bug#57005: [PATCH v3] gnu: petsc: scrub build machine specifics

[Lars Bilke]

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/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

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