Ocean Modeling Discussion

Kosa

Depending on what you're trying to achieve, passive tracers can also be introduced via rivers. And you can adjust their concentration to only release at a certain time.

Kosa

Your initial conditions file only needs a single timestep, so I would subset your year of data and just write the model start time data into a ROMS-compatible NetCDF file.

Kosa

What was your process like when using the global model data? If you have regional model data in the same format, and it fully covers your ROMS model, you should be able to follow a similar procedure. I generally I just write a custom script so I know the full assumptions that going into the ...

Kosa

I haven't tested on Macs, the toolbox installed ok on a Matlab R2022b prerelease running on a PC, it doesn't use any mex files so I'm not sure why it wouldn't install on a Mac, if you can install the toolbox on a PC and do '>>which GridBuilder' in Matlab you should get the location of the ...

Kosa

Has anyone had success installing GridBuilder_toolbox.mltbx on the new ARM-based Macs?

I get the error "toolbox cannot be installed because it is not a valid toolbox file"

My setup:
- Hardware: M2 Macbook Air
- Operating system: macOS 12.4
- Matlab: R2022a

Kosa

It looks like there is M1 Mac optimization happening. See this post: https://www.myroms.org/forum/viewtopic.php?p=24122&sid=495bc79f13d0d3d04e66d6c25bf70214#p24122 We updated the code last week to use the NAGFOR compiler directly with Apple Silicon. See Darwin-nag.mk . David Robertson is ...

Kosa

Are you using WET_DRY option? It's my guess since -10 m zeta didn't cause a blowup. If so, I would try without WET_DRY unless you actually need it. And then you will need to set a minimum depth so that no grid points become fully dry at low tide. So e.g. set all depths to be at least 3 m.

Kosa

Could you post the rest of the output?

Kosa

I think I know what went wrong in the original post by Xegone. If ANA_INITIAL is activated, an initial conditions netcdf file is not considered as long as NRREC=0 to indicate that we are starting a new solution. But in this case NRREC=-1 so ROMS looked for an initial conditions file, and since it ...

Kosa

@skastner: My understanding is that TIDE_START is relative to TIME_REF, not DSTART. There's multiple different ways to get the timing correct but here's how I personally like to set up my models: t0=datenum(2019,1,1,0,0,0); % for TPXO function DSTART = 212.0d0 ! 01-Aug-2019 TIDE_START = 0.0d0 TIME ...

Kosa

osean wrote: ↑Wed Sep 08, 2021 12:51 pm
I noticed that there's a restart file option. How does one go about restarting with a different output frequency from a restart .nc file?

You will create a 2nd ocean.in file with a new NHIS and set ININAME to point to your restart file. Note that you will also want to set NRREC to -1.

Kosa

Does anyone know if output from the Chinese operational models are available online like the US/European-run systems? According to this 2020 preprint the SCSOFS should still be under active development. If not, it looks like Korea may have some ROMS models of the region if I can find how to access ...

Kosa

Thanks Kosa , my usual go to grid size is L300xM150; Well xi and eta differs from case to case. When making grids for a large region my xi x eta dimensions usually becomes large. I believe I do reduce the number of grid points while making my mesh coarser. I'm confused, so do the coarser grids have ...

Kosa

1. What size grids did you use in these different tests? (xi, eta, and vertical dimensions)

2. Have you tried using OpenMP?

3. What are your CPP options?

Kosa

1. I used homebrew, not macports, and had success. So if you're more familiar with homebrew take that route. 2. Looking through my notes, I believe I got the same (or at least a similar) netcdf error as you. I tried a bunch of different things but it looks like the fix came from altering the trunk ...

Kosa

I've run on Catalina. I haven't tried on Big Sur though.

I'm very curious about ROMS performance on the new M1 chip so if you get one of those machines please keep us updated.

Kosa

CoSiNE might be another one to consider.

Kosa

Where are you getting your net longwave heat flux? I've had issues with unrealistic temperatures in shallow regions when applying heat fluxes. The problem is that the heat flux depends on the temperature difference between the air and the ocean, but when we take heat fluxes from some other model ...

Kosa

Thank you! I had never looked into the Quick output.

Kosa

I'm trying to add new history file output fields that take a 3D field but only write the top sigma layer (e.g. SST or surface velocity). Thought I'd check if anyone else has already done this and could share some tips.

Thanks

Kosa

I only added the initial condition, the tidal forcing and the contact files for the refined grid. Can you clarify this sentence? You don't have a tidal forcing file for the refined grid so are you saying that you haven't run the coarse grid standalone with its initial conditions file or its tidal ...

Kosa

1. Is that your full output file? Where are the lateral boundary conditions and C-preprocessing options etc.? 2. What is your grid refinement factor? This should dictate your DT. E.g. if it is 3x refined, it's typical to use a 1/3 smaller DT for the refined grid (so 3 s instead of 15 s). I don't ...

Kosa

When you downloaded the ROMS trunk, you got the latest version. There have been some naming changes that are not reflected in the wiki yet but roms_Upwelling.in and ocean_Upwelling.in are effectively the same, just with a different filename. That particular change is only a few weeks old: https ...

Kosa

Can you post the rest of the output? The information about what's causing the problem will be higher up in the file.

Kosa

I had this issue in the past but I don't remember what I'm doing differently now so that I don't have the issue anymore. My work around: sort the time variable (so that time is strictly increasing) and then sort your other variables' time dimensions to match.

Kosa

Thanks Kate

kate wrote:Also, HYCOM has done this for many years.

Page 56 of the HYCOM user's guide https://hycom.org/attachments/063_hycom_users_guide.pdf 20.3 Generating "Equal-Ocean" Tile Partitions, looks like the most promising lead so far.

Kosa

I'm interested in defining an application-specific grid. Motivation: if we have a grid where the standard domain decomposition results in one or more tiles (MPI processes) that are composed entirely of masked out land cells, then this seems like an inefficient allocation of our computing resources ...

Kosa

Hi I'm looking for some hints pointing me towards papers that have looked at the role of baroclinic processes in water mass exchange/flushing. I'm having trouble finding what I'm looking for and I wonder if maybe I'm using the wrong jargon. I've been shocked by the magnitude of the differences ...

Kosa

Hi I didn't see your log file attached but if it's blowing up at the beginning of the run you could try adding the option

Code: Select all

#define RAMP_TIDES

and recompiling.

Kosa

Hi, attempting to build a NetCDF forcing file with the included frc_rivers.cdl (found in Data/ROMS/CDL/) may return errors due to a few missing commas. Pasted below is 1. the difference between the fixed and the original, 2. the original version, and 3. the fixed version. $ diff frc_rivers_original ...

Kosa

Upon moving to a new machine I am experiencing this exact problem. I wish the other users who experienced this problem had reported back with their solution...

Kosa

Thank you for your reply Charles. A couple of days ago I did switch out all the instances of function " any " to agree with the new r2014b graphics handles but you are right about there still being other issues. Unfortunately, I am not a Windows machine so I think for now I will just locate an older ...

Kosa

John, I too would greatly benefit for your colleague's seagrid advancements. I am attempting to get seagrid working with r2014b but the new graphics system is causing many compatibility issues.

Thank you

Kosa

Have you updated your mex files yet? I believe that is my issue, though maybe you have already updated them. From the SEAGRID README.txt in the mex file subdirectory Building SEAGRID requires building 3 mex files: mexsepeli.F mexrect.F mexinside.c These mex files are machine dependent, and can also ...

Kosa

I am having the same problem, kindly let me know if you find a solution.

Thank you

Ocean Modeling Discussion

Search found 35 matches

Re: Release passive tracers at a certain time instead of begining

Re: HDF5 file for initial input in Model ROMS

Re: How make initial condition from other model to ROMS

Re: Which tool is the stablest tools to create ROMS grid?

Re: Which tool is the stablest tools to create ROMS grid?

Re: ROMS for MacOS v. 10.15.2 Catalina / v. 11 Big Sur system

Re: Different boundary scenarios

Re: netcdf closing error

Re: Running error: unable to open existing NetCDF file

Re: TPXO to ROMS EXPRESS (tide extraction software)

Re: Change Output Frequency?

Accessing SCSOFS South China Sea Ocean Forecast System and other operational regional models

Re: Speeding up ROMS Model simulation

Re: Speeding up ROMS Model simulation

Re: ROMS for MacOS v. 10.15.2 Catalina / v. 11 Big Sur system

Re: ROMS for MacOS v. 10.15.2 Catalina / v. 11 Big Sur system

Re: Differences with CROCO

Re: Abnormal Cooling at Shallow Water Area

Re: History/Averages file output for a single sigma layer

History/Averages file output for a single sigma layer

Re: BLOWING UP during nesting

Re: BLOWING UP during nesting

Re: Roms Upwelling testing case

Re: Found Error: 02 Line: 350 Source: ROMS/Utility/close_i

Re: Problem with the time of the ECMWF files

Re: Domain decomposition for grid with large masked regions

Domain decomposition for grid with large masked regions

Role of statification on shelf-estuary exchanges

Re: SSH tides cause blow up in corner of big domain

Small errors found in frc_rivers.cdl

Re: mpirun problem?

Re: SEAGRID.m with MATLAB R2014b

Re: problem in seagrid2roms (built in win32 system)

Re: SEAGRID.m with MATLAB R2014b

Re: SEAGRID.m with MATLAB R2014b