Ocean Modeling Discussion

wzhu

kate wrote:Are you really running ROMS 3.0? This has been fixed in newer versions.

Yes, but I just changed the DSTART according to the ocean_time, it works. Thanks.

wzhu

You should be able to set NDEFHIS to NHIS, no problem. If you have a problem, something is wrong. You should be able to set the time origin and DSTART as you have below. The tides will depend on how you create your tides file. Thank you very much, kate. I tried I listed above, it works, :) not only ...

wzhu

Dear all, I am a little confused with the ocean_time, DSTART, TIDE_START and TIME_REF. I prepared all my input files with the time period from 00:00 01/01/2006 to 00:00 10/31/2008, if I want to start the simulating time from 00:00 09/01/2006, so I have to set the ocean_time in the initial condition ...

wzhu

Hi, I'm having a problem that ROMS only runs when NDEFHIS=0 in the ocean.in file. This means it produces one very large history file. I would like to produce multiple history files so my model does not encounter problems when it runs for long periods of time. But if I change the value of NDEFHIS ...

wzhu

Did you check your initial condition there? If that's clean, I would set up some STATIONS there to see how it goes bad. Is it two isolated grid points or a small area? If your STATIONS write every timestep, you can watch it go bad in time. Are you right on the edge of your timestep stability? Since ...

wzhu

Hi Kate, Thank you very much for your suggestion. I have looked into the restart file and found the ranges of the following: Salinity: -0.065-176.729; Temperature: 0.1317-144.412 ℃; Density anomaly: -19.1-210.97 kg/m3; Free surface: -1.145-0.777 m; u : -1.13857-2.08 m/s; v : -2.213-1.2375 m/s. ...

wzhu

Someone once told me that the later a model gets into trouble, the harder it is to figure out. It could be anything. I assume you are running the model with a purpose in mind, involving looking at the model output. It is time to work on those skills. Start with ncview - it's really simple. OK ...

wzhu

Before restarting, you need to find a way to look at your solution. Is it otherwise looking reasonable? Where in the domain did the blowup happen? What sort of blowup is it, anyway? Top, bottom, middle? Velocity or density first? How quickly did things go from good to bad? On restart, check NTIMES ...

wzhu

Hi Kate, It again blew up after 148 days, How could I do? use the smaller time steps?
How to restart with the rst file?

wzhu

Both DSTART and TIME_REF are set in the ocean.in file. diag.F checks for out-of-bounds values for both density and velocity and reports what you see when it finds such. If it's a velocity problem, you can probably tell that from the last report of this sort (Max speed): STEP Day HH:MM:SS KINETIC ...

wzhu

Thank you so much, Kate. It seems that we can set both the DSTART and Time_ref to 0 because I ran a model with them set to 0 succesfully. My own model is just based on that model. It seems there is no report shown it is a velocity or density problem. Yes, the NINFO is 1. I have three output files ...

wzhu

Thank you very much, Kate. I have taken the 1/1/2006 00:00:00 as the starting time for all the time parameters. The units of ocean_time in my initial file is second, the long name is 'time since initialization' and I set it to 0, the model seemed work, but blew up after one day more time with ...

wzhu

You have: TDAYS = -24855.1348 What is the time value in your initial conditions file? What is your DSTART and what is your TIME_REF? Do you have the time results from GET_STATE? Here is an example of some times: 40907.000 dstart Time-stamp assigned to model initialization (days). 19000101.00 time ...

wzhu

Hi everyone, When I tried to run the model, I got the error message: GET_CYCLE - starting time for variable: river_time is greater than current model time. TMIN = 1.0000 TDAYS = -24855.1348 my river_time is from 1 to 1036, the interval is 15 minutes. Any reply will be highly appreciated! Best

wzhu

I am also trying to do the job like this. I am trying to use Matlab to interpolate the 1 degree temperature data (WOA09) onto the open boundary line. It is obvious a kind of 2-D interpolation, but what we want are not the meshgrid data, we need the data on the model grid nodes. But it seems that it ...

wzhu

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 ...

wzhu

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 ...

wzhu

Depending on the total size of your domain have you consider using TPXO for the free surface boundary condition? Hey, Patrick, For the free surface boundary condition, Is just only using the TPXO data ok, right? I have looked into the Tidal Forcing documentation and downloaded the TPXO7 and ...

wzhu

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 ...

wzhu

Depending on the total size of your domain have you consider using TPXO for the free surface boundary condition? Thank you very much for your kind, ptimko. The zeta_east equals to tidal data (From TPXO) + non-tidal data (subtidal),right? When I look into the TPXO data set, there are three files ...

wzhu

Hi all, I am preparing the boundary file, how can I get the free-surface eastern boundary condition using data from only two NOAA stations, which locate on the coast near the each side of the open boundary, respectively? I am trying to use Matlab to interpolate2D, but it seems not so good. Any reply ...

wzhu

No, you don't need both. If you like Matlab, go with it. As I said before: I was intentionally vague because you need to build up some tools for manipulating netcdf files that you are comfortable with. I used to use some horrible fortran codes, I then switched to primarily NCL and NCO for these ...

wzhu

This is coming up a lot so I just checked the FAQ: https://www.myroms.org/wiki/index.php/Frequently_Asked_Questions#How_can_I_create_the_initial.2Fboundary.2Fforcing_NetCDF_files_for_ROMS.3F Thank you, kate. Actually, I have downloaded the whole ROMS matlab repository, what's the next step? Do I ...

wzhu

Hello, everyone, How are you doing these days?
I have run the test case successfully, Now I am trying to start my own case, But I have no idea how to create input files? what software or toolkit should I use?

Any help will be highly appreciated!

Peter

wzhu

I would start by looking at the restart file with ncview. If it says it wrote to record 3 while blowing up, focus on record 3. Find out which field went bad and where it went bad. Can you try a serial run? Can you try a different compiler? How about optimized vs. unoptimized? Which compiler are you ...

wzhu

Hi everyone, I am running a Roms-sediment model, but it is always blowing-up at the same timestep with a only message: Blowing-up: Saving latest model state into RESTART file, although I reduce the number of threats and timestep. The same model was run successfully on another machine with mpirun, I ...

wzhu

Hi everyone, When I use the mpirun, it can not work.The error message is: bash: line 0: cd: /home/wzhu/chesapeake_sed: No such file or directory /usr/bin/env: ./oceanM: No such file or directory bash: line 0: cd: /home/wzhu/chesapeake_sed: No such file or directory /usr/bin/env: ./oceanM: No such ...

wzhu

Hi justina0622,
I am now having the same problem, where is the .bashrc file, I only have a .bash file and I can not find the directory in the file.

Wenwu

wzhu

The problem was ultimately solved. The server is a single-processor machine, it is not so powerful to run this model. when I changed to a more powerful server, it worked.
Thanks to all the kind people: kate and ckerry.

Best.

wzhu

No, they're in the ocean_upwelling.in. Hi Friends， How are you doing these days? I have not got the problem silved yet, but when I type:sudo tail -f /var/log/syslog to see the syslog: Nov 14 18:33:18 lsvm kernel: [1244276.692068] [22113] 1003 22113 5902 1 0 0 0 bash Nov 14 18:33:18 lsvm kernel: ...

wzhu

I have had this error message before when my set-up files are in a directory which is several sub-directories away from my home directory eg. /home/subdir1/subdir2/subdir3/subdir4/run By copying the exact same set-up files to a folder /home/run for example I no longer got the error. I don't ...

wzhu

No, they're in the ocean_upwelling.in. I have done that, when I double increase the values, it is OK; when I thrice increase the values or more, it says 'Segmentation fault (core dumped)', but does not dispaly 'killed'. Then I compared the 'ocean_upwelling.in' file with my domain 'Lee.in' file, I ...

wzhu

The only thing I see there is the stack size limit, though my experience has been a seg fault, rather than "killed" as the message. One thing you can try with the upwelling problem is simply increasing the values of Lm, Mm, N to see if larger values fail as your domain did. Thank you. But what and ...

wzhu

Thank you for reply. When I typed 'ulimit -a', it displayed: core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 55260 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) unlimited open files ...

wzhu

Processes usually get killed for running beyond some limit - time limit, open files limit, memory limit. I can't tell which you ran into. How big is your grid? Did it hang there trying to write for a very long time? Did you get any output file at all? I think the grid is 160x240. The contents in my ...

wzhu

Processes usually get killed for running beyond some limit - time limit, open files limit, memory limit. I can't tell which you ran into. How big is your grid? Did it hang there trying to write for a very long time? Did you get any output file at all? Thank you. It took about several minutes(not ...

wzhu

Sorry, I don't know what's wrong. Have you successfully run ROMS in a simpler domain? Have you tested your NetCDF library in any way? I would investigate this in a debugger, poking to find out what ID is in error - the file ID or the variable ID? You might get the same answer from print statements ...

wzhu

Help! Help! I am waiting for you online.

wzhu

When I run the ROMS model, I got the following informaton: NETCDF_PUT_FVAR_1D - error while writing variable: ocean_time in input file: ./Lee.nc call from: wrt_his.F ROMS/TOMS - Output error ............ exit_flag: 3 ERROR: Abnormal termination: NetCDF OUTPUT. REASON: NetCDF: Not a valid ID Part ...

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