Ocean Modeling Discussion

ymamoutos

Greetings John

Many thanks for the correction on
my post. I misinterpreted the
description on roms*.in file.

Kind Regards

Giannis

ymamoutos

Greetings

you need to set NDEFHIS and NDEFAVG not equal to zero.
roms*.in file has an extensive description about these switches

Kind Regards

Giannis

ymamoutos

Greetings Recently I change the atmospheric dateset that I was using with another from a local operational weather model because of its high spatial resolution. Model's operational output doesn't include shortwave and longwave radiation data and includes cloud fraction. So I am trying to compile the ...

ymamoutos

Greetings

Is it possible to post your log file?
What are the options you are using
at the *.h? What is your dt and dtfast?

Giannis

ymamoutos

Greetings I am trying to setup a coupled ROMS-SWAN coastal application using COAWST. ROMS setup is OK and running smoothly but SWAN - coupled and not - gives the following error when I run it using debugger : forrtl: error (182): floating invalid - possible uninitialized real/complex variable. Image ...

ymamoutos

Greetings from the log file you attached it seems that you have inconsistent calendar 18485.000 dstart 755666.00 time_ref dstart is the initialization time and your value (18485) refers to 01-January-2019 00:00:00 if your are using modified Julian days calendar and time_ref = -2.0 (see roms.in ...

ymamoutos

Greetings

nc_constant.m is part of ROMS matlab toolbox.
You can download it with svn using your ROMS credentials
from here:

https://www.myroms.org/svn/src/matlab/

Giannis

ymamoutos

Greetings

check this link https://github.com/wesleybowman/UTide
is the implementation of Matlab's UTIDE package.
According to author is still under development so
use it with some caution. Another option is TAPPY
(https://sourceforge.net/projects/tappy/)

Giannis

ymamoutos

Hi Matheus check here https://confluence.ecmwf.int/display/CKB/ERA5%3A+data+documentation#ERA5:datadocumentation in Temporal frequency section. Also if you download, let's say, recent reanalysis data for example July 2020 some fields are not complete (i.e. total precipitation). There is a ~ 2 month ...

ymamoutos

Greetings, Are you using 6hr timestep ERA5 data? if yes your conversion from J/m^2 to W/m^2 (1/(6*3600)) is valid. If you are using a different timestep then you must change it accordingly i.e 1hr 1/3600, 3hr 1/(3*3600) etc. Also are you downloading from ECMWF site directly or from CDS (https://cds ...

ymamoutos

Greetings once more Try to run using the same options for boundary conditions, i.e. set NLM obc to be the same with adjoint. Another suggestion is to unset the relaxation options (QCORRECTION, SRELAXATION) and run the nonlinear model with BULK_FLUXES enable. Also which of the available 4DVAR schemes ...

ymamoutos

Greetings

You are using nested boundary conditions in NLM model
but it seems you didn't enable the NESTING cpp option.
Also why you are using mixed radiation conditions in
NLM model? In general the choice of the boundary conditions
in the NLM model I think is completely inconsistent.

Giannis

ymamoutos

Greetings once more Raquel, Hernan and Joonho I am more than grateful for your suggestions. Finally I was able to run without any problem the 4DPSAS model :D . Raquel you had a point about my decorrelation scales. I found some literature about using variograms in order to estimate decorrelation ...

ymamoutos

Greetings once more

After several test runs with small to very small dt (30sec to 1 sec and Maximum barotropic Courant Number = 3.56216612E-03)
the problem persists.

Any help or suggestion is more than welcome.

Kind Regards

Giannis

ymamoutos

Greetings after several weeks i was able to solve the blowup at the first step of the adjoint model. To be honest I had to redesign completely my approach in order to run - at some point - the PSAS model. At the moment I am assimilating only SST. The model again blows up at the first inner loop. I ...

ymamoutos

Greetings, the last few weeks I am trying to set up a stable 4DVAR setup but I think that there is something fundamentally wrong on my approach. My application has relative high resolution - approximately 1.7km - with 30 vertical levels. The free runs - with or without tides - are completely stable ...

ymamoutos

oops I missed that

I am apologizing. Please ignore my post

Giannis

ymamoutos

Greetings Are you downloading ERA5 data from ECMWF site or from Copernicus CDS (https://cds.climate.copernicus.eu)? If your are downloading from 2nd source there is no need to use d_ecmwf2roms.m script because the fields that need to be accumulated are already accumulated according to ERA5 CDS ...

ymamoutos

Greetings,

how many barotropic steps you set (ndtfast)?

if ndtdast=1 try more i.e 10 for beginning and
check the value of maximum barotropic Courant number.
In any case - if i recall correctly - for stability
reasons it cannot exceed 0.8

Giannis

ymamoutos

Greetings Do you have any specific reason to use the 3rd-order upstream split advection scheme for momentum and tracers? I am asking because I recall that whenever it tried to use these options in horizontal resolutions similar or higher than yours - 2km to 1km - I had stability issues. Undefine ...

ymamoutos

Greetings At the last record (328) - when your model is blowing up - you have a maximum speed at point (i,j,k)(006,023,20) of 48.6 m/s... It's clear that the problem is on your physical model as already mentioned. Check your restart file to see where this point is and what is going on. Try to reduce ...

ymamoutos

Greetings Kate and sorry for my late reply. Yes it is possible to run it both ways. Currently I am using the default option. I'll probably use the non periodic option to check if there are any significant differences to my results. I don't know if it's right but my domain is relatively small and I ...

ymamoutos

Thanks a million Kate. From the above script I understand that you
use the default option - when you don't set explicitly -p (periodicity)
flag - which is east-west periodicity with zero (0) overlapping points.

Giannis

ymamoutos

Hi Kate Sorry for writing to this old post but I don't think there is a point to start a new thread. When you using sosie to extrapolate MERRA2 dataset are you using east-west periodicity (ewper flag) for the input grid? I am searching to MERRA2 site and manual to find information about MERRA2 grid ...

ymamoutos

Greetings Miguel thanks for your reply. I am using two different regional models (Global Mercator with 1/12 degrees resolution and MFS 1/16 degrees resolution) to create the input data for mine and to check for any significant differences on my results. According to myocean Copernicus service ...

ymamoutos

John The sum of M2 and S2 harmonics is a bit bigger than 0.15m... :shock: I suppose that I can't use this dataset to validate my results. Once more any suggestions??? Kind Regards Giannis P.S. Sorry editing the post multiple times. I had to double check the harmonics because I was looking on the ...

ymamoutos

Greetings John first of all many thanks for your reply. I am using the latest version of ROMS code and time_ref = -2 still uses the same calendar with the older versions. Yes my domain is inside the Mediterranean sea. I forgot to mention to my previous post that I had already used the regional ...

ymamoutos

Greetings, I am also having - let's say - a similar problem. When I am applying tides on my model I get almost 2 times higher amplitude than the actual (I am comparing with a tide gauge data, see attached figure). During my tests I change several things and rerun but the results in all of the cases ...

ymamoutos

Greetings

FYI I am also experiencing the same
problem after updating to version 841.
I am using gfortran 4.9.2 on Debian.

Giannis

ymamoutos

Hi Kate and sorry for the late response

I run it at the debugger using -g -fbounds-check flag
(I am using gfortran 4.8.4) just for a day (480 timesteps)
and it didn't have any problem. The 2D and 3D fields as far
I can see looks ok. Any other suggestion?

Giannis

ymamoutos

Yes I was defining SOLAR_SOURCE with the other vertical
mixing schemes (MY25 and GLS) and the water
type variable was read from the grid file - the
figure that I previously post.

Giannis

ymamoutos

Kate you are absolutely right. I change the values of
land - just set 2 and 3 all over the grid
- and the model run without blowing up. But I am still
curious. Why that happened with LMD and not with the
other schemes. Once more, many thanks Kate.

Giannis

ymamoutos

Hi Kate

I am setting it through the wtype_grid
variable in my grid file. I had already used
the same grid with MY25 and GLS with
SOLAR_SOURCE and WTYPE_GRID options and
the model run without any problem.
I am attaching a figure with my wtype_grid
variable to see it.

ymamoutos

Even more interesting. Turning off WTYPE_GRID
makes the model to run smoothly. Any ideas why
that is happening?

Giannis

ymamoutos

I run it on the debugger (I am using gfortran) and gave me that: At line 123 of file lmd_swfrac.f90 Fortran runtime error: Index '0' of dimension 1 of array 'lmd_mu1' below lower bound of 1 That's interesting because, I am using WTYPE_GRID option. I 'll switch it of and see what is going to happen ...

ymamoutos

Hi Kate and greetings from Greece,

no I am not using WET_DRY option.
It is also weird because in another
setup - only the central and north
part of the grid I am using with
almost 1km resolution - BKPP and
SKPP works without any problem.
Any suggestions?

Again thanks for the answer.

Giannis

ymamoutos

Greetings, When I am trying to use LMD_SKPP and LMD_BKPP at the same time I am experiencing a weird blowup. The model blows up at the first step and according to log file, the point that the model blows up it's on the mask. I also use PERFECT_RESTART option and I notice that my mask at rho points is ...

ymamoutos

Greetings, from your logfile, it seems that you have a fairly large vertical courant number (Cw) and maximum speed. From step 86 and after at point 078,153,32/31 the maximum speed is almost 8.0+(!!!) m/s. Is this one of your point sources (river)? Is river runoff mass transport vertical profile ...

ymamoutos

Greetings,

check this thread

viewtopic.php?f=14&t=3066

it's very helpful, especially Hernan's post. I think answers a part
of your question.

Giannis

ymamoutos

Kate thank you very much for your immediate reply. Indeed i forgot to attach the interesting part :oops: . I am attaching now and is huge :shock: Thanks again. Nonlinear model elapsed time profile, Grid: 01 Allocation and array initialization .............. 19.252 ( 0.0001 %) Ocean state ...

ymamoutos

Greetings, I understand that asking once more about this matter is kind of annoying and i am apologizing in advance, but to be completely honest I am completely confused /lost after reading several posts concerning ROMS tilling. I recently gained access to a HPC system ( https://hpc.grnet.gr/en ...

ymamoutos

Change your OBCFAC to a bigger number (ex. 120.0)
As Kate said check your surface heat fluxes and you
should turn off WET_DRY.I suggest to run with
BULK_FLUXES activated. Use TS_U3HADVECTION and
TS_C4VADVECTION for tracers.

Giannis

ymamoutos

Greetings, I suggest first to change the lateral boundary conditions for zeta and ubar,vbar. Use chapman implicit if you are planning to use flather for ubar,vbar or Chapman explicit for Shchepetkin. As Kate already told you at that post https://www.myroms.org/forum/viewtopic.php?f=31&t=4072 if your ...

ymamoutos

Greetings, recently i gain access to a HPC system and I had the same problem. System has various mpi libraries (openmpi and intelmpi). With openmpi 1.8.5 for all available compilers (gnu,intel) i had no luck but when i start using openmpi 1.8.7 had no problem at all. I suggest to change your openmpi ...

ymamoutos

Greetings to all, here at the University of the Aegean we have been using ROMS to simulate processes taking place in deep secluded sub-basins during and following dense-water formation episodes. We try to close the mass budgets during and following deep-water formation episodes. In order to ...

ymamoutos

Hernan, thank you very much for making clear to me all this. The script I've used for the forcing files is d_ecmwf2roms.m. Concerning Tmax, the total number of days for this run this is 5114, 1096 is the last day of the aeg_wind_era_2002.nc file. ... Input Forcing File 07: /home/yiannis/ROMS/aegean ...

ymamoutos

Greetings, Lanerolle thanks for your advise, I'll check H+zeta and I'll make a new grid with different hmin. Kate i don't have any problem viewing my wind file with ncview (i'll attach a figure). The minimum value for all records is -20.12764 m/s the maximum 18.314148 m/s and for the last record min ...

ymamoutos

:shock: :shock: :shock: Kate thank you so much once more. I have check everything except from that... The weird is that when i open the aeg_wind_era_2002.nc file on that record (2920) doesn't have any extreme value.How is that possible? To be honest i feel bit silly but I've never seen anything like ...

ymamoutos

Greetings, I am running a 14 year simulation over the Aegean sea but for some reason, which I am struggling to understand, the model blows up after 4 years. To be honest I am surprised because the current configuration of the model appeared to be ok. I have run the same region for 6 years with ...

ymamoutos

Dear fereshteh,

if you check the lines from 465 to 468 of d_ecmwf2roms.m you will see
that evaporation is used on case "swflux".

Have a pleasant evening
Giannis

ymamoutos

Greetings,

varinfo.dat, which is located at /<your folder>/trunk/ROMS/External
have a short description of every field that ROMS can handle (input
and output). Also check roms_metadata.m (~/trunk/matlab/netcdf/).

Have a pleasant evening.
Giannis

ymamoutos

Hi Thanos, I have never used Roms_tools for grid and forcing files. I am using the last 2.5 years the matlab routines that are provided through the svn repository. If you download the latest version of Rutgers ROMS matlab tools I am sure that you are not going to have any problems with the netcdf ...

ymamoutos

Greetings, you can use geodesic_dist.m script which is located in ROMS/matlab/utility folder. It's the same with the old spheric_dist.m plus it gives you the term galpha which is the Geodesic azimuth from point 1 to point 2 clockwise from North in decimal degrees. To be honest I am using seagrid ...

ymamoutos

Greetings, I have been running simulations for the north Aegean region over a month now, and I have used two different atmospheric datasets. The configuration for all simulations was the same and the only difference was the atmospheric forcing files. I used the BULK_FLUXES formula, clamped obc for ...

ymamoutos

Evridiki,

if your POM outputs are in netcdf form and in mercator
projection you can use the d_mercator2roms.m script
to create your initial conditions file. Also I have
the same question with Kate about the vertical interpolation.

Giannis

ymamoutos

Greetings, When I try to open your log file my editor tells me that there was a problem opening the file... At boundary conditions section I see weird characters for salt and I don't see any choice for TKE. I think a good choice for your log file is to set on your *.in file NINFO == 1 to see at each ...

ymamoutos

fereshteh, perhaps you have download and build only the C libraries of netcdf. Check here http://www.unidata.ucar.edu/downloads/netcdf/index.jsp and you will see that if you want to use the latest version of the netcdf library you must download two zip files. The first contains the C language ...

ymamoutos

Greetings from Greece and many thanks again Hernan.

Giannis

ymamoutos

Hi, I am currently using BULK_FLUXES for my application and i have a kind of silly/stupid question because i am bit confused. Which atmospheric fields are necessary, if bulk_fluxes isn't defined, except from uv surface stresses, solar shortwave radiation, surface freshwater flux, surface net heat ...

ymamoutos

Greetings mashinde,

I would like to ask you if you are using any point sources (forcing file) for the inflow into the Mediterranean from the Dardanelles straits, Gibraltar and Nile river. If not why? These sources are critical for the circulation and T-S in the Mediterranean.

Giannis

ymamoutos

Greetings, Kate thank you very much for your answer. I would like to ask a couple more thing about what you have suggested. If i am understanding right you suggest to use RadNud boundary conditions for my 3D fields (T,S,U,V). Is there any specific/accurate(??) way to calculate/set some how optimum ...

ymamoutos

Greetings, I am running a simulation of the North Aegean region for the period 2002-2007. The general picture, concerning circulation and tracers, seems ok except an small area close to the southern boundary. A cyclone is created in that area and also the temperature field is cooler from that was ...

ymamoutos

Hi Kee, try to compile your code by enabling the MPI option on the build.bash/build.sh script, specifically uncomment USE_MPI and USE_MPIF90 commands. Now if your machine have, for example, the mpich2 library after your compile is finished type this echo MPD_SECRETWORD=roms > ~/.mpd.conf chmod 600 ...

ymamoutos

Kate thank you for your reply and for your time, i would like to ask a couple more things. From your answer and from Marchesiello's paper i understand that i have to set Radiation and Nudging boundary conditions for the tracers (salinity and temperature), for the 3D u,v momentum components and ...

ymamoutos

Greetings, i am trying to simulate the circulation of the North Aegean region. My problem is that after a year run zeta value ends to be approximately 5.7( :shock: :shock: !!!!) meters. I understand that probably one of the reasons (or the main ?) that causes the problem is that i am using the river ...

ymamoutos

Hi to all,

My Problem is solved. It appears
that occurred due to small
number of points (5 points) for a relatively big
volume flow.

Yiannis.

ymamoutos

Hi to everybody, I am having a problem with point source option. I am giving with an external file the flow of sea of Marmara (5 points) through to Dardanelles straits to North Aegean sea but the only thing i am getting is blow ups...I am sure that my CFL condition is ok and the values of rx1 and ...

ymamoutos

Hi Kate and greetings from Greece, My problem is solved.I modified the ana_*.h files that i wanted for my test case following your suggestion (i set the variables that i needed equal to zero) and my model configuration is running smoothly until now. Thanks again for your help and have a pleasant ...

ymamoutos

Kate hi, on line 74 get_data.f90 calls subroutine get_2dfld for surface wind stress components. You need to provide a bottom salinity flux one way or another - most of us analytically set it to zero. So if am not providing an external file i have to modify ana_btflux.h and the other files if am ...

ymamoutos

Thanks for your advise Kate. My compiler is gfortran 4.4.3 and i used -fbounds-check flag. The result for my current cpp definitions file (myapp.h) is: At line 74 of file get_data.f90 Fortran runtime error: Array reference out of bounds for array 'frc', upper bound of dimension 1 exceeded (1 > 0) If ...

ymamoutos

Hi to everyone,

I've got "similar" problem.My ROMS version is 3.6. Kate you suggest to recompile with bounds checking. How can i do that?

Thanks for any help and for your time.

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