Ocean Modeling Discussion

JDTilley

So looking at my zeta vs tide gauge data, it seems that the amplitudes of my tides are reasonable, although I must have miscalculated my TIDE_START. Let me show you an example of what I have, and maybe someone can tell me if it looks ridiculous to them. Tides certainly have a big effect on our syste...

JDTilley

So something is wrong with my tidal forcing. I am getting an extremely tidally dominated system, when in reality, my system is mixed between wind and tide. Do I need to adjust viscosity if I add tides? I think it is a units problem. Something is way off. My tidal forcing netcdf file has amplitudes i...

JDTilley

I managed to get the data I needed by translating the MATLAB code from here into Python: https://www.myroms.org/index.php?page=forcing I can't make any guarantees, but it seems to work. def ap2ep(Au, PHIu, Av, PHIv): PHIu = PHIu / 180. * np.pi PHIv = PHIv / 180. * np.pi # Make complex amplitudes for...

JDTilley

So I decided to go with ADCIRC. It gives me higher resolution, required less hard drive space to install, and has decent documentation online. I created the dataset, and now I just need to get the data into my forcing file. I get two output files, elev_hc.out and vel_hc.out. In elev_hc.out the first...

JDTilley

So you mean the UV data? I have found a DAP server for the hf data: http://geoport.whoi.edu/thredds/dodsC/usgs/data2/rsignell/data/tpx08/catalog.html But unfortunately, I don't see the UV data. Would you happen to know any DAP servers for TPXO8? I would like to avoid downloading 20 GB of data if pos...

JDTilley

Great. I was looking at TPXO Atlas 8. Unfortunately, I do not have a Matlab license available. I have seen a Python script here: https://github.com/ESMG/pyroms/blob/master/examples/make_tide/make_tide.py Also, I see another package that may be of use here: https://ocefpaf.github.io/python4oceanograp...

JDTilley

I am just starting to create my first tidal forcing file and I have a few questions. I have created a blank file based off of frc_tides.cdl. Where is time in this file? Do I need to add it manually? To me it seems a tidal forcing file should contain spatial arrays of tidal heights over time. Is this...

JDTilley

Oh! I hope that's right. So much better! Can't wait to do a longer run. You are always so helpful. I can't thank you enough.

JDTilley

Oops. OK. So my equation for viscosity would be

visc2 = (800*2/pi)**2/150 ?

JDTilley

So it seems there are several approaches to honing the diffusivity value, and I might end up having to break out my calculus textbook. However, I see from another page that a decent "rule-of-thumb" approximation is: visc2 ~ (delta_x / pi)**2 / timescale and that TNU2 can often be set to 10...

JDTilley

hmm... is this the location of the parameter? ! Harmonic/biharmonic horizontal diffusion of tracer for nonlinear model ! and adjoint-based algorithms: [1:NAT+NPT,Ngrids]. TNU2 == 0.0d0 0.0d0 ! m2/s TNU4 == 2*0.0d0 ! m4/s ad_TNU2 == 0.0d0 0.0d0 ! m2/s ad_TNU4 == 0.0d0 0.0d0 ! m4/s ! Harmonic/biharmon...

JDTilley

I appreciate the suggestion, but so far I have not had any success. I tried using MIX_GEO_TS along with TS_DIF4. It might help if I show you what seem to the relevant macros in the header file. Its probably some glaring novice mistake. /* Define to compute the momentum advection terms */ #define UV_...

JDTilley

Great. Thanks for the help. I did not explicitly add diffusion after removing U3 advection. I will try that. As this is late spring, it is sensible that the offshore waters would be warmer, so it is good to know that the boundaries might be behaving properly. This is a map of surface temperature. I ...

JDTilley

I have been working on developing a circulation model for my area. I've managed to get the model running, but I'm getting strange strip artifacts in my model output. In addition, I'm not sure if my boundaries are behaving properly either. You can see as it spins up that there are not the strange lin...

JDTilley

I run ROMS on Sierra with Macports. One thing I learned is that you need to use the same compiler for everything. So for a gfortran build, the command to install all dependencies using gcc5 would be something like: sudo port install hdf5 +fortran +gcc5 +hl +szip +cxx netcdf +gcc5 +netcdf4 netcdf-for...

JDTilley

They were indeed upside down, and I'm happy to report I worked past my boundary issue! Turns out I had some nans in ubar and vbar that I had carelessly not dealt with. Once I fixed those the model would run with TKE mixing boundary conditions set to closed. The model still looks like it could use so...

JDTilley

Something that may help me would be a better understanding of sigma coordinates and array index order in the netcdf files. I'm noticing that in my climatology that the surface is at the 0 index and the bottom is at the highest index. However, if I check my grid, I see that s_w[0] is -1 and 0 at the ...

JDTilley

I'll give it a shot. It's not ancient code. I even created a new folder with the ROMS source pulled fresh with svn and the problem remains. My best guesses so far are problems in the code I wrote to create my climatology or possibly the way SeaPy handles importing grids from netcdf. In SeaPy, flippi...

JDTilley

OK. I have this: LBC(isFsur) == Che Che Che Che ! free-surface LBC(isUbar) == Shc Shc Shc Shc ! 2D U-momentum LBC(isVbar) == Shc Shc Shc Shc ! 2D V-momentum LBC(isUvel) == RadNud RadNud RadNud RadNud ! 3D U-momentum LBC(isVvel) == RadNud RadNud RadNud RadNud ! 3D V-momentum LBC(isMtke) == Per Per Pe...

JDTilley

I'm not sure. That was not my intention, but it is possible something is set that shouldn't be since I used ocean_upwelling.in as a starting point to making my input file. How would I go about checking if my model is doubly periodic?

JDTilley

I guess what would be really helpful to know is whether it is possible that something in my netcdf configuration, build.bash, ocean.in, or my header file would cause this. Or is it something wrong in my grid, clim, bry, or ini file?

JDTilley

I have been working on a model, but the output shows that my boundaries are swapped (north is south, east is west, etc). I have been unable to figure out what the root of the problem is whether it be a misspecified grid, a bad setting, something installed incorrectly, etc. If you look at my input fi...

JDTilley

I think I've figured out my problem. I think the data arrays in my boundary files are backward. At first I thought the lines at the edges of my animations were artifacts of my laziness. But that is the actually output in my _his file. It seems the script I used to create my boundary file was expecti...

JDTilley

Well the error above was cause by me not having set temp:time in my climatology file. So I managed to get the model running again, but I still have the same problem. Any insights would be greatly appreciated.

JDTilley

Actually, looking over my ocean.in file it seems that the TCLM_NUDGING macro (among others) is obsolete. So I will try to turn on the logical switches for LTracerCLM and LnudgeTCLM and defining ANA_NUDGCOEF in the header file. EDIT: scratch that, now it gives an error: NETCDF_GET_FVAR_1D - error whi...

JDTilley

Thanks. I set my nudging coefficients as: ! Nudging/relaxation time scales, inverse scales will be computed ! internally, [1:Ngrids]. TNUDG == 2*10.0d0 ! days ZNUDG == 0.0d0 ! days M2NUDG == 0.0d0 ! days M3NUDG == 0.0d0 ! days ! Factor between passive (outflow) and active (inflow) open boundary ! co...

JDTilley

My boundaries were derived from my climatology file using SeaPy. I created an animation of the cross-section of the southern boundary and everything looked reasonable. So how would I set my inflow/outflow to 1 and 10 days? Thanks.

JDTilley

So I figured out you can upload animated gifs, so I am attaching a couple here. I am only doing short model runs at this point. It is the bottom layer that the cold is creeping in, and the surface has the opposite problem. I did try setting my nudging timescales, but the problem still remains: ! Nud...

JDTilley

The cold water is forming at the ocean boundaries, not at the land/sea boundaries. I have TNUDG set to 2*0.0d0, which now that I look at it, seems to imply zero. Could that be my problem? As far as my grid goes, it is the same resolution as my climatology and boundary files, although finer than my f...

JDTilley

I am still a novice at ocean modeling, and I am having an issue with cold water (< 5º in shallow water) forming at my boundaries during August in the Gulf of Mexico. I have checked and double checked my climatology, boundary, and forcing files, but can't see anything that should cause this. I have m...

JDTilley

Great. Thanks. I might take a few days to test again. Right now I am redoing my climatology from the ground up. Making good progress. Only have 3D u and v left to do at this point.

JDTilley

So I believe I have addressed my climatology and boundary problems. However, I'm still blowing up at iteration 4225 of 8640. I already pushed DT down to 150 s. Should I decrease this or would I be covering up some bigger issue? Also, I am curious about closed boundary conditions. In your example abo...

JDTilley

You were right on. I see that my boundary file has bad data that originates from my climatology file. Looks like I'll have to sort through that to get my model working properly.

JDTilley

Thanks for all the great information. I didn't realize those cppdefs were unnecessary. I will try to figure out what's going on with my boundary file and hopefully will have an update soon.

JDTilley

I am working on a circulation model, that runs fine until I apply a Flather condition for 2D momentum to one of my boundaries. A Flather condition works fine for all my other boundaries. For example, in my .in file, the following works: ! W S E N ! e o a o ! s u s r ! t t t t ! h h ! ! 1 2 3 4 LBC(i...

JDTilley

Well turns out I had

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#define ana_grid

in my header file.

Removing that fixed the problem. Sorry to bother.

JDTilley

So surprisingly, my input files are set up to the point where I can run a 3D model. When I visualize the output from ocean_his.nc, I see that the land is not masked. The fields mask_rho, mask_u, mask_v, and mask_psi are all in my input grid file. I thought if I set: #define MASKING in my .h file, th...

JDTilley

I'm so new to this I honestly don't know. I have successfully run the upwelling and bio_toy examples, but this is my first attempt at a 3d grid. There is land in my grid. I should have it masked out, but I don't know how the program will treat it. It seems if there is some minimum sigma thickness, m...

JDTilley

Thank you very much! I don't know how I missed that. That might be enough to get me on the right track. EDIT: surely enough, handling the minimum values as in `pyroms/examples/stuff/make_grid.py` fixed it. In addition, I wasn't making the bathymetry depth positive. With these changes the climatology...

JDTilley

I am trying to generate my first vertical grid using pyroms. I am having trouble understanding how to handle land points where the bathymetry is positive (negative actually). So far I've tried to deal with it by setting: hmin = -10 idx = np.where(hgrd.mask_rho == 0) h[idx] = hmin but I still end up ...

JDTilley

In addition to the netcdf4 library, rgdal works great with many spatial datatypes.

JDTilley

The bio_toy test case allows you to run a 1d test case of the various biological models.

https://www.myroms.org/wiki/Test_Cases

You can find the ROMS user guide here.

https://www.myroms.org/Workshops/ROMS20 ... manual.pdf

JDTilley

ROMS includes some coupled ecological models in the source code (Fennel, ecosim, etc.). I know nitrate is in many of them, I don't know how many do phosphorus. It seems ecosim has a couple parameters related to it.

https://www.myroms.org/wiki/ecosim.in

Hope this helps.

JDTilley

I decided to use pyroms to create my input netCDFs. I have successfully created a grid file, and now I'm trying to create a boundary file. I see the function for this is: pyroms_toolbox.nc_create_roms_bdry_file The function call is: nc_create_roms_bdry_file(filename, grd, ocean_time) so I tried: pyr...

JDTilley

Thanks for the info. I managed to get Octant running, so I'll look for the same function in there. I'll give the CDL example a shot. Thanks.

JDTilley

Thanks. I am mostly interested in what you are talking about, particularly the boundary file part. Still it would be nice to have some libraries for visualization and other things. I already made a grid file in Python on my own, and it looked right when I looked at it in Okean. Its the boundary file...

JDTilley

I am curious what the difference is between these two distributions found on GitHub. I mainly use Python and think one of these will be useful for me creating grids and boundary files. However, I can't tell which one I should use. According to the PyROMS page: Pyroms is a collection of tools to help...

JDTilley

Wow. Thanks so much for all the great information!

JDTilley

So I've managed to get ROMS installed and run multiple test cases. So now I am trying to take the next step and run the model for my study area. I am trying to build a netcdf file in Python, but there are a few things I'm not sure about. First, what is the spherical variable? I'm only trying to make...

JDTilley

Thanks. I deleted the sudo built executables and changed the owner of the build directory and build.bash executed correctly.

JDTilley

I appreciate all your help. I managed to get the project to compile. I had to uninstall all traces of netcdf4 and hdf5 from macports, and build everything from source. It was not trivial for me, but I'm happy you could steer me in the right direction. It took about 3 min to run (without debug). I ho...

JDTilley

Yes I uninstalled the old one. Netcdf is working as far as I can tell. Both nc-config --all and nf-config --all are giving me output.

edit: you are right. I am getting a segmentation fault using ncdump on some test .nc files.

JDTilley

Thanks. I was able to get CC to gcc by doing:

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sudo port install netcdf-fortran configure.compiler=macports-gcc-5

Unfortunately I still get the error.

JDTilley

This may be a shot in the dark, but after some reading I am beginning to think that I should be using nf-config instead of nc-config. But in this I also noticed that nf-config seems to have some questionable settings. This netCDF-Fortran 4.4.2 has been built with the following features: --cc -> /usr...

JDTilley

So -fbacktrace didn't reveal the line number. Any suggestions?

JDTilley

Thanks. I will try editing the .mk file with the following, and see if I can get it.

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ifdef USE_DEBUG
           FFLAGS += -g -fbounds-check -fbacktrace
else
           FFLAGS += -O3 -ffast-math
endif

JDTilley

I think I saw the line number during compilation. I get the line here:

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makefile:234: INCLUDING FILE /Users/redacted/ROMS/Projects/Upwelling/Build/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS

JDTilley

Sorry, I did not realize the output.log didn't include the error. Here it is. I must have been mistaken about it giving a line number. DEF_HIS - creating history file, Grid 01: ocean_his.nc Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0...

JDTilley

I retried with USE_DEBUG on, and I get the same result using oceanG. Attached is my log. You may notice I changed the OS setting to Darwin, although I'm not sure that's required (or advised) from the Mac installation wiki.

JDTilley

Another question. I see that I have hdf5 installed as hdf5 @1.8.15-patch1_0+cxx+gcc5. There is a +fortran variant. Could my problem be related to this. I just noticed you mentioned hdf5 in the above post. I also find that the ocean_his.nc is corrupted when I try ncdump (although the fact it is only ...

JDTilley

I have attached the output log.

JDTilley

Thanks for the help. I apologize, I put the wrong link up there. It should be corrected now. My segmentation fault is occurring at run time. I was able to compile by setting USE_NETCDF4 to on. I also set my NETCDF_CONFIG to /opt/local/bin/nc-config and NETCDF_INCDIR to /opt/local/include (both the m...

JDTilley

Hi. I am brand new to ROMS and compiled the source code for the first time yesterday. I use macports so my dependencies were installed using the gcc5, netcdf +netcdf4 +dap +gcc5, and netcdf-fortran +gcc5 ports. The compilation seemed to work, but I am having a problem running the Upwelling test case...

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