* [bug#73603] [PATCH 0/2] Add support for parallel I/O in netcdf
@ 2024-10-02 15:32 Romain GARBAGE
2024-10-02 15:40 ` [bug#73603] [PATCH 1/2] gnu: Add pnetcdf Romain GARBAGE
2024-10-04 11:53 ` bug#73603: [PATCH 0/2] Add support for parallel I/O in netcdf Ludovic Courtès
0 siblings, 2 replies; 4+ messages in thread
From: Romain GARBAGE @ 2024-10-02 15:32 UTC (permalink / raw)
To: 73603; +Cc: ludovic.courtes, 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
^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#73603] [PATCH 1/2] gnu: Add pnetcdf.
2024-10-02 15:32 [bug#73603] [PATCH 0/2] Add support for parallel I/O in netcdf Romain GARBAGE
@ 2024-10-02 15:40 ` Romain GARBAGE
2024-10-02 15:40 ` [bug#73603] [PATCH 2/2] gnu: netcdf-parallel-openmpi: Enable pnetcdf support Romain GARBAGE
2024-10-04 11:53 ` bug#73603: [PATCH 0/2] Add support for parallel I/O in netcdf Ludovic Courtès
1 sibling, 1 reply; 4+ messages in thread
From: Romain GARBAGE @ 2024-10-02 15:40 UTC (permalink / raw)
To: 73603; +Cc: ludovic.courtes, 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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#73603] [PATCH 2/2] gnu: netcdf-parallel-openmpi: Enable pnetcdf support.
2024-10-02 15:40 ` [bug#73603] [PATCH 1/2] gnu: Add pnetcdf Romain GARBAGE
@ 2024-10-02 15:40 ` Romain GARBAGE
0 siblings, 0 replies; 4+ messages in thread
From: Romain GARBAGE @ 2024-10-02 15:40 UTC (permalink / raw)
To: 73603; +Cc: ludovic.courtes, 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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#73603: [PATCH 0/2] Add support for parallel I/O in netcdf
2024-10-02 15:32 [bug#73603] [PATCH 0/2] Add support for parallel I/O in netcdf Romain GARBAGE
2024-10-02 15:40 ` [bug#73603] [PATCH 1/2] gnu: Add pnetcdf Romain GARBAGE
@ 2024-10-04 11:53 ` Ludovic Courtès
1 sibling, 0 replies; 4+ messages in thread
From: Ludovic Courtès @ 2024-10-04 11:53 UTC (permalink / raw)
To: Romain GARBAGE; +Cc: 73603-done
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!
^ permalink raw reply [flat|nested] 4+ messages in thread
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2024-10-02 15:32 [bug#73603] [PATCH 0/2] Add support for parallel I/O in netcdf Romain GARBAGE
2024-10-02 15:40 ` [bug#73603] [PATCH 1/2] gnu: Add pnetcdf Romain GARBAGE
2024-10-02 15:40 ` [bug#73603] [PATCH 2/2] gnu: netcdf-parallel-openmpi: Enable pnetcdf support Romain GARBAGE
2024-10-04 11:53 ` bug#73603: [PATCH 0/2] Add support for parallel I/O in netcdf Ludovic Courtès
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