Received: (at 57005) by debbugs.gnu.org; 6 Mar 2024 11:55:31 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Mar 06 06:55:31 2024 Received: from localhost ([127.0.0.1]:49943 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rhpru-0006ok-AQ for submit <at> debbugs.gnu.org; Wed, 06 Mar 2024 06:55:31 -0500 Received: from mailgate5.ufz.de ([141.65.7.212]:52014 helo=mailgate.ufz.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <lars.bilke@HIDDEN>) id 1rhprr-0006oO-91 for 57005 <at> debbugs.gnu.org; Wed, 06 Mar 2024 06:55:28 -0500 Received: from imap.intranet.ufz.de (dcs1.intranet.ufz.de [141.65.125.135]) by mailgate.ufz.de (Mailgate5-UFZ) with ESMTP id 009721602C4 for <57005 <at> debbugs.gnu.org>; Wed, 6 Mar 2024 12:54:51 +0100 (CET) MIME-version: 1.0 Received: from conversion-daemon.imap.intranet.ufz.de by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) id <0S9X00L00CVLWZ00@HIDDEN> for 57005 <at> debbugs.gnu.org; Wed, 06 Mar 2024 12:54:50 +0100 (CET) Received: from smtp1.ufz.de ([141.65.7.216]) by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) with ESMTPS id <0S9X00EEID3EUJF0@HIDDEN> for 57005 <at> debbugs.gnu.org; Wed, 06 Mar 2024 12:54:50 +0100 (CET) Received: from [198.19.249.3] (ufz542757.intranet.ufz.de [141.65.235.71]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp1.ufz.de (smtp1-UFZ) with ESMTPSA id 6F4028020B for <57005 <at> debbugs.gnu.org>; Wed, 6 Mar 2024 12:54:50 +0100 (CET) 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 In-reply-to: <8d1edc3769b3994fc2a7be34470509e7f45aee31.1709725874.git.lars.bilke@HIDDEN> To: 57005 <at> debbugs.gnu.org Message-id: <8412A210-E386-46B9-A3E1-10D9240AA484@HIDDEN> X-Mailer: MailMate (1.14r5937) Content-type: multipart/signed; boundary="=_MailMate_B4579DDC-11F1-45A6-9D24-A882A7FA9C79_="; micalg=sha-256; protocol="application/pkcs7-signature" References: <8d1edc3769b3994fc2a7be34470509e7f45aee31.1709725874.git.lars.bilke@HIDDEN> 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 (-) This is an S/MIME signed message (RFC 5652 and 8551). --=_MailMate_B4579DDC-11F1-45A6-9D24-A882A7FA9C79_= Content-Type: multipart/alternative; boundary="=_MailMate_65FDE64D-0B39-4C62-BFE2-D4B6A89FD0A6_=" --=_MailMate_65FDE64D-0B39-4C62-BFE2-D4B6A89FD0A6_= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable 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> --=_MailMate_65FDE64D-0B39-4C62-BFE2-D4B6A89FD0A6_=-- 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bug-guix@HIDDEN
:bug#57005
; Package guix
.
Full text available.Received: (at 57005) by debbugs.gnu.org; 6 Mar 2024 11:52:28 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Mar 06 06:52:28 2024 Received: from localhost ([127.0.0.1]:49929 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rhpoy-0006jg-6q for submit <at> debbugs.gnu.org; Wed, 06 Mar 2024 06:52:28 -0500 Received: from mailgate5.ufz.de ([141.65.7.212]:52748 helo=mailgate.ufz.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <lars.bilke@HIDDEN>) id 1rhpov-0006jS-L2 for 57005 <at> debbugs.gnu.org; Wed, 06 Mar 2024 06:52:26 -0500 Received: from imap.intranet.ufz.de (dcs1.intranet.ufz.de [141.65.125.135]) by mailgate.ufz.de (Mailgate5-UFZ) with ESMTP id 6D6571602C4 for <57005 <at> debbugs.gnu.org>; Wed, 6 Mar 2024 12:51:48 +0100 (CET) MIME-version: 1.0 Content-transfer-encoding: 7BIT Content-type: TEXT/PLAIN Received: from conversion-daemon.imap.intranet.ufz.de by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) id <0S9X00L00CVLWZ00@HIDDEN> for 57005 <at> debbugs.gnu.org; Wed, 06 Mar 2024 12:51:48 +0100 (CET) Received: from smtp2.ufz.de ([141.65.7.217]) by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) with ESMTPS id <0S9X00E7ECYCUJF0@HIDDEN> for 57005 <at> debbugs.gnu.org; Wed, 06 Mar 2024 12:51:48 +0100 (CET) Received: from envinf4.minotaur-alpha.ts.net (unknown [141.65.34.85]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-256) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp2.ufz.de (smtp2-UFZ) with ESMTPSA id 3B806E005C; Wed, 6 Mar 2024 12:51:48 +0100 (CET) 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 Message-id: <8d1edc3769b3994fc2a7be34470509e7f45aee31.1709725874.git.lars.bilke@HIDDEN> X-Mailer: git-send-email 2.43.0 X-Debbugs-Cc: Andreas Enge <andreas@HIDDEN>, Eric Bavier <bavier@HIDDEN>, Sharlatan Hellseher <sharlatanus@HIDDEN> X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 57005 Cc: Lars Bilke <lars.bilke@HIDDEN> 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 (-) '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.Received: (at 57005) by debbugs.gnu.org; 5 Mar 2024 15:02:06 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Mar 05 10:02:06 2024 Received: from localhost ([127.0.0.1]:48605 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rhWIw-0006aO-5m for submit <at> debbugs.gnu.org; Tue, 05 Mar 2024 10:02:06 -0500 Received: from mailgate5.ufz.de ([141.65.7.212]:57890 helo=mailgate.ufz.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <lars.bilke@HIDDEN>) id 1rhWIu-0006Ze-83 for 57005 <at> debbugs.gnu.org; Tue, 05 Mar 2024 10:02:05 -0500 Received: from imap.intranet.ufz.de (dcs1.intranet.ufz.de [141.65.125.135]) by mailgate.ufz.de (Mailgate5-UFZ) with ESMTP id 7B2E71602D5; Tue, 5 Mar 2024 16:01:28 +0100 (CET) MIME-version: 1.0 Received: from conversion-daemon.imap.intranet.ufz.de by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) id <0S9V00500QHGFR00@HIDDEN>; Tue, 05 Mar 2024 16:01:28 +0100 (CET) Received: from smtp2.ufz.de ([141.65.7.217]) by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) with ESMTPS id <0S9V00A7OR2G8T90@HIDDEN>; Tue, 05 Mar 2024 16:01:28 +0100 (CET) Received: from [169.254.181.90] (ufz542757.intranet.ufz.de [141.65.235.71]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp2.ufz.de (smtp2-UFZ) with ESMTPSA id 52DD7E0056; Tue, 5 Mar 2024 16:01:28 +0100 (CET) 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> To: 57005 <at> debbugs.gnu.org Message-id: <AB996BF0-5CDD-4BE5-9715-16C586C24784@HIDDEN> X-Mailer: MailMate (1.14r5937) Content-type: multipart/signed; boundary="=_MailMate_5935C150-E3B4-49BE-838C-FEA286D317A7_="; micalg=sha-256; protocol="application/pkcs7-signature" References: <65e5bfc8e0e0580eb9c86e1cc0dc8bb89b286a7a.1709650693.git.lars.bilke@HIDDEN> X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 57005 Cc: andreas@HIDDEN, =?utf-8?q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN> 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 (-) This is an S/MIME signed message (RFC 5652 and 8551). --=_MailMate_5935C150-E3B4-49BE-838C-FEA286D317A7_= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable 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") 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--=_MailMate_5935C150-E3B4-49BE-838C-FEA286D317A7_=--
bug-guix@HIDDEN
:bug#57005
; Package guix
.
Full text available.Received: (at 57005) by debbugs.gnu.org; 5 Mar 2024 14:59:44 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Mar 05 09:59:44 2024 Received: from localhost ([127.0.0.1]:48590 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rhWGd-0006U5-Ia for submit <at> debbugs.gnu.org; Tue, 05 Mar 2024 09:59:44 -0500 Received: from mailgate5.ufz.de ([141.65.7.212]:43012 helo=mailgate.ufz.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <lars.bilke@HIDDEN>) id 1rhWGZ-0006Tn-Mm for 57005 <at> debbugs.gnu.org; Tue, 05 Mar 2024 09:59:42 -0500 Received: from imap.intranet.ufz.de (dcs1.intranet.ufz.de [141.65.125.135]) by mailgate.ufz.de (Mailgate5-UFZ) with ESMTP id 300311602D4 for <57005 <at> debbugs.gnu.org>; Tue, 5 Mar 2024 15:59:03 +0100 (CET) MIME-version: 1.0 Content-transfer-encoding: 7BIT Content-type: TEXT/PLAIN Received: from conversion-daemon.imap.intranet.ufz.de by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) id <0S9V00500QHGFR00@HIDDEN> for 57005 <at> debbugs.gnu.org; Tue, 05 Mar 2024 15:59:03 +0100 (CET) Received: from smtp2.ufz.de ([141.65.7.217]) by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) with ESMTPS id <0S9V00A2SQYD8T90@HIDDEN> for 57005 <at> debbugs.gnu.org; Tue, 05 Mar 2024 15:59:01 +0100 (CET) Received: from envinf4.minotaur-alpha.ts.net (unknown [141.65.34.85]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-256) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp2.ufz.de (smtp2-UFZ) with ESMTPSA id 9AE95E0056; Tue, 5 Mar 2024 15:59:01 +0100 (CET) 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 Message-id: <65e5bfc8e0e0580eb9c86e1cc0dc8bb89b286a7a.1709650693.git.lars.bilke@HIDDEN> X-Mailer: git-send-email 2.43.0 X-Debbugs-Cc: Andreas Enge <andreas@HIDDEN>, Eric Bavier <bavier@HIDDEN>, Sharlatan Hellseher <sharlatanus@HIDDEN> X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 57005 Cc: Lars Bilke <lars.bilke@HIDDEN> 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 (-) '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
.
Full text available.Received: (at 57005) by debbugs.gnu.org; 1 Mar 2024 08:28:00 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Fri Mar 01 03:28:00 2024 Received: from localhost ([127.0.0.1]:36002 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rfyFL-0001YQ-IQ for submit <at> debbugs.gnu.org; Fri, 01 Mar 2024 03:27:59 -0500 Received: from mailgate5.ufz.de ([141.65.7.212]:36830 helo=mailgate.ufz.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <lars.bilke@HIDDEN>) id 1rfyFH-0001YA-4Z for 57005 <at> debbugs.gnu.org; Fri, 01 Mar 2024 03:27:58 -0500 Received: from imap.intranet.ufz.de (dcs1.intranet.ufz.de [141.65.125.135]) by mailgate.ufz.de (Mailgate5-UFZ) with ESMTP id 13E3E16002D for <57005 <at> debbugs.gnu.org>; Fri, 1 Mar 2024 09:27:21 +0100 (CET) MIME-version: 1.0 Content-transfer-encoding: 7BIT Content-type: TEXT/PLAIN Received: from conversion-daemon.imap.intranet.ufz.de by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) id <0S9N00H00TLLSG00@HIDDEN> for 57005 <at> debbugs.gnu.org; Fri, 01 Mar 2024 09:27:21 +0100 (CET) Received: from smtp2.ufz.de ([141.65.7.217]) by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) with ESMTPS id <0S9N00JMOU5KGMC0@HIDDEN> for 57005 <at> debbugs.gnu.org; Fri, 01 Mar 2024 09:27:20 +0100 (CET) Received: from envinf4.minotaur-alpha.ts.net (unknown [141.65.34.85]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-256) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp2.ufz.de (smtp2-UFZ) with ESMTPSA id B8CA1E0069; Fri, 1 Mar 2024 09:27:20 +0100 (CET) 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> X-Mailer: git-send-email 2.43.0 X-Debbugs-Cc: Andreas Enge <andreas@HIDDEN>, Eric Bavier <bavier@HIDDEN>, Sharlatan Hellseher <sharlatanus@HIDDEN> X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 57005 Cc: Lars Bilke <lars.bilke@HIDDEN> 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 (-) '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
.
Full text available.Received: (at 57005) by debbugs.gnu.org; 29 Feb 2024 10:00:58 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Feb 29 05:00:58 2024 Received: from localhost ([127.0.0.1]:33588 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rfdDl-0001R4-Sa for submit <at> debbugs.gnu.org; Thu, 29 Feb 2024 05:00:58 -0500 Received: from mailgate4.ufz.de ([141.65.7.211]:59438 helo=mailgate.ufz.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <lars.bilke@HIDDEN>) id 1rfdDj-0001Qq-AS for 57005 <at> debbugs.gnu.org; Thu, 29 Feb 2024 05:00:56 -0500 Received: from imap.intranet.ufz.de (dcs1.intranet.ufz.de [141.65.125.135]) by mailgate.ufz.de (Mailgate4-UFZ) with ESMTP id AE2BB1602BC for <57005 <at> debbugs.gnu.org>; Thu, 29 Feb 2024 11:00:21 +0100 (CET) MIME-version: 1.0 Received: from conversion-daemon.imap.intranet.ufz.de by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) id <0S9M007002Y55I00@HIDDEN> for 57005 <at> debbugs.gnu.org; Thu, 29 Feb 2024 11:00:21 +0100 (CET) Received: from smtp1.ufz.de ([141.65.7.216]) by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) with ESMTPS id <0S9M00HNI3SK4TF0@HIDDEN> for 57005 <at> debbugs.gnu.org; Thu, 29 Feb 2024 11:00:20 +0100 (CET) Received: from [198.19.249.3] (ufz542757.intranet.ufz.de [141.65.235.71]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp1.ufz.de (smtp1-UFZ) with ESMTPSA id 1594280211 for <57005 <at> debbugs.gnu.org>; Thu, 29 Feb 2024 11:00:20 +0100 (CET) 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 In-reply-to: <de4e8fff610a489bb8c14b1d260a5bd542dfc7d6.1709200010.git.lars.bilke@HIDDEN> To: 57005 <at> debbugs.gnu.org Message-id: <44D266D4-7B4A-4486-AA7E-24CC9E4622B0@HIDDEN> X-Mailer: MailMate (1.14r5937) Content-type: multipart/signed; boundary="=_MailMate_DDBCECFE-F3E3-43C3-A5C2-954E507A6E99_="; micalg=sha-256; protocol="application/pkcs7-signature" References: <de4e8fff610a489bb8c14b1d260a5bd542dfc7d6.1709200010.git.lars.bilke@HIDDEN> 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 (-) This is an S/MIME signed message (RFC 5652 and 8551). --=_MailMate_DDBCECFE-F3E3-43C3-A5C2-954E507A6E99_= Content-Type: multipart/alternative; boundary="=_MailMate_C07CF1BE-6717-41EE-8772-7248BCEDD4A7_=" --=_MailMate_C07CF1BE-6717-41EE-8772-7248BCEDD4A7_= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable 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
.
Full text available.Received: (at 57005) by debbugs.gnu.org; 29 Feb 2024 09:49:39 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Feb 29 04:49:38 2024 Received: from localhost ([127.0.0.1]:33569 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rfd2m-00018s-A3 for submit <at> debbugs.gnu.org; Thu, 29 Feb 2024 04:49:38 -0500 Received: from mailgate4.ufz.de ([141.65.7.211]:45080 helo=mailgate.ufz.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <lars.bilke@HIDDEN>) id 1rfd2Z-000179-A6 for 57005 <at> debbugs.gnu.org; Thu, 29 Feb 2024 04:49:35 -0500 Received: from imap.intranet.ufz.de (dcs1.intranet.ufz.de [141.65.125.135]) by mailgate.ufz.de (Mailgate4-UFZ) with ESMTP id C65121602BC for <57005 <at> debbugs.gnu.org>; Thu, 29 Feb 2024 10:48:49 +0100 (CET) MIME-version: 1.0 Content-transfer-encoding: 7BIT Content-type: TEXT/PLAIN Received: from conversion-daemon.imap.intranet.ufz.de by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) id <0S9M007002Y55I00@HIDDEN> for 57005 <at> debbugs.gnu.org; Thu, 29 Feb 2024 10:48:49 +0100 (CET) Received: from smtp1.ufz.de ([141.65.7.216]) by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) with ESMTPS id <0S9M00H0T3904TF0@HIDDEN> for 57005 <at> debbugs.gnu.org; Thu, 29 Feb 2024 10:48:37 +0100 (CET) Received: from envinf4.minotaur-alpha.ts.net (unknown [141.65.34.85]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-256) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp1.ufz.de (smtp1-UFZ) with ESMTPSA id E50C380211; Thu, 29 Feb 2024 10:48:36 +0100 (CET) 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 Message-id: <de4e8fff610a489bb8c14b1d260a5bd542dfc7d6.1709200010.git.lars.bilke@HIDDEN> X-Mailer: git-send-email 2.43.0 X-Debbugs-Cc: Andreas Enge <andreas@HIDDEN>, Eric Bavier <bavier@HIDDEN>, Sharlatan Hellseher <sharlatanus@HIDDEN> X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 57005 Cc: Lars Bilke <lars.bilke@HIDDEN> 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 (-) '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
.
Full text available.Received: (at submit) by debbugs.gnu.org; 5 Aug 2022 14:51:43 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Fri Aug 05 10:51:43 2022 Received: from localhost ([127.0.0.1]:60228 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1oJyfv-0004ql-51 for submit <at> debbugs.gnu.org; Fri, 05 Aug 2022 10:51:43 -0400 Received: from lists.gnu.org ([209.51.188.17]:34734) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <ludovic.courtes@HIDDEN>) id 1oJyfp-0004qX-Sj for submit <at> debbugs.gnu.org; Fri, 05 Aug 2022 10:51:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51988) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <ludovic.courtes@HIDDEN>) id 1oJyfl-0002sI-Sf for bug-guix@HIDDEN; Fri, 05 Aug 2022 10:51:34 -0400 Received: from mail3-relais-sop.national.inria.fr ([192.134.164.104]:15073) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <ludovic.courtes@HIDDEN>) id 1oJyfj-0002ga-FK for bug-guix@HIDDEN; Fri, 05 Aug 2022 10:51:33 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:subject:date:message-id:mime-version: content-transfer-encoding; bh=7UGx9wljy6i87iY1/AXnSvv099JmAaFFU1rDF2jbe1w=; b=YUef1wJ8f9IzjmleAsQCxj4uicL42Wr7ieQ9g5Ih8aE5R/cZR/7kpK2K Ly3vWE0TQNHbVMorg/CfZTkXrlHeJ008HmarKsbdh3Lww8h91dpMWiapk qYT0yKGO8XmCjhgLDPIYjPc7heXo5/sBN8LuyHRiq6T8VsIrqXVvKz8CP A=; Authentication-Results: mail3-relais-sop.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=ludovic.courtes@HIDDEN; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="5.93,216,1654552800"; d="scan'208";a="20854797" Received: from unknown (HELO ribbon) ([193.50.111.124]) by mail3-relais-sop.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 05 Aug 2022 16:51:26 +0200 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludovic.courtes@HIDDEN> To: bug-guix@HIDDEN Subject: PETSc is not reproducible X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: Octidi 18 Thermidor an 230 de la =?utf-8?Q?R=C3=A9vo?= =?utf-8?Q?lution=2C?= jour de l'Amande X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Fri, 05 Aug 2022 16:51:25 +0200 Message-ID: <87fsiag2vm.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=192.134.164.104; envelope-from=ludovic.courtes@HIDDEN; helo=mail3-relais-sop.national.inria.fr X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H3=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit 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: -2.3 (--) 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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