What is a product produced from a numerical model?

It is the product of a mathematical ocean model governed by equations from fluid dynamics, known as “primitive equations” (e.g. NEMO-OPA). These numerical equations are resolved by millions of calculations on super-computers. Observation data are then assimilated in the model, i.e. the results of the mathematical model are combined with observation data (e.g. from satellites or in-situ buoys) in order to generate the most realistic possible final representation of the ocean state. This also makes it possible to provide 7-day forecasts of the ocean state. A numerical model therefore enables forecasters to provide a three-dimensional representation, current, past or future, of the ocean’s physical or biogeochemical state.

Both the Mercator Ocean Service and the Copernicus Marine Service offer products generated by numerical models:

Mercator Ocean Service’s reference products are described in the following table.

The products of the Copernicus Marine Service are available here.

What is a product produced from satellite or in-situ observations ?

An observation product is generated directly by using raw data from satellite and in-situ observations, after scientific validation and calibration. These results are also sometimes smoothed and interpolated with other data in order to make the product more readable and with broader geographical coverage.

Only the Copernicus Marine Service offers products produced from in-situ or satellite observations.

The products of the Copernicus Marine Service are available here.

What is a numerical product ?

It is a set of data files generated by a numerical model or from satellite or in-situ observations, containing a set of ocean variables, describing the physical or biogeochemical state of the ocean at the global or regional scale, both on the surface and at depth, currently, in the past or in the future. A product may also be a map, representing the ocean state.

Mercator Ocean Service?s reference products are described in the following offer.

The products of the Copernicus Marine Service are available here.

What time periods do these products cover?

The products are divided into two categories, whether for Mercator Ocean or the Copernicus Marine Service:

  • NEAR REAL TIME products are those that represent the recent state of the ocean and which are updated regularly (every day or every week).
  • MULTIYEAR TIME SERIES products represent the state of the ocean in the past (typically within the previous 20 years) and are not updated regularly but only once a year.

Mercator Ocean Service’s reference products are described in the following table.

The products of the Copernicus Marine Service are available here.

What geographical areas do these products cover?

The Mercator Ocean Service covers three geographical regions:

  • The global ocean: all the oceans and major seas of the globe (180°W-180°E; 80°S-90°N).
  • The southern part of the Northeastern Atlantic Ocean and the Western Mediterranean Sea up to the east of Corsica (20°W-10°E; 26°N-64°N).
  • The Mediterranean Sea (11°W-37°E; 30°N-46°N).

The Copernicus Marine Service covers six geographical regions:

  • The global ocean: all the oceans and major seas of the globe (180°W-180°E; 80°S-90°N).
  • The northern part of the Northeastern Atlantic Ocean (20°W-13°E; 48°N-62°N).
  • The southern part of the Northeastern Atlantic Ocean and the Western Mediterranean up to the east of Corsica (20°W-10°E; 26°N-56°N).
  • The Mediterranean (11°W-37°E; 30°N-46°N).
  • The Baltic
  • The Arctic Ocean
  • The Black Sea to the Bosphorus

Mercator Ocean Service’s reference products are described in the following table.

The products of the Copernicus Marine Service are available

What is a grid? Which grid types for our models ?

A grid is a mesh composed of two (or more) sets of curves, each set intersecting the other according to an algorithm.

In most cases, one of two types of grid are used:

The Native Grid is the one on which the ocean fields of the numerical model are calculated (e.g. the ARAKAWA C grid). There are no interpolations. This Native Grid offers the advantage of exactly representing what the system has calculated, but with the drawback that it is difficult to manipulate as all the variables are not located on the same node of the grid (i.e. they are “staggered”) and the lines running from the North Pole to the South Pole in the system do not correspond to the lines of the traditional geographic meridians (which are “stretched” and “rotated”).

The Standard Grid is the one on which the ocean fields initially calculated on a Native Grid are interpolated. It is simpler to use and easier to manipulate. All variables are located on the same node. It uses a cylindrical equidistant projection, for example. As an illustration, the oceanic currents expressed by U and V on the Standard Grid no longer depend on the grid and correspond to conventional zonal and meridional currents. In addition, the interpolated Standard Grid is suitable for sampling eddies. Eddies are thus correctly represented on the interpolated Standard Grid.

To know more about our models’ grids, let’s go!

Which variables are provided?

For the Mercator Ocean Service:

  • The variables concerning ocean physics are mainly the ocean potential temperature, ocean salinity, sea level, ocean currents, and the concentration, thickness and drift of sea ice. Other variables may be available.
  • The variables concerning ocean biogeochemistry are mainly for chlorophyll, nitrates, phosphates and oxygen, as well as phytoplankton carbon biomass and primary production. Other variables may be available.

For the Copernicus Marine Service:

  • The variables for ocean physics are: potential temperature (for models or satellite and in-situ observations), salinity, currents, Stokes drift (current due to waves), sea surface height, geopotential height, sea ice (concentration, thickness, drift, surface temperature, iceberg density, ice type, ice boundaries, etc.), depth of the mixed layer, radiative fluxes and winds.
  • The variables for ocean biogeochemistry are: nitrates, phosphates, primary production, silicate, phytoplankton, zooplankton, depth of the euphotic layer, chlorophyll, dissolved oxygen, dissolved iron, optical properties of sea water, dissolved ammonium.

How often are these products updated?

The frequency varies according to the product: a product may be updated several times per day, or once a day, once a week, once a year, etc.

What are the names given to the different estimates of ocean states, past, present or future?

Ocean Forecast: Output from an ocean model to predict the future state of the ocean for periods from 1 day to 14 days ahead. Ocean Forecast products are updated weekly or daily, depending on the ocean model concerned.

Ocean Analysis: Output from an ocean model giving the best possible estimate of the recent and present ocean state. These results are aggregated in time, making up time series that are updated and incremented with the latest results either daily or weekly, depending on the ocean model concerned. These analyses represent ocean states that are almost simultaneous with the present time.

Ocean Reanalysis: Output from an ocean model giving the best possible estimate of a past ocean state. These results are derived from a dedicated numerical ocean model, forced by and assimilating consistent reprocessed observations acquired in-situ and by satellite. Reanalysis products display a time series in the past which is at least 20 years long.

A Model simulation without data assimilation is a time series in the past, at least 20 years long, into which no data have been assimilated (unlike ocean reanalysis).

What is data assimilation?

In meteorology, data assimilation involves using actual observations to correct a forecast of the state of the atmosphere. Likewise, assimilation in physical oceanography data is the mathematical process of using actual observations (from satellites or in-situ) to correct a forecast of the state of the ocean in order to produce an analysis of the ocean state.

The SEEK-SAM2 method for sequential reduced-order data assimilation (the Mercator Ocean data assimilation system version 2) was developed by Mercator Ocean and is used in most operational Mercator systems. This pattern of assimilation enables the optimum combination of observations and forecasts by ocean models to be achieved for producing an ocean analysis. This analysis is deemed to provide the most probable representation of an ocean state taking into account both the available observations and the forecast. The SAM2 method is a reduced-order Kalman filter based on the SEEK formulation (Singular Scalable Extended Kalman). The solution that minimizes the least-squares deviation between observations and their equivalent model is calculated in a reduced space, in the form of a linear combination of the model’s error modes. The calculated correction, known as the increment, is applied progressively to all or part of the assimilation window to limit the initialisation shock at the instant the corrected model is restarted (Incremental Analysis Update).

Which format is used for numerical files?

NetCDF (Network Common Data Form) is a data format containing its own metadata (and thus independent of the hardware used), enabling the creation, accessibility and sharing of scientific data stored in table form.

Mercator Ocean numerical files are in NetCDF-3 or NetCDF-4 format, using the CF convention.

How are products delivered?

For the Mercator Ocean Service:

  • Mercator Ocean website: https://www.mercator-ocean.fr/en/
  • Email: email is a service for the transmission of written messages and documents sent electronically via a computer network (the internet).
  • Cloud: the cloud is a way of using the power of computing or storage on remote servers over a network (the internet).
  • FTP: the File Transfer Protocol, or FTP, is a communication protocol for exchanging computer files over a TCP/IP network. It enables files to be copied from one computer to another. This delivery solution is preferred for daily or weekly real-time services.
  • Opendap: differed time data downloads by users can be performed via an authenticated external opendap. This is the main choice in place of the external hard disk drive.
  • External drive: delayed data can be delivered to users via an external drive. This option is an exception, when the data are too voluminous for Internet transfer, or depending on user constraints. The choice of medium depends on i) the volume to be transferred, ii) the physical formats that the user is equipped to read. The portable hard disk is recommended.

For the Copernicus Marine Service:

You can choose the products in which you are interested from the Copernicus Marine Service’s online catalogue and download them (registration required for the first download). The Copernicus Marine Service is open and free to any user and for any use in compliance with the conditions of use.

Why should an opendap be used as part of an oceanographic data service?

OPeNDAP is an acronym for “Open-source Project for a Network Data Access Protocol,” an endeavor focused on enhancing the retrieval of remote, structured data through a Web-based architecture and a discipline-neutral Data Access Protocol (DAP). It allows end users, whoever they may be, to access immediately whatever data they require in a form they can use, all while using applications they already possess and are familiar with. In the field of oceanography, OPeNDAP has already helped the research community make significant progress towards this end.The protocol is layered on HTTP
With OPeNDAP, you can access data using an OPeNDAP URL. You can do this via command-line, Internet browser, or a custom UI. Typical DAP clients are:
    • Data-analysis or data-visualization tools (such as MATLAB, IDL, Panoply, GrADS, Integrated Data Viewer, Ferret and ncBrowse[5]) which their authors have adapted to enable DAP-based data input;
    • Similarly adapted Web applications (such as Dapper Data Viewer, aka DChart)[6]
    • Similarly adapted end-user programs (in common languages such as C++, JAVA, Python, R, …)

How to access an authenticated opendap?

Source opendap documentation chap. 8:

https://docs.opendap.org/index.php/DAP_Clients_-_Authentication#Matlab.2C_Ferret.2C_Other_applications_that_use_NetCDF_C

Extract from the documentation:

The LDAP-backed HTTP/S-Basic authentication should work by reading credentials from the .netrc file given that the .dodsrc file is set to point to them. Here’s a short summary of the configuration Add your URS/LDAP credentials to the .netrc file, associating them with the URS/OpenDAP server that you normally authenticate with, like this:

machine tds.mercator-ocean.fr
login 
password 

Next, edit the .dodsrc file in your HOME directory so that it tells DAP clients to use the .netrc file for password information:

HTTP.NETRC=/home/jdoe/.netrc

At the end, you must change the rights on the .netrc file using the following command:

chmod 600 .netrc

What tools do I need to manipulate these products?/ Download a sample to test the product

  • A- Definition

What is the NetCDF format?

http://www.unidata.ucar.edu/software/netcdf/

Go to a list of tools for manipulating or displaying NetCDF data:

http://www.unidata.ucar.edu/software/netcdf/software.html

Here are samples of NetCDF files of Mercator Ocean products:

Example of viewing with ncview

Above, a screenshot of the GLO12 sample, 1/12 degree grid, open with ncview. For data volume issues, we only offer a zoom, for this configuration, a single parameter on all vertical levels, from the surface to the bottom. It is about the salinity in the Gulf of Mexico.

 

Example of viewing with ncview

Above, a screenshot of the GLO4 sample, 1/4 degree grid, open with ncview. We offer you a sample, on the global ocean, for this configuration, with a single parameter on the first two vertical levels, from the surface to -1.5m. It is about the temperature on the global ocean.

 

  •  B- Decompression (non exhaustive list)

Bzip2 decompressor (Windows : http://www.7-zip.org/) or pages of the Bzip2 project: http://www.bzip.org/

  •  C- Visualisation (non-exhaustive list of tools for viewing, that are easy to install)

Ncview http://meteora.ucsd.edu/~pierce/ncview_home_page.html

Visualisation and first-level analysis (easy to install on Unix/Linux platforms, possible under Windows)

Ferret http://ferret.pmel.noaa.gov/Ferret/

Viewing and advanced analysis (you need to develop your own program)

Panoply (http://www.giss.nasa.gov/tools/panoply/) Cross-platform application that plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets

Matplotlib, python library http://matplotlib.sourceforge.net/

ncl http://www.ncl.ucar.edu

idv http://www.unidata.ucar.edu/software/idv/ Visualisation avancée avec animation 3D

  •  D- Extraction/Manipulation

Concatenation/Computing the mean/Adding variables and attributes, etc. (non-exhaustive list)

List of software for manipulating NetCDF, http://www.unidata.ucar.edu/software/netcdf/software.html

The NetCDF software package, which includes libraries for Fortran and C++, can be downloaded for free, please see: http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#howtoget.

This coding package offers the best performance for manipulating files in NetCDF format, including conversion to ASCII and other formats.

The NCO operators constitute a powerful set of tools (for Extraction/Concatenation/Computing the mean/Adding variables and attributes) for working with NetCDF files. They can be obtained free of charge from  http://nco.sourceforge.net/

cdo https://code.zmaw.de/projects/cdo

xarray http://xarray.pydata.org/en/stable/

  •  E- Conversion (from NetCDF format to GRIB for example)

ncl http://www.ncl.ucar.edu

To which sectors of the blue economy are our products and services addressed?

1_Polar Environment Monitoring: we provide key data products for the Polar Environment Monitoring sector to assess environmental impacts at both poles.

2_Climate&Adaptation: we provide scientists ocean data and information to conduct their environmental, climate and oceanographic research to support climate adaptation.

3_Ocean Health: we provide important inputs to monitor the ocean's state and vital health signs, essential for the well-being of life on Earth.

4_Marine Conservation & Biodiversity: we provide resources in terms of knowledge, expertise and ocean culture to support committed organizations and actively support their actions to implement policies for a sustainable ocean. We provide key data to monitor marine biodiversity and to protect Marine Protected Areas, preserving at-risk ecosystems

5_Science&Innovation: we collaborate with many international scientific partners, we provide scientists and businesses with ocean data, allowing them to innovate their practices and build new applications and services for intermediate and final users, including citizens.

6_Policies&Ocean Governance &Mitigation: we provide key data to support European Member States in the implementation of European Directives. we also collaborate with international institutions to support Ocean Governance.

7_Education, Public Health & Recreation: When raising awareness about the many challenges facing the ocean, we develop partnerships with non-profit organizations and leads awareness events. These actions take different forms such as providing access to marine data and ocean literacy information, technical support to build educational tools or letting scientists explain what they do during awareness events.

Through ocean literacy networks, non-profit partners (e.g. Children for the Oceans, Coral Guardian, Emily Penn’s Exxpedition) and events, Mercator Ocean and Copernicus Marine share scientific knowledge with civil society and promote sustainable ocean initiatives. 8_Extremes, Hazards & Safety: we support safety at sea and pollution response by providing oceanic parameters for extreme situations at sea and pollutant drift forecast.

8_Extremes, Hazards & Safety: we support safety at sea and pollution response by providing oceanic parameters for extreme situations at sea and pollutant drift forecast.

9_Marine Food: we support the management of aquaculture farms and the sustainable exploitation of ocean’s living resources.

10_Coastal Services: we provide key data that can be used to develop high-resolution coastal models to manage and monitor coastal areas.

11_Trade&Marine Navigation: we provide key ocean parameters contributing to safer and more ecological marine navigation.

12_Natural Resources & Energy: we provide key data products for the oil & gas, deep sea mining and marine renewable energy sectors.

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