BLZ_SURGE

Belize surge model

This recipe describes how to build NEMO and XIOS appropriate for a surge model using Docker.

Note the is a slight modification to the MY_SRC/diaharm_fast.F90 (line 68) relative to surge configurations built on other machines (e.g. AMM7_SURGE on ARCHER[1,2] https://doi.org/10.5281/zenodo.4022309). This is because of incompatability of compilers used across machines. Cray (e.g. ARCHER2): CHARACTER( LEN = 10 ), DIMENSION(5), PARAMETER :: m_varName2d = (/'ssh','u2d','v2d','ubfr','vbfr'/) GNU (here): CHARACTER( LEN = 10 ), DIMENSION(3), PARAMETER :: m_varName2d = (/'ssh','u2d','v2d'/)

The notes for the docker build were built on those made by Pierre DERIAN https://github.com/pderian/NEMOGCM-Docker (see also BUILD_NEMO/readme.txt)

0. Prerequisites and path definitions =====================================

Prerequisites to be placed in a INPUTS directory (see below)::

• domain_cfg.nc
• BLZE12_bdytide_rotT_*.nc (FES boundary tidal forcing)
• coordinates.bdy.nc (coordinates for FES boundary forcing)

Structure: The git repo contains BUILD_NEMO and RUN_NEMO. The compilation of XIOS and NEMO executables and done once and then copied into RUN_NEMO. BUILD_NEMO could then be removed or cleaned to save space.

The INPUTS directory is empty on cloning. It needs to contain the forcing and domain files that are generated externally to this instruction set. These files are copied/linked into the bdydta folder in the experiment directory.

1. Clone this repository ========================

Clone the repository ::

cd $HOME git clone https://github.com/NOC-MSM/BLZ_SURGE.git BLZ_SURGE

Copy the INPUTS in place. EDIT <INPUTS_SOURCE> appropriately::

rsync -uvt <INPUTS_SOURCE>/* $HOME/BLZ_SURGE/INPUTS/.

2. Get XIOS2.5 @ r2022 code ===========================

Note when NEMO (nemo.exe / opa) is compiled it is done with reference to a particular version of XIOS. So on NEMO run time the version of XIOS that built xios_server.exe must be compatible with the version of XIOS that built nemo.exe / opa.

Download XIOS2.5 and prep::

cd $HOME/BLZ_SURGE/BUILD_NEMO svn co -r2022 http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5/ xios-2.5_r2022 cd xios-2.5_r2022

Link the xios-2.5_r2022 to a generic XIOS directory name (The generic name is used in the NEMO build arch files). Note you have to use relative paths for the link to work within the docker container::

cd $HOME/BLZ_SURGE/BUILD_NEMO ln -s xios-2.5_r2022 XIOS2

3. Get NEMO codebase ====================

Get the code::

cd $HOME/BLZ_SURGE/BUILD_NEMO svn co http://forge.ipsl.jussieu.fr/nemo/svn/branches/UKMO/dev_r8814_surge_modelling_Nemo4/NEMOGCM dev_r8814_surge_modelling_Nemo4

Copy the MY_SRC modifications to the compilation location::

cp MY_SRC/* dev_r8814_surge_modelling_Nemo4/CONFIG/BLZ_SURGE/MY_SRC/.

Copy the compiler flag file into location::

cp cpp_BLZ_SURGE.fcm dev_r8814_surge_modelling_Nemo4/CONFIG/BLZ_SURGE/.

4. Copy the architecture files ==============================

Copy NEMO and XIOS arch files to appropriate folder for building::

cp $HOME/BLZ_SURGE/BUILD_NEMO/arch_NEMOGCM/arch* $HOME/BLZ_SURGE/BUILD_NEMO/dev_r8814_surge_modelling_Nemo4/ARCH cp $HOME/BLZ_SURGE/BUILD_NEMO/arch_XIOS/arch* $HOME/BLZ_SURGE/BUILD_NEMO/xios-2.5_r2022/arch

5. Build the Debian Docker image ================================

Launch docker application. Then back in a terminal::

cd $HOME/BLZ_SURGE/BUILD_NEMO/Docker docker build -t nemo/compiler .

6. Start an interactive container =================================

Start an interactive container sharing the source files as a Volume. This way the host SRC will be available from within the container as /SRC. /!\ Note: /host/path/to/SRC must be the absolute path to the host SRC directory (at least on Mac OS X)::

docker run -v $HOME/BLZ_SURGE:/BLZ_SURGE -t -i nemo/compiler /bin/bash

I.e. docker run -v /host/path/to/BLZ_SURGE:/BLZ_SURGE -t -i nemo/compiler /bin/bash

From here on, unless otherwise stated, all the commands are executed within the docker container.

7. Compile XIOS ===============

This took about an hour, so make a cup of tea::

cd /BLZ_SURGE/BUILD_NEMO/xios-2.5_r2022 ./make_xios --dev --netcdf_lib netcdf4_seq --arch DEBIAN

Copy the executable to the experiment directory::

cp /BLZ_SURGE/BUILD_NEMO/xios-2.5_r2022/bin/xios_server.exe /BLZ_SURGE/RUN_NEMO/EXP_tideonly/.

8. Build NEMO executable ========================

Make NEMO executable (select 'Y' for OPA_SRC, otherwise select 'N')::

cd /BLZ_SURGE/BUILD_NEMO/dev_r8814_surge_modelling_Nemo4/CONFIG ./makenemo -v 3 -m DEBIAN -n BLZ_SURGE

Copy the executable to the experiment directory::

cp /BLZ_SURGE/BUILD_NEMO/dev_r8814_surge_modelling_Nemo4/CONFIG/BLZ_SURGE/BLD/bin/nemo.exe /BLZ_SURGE/RUN_NEMO/EXP_tideonly/.

9. Run NEMO ===========

Make a link between where the inputs files are and where the model expects them ::

cd /BLZ_SURGE/RUN_NEMO/EXP_tideonly
ln -s ../../INPUTS bdydta
ln -s ../../INPUTS/domain_cfg.nc .

NB I HAD A PROBLEM WITH A LURKING SYM LINK. YOU MIGHT NEED TO DELETE $HOME/BLZ_SURGE/RUN_NEMO/EXP_tideonly/bdydta BEFORE THE LINK CAN BE MADE. IF NOT, THEN DELETE ME.

Now EXP_tideonly/bdydta should directly contain BLZE12_bdytide_rotT_*.nc and coordinates.bdy.nc ::

cd /BLZ_SURGE/RUN_NEMO/EXP_tideonly/ mpirun -n 2 ./nemo.exe : -n 1 ./xios_server.exe

NB the timestep, run length etc is not optimal, but it works!