|build-status| |conda-install|
| Version: | 0.6.7-41c_conv |
|---|
The Quality Assurance tool QA-DKRZ developed at DKRZ checks data and conformance of meta-data of climate simulations given in netCDF format with conventions and rules of projects. At present, checking of CF Conventions, CORDEX, CMIP5, and CMIP6, the latter with the option to run PrePARE (D. Nadeau, LLNL) is supported. The check results are summarised in json-formatted files.
THIS is the adaptation of the AQ-DKRZ tool (a.k.a. QA-checker) for the CORDEX FPS Convection project.
This is a step-by-step guide to getting started in using the pre-installed
QA-checker at the project-internal jsc-cordex data processing exchange
infrastructure. This is not a documentation or HowTo guide for using the
jsc-cordex machine in general.
1. Prerequisites
You need a personal account on the jsc-cordex server.
For bash shell, set the FPSCONV root directory; this variable is just used in this manual for clarity (it is not needed to run the QA-checker):
export FPSCONV_ROOT=/mnt/CORDEX_FPS_CPCM
The QA-checker does not need any environment variables to be set.
2. Install directory of the QA-checker
The centrally installed and maintained production version of the QA-checker is under (based on this github repo):
$FPSCONV_ROOT/Software/adobler/git/QA-DKRZ_FPSCONV
The configuration tables, needed to adjust the QA-checker to specific experiments are in the their most current version here:
$FPSCONV_ROOTS/Software/adobler/git/QA-DKRZ_FPSCONV/tables/projects/CORDEX-FPSCONV
3. Preparation per user
Has to be done only once, permission setting for using the installed version
and configuration of the individual QA-checker working directory, the
$FPSCONV_ROOT/tmp/$USER is the preferred temporary working directory for
the users:
git config --global --add safe.directory $FPSCONV_ROOT/Software/adobler/git/QA-DKRZ_FPSCONV mkdir -p $FPSCONV_ROOT/tmp/$USER/qa-dkrz-check mkdir -p $FPSCONV_ROOT/tmp/$USER/QA/results
Now get the task file, which is a runcontrol or namelist file for the QA-checker. Copy the default, you may have as many of these files as needed, they contain the instructions which tasks the QA-checker is supposed to do this file will be edited later:
cd $FPSCONV_ROOT/tmp/$USER/qa-dkrz-check cp $FPSCONV_ROOT/Software/adobler/git/QA-DKRZ_FPSCONV/qa-test.task .
The QA-checker works with tabulated information that describes what to check
and which results to expect; the QA-checker needs to know where to find these
tables; one may either use the "official" tables that are provided with the
checker (our default here) or use modified tables at alternative locations. Run
the following command which creates a mandatory config file under
$HOME/.qa-dkrz/config.txt whith the location of the tables; when run for
the first time or when no config file is found it asks for the location of the
QA-tables:
./$FPSCONV_ROOT/Software/adobler/git/QA-DKRZ_FPSCONV/install
This is the content of the $HOME/.qa-dkrz/config.txt and for a first test
leave this unchanged (now without the $FPSCONV_ROOT nomenclature:
/mnt/CORDEX_FPS_CPCM/Software/adobler/git/QA-DKRZ_FPSCONV: QA_TABLES=/mnt/CORDEX_FPS_CPCM/Software/adobler/git/QA-DKRZ_FPSCONV/tables UPDATE=frozen
4. Set-up the QA-checker task
In the working directory adjust the task-file, it contains several
examples on how it might be modified:
cd $FPSCONV_ROOT/tmp/kgoergen/qa-dkrz-check vim qa-test.task
If you want to run the QA-checker with a default configuration in terms of range
checking etc., then the most important / only things to adjust are the
following variables in qa-test.task.
The path to the CMORized netCDF files to be checked, on jsc-cordex
(replace $USER and $FPSCONV_ROOT accordingly); the checker goes through
directory hierarchy recursively:
PROJECT_DATA=$FPSCONV_ROOT/CORDEX-FPSCONV/output/ALP-3/FZJ-IDL/SMHI-EC-Earth/rcp85
The results of the check, this is highly structured output:
QA_RESULTS=$FPSCONV_ROOT/tmp/$USER/QA/results
Which variables and and which time interval to check; many more options are
possible; here: check hourly data, check everything the QA-checker recursivly
finds under $PROJECT_DATA:
SELECT .*/1hr/*
5. Run the QA-checker
Finally, to run it:
cd $FPSCONV_ROOT/tmp/kgoergen/qa-dkrz-check ./$FPSCONV_ROOT/Software/adobler/git/QA-DKRZ_FPSCONV/scripts/qa-dkrz -f qa-test.task
On a daily basis mainly Step 4 and 5 will be repeated. It may be useful to have multiple task files, dependent on the temporal rersolution and experiment to check. You can find a set of templates for that in:
$FPSCONV_ROOT/Software/adobler/git/QA-DKRZ_FPSCONV/example/templates/
6. Results
The outcome of the checking, via ASCII log files, can be found in the QA_RESULT directory you defined in the task file, e.g.:
$FPSCONV_ROOT/tmp/$USER/QA/results/check_logs/FZJ-IDL_SMHI-EC-EARTH_historical_fpsconv-x1n2-v1_r12i1p1_1hr.log
For testing the checker, it is useful to move, remove or have a unique name for the results folder each time you start the checker. Otherwise the reusults may be confusing. Once you enter the final checking stage however, keep the logs, they might be needed or at least useful as proof later on.
7. Performance
To run the QA-checker concurrently (x4) on several netCDF files and / or variables,
set this in the qa-test.task:
NUM_EXEC_THREADS=4
8. Custom QA-tables
Customized tables in addition / combination with the official tables might help to capture real issues with the data which may just be ignored as warnings with the default tables otherwise.
For the CORDEX FPSCONV implementation, this README file is the primary
documentation.
QA-DKRZ applies Sphinx, and the latest documentation can be found on ReadTheDocs.
Feel free to use the slack channel https://app.slack.com/client/T01FXMXLE4S/C01FR0ENXC6
Please use the issue tracker here on github
The sources of QA-DKRZ are available on Github: https://github.com/h-dh/QA-DKRZ
You are highly encouraged to participate in the development.
For research purposes only.