: I41d82339e43187d7dc7e3fc189a338784c363c68</p>
<p dir=3D"auto">---
<br>
gnu/packages/maths.scm | 13 ++++++++-----
<br>
1 file changed, 8 insertions(+), 5 deletions(-)</p>
<p dir=3D"auto">diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.=
scm
<br>
index 1f61ee0583..f09cbee48b 100644
<br>
--- a/gnu/packages/maths.scm
<br>
+++ b/gnu/packages/maths.scm
<br>
@@ -3455,18 +3455,21 @@ (define-public petsc
<br>
(substitute* "config/example_template.py"
<br>
(("#!/usr/bin/env bash")
<br>
(string-append "#!" (which "bash")))))))
<br>
- (add-after 'configure 'clean-local-references
<br>
+ (add-after 'install 'clean-local-references
<br>
(lambda* (#:key outputs #:allow-other-keys)
<br>
(let ((out (assoc-ref outputs "out")))
<br>
(substitute* (find-files "." "^petsc(conf|machineinfo).h=
$")
<br>
;; Prevent build directory from leaking into compiled =
code
<br>
(((getcwd)) out)
<br>
- ;; Scrub timestamp for reproducibility
<br>
- ((".*Libraries compiled on.*") ""))
<br>
+ ;; Scrub build machine characteristic
<br>
+ (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.[0=
-9]+")
<br>
+ "Machine characteristics: Linux-x.x.x"))
<br>
(substitute* (find-files "." "petscvariables")
<br>
;; Do not expose build machine characteristics, set to=
defaults.
<br>
- (("MAKE_NP =3D [:digit:]+") "MAKE_NP =3D 2")
<br>
- (("NPMAX =3D [:digit:]+") "NPMAX =3D 2")))))
<br>
+ (("MAKE_NP =3D [[:digit:]]+") "MAKE_NP =3D 2")
<br>
+ (("MAKE_TEST_NP =3D [[:digit:]]+") "MAKE_TEST_NP =3D 2=
")
<br>
+ (("MAKE_LOAD =3D [[:digit:]]+\\.[[:digit:]]+") "MAKE_L=
OAD =3D 2.0")
<br>
+ (("NPMAX =3D [[:digit:]]+") "NPMAX =3D 2")))))
<br>
(add-after 'install 'clean-install
<br>
;; Try to keep installed files from leaking build directory =
names.
<br>
(lambda* (#:key inputs outputs #:allow-other-keys)</p>
<p dir=3D"auto">base-commit: 75bad75367fcf2c289fae3b40dbcc850f92177be
<br>
-- </p>
</blockquote></div>
<div class=3D"markdown" style=3D"white-space: normal;">
<blockquote style=3D"margin: 0 0 5px; padding-left: 5px; border-left: 2px=
solid #777777; color: #777777;">
<p dir=3D"auto">2.43.0</p>
</blockquote>
</div>
</div>
</body>
</html>
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bug-guix@HIDDEN:bug#57005; Package guix.
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Date: Thu, 29 Feb 2024 10:46:50 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH v1] gnu: petsc: scrub build machine specifics
To: 57005 <at> debbugs.gnu.org
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'Libraries compiled on' does not have to be removed since PETSc 3.9:
https: //gitlab.com/petsc/petsc/-/commit/a970bd748978a4e12790be7c36b10e832ec0149f
Change-Id: I41d82339e43187d7dc7e3fc189a338784c363c68
---
gnu/packages/maths.scm | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1f61ee0583..f09cbee48b 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3455,18 +3455,21 @@ (define-public petsc
(substitute* "config/example_template.py"
(("#!/usr/bin/env bash")
(string-append "#!" (which "bash")))))))
- (add-after 'configure 'clean-local-references
+ (add-after 'install 'clean-local-references
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
;; Prevent build directory from leaking into compiled code
(((getcwd)) out)
- ;; Scrub timestamp for reproducibility
- ((".*Libraries compiled on.*") ""))
+ ;; Scrub build machine characteristic
+ (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.[0-9]+")
+ "Machine characteristics: Linux-x.x.x"))
(substitute* (find-files "." "petscvariables")
;; Do not expose build machine characteristics, set to defaults.
- (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
- (("NPMAX = [:digit:]+") "NPMAX = 2")))))
+ (("MAKE_NP = [[:digit:]]+") "MAKE_NP = 2")
+ (("MAKE_TEST_NP = [[:digit:]]+") "MAKE_TEST_NP = 2")
+ (("MAKE_LOAD = [[:digit:]]+\\.[[:digit:]]+") "MAKE_LOAD = 2.0")
+ (("NPMAX = [[:digit:]]+") "NPMAX = 2")))))
(add-after 'install 'clean-install
;; Try to keep installed files from leaking build directory names.
(lambda* (#:key inputs outputs #:allow-other-keys)
base-commit: 75bad75367fcf2c289fae3b40dbcc850f92177be
--
2.43.0
andreas@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, bug-guix@HIDDEN:bug#57005; Package guix.
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Subject: PETSc is not reproducible
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PETSc 3.16.1 is not reproducible as it captures the kernel version and
number of processors of the machine it=E2=80=99s built on:
--8<---------------cut here---------------start------------->8---
$ guix describe
Generation 223 Aug 01 2022 00:30:24 (current)
guix ab59155
repository URL: https://git.savannah.gnu.org/git/guix.git
branch: master
commit: ab59155c5a38dda7efaceb47c7528578fcf0def4
$ guix challenge petsc --diff=3D"$(type -P diff) -ru"
/gnu/store/4dii69ddwxjiyf2pnay82l4w64s03n60-petsc-3.16.1 contents differ:
no local build for '/gnu/store/4dii69ddwxjiyf2pnay82l4w64s03n60-petsc-3.1=
6.1'
https://ci.guix.gnu.org/nar/lzip/4dii69ddwxjiyf2pnay82l4w64s03n60-petsc-3=
.16.1: 1fqg24x0qq0vww8a21a4ifyxlwy0l7bg8zzrzvg024lk76n54kxh
https://bordeaux.guix.gnu.org/nar/lzip/4dii69ddwxjiyf2pnay82l4w64s03n60-p=
etsc-3.16.1: 162fp2wsxxjjl1pd42522jb3i37hpq8lnfs12qaipzhkzqda5h34
bordeaux.guix.gnu.org 10.3MiB =
9=
.7MiB/s 00:01 [##################] 100.0%diff -ru /tmp/guix-directory.4kiUD=
I/include/petscmachineinfo.h /tmp/guix-directory.0i2wFi/include/petscmachin=
einfo.h
--- /tmp/guix-directory.4kiUDI/include/petscmachineinfo.h 1970-01-01 01:00:=
01.000000000 +0100
+++ /tmp/guix-directory.0i2wFi/include/petscmachineinfo.h 1970-01-01 01:00:=
01.000000000 +0100
@@ -1,6 +1,6 @@
static const char *petscmachineinfo =3D "\n"
"-----------------------------------------\n"
-"Machine characteristics: Linux-5.15.10-gnu-x86_64-with-glibc2.33\n"
+"Machine characteristics: Linux-5.15.11-gnu-x86_64-with-glibc2.33\n"
"Using PETSc directory: /gnu/store/4dii69ddwxjiyf2pnay82l4w64s03n60-petsc-=
3.16.1\n"
"Using PETSc arch: \n"
"-----------------------------------------\n";
Binary files /tmp/guix-directory.4kiUDI/lib/libpetsc.so and /tmp/guix-direc=
tory.0i2wFi/lib/libpetsc.so differ
Binary files /tmp/guix-directory.4kiUDI/lib/libpetsc.so.3.16 and /tmp/guix-=
directory.0i2wFi/lib/libpetsc.so.3.16 differ
Binary files /tmp/guix-directory.4kiUDI/lib/libpetsc.so.3.16.1 and /tmp/gui=
x-directory.0i2wFi/lib/libpetsc.so.3.16.1 differ
diff -ru /tmp/guix-directory.4kiUDI/lib/petsc/conf/petscvariables /tmp/guix=
-directory.0i2wFi/lib/petsc/conf/petscvariables
--- /tmp/guix-directory.4kiUDI/lib/petsc/conf/petscvariables 1970-01-01 01:=
00:01.000000000 +0100
+++ /tmp/guix-directory.0i2wFi/lib/petsc/conf/petscvariables 1970-01-01 01:=
00:01.000000000 +0100
@@ -107,10 +107,10 @@
OMAKE_PRINTDIR =3D /gnu/store/55cbpsi18mahg131nmiya6km5b4mscfa-make-4.3/b=
in/make --print-directory
OMAKE =3D /gnu/store/55cbpsi18mahg131nmiya6km5b4mscfa-make-4.3/bin/make -=
-no-print-directory
MAKE_PAR_OUT_FLG =3D --output-sync=3Drecurse
-MAKE_NP =3D 40
-MAKE_TEST_NP =3D 40
-MAKE_LOAD =3D 96.0
-NPMAX =3D 64
+MAKE_NP =3D 24
+MAKE_TEST_NP =3D 24
+MAKE_LOAD =3D 48.0
+NPMAX =3D 32
SONAME_FUNCTION =3D $(1).$(SL_LINKER_SUFFIX).$(2)
SL_LINKER_FUNCTION =3D -shared -fPIC -Wall -Wwrite-strings -Wno-strict-a=
liasing -Wno-unknown-pragmas -fstack-protector -fvisibility=3Dhidden -g3 -O=
0 -Wl,-soname,$(call SONAME_FUNCTION,$(notdir $(1)),$(2))
BUILDSHAREDLIB =3D yes
1 store items were analyzed:
- 0 (0.0%) were identical
- 1 (100.0%) differed
- 0 (0.0%) were inconclusive
--8<---------------cut here---------------end--------------->8---
Ludo=E2=80=99.
Ludovic Courtès <ludovic.courtes@HIDDEN>:bug-guix@HIDDEN.
Full text available.bug-guix@HIDDEN:bug#57005; Package guix.
Full text available.
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