From db7b16e3afa0d432b2ee61c7cbb825caf52a9bf4 Mon Sep 17 00:00:00 2001 From: bcumming Date: Wed, 29 Oct 2025 11:26:15 +0100 Subject: [PATCH 1/3] add notes for netcdf-tools uenv --- docs/software/cw/netcdf-tools.md | 88 ++++++++++++++++++++++++++++++++ mkdocs.yml | 1 + 2 files changed, 89 insertions(+) create mode 100644 docs/software/cw/netcdf-tools.md diff --git a/docs/software/cw/netcdf-tools.md b/docs/software/cw/netcdf-tools.md new file mode 100644 index 00000000..01a20be3 --- /dev/null +++ b/docs/software/cw/netcdf-tools.md @@ -0,0 +1,88 @@ +[](){#ref-uenv-netcdf-tools} +# netcdf-tools + +The `netcdf-tools` uenv provides a set of CLI tools and GUI tools frequently used in climate and weather workflows. + +The release schedule is not fixed, with new releases when required. + +| version | node types | system | status | +|--------------------|-------------------|-----------------------------------------|--------| +| 2024 | zen2, gh200 | daint, eiger, santis, clariden | **DEPRECATED** | +| 2025 | zen2, gh200 | daint, eiger, santis, clariden | :white_check_mark: | + +!!! warning + If you are using the `netcdf-tools/2024` version, please upgrade to the `2025` version, because the `2024` version uses an old interface that won't load views correctly. + + +The packages exposed via the `default` and `modules` views in `2025:v1` are: + +* [cdo@2.5.2](https://packages.spack.io/package.html?name=cdo) +* [cray-mpich@8.1.32](https://packages.spack.io/package.html?name=cray-mpich) +* [eccodes@2.41.0](https://packages.spack.io/package.html?name=eccodes) +* [ferret@7.6.0](https://packages.spack.io/package.html?name=ferret) + * Only provided in Eiger because its build configuration hard-codes x86 instructions. +* [gcc@14.3.0](https://packages.spack.io/package.html?name=gcc) +* [gdal@3.11.0](https://packages.spack.io/package.html?name=gdal) +* [geos@3.13.1](https://packages.spack.io/package.html?name=geos) +* [hdf5@1.14.6](https://packages.spack.io/package.html?name=hdf5) +* [nco@5.3.3](https://packages.spack.io/package.html?name=nco) +* [ncview@2.1.9](https://packages.spack.io/package.html?name=ncview) +* [netcdf-c@4.9.2](https://packages.spack.io/package.html?name=netcdf-c) +* [netcdf-cxx4@4.3.1](https://packages.spack.io/package.html?name=netcdf-cxx4) +* [netcdf-fortran@4.6.1](https://packages.spack.io/package.html?name=netcdf-fortran) +* [python@3.13.5](https://packages.spack.io/package.html?name=python) +* [udunits@2.2.28](https://packages.spack.io/package.html?name=udunits) + +## How to use + +Use the different views to access the software + +=== "the `netcdf` view" + + The simplest way to get started is to use the `netcdf` file system view, which automatically loads all of the packages when the uenv is started. + + !!! example "test mpi compilers and python provided by netcdf-tools/2025" + ```console + # start using the netcdf view + $ uenv start --view=netcdf netcdf-tools/2025:v1 + + # the software is available + $ which cdo + /user-environment/env/netcdf/bin/cdo + $ which gdal + /user-environment/env/netcdf/bin/gdal + $ gdal --version + GDAL 3.11.0 "Eganville", released 2025/05/06 + ``` + + !!! example "run applications directly using uenv run" + ```console + # run ncview without having to start a uenv session + $ uenv run netcdf-tools/2025:v1 --view=netcdf -- ncview + + # create an alias that launches tools in netcdf-tools (add it to bashrc) + $ alias ncx='uenv run --view=netcdf netcdf-tools/2025:v1 --' + # then run commands: + $ ncx ncview + $ ncx cdo + ``` + +=== "modules" + + The uenv provides modules for all of the software packages, which can be made available by using the `modules` view in + No modules are loaded when a uenv starts, and have to be loaded individually using `module load`. + + !!! example "starting netcdf-tools and using the provided modules" + ```console + $ uenv start netcdf-tools/2025:v1 --view=modules + $ module avail + ---------------------------- /user-environment/modules ----------------------------- + cdo/2.5.2 gdal/3.11.0 ncview/2.1.9 squashfs/4.6.1 + cray-mpich/8.1.32 geos/3.13.1 netcdf-c/4.9.2 udunits/2.2.28 + eccodes/2.41.0 hdf5/1.14.6 netcdf-cxx4/4.3.1 + ferret/7.6.0 libfabric/1.22.0 netcdf-fortran/4.6.1 + gcc/14.3.0 nco/5.3.3 python/3.13.5 + $ module load gdal + $ gdal --version + GDAL 3.11.0 "Eganville", released 2025/05/06 + ``` diff --git a/mkdocs.yml b/mkdocs.yml index 54dddf8c..91209b66 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -102,6 +102,7 @@ nav: - 'Climate and Weather': - software/cw/index.md - 'WRF': software/cw/wrf.md + - 'netcdf-tools': software/cw/netcdf-tools.md - 'Communication Libraries': - software/communication/index.md - 'Cray MPICH': software/communication/cray-mpich.md From fa03b9459e6dedc1efd3fe9509d3d3018ddfbd50 Mon Sep 17 00:00:00 2001 From: bcumming Date: Wed, 29 Oct 2025 11:33:09 +0100 Subject: [PATCH 2/3] reorder versions in table --- docs/software/cw/netcdf-tools.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/software/cw/netcdf-tools.md b/docs/software/cw/netcdf-tools.md index 01a20be3..2b8fbcb3 100644 --- a/docs/software/cw/netcdf-tools.md +++ b/docs/software/cw/netcdf-tools.md @@ -7,14 +7,14 @@ The release schedule is not fixed, with new releases when required. | version | node types | system | status | |--------------------|-------------------|-----------------------------------------|--------| -| 2024 | zen2, gh200 | daint, eiger, santis, clariden | **DEPRECATED** | | 2025 | zen2, gh200 | daint, eiger, santis, clariden | :white_check_mark: | +| 2024 | zen2, gh200 | daint, eiger, santis, clariden | **DEPRECATED** | !!! warning If you are using the `netcdf-tools/2024` version, please upgrade to the `2025` version, because the `2024` version uses an old interface that won't load views correctly. -The packages exposed via the `default` and `modules` views in `2025:v1` are: +The packages exposed via the `default` and `modules` views in `netcdf-tools/2025:v1` are: * [cdo@2.5.2](https://packages.spack.io/package.html?name=cdo) * [cray-mpich@8.1.32](https://packages.spack.io/package.html?name=cray-mpich) From 9de7eef9f2a2ee60bfbf56b7fadf89fcbbf538c5 Mon Sep 17 00:00:00 2001 From: bcumming Date: Wed, 29 Oct 2025 11:41:11 +0100 Subject: [PATCH 3/3] clarify deprecation notice --- docs/software/cw/netcdf-tools.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/software/cw/netcdf-tools.md b/docs/software/cw/netcdf-tools.md index 2b8fbcb3..371fe436 100644 --- a/docs/software/cw/netcdf-tools.md +++ b/docs/software/cw/netcdf-tools.md @@ -11,7 +11,9 @@ The release schedule is not fixed, with new releases when required. | 2024 | zen2, gh200 | daint, eiger, santis, clariden | **DEPRECATED** | !!! warning - If you are using the `netcdf-tools/2024` version, please upgrade to the `2025` version, because the `2024` version uses an old interface that won't load views correctly. + The `netcdf-tools/2024` version uses an old interface that won't load views correctly. + + All users of version `2024` should upgrade to `2025` as soon as possible. The packages exposed via the `default` and `modules` views in `netcdf-tools/2025:v1` are: