A new method for computing depth in Fetch based applications was added: average depth along wind direction. The previous method uses the local cell depth and this new method accounts for the depth effect along wind path. Another upgrade was made to ModuleWaves, namely the option for the user to output fetch distance and depth (in case of average depth in wind direction). This creates a grid data file for each cardinal direction. 

The KEYWORDS to define the new method must be defined in Waves data file:

! Connect fetch in wave generation
WAVEGEN_TYPE            : 1

! Connect the new depth method (average depth in wind direction)
DEPTH_METHOD            : 1
MEAN_SEA_LEVEL          : 2.08     !for average depth (bathymetry + MSL)

! Connect the output of defined grids in each cardinal direction
OUTPUT_FETCH_DISTANCES  : 1
OUTPUT_FETCH_DEPTHS     : 1

This upgrade is available from MOHID Codeplex Revision Number 76682 onward.

A Supplement of the Journal of Marine Systems (Vol. 94) has just been published under the title Remote sensing, mathematical modeling and in-situ data for improving coastal management supporting tools (see it here), compiling some of the major results from project INSEA.

This Special Issue contains 3 original papers featuring the MOHID model. Two papers deal with the biogeochemical model built-in the MOHID system (model description and application to the Tagus estuary). The other paper describes the use of the model to test a hypothesis related with modeling Chla synthesis. The papers can be accessed and downloaded via Sciencedirect web portal, through the following links:

A process-oriented model of pelagic biogeochemistry for marine systems. Part I: Model description

A process-oriented model of pelagic biogeochemistry for marine systems. Part II: Application to a mesotidal estuary

Is it relevant to explicitly parameterize chlorophyll synthesis in marine ecological models?

MOHID users involved in coastal zone management and water pollution modelling may have particular interest in a work that was recently presented at the 11^th Water Congress in Portugal. The work addresses the role of MOHID as a decision-support toll in pollution related scenarios, and also shows the state-of-the-art in modeling interfaces using the MOHID platform. 

The conference paper can be downloaded here (in Portuguese):

Modelação de derrames de poluentes: Desenvolvimento e integração na nova geração de ferramentas de apoio à decisão – Aplicação na Costa Continental Portuguesa e no Estuário do Tejo

It’s now possible to have an output for phytoplankton Chla (ug/L) in the HDF results file for module WaterQuality. This is an additional output for the standard phytoplankton output expressed in biomass (mg C/L).

The output for Phytoplankton Chla is not setup by default and to activate this option, users must flag it and define the C:Chla ratio to be used in the conversion from mg C/L to ug Chla/L. The Chla output is a diagnostic variable since the model does not account for explicit parameterization of the pigment synthesis.

This upgrade is available from MOHID Codeplex Revision Number 72841 onward.

The KEYWORDS to define the output must be defined inside the Phytoplankton property block:

<beginproperty>
NAME : Phytoplankton
…
CHLA_WQ_OUTPUT : 1
C_CHLA_OUTPUT : 60.0
<endproperty>

A short segment was recently published in Harmful Algae News 45 under the title First bloom of Ostreopsis cf. ovata in the continental Portuguese coast. The article reports on a Harmful Algae Bloom of this particular species that was spotted in Algarve (south coast of Portugal) in late September 2011.

Results (hindcast) and forecasts from MOHID-PCOMS were used to predict bloom dispersion. The model predictions were then used in the decision making process that lead to the closing of some beaches by local authorities.

The work was done in the framework of project ASIMUTH that aims to develop forecasting capabilities to warn of impending harmful algal blooms (HABs).

MOHID – PCOMS forecast for potential impacted areas by the tracking of bloom position. Lower-right side image from a national newspaper (Correio da Manhã).

MOHID users and developers can now have access to an exhaustive list of publications featuring MOHID applications and developments. A profile for MOHID was created in Mendeley, a free reference manager and academic social network, where the publications are available for download. This work was mostly developed by Jorge Roldan, a Biology graduated from Spain, during a professional upgrade at MARETEC.

From now on this repository of documents can be accessed through the Mendeley ribbon in the vertical panel on the right-side of the blog.

Our aim is to keep the profile updated so the MOHID community is stimulated to send their own MOHID publications or missing ones from the list in pdf format, using the email: mohid.in.mendeley [at] gmail.com

Alternately, you can leave a reply on this post with the bibliographic reference and send the file afterwards.

A new manual describing light related processes and parameterization in MOHID is now available for download. This manual contains both a conceptual explanation of the processes, and a technical description on how they are handled in the model.

Modules, keywords, input files and options are addressed, and the methods to estimate light extinction factors in the water column illustrated.

MOHID users are encouraged to read the manual for a better understanding on how the model is reproducing the light ambient in the water column, especially if working on water-quality/ecological applications where light plays a major role.

Parameterization of light-related processes in MOHID is a work-in-progress and so the manual will be updated on a systematic basis to encompass new features or code upgrades related with light parameterization. Amendments and suggestions are welcomed.

Manual
Light parameterization in MOHID
Version 1.0 

A new code upgrade was made recently by Paulo Chambel at HIDROMOD allowing MOHID to calculate backtracking for lagrangian tracers. This upgrade is available from MOHID Codeplex Revision Number 71268 onward.

This feature is activated in model_x.dat with the keyword BACKTRACKING : 1

click on the figure to see the animation

The MARETEC research group plans to publish a book featuring MOHID applications in the context of coastal/watershed management, somewhere during next year. The book will contain study cases in the form of chapters, and MOHID users worldwide are encouraged to contribute, thus sharing their experience and knowledge with other users, disseminating at the same time their own work, past or present.

The book aims to be a portfolio of key MOHID applications to illustrate its potential to provide insights or answers in the management of marine and terrestrial systems. 

Potential contributors are invited to check additional information that can be downloaded here or consulted online here. Chapter templates for both Word and LaTex can also be found at the book call page in this blog.

A new feature for shortwave radiation output has been added by Isabella Kenov to the water properties time-series file (*.srw). This code upgrade, available from MOHID Codeplex Revision Number 71263 onward, enables by default the output of three distinct parameters related with shortwave radiation in the water column:

- Average shortwave radiation in each cell/layer
- Shortwave extinction coefficient
- Shortwave radiation at the top of each cell/layer

An MSc thesis featuring the use of MOHID has recently been released, with the original title:

Avaliação da correlação entre parâmetros de qualidade da água e socioeconômicos no complexo estuarino de Santos – São Vicente, através de modelagem numérica ambiental

This work has been developed by Alexandra Sampaio from UNISANTA (Universidade de Santa Cecília) in Santos, Brazil, in the aftermath of project ECOMANAGE (2005-2008). In this work MOHID has been used to model the Santos estuary dynamics and water-quality processes. The main purpose of the thesis was to correlate water-quality and socioeconomic parameters.

Back in 1970’s the Santos estuary was considered one of the most polluted places on earth. Since then there has been considerable effort to conciliate human occupation, environmental protection and industrial and port development. Numerical models are a fundamental tool to address the management challenges posed by these sometimes conflictive uses, as shown by Alexandra’s MSc thesis. 

The thesis (in Portuguese) can be downloaded here. 

Jonathan van der Wielen, currently working at MARETEC integrating CUDA C/C++ into MOHID, is making a presentation tomorrow (November 15^th) at Faculdade de Ciências da Universidade de Lisboa (1 P.M., building C8, room 8.2.14).

The following topics will be addressed:

• Goal: achieve performance gains for numerical models by using CUDA.
• What is CUDA?
• Thomas in CUDA
• How to parallelize?
• Binding between FORTRAN and C
• Correctness benchmarks
• Performance benchmarks: achieved result
• Future prospect based on Thomas results

Free entrance!

[Added on 25/11/2011: the slideshow of the presentation can be downloaded here]

From now on MOHID Land users can have regular news posted directly in their Facebook wall.

Please have a look at MOHID Land FB profile for more info and share it with other modelers. And by the way, if you happen to visit the profile, just click on the ‘Like’ and show your support for this new way of dissemination.

A new version of MOHID Studio has been released (V 1.1.5) by Action Modulers, with some bugs fixed from the previous one.
More information can be found at Action Modulers website. Check the list of fixes for MOHID Studio V1.1.5 here.

A successful attempt has been made to integrate CUDA C/C++ into MOHID. CUDA is an NVIDIA technology that makes programming on a graphics card easier. Graphics cards (GPU’s) bring performance gains for applications that allow massive parallelization. Hydro-dynamical models are very suitable for this kind of applications due to the 2D or 3D grid structure.

The Thomas algorithm (a widely used tri-diagonal solver) can now run in CUDA while being called from within MOHID. Performance tests show that the Thomas algorithm runs 5.3x and 7.8x faster for respectively the Z and the X – Y direction on a TESLA C1060 (a standard CUDA card, current value around €1200). The results were compared to the FORTRAN implementation running on one core of a high-end CPU. Also, the overall execution time of MOHID was reduced by doing some memory optimizations (array padding and page-locked memory).

The roughly estimated potential speed up for running the complete hydro-dynamical MOHID module in CUDA is 15x to 50x for a TESLA C1060. In computation time requirements this means that a model that currently takes a month of real-time simulation will take two days or less. The estimated performance gain is higher than the currently achieved speed up, since a lot of communication is required between host (CPU) and device (GPU) for the Thomas algorithm. If a complete model is contained on the GPU, this communication operating cost can become insignificant. Of course there is always some overhead of code that cannot be parallelized (the blue part in figure 2, estimated at 5%).

Two reports have been produced, describing the work and the main results:

• Report: Hydro-dynamics in CUDA – Performance optimizations in MOHID
• Report: MOHID in CUDA Test report

This work has been developed by Jonathan van der Wielen, a 24 year old Dutch Technical Computer Scientist student who is currently working on his final project for his Bachelor degree. The preliminary results here presented were achieved after integrating CUDA into MOHID, in a work developed in less than three months and with relatively cheap equipment. Jonathan believes CUDA has enough potential to convince FORTRAN programmers to take the effort of learning C++.

Performance test results Thomas in CUDA and FORTRAN, total execution time

Rough estimation of performance gain for ModuleHydroDynamic

Action modulers has recently release version 1.1 of MOHID Studio, an integrated graphical user interface (GUI) for the MOHID Water Modelling System.

More details on this tool can be found at Action Modulers website.

In a few weeks this will became the official MOHID News channel. Our aim is to keep the fast-growing community of MOHID users up-to-date with all the MOHID latest and hottest news, ranging from code developments, new releases, training courses, current applications (case studies), related publications, etc.

Additional information on the MOHID model will be permanently available at this blog’s pages acessed through the top horizontal menu located at the top of this page.