Ocean Modeling Discussion

flcastej

Hi Arango, I am sorry for bothering you. I was writing the result in the forum just in case it could help other users and perhaps get some feedback. I have started to do the performance test with the different configuration explained in the ticket and trying to learn a little about distributed ...

flcastej

Dear Arango, I really appreciate your help. I was trying to test the different configuration to try to speed up my runs, but then I got in trouble with the segmentation fault. I will talk with the administrator to analyze the output to see in what region of the code are slower. About the heap-array ...

flcastej

Dear Arango, I have updated the code with the last revision. Now I have been able to run the model without the option -heap-arrays but it still take more time than older revisions. OceanM Versión 3.7 rev.923 // 2 Nested grid // 2 nodes 16 CPU/node // Total Elapsed CPU Time = 28580.836 sec OceanM ...

flcastej

Today I have been able to run the model without error using the option -heap-arrays but it affect a lot the performance. Below you will find a comparative table OceanM Versión 3.7 rev.922 // 2 Nested grid // 2 nodes 16 CPU/node // Total Elapsed CPU Time = 30138.171 sec OceanM Versión 3.7 rev.836 / ...

flcastej

Dear Arango, I am sorry for not explaining it properly. I followed your advice at the ticket doing: .cshrc, .tcshrc, etc. limit stacksize unlimited or .bashrc ulimit -s unlimited But I got the same error. The next step was to compile the model with the option -heap-arrays (I am using ifort). So I ...

flcastej

Dear Arango,

Thanks a lot for your answer. I will talk with the administrator of our HPC system to try to configure the stack size properly.

Regards,

-Francisco

flcastej

Thanks a lot Kate. Let´s see if someone could give us any clue about what´s happening. Meanwhile I will try to use the old code as you suggested.

flcastej

Dear all, I know that this error (the one that I am more afraid to get) can be caused by a lot of things, so I will try to give as much information as possible. I have been working for a while with ROMS. Now I am using ROMS/TOMS version 3.7, revision 921. After last updates, when I try to run the ...

flcastej

Hi, Six years ago I worked on the same problem as you but for the model COHERENS, trying to find the best number of core to be used. I presented the result " Auto-optimization on parallel hydrodynamic codes: an example of COHERENS with OpenMP for multicore " in a conference and I want to share it ...

flcastej

Hi, I am not an expert but: current model time exceeds ending value for variable: zeta_west [/i] It seems that you want to run de model (NTIMES) longer that the data available in your boundary file. So, you have to use a lower value for NTIMES or produce a new boundary file with more data. I hope I ...

flcastej

Richard, thanks a lot for your suggestion about the use of standard names. Hernan thanks a lot for updating the code with this change I am very glad to be able to help a little to the ROMs community.

flcastej

Dear all, I have uploaded my ROMS model output to a ncWMS server and it works without problems, so I am able to visualize my output perfectly. The only problem is that ncWMS, in order to plot vectors, looks for the word "eastward or northward" in the standard_name to recognize this variable as ...

flcastej

Dear Kate and Lyon,

Thanks a lot for your help. Finally it seem that I have been able to get rid off the instability trying different values for VISC2 and Zob. Now I have another problem but I think that I am going to be able to handle it by my own.

Thanks !!

flcastej

Dear Lyon,

Thanks a lot for your advice. I have launched the model following Kate suggestion and changing the value of VISC2 and it seem that it´s working. Once it finished I will follow your suggestion and test to run the model with different bottom stress formulation.

flcastej

Dear Kate, Thanks a lot for your help. Attached you will find a plot of the coarser grid and the three nested grids. Two of the nested grids are refined to a scale of 3 and another one to 4. In the plot is showed this values. I have changed the values of VISC2 increasing the value for the coarser ...

flcastej

Thanks a lot for your suggestion, I will try to do so.

flcastej

The white area in the pictures showed in my post correspond to the mask_rho. Yes, the minimum depth in my domain is 0.5 meters to ensure that I am not going to have any dry area. My problem come using the MY25 vertical scheme, if I use other scheme my model is stable but I get low velocities. Thanks ...

flcastej

Dear Lyon Lanerolle,

Thanks a lot for your answer I am working in a quite shallow area. I have tides but the tidal range is very small (max. 20 cm) so the area never get dry.

Regards,

-Francisco

flcastej

Dear Kate, Thanks a lot for your answer and your help. The model get unstable after 4 hours, the wind blowing at this time is not very strong (5 m/s) and the sea level variations quite small. I have tried to use smaller time steps, different values for RDRG2 and several sigma layer distributions but ...

flcastej

Dear all, I am running a nested simulation. It have 3 child grids for 3 channels with a resolution about 10 meters. The channels are quite narrow (50/70 m width) and shallow (5 meters). I have used different vertical mixing schemes: MY25, GLS and LMD. If I use GLS or LMD my model is very stable but ...

flcastej

Hi Yisen, ¿Have you tried to use a different vertical sigma coordinates distribution? Sometimes playing with theta_s,theta_b... could be really useful. Here is some information: https://www.myroms.org/wiki/Vertical_S-coordinate Also, it could help you to check if you get a better stability using ...

flcastej

Dear Kate and Rodrigo, Thanks a lot for your answers. I hope to be able to find a solution using ROMS, I have worked really hard to have my model working properly including 3 nesting layers and it could be a pity that finally I wasn't able to use ROMS. Also I like ROMS and all the community behind ...

flcastej

Dear all, I am working on a coastal lagoon and I have been able to run model properly, but I have a problem and I will be really grateful if someone could give me some hints that allow me to resolve it. We deployed several ADCP in order to validate the model, the vertical velocities recorder are in ...

flcastej

Dear Arango,

Thanks a lot for fixing it. I am really glad to have been able to contribute to improve ROMS.

flcastej

Thanks a lot !!

I know that my fix is not correct I share it in the forum just in case it could help to figure out where was my problem. Now I have forgotten about it and I am trying to find where is my misconfiguration.

-Francisco

flcastej

Dear Arango, Thanks a lot for your answer. The issue with the contact function it ´s my fault. It works well and it gave me the warning but I have had bad experience (instabilities) working with other models (ROMS-AGRIF) with refine factor higher than 3, so I decided (a really bad decision) to use ...

flcastej

Dear Arango, Thanks a lot for your help, I really appreciate your effort. Attached you will find a diagram of my grids with the refinement factors for each grid. grids_diagram.png My contact file has been made : Gnames = {'parent_grid.nc', 'refined_grid_1.nc', 'refined_grid_2.nc', ,'refined_grid_3 ...

flcastej

Dear Arango, Thanks a lot for your answer. I have followed your advice and first I examined the Lake Jersey case example and use it for my first simple case, one parent grid and one refined grid. Only after have been able to run it I moved to the next step, one parent grid and two refined grid as ...

flcastej

Dear all, After reviewing all the nesting code several time I have been able to resolve my problem, although not in a very nice way. I am pretty sure that there is something I have made wrong but with this change in the main3d.F all my refined grids run in two-ways model. I have change from the ...

flcastej

I have been reviewing the output log and it always gives : FINE2COARSE - exchanging data between grids: dg = 02 and rg = 01 at cr = 03 If I am working with two refined nestings, should it be? FINE2COARSE - exchanging data between grids: dg = 02 and rg = 01 at cr = 03 FINE2COARSE - exchanging data ...

flcastej

Dear all, Finally I have been able to run my model with 3 refined grid, but something strange is happening. When I run the model the first refined grid works in a two-way mode feeding the refined grid the parent grid and the parent grid the refined grid. But the other two refined grid work in one ...

flcastej

Dear John, I have tried different values for THETA_S, including values higher than 3. In my last runs, I have defined my initial condition by ANA_INITIAL, so I am not using any initial condition files. Trying different things I have used several values for DT and NDTFAST but I haven´t get any ...

flcastej

Dear John, Thanks a lot for your help, every answer give me hopes to resolve this problem. :D I did the changes proposed but I am still getting the error. In order to be sure that I don´t have any problem with my initial files or forcing files, I have defined them analytically, but without any ...

flcastej

Dear John, First of all, thanks a lot for your help. I really appreciate it a lot. I tested the parent and the grid alone, and they run without problems. Although I tried different values of theta_s, theta_b.. without any advance, today I have tried it again. Reviewing the value in the logfile and I ...

flcastej

Dear Kate, You were right, after some test, set the debugging mode, activate the floating point for gfortran and set the initial conditions analytical, finally has been able to detect the problem, although I haven´t been able to resolve it. The results obtained in my test point out to the NDTFAST as ...

flcastej

Dear Kate,

THANKS !!!

a lot for your answer. I am going to start to follow your instruction and I will inform about the results obtained.

-Francisco

flcastej

Dear all, Finally I have been able to prepare all the needed files for my nesting aplication, a very simple case, a coarse grid and one refined grid. I have used coarse2fine to generate the refined grid and contact.m to get the contact file. I have been able to compile the model and I am able to run ...

flcastej

Dear all, Finally I have been able to find the problem and it was quite simple. My matlab svn repositoy hasn´t been update. I thought that doing "svn update" in my ROMS root folder, it updated all the subfolders (ie: matlab) so I thought that I was using the last updated code. Finally looking on ...

flcastej

Dear all, I have started to work with nested grids in ROMS. I have started trying to run the Lake Jersey example test, but when I run the model it give me this error: NETCDF_GET_DIM - requested dimension: nLweights not found in input file: ../Data/lake_jersey_ngc_2grids_bot.nc call from: The only ...

flcastej

Finally, after reading several times the forum and review the code, I have been able to fixed it and set the forcing file properly. I have done two things: 1.) Change the reference time from 0001-01-01 00:00:00 to 1968-05-23 00:00:00 in order to work with smaller number and prevent any precision or ...

flcastej

Dear all,

I have been reviewing my boundary forcing file and I realized that I set the time reversed (the end time was the start time) and the my simulation runs longer than my boundary file. Once I fixed it, my model runs without problems.

flcastej

Dear all, I have realised of a issue about the time variable in my forcing file and I will like to share it with you to get your feedback about it. I have prepared my forcing file and ncdump -v sms_time mysimulation_frc.nc gives me: double shf_time(shf_time) ; shf_time:long_name = "surface heat flux ...

flcastej

Dear John, Thanks a lot for your help, this error is the same that I obtained running the model force with tides. In that case the error was fixed adding to my *.h file: #define ANA_FSOBC #define ANA_M2OBC I have been reviewing the time variable for all my files and I have some doubt about it. I am ...

flcastej

Dear all, I am obtaining the same error as xwbin. I am trying to run a simulation forced with wind, tides and a sea level imposed at the boundaries. If I force the model only with tides and wind, it run without problems, but when I add the bry file, it give me the error: CHECK_MULTIFILE - Error ...

flcastej

Dear Marck and John,

Thanks a lot for your answer. Right now I am on holidays so I am not able to check your suggestions. On thursday I will return to the office and test them.

Regards,

-Francisco

flcastej

Dear all ROM´s users, I have been able to run my simulation with tides. I have prepared my tides forcing files and now it´s running without problems. The point is that I will like to add to the tides the inversed barometer effect on the sea level but my working area isn´t enough big to allow the mo ...

flcastej

Dear John,

Thanks a lot for your help, now the model is running!!!!!

flcastej

I don´t have any lateral boundary conditions. Do I need to have it in order to force the model with tides?

When I run the model without tides It doesn´t give me any error.

Thanks.

flcastej

John,

Thanks a lot for your help. I have applied the changes :

DSTART = 734323.0d0 ! days
TIDE_START = 734690.0d0 ! days
TIME_REF = -1.0d0 ! yyyymmdd.d

But I am still getting the same error.

flcastej

I wanted to start my simulation on 2011/07/06 (yyyy/mm/dd), so I defined: In my init file I have defined: double ocean_time(ocean_time) ; ocean_time:units = "seconds since 0001-01-01 00:00:00" ; and ocean_time have a value of 63445507200. In mymode.in : DSTART = 734323 ! days TIDE_START = 0.0d0 ...

flcastej

Thanks a lot for your answer !!

I tried in both ways getting the same error.

flcastej

Dear ROMS users, I am having some problems running my tide force simulation and I will like to get any advise that you could give me. I have read the information at the Wiki and Forum. The steps followed to run the simulation has been: 1.) Prepare the tide forcing file following the instructions on ...

flcastej

Hi, I am using ROMS in a shallow coastal lagoon, and forcing it with real wind data from a meteorological station near the place where a current meter was deployed. I am getting low velocities in the E-W axis, comparing the model result with the current data registered. In the N-S axis it works ok ...

flcastej

Thanks a lot!!

Tomorrow I start my holidays, so I will look the code and test it for my case at the end August. But thanks a lot for your answer, the code and the link cause I need to change the points by hand too.

flcastej

Hi everybody!! I will like to know if there are any software o matlab script that allow me to modify my netcdf bathy file. Sometimes I detected an error in some points on the bathymetry and I will like to change this values, but I don't know how. it could be something like the editmask.m used to ...

flcastej

I am using it for my phD, studying the interaction wave-current in a coastal lagoon in Spain.

flcastej

Finally I fix the problem!!! It has been dificult to find the real error, cause it only appeared when I find the code line in makefile and commented it. In a step during the update, I used windows, and it put me a "beatiful" Â character on the name of the makefile file. So I updated again the code ...

flcastej

Dear Kate, I will try to answer some of your questions. The gmake version is 3.81. It s something strange, cause the make_macros.mk file are build and copy to the folder Build/, after that I get the error "the file doesn´t exist"m the same happen with abort.F90 I only run one build.bash at the same ...

flcastej

Hi kate, Thanks a lot for your answer. I thought that the error was in sfmakedepend, cause if i use the older one, the error dissapeared. Most probably, I am doing something wrong. When I run /build/bash, I get: rm -f -r core *.ipo /modelos/ROMs/projects/upwelling_paral_mpi/Build /home/francisco ...

flcastej

Hi, I has been working with ROMs without problems, but yesterday I made a svn update of the code, and now when I execute ./build.bash , I get an error. I think the problem is on sfmakedepend update, if I update all the files except sfmakedepend, I don´t get any error. Anyone has any idea about this ...

flcastej

Thank´s a lot for your help, finally I will try to use a lagoon model nested (1-way, off-line nesting should do) inside a shelf model (2D) to model correctly the sea level fluctuations.

Happy new year !!!

flcastej

So, if I want to model the inverse barometer effect, should I use a grid big enough to have an atmospheric pressure gradient? Use a bigger grid will have a higher computational time cost, so I should use a nesting model, isn´t it?

Thanks a lot for your answer.

flcastej

Hi !! I am trying to model the sea level fluctuations on a coastal lagoon,after getting good result forcing the model with winds, I want to simulate the inverse barometer effect. I have use the preprocessor option ATM_PRESS with PJ_GRADP, but I don´t get any fluctuation on the sea level. As I ...

flcastej

Hi, After a lot of test done, messages in the forum read and a bit of luck, I has resolve my problem. I dont know if it ´s the right answer, but at the moment, I get the expected results. With bulk fluxes, using the value of BLK_ZW =1 instead usual one BLK_ZW = 10. BLK_ZW Height (m) of surface winds ...

flcastej

Hi, I am trying to simulate a coastal lagoon, (max. depth=6m, area=170 mk2 ) only forcing with real wind data. I use the Bulk_fluxes, but comparing the ROMs data with the registred data for the same period simulated, I get smaller values with ROMs. Registered data is around 0.1 m sea level ...

flcastej

I can´t give you an answer, but I made a research about auto-optimization with OpenMP for Coherens(another ocean model) and one of the conclusion obtained were the use of more cpu dont mean that you model will run faster, depending of the grid use,the machine were you run the model, if you are ...

flcastej

Hi!! I wanted to plot velocity overlay with rslice of my 2D case, but I couldn´t manage to do it with the original rslice, so I have modified the code in a way that, if your file has ubar,vbar, rslice read it and allow you to make velocity overlay. The lines modified, are : Line 527 Line 2023 I have ...

flcastej

Hello, I have recently started to use rslice, when I try to open my netcdf file, rslice doesn´t give me any error, but I only get a white figure. When I run rslice, I get: >> rslice('file','mycase_his.nc') Acquiring h... Acquiring pm... Acquiring pn... Acquiring x_rho... Acquiring y_rho... Acquiring ...

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