Metos3D

Marine Ecosystem Toolkit for Optimization and Simulation in 3-D

Installer

$>
curl -O https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

conda install -c jpicau metos3d

Base system

You've cloned the base Metos3D system. This includes ...

metos3d         # work horse, Python script
src/            # transport driver, C code
model/          # bgc models, Fortran code

Environment

Metos3D needs a sane compile environment, this includes ...

If you are working on a known machine and want to use one of the standard models, have a look at our environment section, we have prepared a set of standard versions,

however, if you want the full control, you'll need, sequential execution: C/C++, Fortran compiler, parallel execution, MPI versions of C/C++,

with those compilers, a compiled PETSc library, version 3.7., which means, two environment variables set, named PETSC_DIR and PETSC_ARCH,

Data

You're missing the data, yet. You can clone it. However, you'll need Git LFS (large file support).

$> git clone http://

or you can download an compressed archive, using curl or wget

$> wget https://
$> curl -O https://

unzip,

Compile and run

Now, you can ... compile an executable and run a simulation

for instance:

$> metos3d simpack NPZD-DOP
$> ./metos3d-simpack-NPZD-DOP.exe model/NPZD-DOP/option/test.NPZD-DOP.option.yaml

see Metos3D cheat sheet for a detailed reference of the subcommands of the metos3d script,

Introducing Metos3D version 1.0.0

following sematic versioning (major.minor.patch), change in major version means loss of compatibility

we hybernated the development of Metos3D in separated repositories, the last avaiable versions were: metos3d v0.6.0, simpack v0.5.0, model v0.4.0 and data v0.2.1 all git repositories were archieved as one file and can be downloaded here, each repo includes its earlier versions, in particular access to versions used in Piwonski and Slawig, 2016

New concept

Metos3D 1.0.0 introduces a new concept of usage, one repository,

we distinguish two installation types:

• container, easy to install and use, hard-coded, one executable for each model, inflexible, including everything, huge
• script/system, requires mpi versions of c and fortran compilers, as well as a compiled version of petsc, fully flexible, lean

Documentation

• cheat sheet, BGC cheat sheet, templates
• tutorial
• manual
• code reference

References

• Piwonski and Slawig, 2016 Metos3D: ...