GNU bug report logs - #67822
[PATCH] gnu: maths: petsc: Reduce closure size.

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Package: guix-patches; Reported by: Lars Bilke <lars.bilke@HIDDEN>; Keywords: patch; dated Thu, 14 Dec 2023 12:57:02 UTC; Maintainer for guix-patches is guix-patches@HIDDEN.

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Date: Tue, 09 Jan 2024 19:15:04 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH v4] gnu: maths: petsc: Reduce closure size.
To: 67822 <at> debbugs.gnu.org
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Reduces closure size by around 350 MB by removing refernces to build
dependencies (e.g. gcc).

New ion v4:

Used proposed :graph: syntax.
Also removed gfortran reference.

Change-Id: I2e6900747b2118546f0a39ceb109b3f2f90e6949
---
 gnu/packages/maths.scm | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index adc7beb655..7dc93ce8ee 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3484,8 +3484,21 @@ (define-public petsc
                           '("configure.log" "make.log" "gmake.log"
                             "test.log" "error.log" "RDict.db"
                             "PETScBuildInternal.cmake"
+                            "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: a1a645337a76cf5fb55d20ee694fcb6a52fcf11b
-- 
2.43.0





Information forwarded to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, guix-patches@HIDDEN:
bug#67822; Package guix-patches. Full text available.

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From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN>
To: Efraim Flashner <efraim@HIDDEN>
Subject: Re: [bug#67822] [PATCH v3] gnu: maths: petsc: Reduce closure size.
In-Reply-To: <ZZpqX6OYjXu-lfB9@3900XT> (Efraim Flashner's message of "Sun, 7
 Jan 2024 11:09:51 +0200")
References: <9ba967c61c66acea4b4c3b1db6e1a446ad9e827e.1702558568.git.lars.bilke@HIDDEN>
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Hi,

Efraim Flashner <efraim@HIDDEN> skribis:

> On Fri, Jan 05, 2024 at 12:52:02PM +0100, Lars Bilke wrote:
>> Hi Ludo,
>>=20
>> On 5 Jan 2024, at 12:08, Ludovic Court=C3=A8s wrote:
>>=20
>> > Can we instead patch the thing that creates =E2=80=98petscvariables=E2=
=80=99 in the
>> > first place?
>> >
>> > The reason I=E2=80=99m suggesting it is because in general we avoid ha=
rdcoding
>> > /gnu/store in substitution patterns because it=E2=80=99s possible to c=
onfigure
>> > Guix with a different store directory.
>>=20
>> Thanks for your feedback!
>>=20
>> In v1 of this patch I removed the 'petscvariables'-file completely but t=
his broke dependent packages as well as not-yet packaged projects which use=
 the file for finding the PETSc library and configuriung their build system.
>>=20
>> Is there a possibility to replace the hard-coded /gnu/store with a varia=
ble which evaluates to the current store directory?
>
> There's %store-directory in (guix build utils).  In fact, it looks like
> git might have some code that you can borrow.

Yes.  However, I think we should use literal strings for patterns in
=E2=80=98substitute*=E2=80=99.  That is, I would avoid:

  (substitute* =E2=80=A6
    (((string-append (%store-directory) "/bin/whatever"))
     =E2=80=A6))

in favor of, say:

  (substitute* =E2=80=A6
    (("([[:graph:]]+)/bin/whatever")
      =E2=80=A6))

This is to make things easier to understand, 100% correct (in theory we
should use =E2=80=98regexp-quote=E2=80=99 when turning strings into regexps=
), and to
leave room for how =E2=80=98substitute*=E2=80=99 is implemented.

Thanks,
Ludo=E2=80=99.




Information forwarded to guix-patches@HIDDEN:
bug#67822; Package guix-patches. Full text available.

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Date: Sun, 7 Jan 2024 11:09:51 +0200
From: Efraim Flashner <efraim@HIDDEN>
To: Lars Bilke <lars.bilke@HIDDEN>
Subject: Re: [bug#67822] [PATCH v3] gnu: maths: petsc: Reduce closure size.
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 67822 <at> debbugs.gnu.org, Andreas Enge <andreas@HIDDEN>,
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On Fri, Jan 05, 2024 at 12:52:02PM +0100, Lars Bilke wrote:
> Hi Ludo,
>=20
> On 5 Jan 2024, at 12:08, Ludovic Court=C3=A8s wrote:
>=20
> > Can we instead patch the thing that creates =E2=80=98petscvariables=E2=
=80=99 in the
> > first place?
> >
> > The reason I=E2=80=99m suggesting it is because in general we avoid har=
dcoding
> > /gnu/store in substitution patterns because it=E2=80=99s possible to co=
nfigure
> > Guix with a different store directory.
>=20
> Thanks for your feedback!
>=20
> In v1 of this patch I removed the 'petscvariables'-file completely but th=
is broke dependent packages as well as not-yet packaged projects which use =
the file for finding the PETSc library and configuriung their build system.
>=20
> Is there a possibility to replace the hard-coded /gnu/store with a variab=
le which evaluates to the current store directory?

There's %store-directory in (guix build utils).  In fact, it looks like
git might have some code that you can borrow.


--=20
Efraim Flashner   <efraim@HIDDEN>   =D7=A8=D7=A0=D7=A9=D7=9C=D7=A4 =
=D7=9D=D7=99=D7=A8=D7=A4=D7=90
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Information forwarded to guix-patches@HIDDEN:
bug#67822; Package guix-patches. Full text available.

Message received at 67822 <at> debbugs.gnu.org:


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Date: Fri, 05 Jan 2024 12:52:02 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: Re: [bug#67822] [PATCH v3] gnu: maths: petsc: Reduce closure size.
In-reply-to: <878r54f35z.fsf@HIDDEN>
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Hi Ludo,

On 5 Jan 2024, at 12:08, Ludovic Court=C3=A8s wrote:

> Can we instead patch the thing that creates =E2=80=98petscvariables=E2=80=
=99 in the
> first place?
>
> The reason I=E2=80=99m suggesting it is because in general we avoid har=
dcoding
> /gnu/store in substitution patterns because it=E2=80=99s possible to co=
nfigure
> Guix with a different store directory.

Thanks for your feedback!

In v1 of this patch I removed the 'petscvariables'-file completely but th=
is broke dependent packages as well as not-yet packaged projects which us=
e the file for finding the PETSc library and configuriung their build sys=
tem.

Is there a possibility to replace the hard-coded /gnu/store with a variab=
le which evaluates to the current store directory?

Sincerely,
Lars

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Information forwarded to guix-patches@HIDDEN:
bug#67822; Package guix-patches. Full text available.

Message received at 67822 <at> debbugs.gnu.org:


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From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN>
To: Lars Bilke <lars.bilke@HIDDEN>
Subject: Re: [bug#67822] [PATCH v3] gnu: maths: petsc: Reduce closure size.
In-Reply-To: <6a6413853ce16af65e143bd727715be6dd7d6048.1702630557.git.lars.bilke@HIDDEN>
 (Lars Bilke's message of "Fri, 15 Dec 2023 09:55:57 +0100")
References: <9ba967c61c66acea4b4c3b1db6e1a446ad9e827e.1702558568.git.lars.bilke@HIDDEN>
 <6a6413853ce16af65e143bd727715be6dd7d6048.1702630557.git.lars.bilke@HIDDEN>
Date: Fri, 05 Jan 2024 12:08:40 +0100
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Hi Lars,

Lars Bilke <lars.bilke@HIDDEN> skribis:

> Reduces closure size by around 350 MB by removing refernces to build depe=
ndencies (e.g. gcc).

Woow, nice!

> +          (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 i=
nputs.
> +              (let ((out (assoc-ref outputs "out")))
> +              (substitute* (string-append out "/lib/petsc/conf/petscvari=
ables")
> +                (("/gnu/store/.*/bin/gcc") "gcc")
> +                (("/gnu/store/.*/bin/g\\+\\+") "g++")
> +                (("/gnu/store/.*/bin/make") "make")
> +                (("/gnu/store/.*/bin/diff") "diff")
> +                (("/gnu/store/.*/bin/sed") "sed")

Can we instead patch the thing that creates =E2=80=98petscvariables=E2=80=
=99 in the
first place?

The reason I=E2=80=99m suggesting it is because in general we avoid hardcod=
ing
/gnu/store in substitution patterns because it=E2=80=99s possible to config=
ure
Guix with a different store directory.

Thanks, and apologies for the delay!

Ludo=E2=80=99.




Information forwarded to guix-patches@HIDDEN:
bug#67822; Package guix-patches. Full text available.

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Date: Fri, 15 Dec 2023 09:55:57 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH v3] gnu: maths: petsc: Reduce closure size.
To: 67822 <at> debbugs.gnu.org
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Reduces closure size by around 350 MB by removing refernces to build dependencies (e.g. gcc).

Fixed a regex from v2.

Change-Id: I2e6900747b2118546f0a39ceb109b3f2f90e6949
---
 gnu/packages/maths.scm | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0f4d29b40f..4b2643e535 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3484,8 +3484,20 @@ (define-public petsc
                           '("configure.log" "make.log" "gmake.log"
                             "test.log" "error.log" "RDict.db"
                             "PETScBuildInternal.cmake"
+                            "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")
+                (("/gnu/store/.*/bin/gcc") "gcc")
+                (("/gnu/store/.*/bin/g\\+\\+") "g++")
+                (("/gnu/store/.*/bin/make") "make")
+                (("/gnu/store/.*/bin/diff") "diff")
+                (("/gnu/store/.*/bin/sed") "sed")
+                ))))
           (add-after 'install 'move-examples
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))

base-commit: ac61e9705fb8c450c6cd0c1731fbb1b909c1f944
-- 
2.43.0





Information forwarded to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, guix-patches@HIDDEN:
bug#67822; Package guix-patches. Full text available.

Message received at 67822 <at> debbugs.gnu.org:


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Date: Thu, 14 Dec 2023 15:53:07 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH v2] gnu: maths: petsc: Reduce closure size.
To: 67822 <at> debbugs.gnu.org
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Reduces closure size by around 350 MB by removing refernces to build
dependencies (e.g. gcc).

The v2 patch does not delete petscvariables but only removes some store
references. This fixes downstream packages such as e.g. dealii-openmpi.

Change-Id: I2e6900747b2118546f0a39ceb109b3f2f90e6949
---
 gnu/packages/maths.scm | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0f4d29b40f..8e8e380336 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3484,8 +3484,20 @@ (define-public petsc
                           '("configure.log" "make.log" "gmake.log"
                             "test.log" "error.log" "RDict.db"
                             "PETScBuildInternal.cmake"
+                            "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")
+                (("/gnu/store/.*/bin/gcc") "gcc")
+                (("/gnu/store/.*/bin/g++") "g++")
+                (("/gnu/store/.*/bin/make") "make")
+                (("/gnu/store/.*/bin/diff") "diff")
+                (("/gnu/store/.*/bin/sed") "sed")
+                ))))
           (add-after 'install 'move-examples
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))

base-commit: ac61e9705fb8c450c6cd0c1731fbb1b909c1f944
-- 
2.43.0





Information forwarded to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, guix-patches@HIDDEN:
bug#67822; Package guix-patches. Full text available.

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


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Date: Thu, 14 Dec 2023 13:56:08 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH] gnu: maths: petsc: Reduce closure size.
To: guix-patches@HIDDEN
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Reduces closure size by around 350 MB.

May break CMake-based projects which use the following script:

https://github.com/jedbrown/cmake-modules/blob/master/FindPETSc.cmake

Use pkg-config based finding instead. See
https://github.com/jedbrown/cmake-modules/blob/master/README.md.

Change-Id: I2e6900747b2118546f0a39ceb109b3f2f90e6949
---
 gnu/packages/maths.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0f4d29b40f..7f3e80efa4 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3484,6 +3484,8 @@ (define-public petsc
                           '("configure.log" "make.log" "gmake.log"
                             "test.log" "error.log" "RDict.db"
                             "PETScBuildInternal.cmake"
+                            "petscvariables"
+                            "configure-hash"
                             ;; Once installed, should uninstall with Guix
                             "uninstall.py")))))
           (add-after 'install 'move-examples

base-commit: ac61e9705fb8c450c6cd0c1731fbb1b909c1f944
-- 
2.43.0





Acknowledgement sent to Lars Bilke <lars.bilke@HIDDEN>:
New bug report received and forwarded. Copy sent to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, guix-patches@HIDDEN. Full text available.
Report forwarded to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, guix-patches@HIDDEN:
bug#67822; Package guix-patches. Full text available.
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