GNU bug report logs - #52124
[PATCH 0/1] Add n2p2-lib

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Package: guix-patches;

Reported by: zimoun <zimon.toutoune <at> gmail.com>

Date: Fri, 26 Nov 2021 13:09:01 UTC

Severity: normal

Tags: patch

Done: Ludovic Courtès <ludo <at> gnu.org>

Bug is archived. No further changes may be made.

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Report forwarded to guix-patches <at> gnu.org:
bug#52124; Package guix-patches. (Fri, 26 Nov 2021 13:09:02 GMT) Full text and rfc822 format available.

Acknowledgement sent to zimoun <zimon.toutoune <at> gmail.com>:
New bug report received and forwarded. Copy sent to guix-patches <at> gnu.org. (Fri, 26 Nov 2021 13:09:02 GMT) Full text and rfc822 format available.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 0/1] Add n2p2-lib
Date: Fri, 26 Nov 2021 14:08:24 +0100
Hi,

This adds n2p2-lib.  It is an example from Café Guix.

Cheers,
simon


Pierre-Antoine Bouttier (1):
  gnu: Add n2p2-lib.

 gnu/packages/maths.scm | 55 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)

-- 
2.33.1





Information forwarded to guix-patches <at> gnu.org:
bug#52124; Package guix-patches. (Thu, 02 Dec 2021 14:47:01 GMT) Full text and rfc822 format available.

Message #8 received at 52124 <at> debbugs.gnu.org (full text, mbox):

From: Mathieu Othacehe <othacehe <at> gnu.org>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 52124 <at> debbugs.gnu.org
Subject: Re: bug#52124: [PATCH 0/1] Add n2p2-lib
Date: Thu, 02 Dec 2021 15:46:31 +0100
Hello zimoun,

> This adds n2p2-lib.  It is an example from Café Guix.

The actual patch seems to be missing here.

Thanks,

Mathieu




Information forwarded to guix-patches <at> gnu.org:
bug#52124; Package guix-patches. (Thu, 02 Dec 2021 15:55:02 GMT) Full text and rfc822 format available.

Message #11 received at 52124 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: Mathieu Othacehe <othacehe <at> gnu.org>
Cc: 52124 <at> debbugs.gnu.org
Subject: Re: bug#52124: [PATCH 0/1] Add n2p2-lib
Date: Thu, 2 Dec 2021 16:54:22 +0100
Hi Mathieu,

On Thu, 2 Dec 2021 at 15:46, Mathieu Othacehe <othacehe <at> gnu.org> wrote:

> > This adds n2p2-lib.  It is an example from Café Guix.
>
> The actual patch seems to be missing here.

Thanks for noticing.  I did a live demo at Café Guix [1] past friday
(2021-11-26) and I ran out of time to complete.  I try to send ASAP.
:-)

https://hpc.guix.info/events/2021/caf%C3%A9-guix/


Thanks,
simon




Information forwarded to guix-patches <at> gnu.org:
bug#52124; Package guix-patches. (Mon, 06 Dec 2021 15:25:02 GMT) Full text and rfc822 format available.

Message #14 received at 52124 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 52124 <at> debbugs.gnu.org
Cc: othacehe <at> gnu.org,
 Pierre-Antoine Bouttier <pierre-antoine.bouttier <at> univ-grenoble-alpes.fr>
Subject: [PATCH] gnu: Add n2p2-lib.
Date: Mon,  6 Dec 2021 16:24:22 +0100
From: Pierre-Antoine Bouttier <pierre-antoine.bouttier <at> univ-grenoble-alpes.fr>

* gnu/packages/maths.scm (n2p2-lib): New variable.
---
 gnu/packages/maths.scm | 55 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 83f31c1396..b08dc6fe67 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -48,6 +48,7 @@
 ;;; Copyright © 2021 Paul A. Patience <paul <at> apatience.com>
 ;;; Copyright © 2021 Ivan Gankevich <i.gankevich <at> spbu.ru>
 ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv <at> pm.me>
+;;; Copyright © 2021 Pierre-Antoine Bouttier <pierre-antoine.bouttier <at> univ-grenoble-alpes.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1753,6 +1754,60 @@ (define-public netcdf-fortran
     (home-page (package-home-page netcdf))
     (license (package-license netcdf))))
 
+(define-public n2p2-lib
+  (package
+    (name "n2p2-lib")
+    (version "2.1.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/CompPhysVienna/n2p2")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1lw195ihpxwh08387i4gamk1glhalpq888q6nj8l5vswbgnrv1pq"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags '("MODE=shared" "-C" "src")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'post-unpack
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "src/makefile.gnu"
+               (("PROJECT_EIGEN=/usr/include/eigen3")
+                (string-append "PROJECT_EIGEN="
+                               (assoc-ref inputs "eigen") "/include/eigen3")))
+             (substitute* "src/makefile.gnu"
+               (("-lblas")
+                (string-append "-L"
+                               (assoc-ref inputs "openblas") "/lib -lopenblas")))))
+         (delete 'configure)
+         (delete 'check)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bindir (string-append out "/bin"))
+                    (libdir (string-append out "/lib"))
+                    (incdir (string-append out "/include")))
+               (for-each (lambda (f) (install-file f libdir))
+                         (find-files "../lib/" "."))
+               (for-each (lambda (f) (install-file f incdir))
+                         (find-files "../include/" "."))))))))
+    (inputs
+     `(("openmpi" ,openmpi)
+       ("gsl" ,gsl)
+       ("openblas" ,openblas)
+       ("eigen" ,eigen)))
+    (synopsis "Neural network potentials for chemistry and physics")
+    (description "This package contains software that will allow you to use
+existing neural network potential parameterizations to predict energies and
+forces (with standalone tools but also in conjunction with the MD software
+LAMMPS). In addition it is possible to train new neural network potentials
+with the provided training tools.")
+    (home-page "https://compphysvienna.github.io/n2p2")
+    (license license:gpl3)))
+
 (define-public nlopt
   (package
     (name "nlopt")

base-commit: 9478a252509a93f3e7f486cbc549631185ba071d
-- 
2.33.1





Information forwarded to guix-patches <at> gnu.org:
bug#52124; Package guix-patches. (Tue, 03 May 2022 12:49:02 GMT) Full text and rfc822 format available.

Message #17 received at 52124 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 52124 <at> debbugs.gnu.org
Cc: othacehe <at> gnu.org, ludo <at> gnu.org,
 Pierre-Antoine Bouttier <pierre-antoine.bouttier <at> univ-grenoble-alpes.fr>
Subject: Re: bug#52124: [PATCH 0/1] Add n2p2-lib
Date: Tue, 03 May 2022 14:38:06 +0200
Hi,

On Mon, 06 Dec 2021 at 16:24, zimoun <zimon.toutoune <at> gmail.com> wrote:
> From: Pierre-Antoine Bouttier <pierre-antoine.bouttier <at> univ-grenoble-alpes.fr>
>
> * gnu/packages/maths.scm (n2p2-lib): New variable.
> ---
>  gnu/packages/maths.scm | 55 ++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 55 insertions(+)
>
> diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
> index 83f31c1396..b08dc6fe67 100644
> --- a/gnu/packages/maths.scm
> +++ b/gnu/packages/maths.scm

Friendly ping about this patch#52124 [1].

1: <http://issues.guix.gnu.org/issue/52124>


Cheers,
simon




Reply sent to Ludovic Courtès <ludo <at> gnu.org>:
You have taken responsibility. (Thu, 05 May 2022 21:29:02 GMT) Full text and rfc822 format available.

Notification sent to zimoun <zimon.toutoune <at> gmail.com>:
bug acknowledged by developer. (Thu, 05 May 2022 21:29:02 GMT) Full text and rfc822 format available.

Message #22 received at 52124-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: othacehe <at> gnu.org, 52124-done <at> debbugs.gnu.org,
 Pierre-Antoine Bouttier <pierre-antoine.bouttier <at> univ-grenoble-alpes.fr>
Subject: Re: bug#52124: [PATCH 0/1] Add n2p2-lib
Date: Thu, 05 May 2022 23:28:37 +0200
[Message part 1 (text/plain, inline)]
Hi,

zimoun <zimon.toutoune <at> gmail.com> skribis:

> From: Pierre-Antoine Bouttier <pierre-antoine.bouttier <at> univ-grenoble-alpes.fr>
>
> * gnu/packages/maths.scm (n2p2-lib): New variable.

The ‘install’ phase was not installing anything, so I had to adjust it.
I also fixed a couple of other issues—patch below.

Finally applied, thanks!

Ludo’.

[Message part 2 (text/x-patch, inline)]
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 613b52f5aa..efa453659c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1855,7 +1855,7 @@ (define-public netcdf-fortran
 
 (define-public n2p2-lib
   (package
-    (name "n2p2-lib")
+    (name "n2p2")
     (version "2.1.4")
     (source (origin
               (method git-fetch)
@@ -1879,8 +1879,13 @@ (define-public n2p2-lib
                                (assoc-ref inputs "eigen") "/include/eigen3")))
              (substitute* "src/makefile.gnu"
                (("-lblas")
-                (string-append "-L"
-                               (assoc-ref inputs "openblas") "/lib -lopenblas")))))
+                (string-append "-L" (assoc-ref inputs "openblas")
+                               "/lib -lopenblas"))
+               (("-march=native")
+                ""))
+             (substitute* "src/application/makefile"
+               (("LDFLAGS=")
+                "LDFLAGS=-Wl,-rpath='$$ORIGIN/../lib' "))))
          (delete 'configure)
          (delete 'check)
          (replace 'install
@@ -1889,23 +1894,23 @@ (define-public n2p2-lib
                     (bindir (string-append out "/bin"))
                     (libdir (string-append out "/lib"))
                     (incdir (string-append out "/include")))
+               (for-each (lambda (f) (install-file f bindir))
+                         (find-files "bin" "^nnp-"))
                (for-each (lambda (f) (install-file f libdir))
-                         (find-files "../lib/" "."))
+                         (find-files "lib" "\\.so$"))
                (for-each (lambda (f) (install-file f incdir))
-                         (find-files "../include/" "."))))))))
+                         (find-files "include" "\\.h$"))))))))
     (inputs
-     `(("openmpi" ,openmpi)
-       ("gsl" ,gsl)
-       ("openblas" ,openblas)
-       ("eigen" ,eigen)))
+     (list openmpi gsl openblas eigen))
     (synopsis "Neural network potentials for chemistry and physics")
     (description "This package contains software that will allow you to use
 existing neural network potential parameterizations to predict energies and
 forces (with standalone tools but also in conjunction with the MD software
-LAMMPS). In addition it is possible to train new neural network potentials
+LAMMPS).  In addition it is possible to train new neural network potentials
 with the provided training tools.")
-    (home-page "https://compphysvienna.github.io/n2p2")
-    (license license:gpl3)))
+    (home-page "https://compphysvienna.github.io/n2p2/")
+    (properties '((tunable? . #t)))        ;to benefit from SIMD code in Eigen
+    (license license:gpl3+)))
 
 (define-public nlopt
   (package

Information forwarded to guix-patches <at> gnu.org:
bug#52124; Package guix-patches. (Fri, 06 May 2022 08:31:01 GMT) Full text and rfc822 format available.

Message #25 received at 52124-done <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: Mathieu Othacehe <othacehe <at> gnu.org>, 52124-done <at> debbugs.gnu.org,
 Pierre-Antoine Bouttier <pierre-antoine.bouttier <at> univ-grenoble-alpes.fr>
Subject: Re: bug#52124: [PATCH 0/1] Add n2p2-lib
Date: Fri, 6 May 2022 10:30:18 +0200
Hi,

On Thu, 5 May 2022 at 23:28, Ludovic Courtès <ludo <at> gnu.org> wrote:

> The ‘install’ phase was not installing anything, so I had to adjust it.
> I also fixed a couple of other issues—patch below.

Thanks.  Sorry to not have catched the errors beforehand.


Cheers,
simon




bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Fri, 03 Jun 2022 11:24:04 GMT) Full text and rfc822 format available.

This bug report was last modified 1 year and 299 days ago.

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