7. Sloop run : Run preprocessing, model and postprocessing
##########################################################
The next step is to run the differents tasks of preprocessing, model and postprocessing
To do so, use :doc:`cli.sloop.run`.
Description
============
Available tasks for Croco
-------------------------
The differents tasks are listed in the following table
.. note:: All tasks can be launched in stand alone mode (as python binary)
.. _tasklist:
.. list-table:: Available tasks for Croco
:header-rows: 1
* - Generic name of the task
- Description
- Python binary name
* - ibc-collect
- Collect and format data from CDOCO PSY4 model
- sloop-croco-run-ibc-0-collect.py
* - init
- build an initial condition from psy4 model output
- sloop-croco-run-ibc-1-init.py
* - obc
- build boundary conditions from psy4 model output
- sloop-croco-run-ibc-2-obc.py
* - atmfrc
- collect and format data from CDOCO to build atmospheric forcing file
- sloop-croco-run-atmfrc.py
* - nudging
- Build the forcing file for Nudging run (extract on the whole Ogcm file)
- sloop-croco-nudging
* - rivers
- Format the rivers data from CDOCO format to Croco netcdf format
- sloop-croco-run-rivers.py
* - model
- Launch croco on PBS cluster
- sloop-croco-run-model.py
* - postprod
- Format outputs and store it
- sloop-croco-run-postprod-0-format-data.py
.. warning::
``sloop run`` has to be executed in the directory of the experiment
created by ``sloop init``.
Syntax
------
.. command-output:: sloop run --help
Run one task
-------------
There are 2 ways to launch the tasks listed above :
* Launch one task with sloop that will send a PBS job
::
sloop --novortex -c croco_med.cfg run -j ibc-collect -b 2017-06-01,00:00 -e 2017-06-05,00:00
.. note:: "--novortex" option is mandatory for CROCO and use on Datarmor
* Launch the task directly with the python routine in interactive mode
::
sloop-croco-run-ibc-0-collect.py exp_dir -b 2017-06-01,00:00 -e 2017-06-05,00:00 --model glorys12v1 --grid croco_grd.nc
.. note:: for the second one you MUST be connected to a compute node (**qsub -I** command)
Chain your tasks with a workflow
--------------------------------
There is a way to chain your tasks thanks to *workflow* capacity : :doc:`env</tuto.rd.run>`
* First define your workflow like this one in a config file :
.. literalinclude:: ../templates/cfg_croco/workflow_conf.cfg
:language: ini
* The tasks in this file are those listed in the table on the top of the page : **the names must be exactly the same as in the table**
* On each line on this file, the tasks have no dependencies
* Each line (and all tasks contained in it) depend on the previous one and will be launched after
* The workflow can be launched in several ways :
* With a begin date and end date
::
-b 2017-06-01,12:00 -e 2017-06-05,00:00
* With a number of cycle and a frequency of this cycle
::
--ncycle 4 --freq 7 (4 cycles of 7 days, frequency can be ommitted and will be 7 by default)
* With the rundate of the experiment
::
--rundate (==1 cycle of default freq)
Custom options
--------------
* Template editing
The user might need to make a change in **croco.in** file before running : The template file is **TPL/croco.in.tpl**
* Change the queues of tasks on Datarmor
If the user want to change for example the number of nodes on which Croco should run
The information is provided in the following file
**conf/croco_med.ini** (med is the name of your application)
The names of the section match with those given in the table `tasklist`_
What to do on Datarmor
======================
#. Be sure to be logged on a interactive node and not on the loggin node
::
qsub -X -I -l mem=20g -l walltime=02:00:00
#. Load your sloop environment (see :doc:`env</tuto.croco.env>`)
#. Launch your workflow
::
sloop --novortex -c croco_med.cfg run -w workflow_med -b 2017-06-01,12:00 -e 2017-06-05,00:00
#. Launch one by one
::
sloop --novortex -c croco_med.cfg run -j ibc-collect -b 2017-06-01,12:00 -e 2017-06-05,00:00
sloop --novortex -c croco_med.cfg run -j init -b 2017-06-01,12:00 -e 2017-06-05,00:00
sloop --novortex -c croco_med.cfg run -j nudging -b 2017-06-01,12:00 -e 2017-06-05,00:00
sloop --novortex -c croco_med.cfg run -j obc -b 2017-06-01,12:00 -e 2017-06-05,00:00
sloop --novortex -c croco_med.cfg run -j atmfrc -b 2017-06-01,12:00 -e 2017-06-05,00:00
sloop --novortex -c croco_med.cfg run -j model -b 2017-06-01,12:00 -e 2017-06-05,00:00
sloop --novortex -c croco_med.cfg run -j postprod -b 2017-06-01,12:00 -e 2017-06-05,00:00
.. warning:: Be carfeul of the format of the date. It Must be YYYY-MM-DD,HH:MM
TIPS
====
#. Be careful of the start hour of your IBC forcing model. It must match the start hour of your model. For example, *glorys12v1* start at 12:00, so you must start your model at 12:00.
#. If you want to use your own initial file generated from an other script you just have to make a link or copy it in FORCING directory with this name (just put the right date)
::
ln -s my_ic_file.nc FORCING/croco_ic_20220503T1200.nc
#. To change the MPI procs :
* edit your config file **croco_config.cfg**
* Compile your model with sloop
* In your experiment directory, edit the **conf/croco_conf.ini** and adjust the queue's name for Datarmor
#. Available models for IBC and Atm forcing are described in **sloop/sloop/data** directory. You'll find a config file by model
#. Format data in postprocessing
If the user want to split the output files by dates and/or by area , it's possible with
the *sloop-croco-run-postprod-0-format-data* routine.
The options are given in the **croco_conf.cfg** file:
* Either write the whole domain splitted in a file by date
* Either split the file in sub area of interest and split it by date
If the user want a subdomain he must fill a subsection in the cfg like this
::
[postprod]
postprod_data_dir="./DATA_OUTPUTS"
write_whole_domain=False
[[zone1]]
activate=True
[[[bounds_lon]]]
min = -4.2
max = 2.0
[[[bounds_lat]]]
min = 35.4
max = 40.6
[[zone2]]
activate=True
[[[bounds_lon]]]
min = 14.2
max = 20.0
[[[bounds_lat]]]
min = 32.4
max = 42.6
Where to see the results
=========================
* Check **sloop.log** file to see if something went wrong
* Check the **logs** directory that contains a log per task
* *Preprocessing* : see **FORCING** directory that should contain all IBC/RIVERS/ATM/NUDGING files
* *Model run* : for each a run a directory with the start and end dates simulation is created
* *Model outputs* after postprod : Check **DATA_OUTPUTS**
Other features
==============
MPI NO LAND
-----------
If the user want to optmize the number of cores to use on the computer he should use the MPI_NOLAND cpp key
#. Get the program in croco src directory (it's called *MPI_NOLAND*)
#. Compile it
#. Fill the namelist with the maximum number of procs you want to use and the name of your croco grid file
#. run **mpp_optimiz** and get the optimized layout
#. You should find a result with a multiple of the number of cores in one node in your HPC (28 for Datarmor)
#. From the output file title you get the NP_XI,NP_ETA, N_NODES params and you copy it in your config file **croco_med.cfg**
#. Re compile the model with SLOOP by adding the **MPI_NOLAND** cppkey in your *TPL/cppdefs.h.tpl* file
#. Change the required number of nodes and MPI queue in *conf/croco_med.ini* in **model** section
AGRIF
-----
What to do in case of Agrif configuration ?
#. Compile the model with AGRIF cpp keys
#. Define the number of childs grid by the variable **nb_agrif** in *croco_config.cfg* as shown below
#. Give the path of each grid in the *croco_config.cfg* with the number of the grid at the end of the name
#. Put the path of required (not mandatory) inputs files as shown in the full example below
#. Don't forget to prepare a croco.in.tpl per grid and put in TPL directory if it's not in your config directory (see :doc:`sloop constants</tuto.croco.constants>`)
#. When launching *sloop run init* a initial file by grid will be build
::
[run_model]
[[croco_inputs]]
start_date="01-01-2016"
end_date="03-01-2016"
freq_rst=24
freq_avg=24
freq_output=72
nb_agrif=2
croco_forcing_dir= /home1/datawork/mcaillau/CROCO/GIBRALTAR_3GRIDS/INPUT/
croco_frc_grid= ${croco_forcing_dir}/croco_GIB100_BR4_N40_grd.nc
croco_frc_grid1= ${croco_forcing_dir}/croco_GIB100_BR4_N40_grd.nc.1
croco_frc_grid2= ${croco_forcing_dir}/croco_GIB100_BR4_N40_grd.nc.2
croco_frc_tides=${croco_forcing_dir}/croco_frc_GFS_282.nc
croco_frc_tides1=${croco_forcing_dir}/croco_frc_GFS_282.nc.1
croco_frc_tides2=${croco_forcing_dir}/croco_frc_GFS_282.nc.2
croco_frc_blk=${croco_forcing_dir}/croco_blk_GFS_282.nc
croco_frc_blk1=${croco_forcing_dir}/croco_blk_GFS_282.nc.1
croco_frc_blk2=${croco_forcing_dir}/croco_blk_GFS_282.nc.2
croco_frc_clm=${croco_forcing_dir}/croco_clm_cmems-global_282.nc
croco_frc_clm1=${croco_forcing_dir}/croco_clm_cmems-global_282.nc.1
croco_frc_clm2=${croco_forcing_dir}/croco_clm_cmems-global_282.nc.2
croco_frc_ini=${croco_forcing_dir}/croco_ini_cmems-medsea_282.nc
croco_frc_ini1=${croco_forcing_dir}/croco_ini_cmems-medsea_282.nc.1
croco_frc_ini2=${croco_forcing_dir}/croco_ini_cmems-medsea_282.nc.2
croco_frc_obc=${croco_forcing_dir}/croco_bry_cmems-medsea_282.nc
croco_child_grids=${croco_frc_grid1} ${croco_frc_grid2}
[[tpl_files]]
croco_tpl_dir= /home1/datawork/mcaillau/CROCO/GIBRALTAR_3GRIDS/
croco_input_file=${croco_tpl_dir}/croco.in.tpl
croco_input_file1=${croco_tpl_dir}/croco.in.1.tpl
croco_input_file2=${croco_tpl_dir}/croco.in.2.tpl