[bug#73603] [PATCH 0/2] Add support for parallel I/O in netcdf

[bug#73603] [PATCH 0/2] Add support for parallel I/O in netcdf

[Romain GARBAGE]

According to the documentation at [1], parallel I/O support for classic
netCDF files, i.e. CDF-1, 2 and 5 formats, requires the PnetCDF library.
This patch series adds the pnetcdf package (first commit) and activates
the pnetcdf support in the parallel variant of the netcdf package.

[1]: https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html#build_parallel

Romain GARBAGE (2):
  gnu: Add pnetcdf.
  gnu: netcdf-parallel-openmpi: Enable pnetcdf support.

 gnu/packages/maths.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)


base-commit: 71fef00c95b22a1d917abdb28de5aa217b023e31
-- 
2.46.0

[bug#73603] [PATCH 1/2] gnu: Add pnetcdf.

[Romain GARBAGE]

* gnu/packages/maths.scm (pnetcdf): New variable.

Change-Id: I419161be82cd45585187abfd1e63a23feac73d59
---
 gnu/packages/maths.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 03fa4d2fae..51812c5a0d 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2350,6 +2350,37 @@ (define-public netcdf
 sharing of scientific data.")
     (license (license:x11-style "file://COPYRIGHT"))))
 
+(define-public pnetcdf
+  (package
+    (name "pnetcdf")
+    (version "1.13.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://parallel-netcdf.github.io/Release/pnetcdf-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "14f4nbcnw80y59cl0kjpxqqfaxzzd62kixnhb6ihp6aigb3z385b"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:configure-flags
+           #~(list "--enable-shared"
+                   (string-append "--with-mpi=" #$(this-package-input "openmpi")))
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'build 'mpi-setup
+                 #$%openmpi-setup))))
+    (inputs (list openmpi))
+    (native-inputs (list m4))
+    (home-page "https://parallel-netcdf.github.io/")
+    (synopsis "Parallel I/O Library for NetCDF File Access")
+    (description "PnetCDF is a high-performance parallel I/O library for accessing
+Unidata's NetCDF, files in classic formats, specifically the formats of CDF-1, 2, and
+5.")
+    (license (license:x11-style "file://COPYRIGHT"))))
+
 (define-public netcdf-parallel-openmpi
   (package (inherit netcdf)
     (name "netcdf-parallel-openmpi")

base-commit: 71fef00c95b22a1d917abdb28de5aa217b023e31
-- 
2.46.0

[bug#73603] [PATCH 2/2] gnu: netcdf-parallel-openmpi: Enable pnetcdf support.

[Romain GARBAGE]

* gnu/packages/maths.scm (netcdf-parallel-openmpi) [arguments]: Enable pnetcdf support.

Change-Id: I7f3fc6abdb262be86840ea3f68bb6416a0ab1fad
---
 gnu/packages/maths.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 51812c5a0d..f4edd546e2 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2386,6 +2386,7 @@ (define-public netcdf-parallel-openmpi
     (name "netcdf-parallel-openmpi")
     (inputs
      `(("mpi" ,openmpi)
+       ("pnetcdf" ,pnetcdf)
        ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
                         (package-inputs netcdf))))
     ;; TODO: Replace pkg-config references in nc-config with absolute references
@@ -2394,6 +2395,8 @@ (define-public netcdf-parallel-openmpi
        ((#:configure-flags flags)
         `(cons* "CC=mpicc" "CXX=mpicxx"
                 "--enable-parallel-tests"
+                ;; Enable support of CDF-1, 2 and 5 formats.
+                "--enable-pnetcdf"
                 ;; NetCDF supports both parallel and shared library building
                 ;; See https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html#build_parallel
                 "--enable-shared" "--with-pic"
-- 
2.46.0

bug#73603: [PATCH 0/2] Add support for parallel I/O in netcdf

[Ludovic Courtès]

Romain GARBAGE <romain.garbage@inria.fr> skribis:

> According to the documentation at [1], parallel I/O support for classic
> netCDF files, i.e. CDF-1, 2 and 5 formats, requires the PnetCDF library.
> This patch series adds the pnetcdf package (first commit) and activates
> the pnetcdf support in the parallel variant of the netcdf package.
>
> [1]: https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html#build_parallel
>
> Romain GARBAGE (2):
>   gnu: Add pnetcdf.
>   gnu: netcdf-parallel-openmpi: Enable pnetcdf support.

Applied, thanks!