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

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 73603 in the body.
You can then email your comments to 73603 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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

From: Romain GARBAGE <romain.garbage <at> inria.fr>
To: guix-patches <at> gnu.org
Cc: ludovic.courtes <at> inria.fr, Romain GARBAGE <romain.garbage <at> inria.fr>
Subject: [PATCH 0/2] Add support for parallel I/O in netcdf
Date: Wed,  2 Oct 2024 17:32:24 +0200

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

Message #8 received at 73603 <at> debbugs.gnu.org (full text, mbox):

From: Romain GARBAGE <romain.garbage <at> inria.fr>
To: 73603 <at> debbugs.gnu.org
Cc: ludovic.courtes <at> inria.fr, Romain GARBAGE <romain.garbage <at> inria.fr>
Subject: [PATCH 1/2] gnu: Add pnetcdf.
Date: Wed,  2 Oct 2024 17:40:00 +0200

* 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

Message #11 received at 73603 <at> debbugs.gnu.org (full text, mbox):

From: Romain GARBAGE <romain.garbage <at> inria.fr>
To: 73603 <at> debbugs.gnu.org
Cc: ludovic.courtes <at> inria.fr, Romain GARBAGE <romain.garbage <at> inria.fr>
Subject: [PATCH 2/2] gnu: netcdf-parallel-openmpi: Enable pnetcdf support.
Date: Wed,  2 Oct 2024 17:40:01 +0200

* 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

Message #16 received at 73603-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludovic.courtes <at> inria.fr>
To: Romain GARBAGE <romain.garbage <at> inria.fr>
Cc: 73603-done <at> debbugs.gnu.org
Subject: Re: [bug#73603] [PATCH 0/2] Add support for parallel I/O in netcdf
Date: Fri, 04 Oct 2024 13:53:09 +0200

Romain GARBAGE <romain.garbage <at> 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!

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.