Ocean Modeling Discussion

ptimko

Monthly means for HYCOM should be available here: https://data.hycom.org/datasets/GLBb0.08/expt_93.0/data/meanstd/ The files are in native HYCOM format but there maybe a utility for converting the files to netcdf format in the source code under utilities or tools, looks like there may be some python ...

ptimko

Have you tried looking at the HYCOM forum for answers at www.hycom.org? If you are having difficulty accessing or downloading HYCOM data it would probably be best to place a question in the HYCOM forum as they understand their data server the best. In most cases they are able to resolve user ...

ptimko

As a former employee I would be happy to provide anyone with information about what it is like to work in the School of Ocean Sciences at Bangor University. Please feel free to contact me at pgtimko1@yahoo.ca

ptimko

Are you trying to read native HYCOM (*.[ab]) output files? If it is a global dataset then the data are on a global tri-polar grid, which is not rectangular. There should be FORTRAN routines available on the HYCOM website for converting native HYCOM (*.[ab]) to netcdf (*.nc) which might help. At ...

ptimko

If anyone wishes to receive further information about working in the School of Ocean Sciences at Bangor University please feel free to contact me at p.timko@bangor.ac.uk

ptimko

For further information regarding studying and working in the School of Ocean Sciences at Bangor University please feel free to contact me at p.timko@bangor.ac.uk

ptimko

Something must be mismatched. I'm not sure I understand why your grid stiffness ratios are changing if you are using the same bathymetry. For your own climatology case you are trying to set up. Have you check the coastline for single point seas? If it's blowing up near the boundary you may want to ...

ptimko

If the model is blowing up with 2 time steps it sounds like you're violating the CFL criteria. Try using a smaller time step.

ptimko

Thanks for correcting me. Now that I've thought about it more you don't need to hold the time series in memory. I'll take a look at the AVERAGES_DETIDE option.

ptimko

Thanks for the additional input. My biggest concern with implementing tidal analysis in ROMS is the memory requirement. If you wanted to include the four largest semi-diurnal and four largest diurnal constituents (M2, S2, N2, K2, K1, O1, P1, and Q1) you would need 183 days of hourly data. That would ...

ptimko

It think it would be rather difficult to implement harmonic tidal analysis within the code since it would require that they entire time series be held in memory. For a large domain that could impose some serious memory usage issues; especially if one wanted to study the 3-D tidal currents. You'd ...

ptimko

Probably best to do the tidal analysis using FORTRAN code on the supercomputing cluster. I did this when I analysed an 8 Terabyte dataset for 3-D global tides from HYCOM. Foreman's FORTRAN harmonic analysis code uses the same algorithm as matlab t_tide but doesn't provide 95% confidence intervals.

ptimko

I believe the correct flag for ifort is -free

ptimko

Question... Why do you have periodic boundary conditions? you say you're trying to model: I am using ROMS model configured for the Arabian Sea in northern Indian Ocean. but your output file says your boundary conditions are: Lateral Boundary Conditions: NLM ============================ Variable Grid ...

ptimko

Thanks for the input, I have plans to run similar size grids myself when I get back to work!

ptimko

thanks for the input... previous message spcecified that the complile flags were: mcmodel=large and i-dynamic that's why I was suggesting an error in the input file and/or a code bug. You're could be right about memory limitations. I've run larger grids for global tide simulations using another ...

ptimko

I'm kinda stuck, I'm currently out of my office and don't have access to the source code to look at the routines themselves. It appears that there is a problem with the way that the variable GridNumber is defined. Is it possible that you are missing or have incorrectly specified something in your ...

ptimko

with ncpus=12 are you running the code with OMP on a single node?

you might want to try compiling under mpi and using 2 or more nodes.

might depend on your job script....

ptimko

What is the physical memory of the system you are using?

Patrick

ptimko

What compiler are using? what compiler options are you using? and what is your computing platform? If you have alternative compilers available or alternative platforms available you may want to see if you can replicate the problem. It may help determine if it's compiler or platform specific. Patrick

ptimko

Another thought just occured to me, You may be trying to print an unprintable ascii or ebcdic character (such as a tab character, control, EOL, etc) for your system. Not sure why that would happen either...

Patrick

ptimko

I've never seen output like that before... I'm wondering if maybe you have a NaN or Inf in your input/output somewhere. Another possibility might be an out of range value that can't be represented by the field descriptor on output. The representation of NaN's, Inf's, or out of range values may be ...

ptimko

This probably isn't going to help much but I checked on Wikipedia and to answer your first question: "What are those characters?" I found the following: The at sign, @, normally read aloud as "at", also commonly called the at symbol or commercial at, and less commonly a wide range of other terms,[1 ...

ptimko

John,

Please let us know when you set up another location to discuss model coupling. I know some people at my location who would definitely be interested and I'm sure there are many other people who are interested as well.

Patrick

ptimko

Peter, Yes, that's the basic idea. If you want to force ROMS then you should use the correct input format for tidal forcing. If all you want is the data then you should be able to use TMD to predict the tidal heights at the boundary. I'm quite a patient guy (normally), glad I could help... :) Patrick

ptimko

TMD will extract the tidal elevations and greenwich phase for the tidal constituents you want. It should also be able to make a prediction. Tidal forcing in ROMS is input in terms of the tidal elevations (amplitude and phase) as well as the tidal ellipses (semi-major axis, semi-minor axis, ellipse ...

ptimko

You may want to review the documentation section on tidal forcing available on the ROMS website and also the "Packages" section for pre- and post-processing packages. There should be a section on tidal forcing if you follow the "Forcing Package" link. There is a TMD toolbox that should be available ...

ptimko

Depending on the total size of your domain have you consider using TPXO for the free surface boundary condition?

ptimko

With regards to choosing the number of processors to use: You always want to make sure that the memory requirements for the job fit within the physical memory of the system you are using. On a stand alone machine you might as well compile the code under OMP (shared memory model); assuming of course ...

ptimko

I'd say that Kate's best guess is correct since a 32 bit representation of a number is only accurate to about 7 decimal places.

I'm curious why you're getting a segmentation fault with -O3 on ifort; might want to try compiling with -traceback to see where the code breaks.

ptimko

Try this... A simulation is a recreation of a past event to examine what has happened in the past... Modelling is a study of the processes and forces involved to understand a physical or other other type of system... If you are only recreating the past from a single event I would say you are doing a ...

ptimko

I'm also using the K-omega option. Not sure what else to suggest right now, if I think I'll let you know.

ptimko

You have what would appear to be a baroclinic instability. I would suggest checking you vertical mixing model. I have had problems in the past with ROMS by not specifying a vertical mixing model. The problem was solved by specifying a GLS mixing model in the model options during the build process ...

ptimko

I would think ROMS should be able to do this with few problems. About 10 years ago I was running a modified version of POM in an fjord that had near super-critical flow over a sill that had a coincident contraction. The horizontal resolution I used was 50 metres. I had 10 layers and depth range was ...

ptimko

Category PhD Studentship Employer School of Ocean Sciences, Bangor University Location United Kingdom, Gwynedd, Bangor Closure Date Sunday, August 19, 2012 Description: For EU and UK students only Project title: Simulating the impacts of climate change on estuarine dynamics using an integrated ...

Ocean Modeling Discussion

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