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

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

[zimoun]

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

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

[Mathieu Othacehe]

Hello zimoun,

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

The actual patch seems to be missing here.

Thanks,

Mathieu

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

[zimoun]

Hi Mathieu,

On Thu, 2 Dec 2021 at 15:46, Mathieu Othacehe <othacehe@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

[bug#52124] [PATCH] gnu: Add n2p2-lib.

[zimoun]

From: Pierre-Antoine Bouttier <pierre-antoine.bouttier@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@apatience.com>
 ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
 ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
+;;; Copyright © 2021 Pierre-Antoine Bouttier <pierre-antoine.bouttier@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

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

[zimoun]

Hi,

On Mon, 06 Dec 2021 at 16:24, zimoun <zimon.toutoune@gmail.com> wrote:
> From: Pierre-Antoine Bouttier <pierre-antoine.bouttier@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

bug#52124: [PATCH 0/1] Add n2p2-lib

[Ludovic Courtès]

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Hi,

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

> From: Pierre-Antoine Bouttier <pierre-antoine.bouttier@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’.


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: Type: text/x-patch, Size: 2742 bytes --]

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

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

[zimoun]

Hi,

On Thu, 5 May 2022 at 23:28, Ludovic Courtès <ludo@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