From a4f346043c4b140ec26fa983645c4d573b705219 Mon Sep 17 00:00:00 2001 From: Matthieu Leclair Date: Fri, 30 Aug 2024 12:22:54 +0200 Subject: [PATCH 1/2] upd(alps): more Alps doc, remove part under ICON (#194) --- docs/alps/uenvs.md | 63 ++++++++++++++++++++++++++++++++++-------- docs/alps/vclusters.md | 12 ++++++++ docs/models/icon.md | 35 ----------------------- 3 files changed, 64 insertions(+), 46 deletions(-) diff --git a/docs/alps/uenvs.md b/docs/alps/uenvs.md index 6487ce1e..1dc4232f 100644 --- a/docs/alps/uenvs.md +++ b/docs/alps/uenvs.md @@ -38,23 +38,59 @@ It can be used to - run a single command with that uenv mounted - access uenv modules -For now, `uenv` isn't available on Balfrin and requires (easy) [manual installation :material-open-in-new:](https://eth-cscs.github.io/uenv/#getting-uenv){:target="_blank"}. +For now, `uenv` isn't available on Balfrin and requires (easy) [manual installation :material-open-in-new:](https://eth-cscs.github.io/uenv/#getting-uenv){:target="_blank"}: +```shell +git clone https://github.com/eth-cscs/uenv.git && ./uenv/install --local +``` + +### Quickstart -!!! note "TODO: Quick start" +In the following, using `name/version:tag` as metadata to target a uenv can be replaced by the absolute path to the image if necessary. + + +#### Create a local images repository +In order to be able to use uenv images, you first need to `pull`them into a local repository. First create the repo with +```shell +uenv repo create +``` - - [ ] `uenv image repo create` - - [ ] `uenv image find` - - [ ] `uenv image pull` - - [ ] `uenv start` - - [ ] `uenv run` +#### List available images +```shell +uenv image find +``` -## `--uenv` SLURM plugin +#### Pull an image in the local repo +```shell +uenv image pull name/version:tag +``` + +#### Start a uenv for interactive use +This will spawn a new shell with the uenv mounted at `/mount-point` (defaulting to `/user-environment`) +```shell +uenv start name/version:tag [/mount-point] +``` +Exit with a usual `exit` or `uenv stop`. + +#### Use modules +Software in a uenv can be accessed by using it as a `spack` upstream (see [`spack-c2sm` integration](#spack-c2sm-integration)) but also by loading modules. For that, use the `--view=modules` option: +```shell +uenv start --view=modules name/version:tag [/mount-point] +``` +A usual `module avail` command would then show you the different modules added by the uenv on top of the original environment + +#### launch a subprocess with a uenv mounted +```shell +uenv run name/version:tag -- my_command +``` +will run `my_command` (can be executing a script) with the uenv mounted. This is particularly useful when inside scripts. + +## The `--uenv` SLURM plugin CSCS developped the `--uenv` slurm plugin in order to mount uenvs at runtime. Either use the name of a uenv in your local repo or the full absolute path to the uenv. ```shell -sbatch --uenv uenv_name:/mount/point -sbatch --uenv /image/path:/mount/point +sbatch --uenv name/version:tag[:/mount/point] +sbatch --uenv /image/path[:/mount/point] ``` `:mount/point` can always be omitted and defaults to `:/user-environment`. @@ -72,8 +108,13 @@ Uenvs cannot be mounted *anywhere*. They are generated with a predefined install ## `spack-c2sm` integration -User environments are used as a spack upstream with +User environments are supported in non-yet released `spack-c2sm` tags. For testing purposes, you can use `v0.21.1.2`, so +```shell +git clone --depth 1 --recurse-submodules --shallow-submodules -b v0.21.1.2 https://github.com/C2SM/spack-c2sm.git +``` +Then start the user environment and use it as a spack upstream with ```shell +uenv start name/version:tag source spack-c2sm/setup-env.sh /user-environment ``` diff --git a/docs/alps/vclusters.md b/docs/alps/vclusters.md index 23948887..af5a81dc 100644 --- a/docs/alps/vclusters.md +++ b/docs/alps/vclusters.md @@ -70,3 +70,15 @@ Santis is dedicated to Weather and Climate and is deployed on ~400 Grace-Hopper !!! note "TODO" - [ ] Storage + + +## Tödi + +Tödi is the testing vCluster and is currently deployed on the entire machine. + +### Uenvs + +| uenv | activity | +|--------------------------|-------------------------------| +| icon-wcp/v1:rc4 | build and run icon | +| netcdf-tools/2024:v1-rc1 | pre and post processing tools | diff --git a/docs/models/icon.md b/docs/models/icon.md index badbd66e..ce83619f 100644 --- a/docs/models/icon.md +++ b/docs/models/icon.md @@ -54,41 +54,6 @@ spack install cosmo-eccodes-definitions srun -N 1 -c 12 --mem-per-cpu=20G spack install -v -j 12 ``` -### Temporary Tödi - -!!! warning "These are only temporary guidelines during the acceptance phase of Alps" - - - Santis will be the official W&C vcluster but Tödi has to be deployed on the entire Alps system for the acceptance phase. These guidelines are for the ones who have access to Tödi. - - The resulting executable is not tested. - - Anything can go wrong - -- Get `spack-c2sm` - ```shell - git clone --depth 1 --recurse-submodules --shallow-submodules https://github.com/C2SM/spack-c2sm.git - ``` - -- Start user environment - ```shell - uenv start /capstor/scratch/cscs/leclairm/uenvs/images/icon_c2sm_v1_rc3.sqfs - ``` - -- Setup `spack-c2sm` - ```shell - source spack-c2sm/setup-env.sh /user-environment - ``` - -- Adapt your spack environment following `/capstor/scratch/cscs/leclairm/icon-nwp/config/cscs/spack/uenv/mch_gpu_double/spack.yaml` and activate it as usual with `spack env activate`. - -- Build as usual from your icon root dir - ```shell - spack install - ``` - -- Submit job with uenv - ```shell - sbatch --uenv /capstor/scratch/cscs/leclairm/uenvs/images/icon_c2sm_v1_rc3.sqfs my_run_script - ``` - ## Run test case with ICON In the *run* folder, you find many prepared test cases, which you can convert into run scripts. To generate the runscript of one of the experiment files, e.g. *mch_ch_lowres*, you can use the `make_runscripts` function. From 59358ca4a1315d566348e185fa32a67b0958b179 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michael=20J=C3=A4hn?= Date: Sun, 1 Sep 2024 04:31:32 +0200 Subject: [PATCH 2/2] GitHub Action: Update datasets (#195) Co-authored-by: github-actions[bot] --- docs/datasets/climate_model_data.md | 12 ++++++------ docs/datasets/obs_reanalysis_data.md | 16 ++++++++-------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/datasets/climate_model_data.md b/docs/datasets/climate_model_data.md index 2854d933..096682e2 100644 --- a/docs/datasets/climate_model_data.md +++ b/docs/datasets/climate_model_data.md @@ -111,8 +111,8 @@ /nfs/atmos/c2sm/cmip6-ng ``` -- Size: 200.63 TB :material-information-outline:{ title="last updated: 2024-08-25 01:47:08" } -- Number of files: 663,802 :material-information-outline:{ title="last updated: 2024-08-25 01:47:08" } +- Size: 200.63 TB :material-information-outline:{ title="last updated: 2024-09-01 01:46:34" } +- Number of files: 663,802 :material-information-outline:{ title="last updated: 2024-09-01 01:46:34" } - Access: direct / rsync - Status: frozen (2019-03) - Variables: @@ -195,8 +195,8 @@ /store/c2sm/c2sme/cordex ``` -- Size: 356.97 TB :material-information-outline:{ title="last updated: 2024-08-25 01:49:02" } -- Number of files: 552,595 :material-information-outline:{ title="last updated: 2024-08-25 01:49:02" } +- Size: 356.97 TB :material-information-outline:{ title="last updated: 2024-09-01 01:48:18" } +- Number of files: 552,595 :material-information-outline:{ title="last updated: 2024-09-01 01:48:18" } - Access: direct / rsync - Status: monthly updated - Resolution: 0.44° and 0.11° @@ -211,8 +211,8 @@ ```console /nfs/atmos/c2sm/cordex-reklies ``` -- Size: 22.41 TB :material-information-outline:{ title="last updated: 2024-08-25 01:45:04" } -- Number of files: 94,936 :material-information-outline:{ title="last updated: 2024-08-25 01:45:04" } +- Size: 22.41 TB :material-information-outline:{ title="last updated: 2024-09-01 01:44:45" } +- Number of files: 94,936 :material-information-outline:{ title="last updated: 2024-09-01 01:44:45" } - Access: direct - Status: monthly updated - Resolution: 0.11° diff --git a/docs/datasets/obs_reanalysis_data.md b/docs/datasets/obs_reanalysis_data.md index b9ac7089..51224be1 100644 --- a/docs/datasets/obs_reanalysis_data.md +++ b/docs/datasets/obs_reanalysis_data.md @@ -157,8 +157,8 @@ /net/atmos/data/cerra/processed/v1/ ``` -- Size: 7.72 TB :material-information-outline:{ title="last updated: 2024-08-25 01:44:39" } -- Number of files: 1,824 :material-information-outline:{ title="last updated: 2024-08-25 01:44:39" } +- Size: 7.72 TB :material-information-outline:{ title="last updated: 2024-09-01 01:44:05" } +- Number of files: 1,824 :material-information-outline:{ title="last updated: 2024-09-01 01:44:05" } - Access: direct - Status: updated - Time period: 1985-2020 @@ -199,8 +199,8 @@ /net/atmos/data/cerra-land/processed/v1/ ``` -- Size: 1.78 TB :material-information-outline:{ title="last updated: 2024-08-25 01:44:39" } -- Number of files: 1,016 :material-information-outline:{ title="last updated: 2024-08-25 01:44:39" } +- Size: 1.78 TB :material-information-outline:{ title="last updated: 2024-09-01 01:44:05" } +- Number of files: 1,016 :material-information-outline:{ title="last updated: 2024-09-01 01:44:05" } - Access: direct - Status: updated - Time period: 1985-2020 @@ -253,8 +253,8 @@ /nfs/atmos/c2sm/era5/processed/v2 ``` -- Size: 45.76 TB :material-information-outline:{ title="last updated: 2024-08-25 01:45:28" } -- Number of files: 138,400 :material-information-outline:{ title="last updated: 2024-08-25 01:45:28" } +- Size: 45.76 TB :material-information-outline:{ title="last updated: 2024-09-01 01:44:07" } +- Number of files: 138,400 :material-information-outline:{ title="last updated: 2024-09-01 01:44:07" } - Access: direct - Status: updated - Time period: v1: 1940-present, v2: 1980-present @@ -294,8 +294,8 @@ /net/atmos/data/era5-land_cds/processed/v1/ ``` -- Size: 6.64 TB :material-information-outline:{ title="last updated: 2024-08-25 01:44:41" } -- Number of files: 1,504 :material-information-outline:{ title="last updated: 2024-08-25 01:44:41" } +- Size: 6.64 TB :material-information-outline:{ title="last updated: 2024-09-01 01:44:06" } +- Number of files: 1,504 :material-information-outline:{ title="last updated: 2024-09-01 01:44:06" } - Access: direct - Status: updated - Time period: 1950-present