diff --git a/README.md b/README.md index 3c9e8aee..cd013e0c 100644 --- a/README.md +++ b/README.md @@ -1,73 +1,4 @@ -[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/Naereen/StrapDown.js/graphs/commit-activity) -[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/) -[![Github Actions Test](https://github.com/valeriupredoi/bgcval2/actions/workflows/run-tests.yml/badge.svg)](https://github.com/valeriupredoi/bgcval2/actions/workflows/run-tests.yml) - -![bgcval2logo](https://github.com/valeriupredoi/bgcval2/blob/main/doc/figures/BGCVal2-logo-2.png) - -bgcval2 -======= - - -bgcval2 is the updated and modernised version of BGC-val. -There are several updates over the previously published version of [BGCVal](https://gmd.copernicus.org/articles/11/4215/2018/). -The primary improvements are to the user interface, the ease of use, ease of installation, -and a general modernisation of the core approach, including the move to python3, -and using a conda enviroment. - -This work was funded through WP1 of the Terrafirma project. - - -Current version notes: - -- Suported versions of Python: 3.9, 3.10 and 3.11 - -Environment and installation -============================ - -**Supported Operating Systems so far**: Linux/UNIX - -To install locally: - -- get the `git` file of this repository: - -``` -git clone https://github.com/valeriupredoi/bgcval2.git -``` - -- then grab [miniconda3](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html). -- This can be installed using (bearing in mind that your file name may differ), and follow the on screen instructions: -``` - bash Miniconda3-py39_4.12.0-Linux-x86_64.sh -``` - -- Once you have a local version of miniconda3 installed, install `mamba` in the `base` environment: - -``` -conda install -c conda-forge mamba -``` - -- mamba is a replacement for conda that is faster, but works exactly the same way. Ie the command “conda env” -> becomes “mamba env”. However, this step is somewhat optional. If you can’t install mamba, but have conda working, just replace “mamba” with “conda” below. - - -- then create the `bgcval2` environment and activate it: - -``` -cd bgcval2 -mamba env create -n bgcval2 -f environment.yml -conda activate bgcval2 -``` - -- then install the development dependencies and the tool itself - (note that all our dependencies are from `conda-forge` so there - is no risk of mixing Conda and PyPI packages): - -``` -pip install -e .[develop] -``` - -Test that the tool has been installed correctly with: -``` -analysis_compare -h +compare -h ``` which should print the module information and instructions on how to run the tool. @@ -115,6 +46,7 @@ Executable name | What it does | Command `bgcval` | runs time series and point to point. | bgcval jobID `bgcval2_make_report` | makes the single model HTML report. | bgcval2_make_report jobID `analysis_compare` | runs comparison of multiple single jobs | analysis_compare +`batch_timeseries` | Submits single job time series analysis to slurm | batch_timeseries ### Checking out development branches @@ -319,6 +251,36 @@ then the report will appear on the [JASMIN public facing page](https://gws-acces which is public facing but password protected. +Batch times series Analysis +=========================== + +The `batch_timeseries` tool can take an `analysis_compare` input yaml file, +and instead of running the time series analysis for each job on +the interactive shell terminal in series, it uses slurm to submit +each job as an independent job. + +On jasmin, users can run up to five jobs simulataneously, +so this can singnificantly boost the speed of the analysis. + +The command to run it is: +``` +batch_timeseries - y comparison_recipe.yml +``` + +There is also an optional flag `-d` or `--dry_run` to test the batch_timeseries, +which outputs the submission command to screen but does not submit the jobs. + +Note that this task does not run the `analysis_compare` suite so it will +not generate the html report. However, the html report can be generated more quickly +with the `-s` skip the `analysis_timeseries` section +described above. + +In addition, note that this will not run the `download_from_mass` +script, so jobs added here will not be included in the automated download. +However, these jobs are added for automated download when `analysis_compare` +is used. + + Downloading data using MASS ===========================