Ocean Modeling Discussion

I also like this book very much. I've been building a Western Baltic Sea ROMS application from scratch recently and have found it to be a very useful reference when I have needed support understanding the various dynamics. Thanks for bringing it to the community!

So, it seems you are not trying to run bio_toys at all. It's your own application. Bio_toys is a 6x6 grid with periodic boundary conditions, useful for doing small scale tests .... and getting familiar with biological models. First, you need to decide which biological model you want to run, there ...

Your *.h file indicates that you have ecosim defined, yet the model is looking for chlorophyll as an input variable which would suggest bio_fennel is defined ... Are you actually calling the correct *.h file? What paths are in your build script and what are you calling your application? and which ...

Try renaming your ocean.ini.nc to ocean_ini.nc and changing this reference in the *.in file too. Make sure your local paths are correct also.

Bronwyn

yes, you should be able to run biotoys with analytical biology. a couple of things, as Kate says, you need to know which biological model you are using. According to your bio_toy.h file, it's ecosim, but the variables listed in the compilation error of your analytical f90 code would suggest bio ...

Look at this topic, your problem looks like it is related.

viewtopic.php?t=1192

I think you may need to update your code ...

I had a similar problem when I updated to revision 294. I tried to rerun a biotoys application which worked fine in previous revision but failed trying to read in time variable with r294 as follows: GET_2DFLD - surface u-wind component, t = 0 00:00:00 (File: frc_biotoys_era4010yrsall.nc, Rec=0000 ...

Hi Tom, Yes, you are right about the inconsistency in the fasham initial conditions ocean_time and dstart in the ocean_biotoy.in file. I'll post a new fasham initial condition file with ocean_time set to 0. As for the second question, you need to define BIO_FASHAM and undef ECOSIM in biotoys.h to ...

Hi Zhou,

That's curious. I've used this initial condition file without problems ... can you tell me what version of NetCdf and ROMS you are using?

Thanks,
Bronwyn

Laura, You are right about point 2). Currently there is no mechanism in place to feedback attenuation of light by organic material in biological models back into water column physics in ROMS. As for point 1) this is also an issue in EcoSim where attenuation of light for photosynthesis is prescribed ...

I have some initialization files for Fasham and EcoSim BioToys applications which I want to make available for general use. Is there somewhere I can post these on the ROMS site or do I need to post elsewhere on an ftp server?

Thanks
- Bronwyn

I've been working with BIOTOYS and Ecosim and Fasham applications a lot and have initialization files for running these. I'm traveling this week but can make them available to the community next week when I'm back at my desk.

- Bronwyn

Thanks Kate ... glad it was something easy to fix. All working now.

Bronwyn

Hi there, I'm trying to get ROMS 3.0 BioToys Application running on a MacBook Pro. I've successfully run previous versions of ROMS / BioToys on the Mac. Here's what I've done so far: I checked out the latest version of ROMS code from the repository and downloaded it onto MacBook Pro. I installed ...

Thanks for the reply, I get it.

Bronwyn

Hi

I notice that VAR_RHO_2D is defined in new globaldefs.h and not in old, is this a new global feature, or was my old globaldefs.h wrongly configured for some reason?

Thanks
Bronwyn

We recently managed to get ROMS 2.2 and BioToys case study running on the Intel MacBook Pro using mpich2 and g95 too. Here's how to configure it. ROMS 2.2 / BioToys setup on Intel MacBook Pro · Install XCode Utilities from the System DVDs. · Install Fink 0.8.1-Intel from fink.sourceforge.net · G95 is ...

This change in get_state.F has not been implemented in the new corrections-2.2.tar file. It's need to read in initial conditions for biological tracers.

line 135:

Code:

from

get_var(idbio(itrc))=.TRUE.

to

get_var(idTvar(idbio(itrc)))=.TRUE.

thanks for the help and suggestions, i'll let you know how it works out.

Not sure what Totalview is, is it for debugging? And, Yes, the last run was NtileI == 1 NtileJ == 2 Just tried it the other way around NtileI == 2 NtileJ == 1 and this happens STEP time[DAYS] KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME trd 103200 107.500000 2.914093E+00 2.047989E+02 2.077130E+02 1 ...

OK, this is what happens with 2 tiles, error message after first step STEP time[DAYS] KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME trd 103200 107.500000 2.914093E+00 2.047989E+02 2.077130E+02 1.364563E+12 0 p1_16392: p4_error: interrupt SIGSEGV: 11 DEF_HIS - creating history file: latte_out/ecosim ...

ok, running with one processor seems to be working so far, it's created a history file and is going through time-steps (slowly).

what does this mean?

Hi, I'm trying to run ROMS/Ecosim using 8 processors. 1) Executable was compiled with MPI on 2) Tiling in input set to: NtileI == 2 NtileJ == 4 3) command line: mpirun -np 8 oceanMlatteecosim External/ocean_latte_2005_Apr_bio.in > & loglatteecosim2 It gets as far as the first line in the time ...

Hi

I'm looking for the ROMS Technical Documentation and link to the Wiki that was discussed at the ROMS User Meeting last week.

A new formulation of EcoSim pigment calculations was included in the 2.2 version of ROMS. In this version, pigment biomass was explicitly tracked as mass, rather than previous formulations that relied on the carbon:pigment ratio. The advantage was greater numerical simplicity and more consistent ...

Technical documentation for EcoSim can be found at: http://www.flenvironmental.org/pubs/index.html Scroll to the end of the publication list to: Bissett, W.P., DeBra, S., and Dye, D. 2004. Ecological Simulation (EcoSim) 2.0 Technical Description. FERI Technical Document Number FERI-2004-0002-U-D. p ...