Ocean Modeling Discussion

leonjld

Here is the mex file for win64 per the request of some users.

Unzip the attached zip file and put the extracted files in the directory which contains similarly-named files (is there a mex folder in the matlab install dir?). Make sure the directory is in the matlab search path. Please test it on ...

leonjld

hi, I have a case in which I want to change the stratification. will it make any difference if I change the BVF_BAK in the input file? will that value has any effect in the momentum equation? it seems from the code that BVF_BAK is only used in brunt-vasaila frequency dependent vertical mixing? just ...

leonjld

thanks for the reply, Arango. So what happens if I have radiation 2D velocity obc and a closed wall 3D velocity bc? I feel the ubar/vbar and u/v are not consistent then, since ubar should be depth-averaged u?

leonjld

hi,

This question is related to older versions of ROMS (e.g. v3.3) when OBC was implemented as preprocessing options: if no option is undefined, e.g. for baroclinic velocity OBC. What will the default M3 OBC be? It seems the ROMS can run without problem even if baroclinic velocity and tracer OBC ...

leonjld

i see what you need now. I think one way to do it is to set:

NTSDIA == 1 ! Starting diagnostics time-step

to another value. If NDIA == 72, for example, you can set NTSDIA to 71, or maybe even 72. I haven't used that, so I can be wrong. Kate and Arango can confirm the meaning of NTSDIA.

leonjld ...

leonjld

You can calculate any momentum terms from the his files by yourself using e.g. MATLAB. The ROMS dia files are averaged fields and are used for diagnosis purposes only.

leonjld

Dear all,

I am trying to adjust the contour intervals since the plotting package's default setting has too many contour lines. Also the color bar has too many labels. I see the .cnt internal parameter has IFLDS and ILEVS set to 29 and 2. I am plotting temperature fields so I set the 23th (since ...

leonjld

I believe it will be useful if you check your tidal forcing netcdf files to see how the M2 current phase changes over the domain (when doing this you need to consider the inclination of the M2 current ellipse). You can even compare the forcing with your response by extracting the M2 current from ...

leonjld

hi all,

I found that roms reports different values for rx0, rx1 and totvolume for identical runs (what I did is just start roms, save the output, kill it, and repeat the process). I am using openmp, can this discrepancy be due to grid partition?

btw, I used the SVN Revision : 508:509M

diff ...

leonjld

Hi Roberto,

the errors came from the matlab mexnc interface (the toolbox you downloaded). Matlab 7.7+ all have native netcdf support so that you don't need netcdf toolbox. But what you need to do is to re-write the netcdf I/O in the m file using matlab native netcdf functions, which is what I have ...

leonjld

thanks, Kate!

In the cdl on that page:

double lat(lat) ;
lat:units = "degrees_north" ;
lat:point_spacing = "uneven" ;
lat:axis = "Y" ;
double lon(lon) ;
lon:units = "degrees_east" ;
lon:modulo = 360. ;
lon:point_spacing = "even" ;
lon:axis = "X" ;

Can I define coordinate as lon(lat,lon ...

leonjld

Hi, dear roms users and developers,

I am trying to force my application directly using the atmospheric model without interpolation to the forcing fields.

on this page: http://www.myroms.org/index.php?page=forcing

it was mentioned that user can use a ascii file as forcing files, I am wondering ...

leonjld

If I am understanding correctly, ROMS will also calculate sensible and latent heat flux if BULK_FLUX is on. My question is: for latent heat flux, does that mean user must provide precipitation data (either by forcing file or analytical function)? and does ROMS calculate evaporation by itself or ...

leonjld

it seems that the plotting program looks for an attribute called 'calender' in the variable dstart or ocean_time. If the value is 'gregorian', it will just ignore the specified year and day in the input file and take dstart as a modified julian date with base time being 1958/5/23. Otherwise it will ...

leonjld

if you downloaded the most recent version of roms (ver 3.3), I think you just need to modify the 'Makefile' and one .mk file in the Compiler directory depending on which OS and compiler you use. If you use linux and ifort, you need to edit Compilers/Linux-ifort.mk. just read https://www.myroms.org ...

leonjld

according to my experience, at least for roms ver. 3.3, openmp run will incorrectly show the cpu time. e.g., if I use 8 threads to run 5 minutes, roms output will show 40 minutes (which is 5 mins times 8 threads I think) for each thread (each thread has exactly the same number as cpu time).

so you ...

leonjld

the time label showed by ccnt is incorrect. Changing the year and yearday of the first line in the ccnt input file does not change the time label. Did I miss something?

leonjld

BAN, did you compare the ADCP currents directly with the tidal currents in the OSU tidal forcing? You can also try adcirc tidal database as forcing or compare with directly: http://www.unc.edu/ims/ccats/tides/tides.htm

if you have tidal elevation measurement it will be good to know first if the O1 ...

leonjld

1. read longitude, latitude, and bathymetry vectors from netcdf into matlab workspace,
2. rename the variables to xbathy, ybathy and zbathy, respectively, and
3. save them into data.mat.

leonjld

thanks for all your suggestions.

it seems that the abnormal temperatures are caused by the discontinuity of the tidal forcing at the boundary. The figure shows where the tidal forcing data are (red area) after interpolating the adcirc data to ROMS grid. The blue area are water cells without adcirc ...

leonjld

Do you need the 3D flow? Have you tried it without SOLVE3D?

On the river input, you have to specify the tracers on influx. You can set it to ten, but you have to set it or you will be doing the unstable downstream advection.

I use the 3D flow. Since other cases also use SOLV3D and no temperature ...

leonjld

I was running a tidal simulation when it blew up after 1 day. This blow-up is really strange: I have checked ubar, vbar, u, v, w and zeta of the last time step at blow-up (in restart file), and found nothing abnormal. However, the temperature has extreme values at two locations, one at the southwest ...

leonjld

Anyone made seagrid run successfully on matlab 2008b (64bit) on a 64bit windows vista?

I solved the problem. You need to change all pointer types (originally "integer*4") in mexrect.F and mexsepeli.F into "integer*8", since 64bit systems have double the size to store the memory address than 32bit ...

leonjld

Anyone made seagrid run successfully on matlab 2008b (64bit) on a 64bit windows vista?

leonjld

It's one of the dirty little secrets in Seagrid. The boundary you provide it goes through the outer rho boundary image points, not where a wall would be.

I am wondering does the masking on the boundary rho points work as regular or not? Say if I masked one boundary rho point at southern boundary ...

leonjld

[quote="kate"]Yes, it is true that ROMS will try to read the tides over the whole grid, then only use them at the boundary. It is applying them as part of the boundary condition, letting them propagate into the grid. If you have a large enough domain to require the body force potential tide, then ...

leonjld

nacholibre wrote:You need to edit following files:
uncomment '>Mask' in doaddmenus.m
add the following line under the case 'mask' in doevent.m
domasktool(self)

and then simply run seagrid. You can now use the Mask command under <Toggle> menu.

Zafer

wow~~it works perfectly. Thanks!

leonjld

Suppose now I have generated the grid, computed the mask and modified it using mouse clicks, and saved it as a MATLAB seagrid file. Now on the other day I tried to further modify the grid. I loaded it, but it would not show the mask it saved. I know the mask data is there, but how to display it and ...

leonjld

Faculty Positions available at Institute of Oceanography, National Taiwan University

The Institute of Oceanography, National Taiwan University (NTU), invites applications for four faculty positions, at the level of assistant professor or higher, starting August 1st, 2009. Applicants should hold a ...

leonjld

I see, thanks!

leonjld

If I just want to see the result of background vertical mixing, can I turn off the vertical turbulent closure by undefine the original mixing scheme in the cppdef.h ?

leonjld

Thanks Nobuhito Kun, The memorandum is very helpful to understand the some of the OBC of ROMS. I hope ROMS group can give a more complete memorandum of the OBC in the similar way, and how to set OBC using netcdf file or analytical expressions.

leonjld

thanks, kate. I didn't know I need to change the ana.hmixcoef.h when specifying SPONGE. For Sasha's boundary condition talk, are you referring to:

Alexander F. Shchepetkin, IGPP, UCLA (30 min)
10 Years of the ROMS Project: An Overview with Emphasis on what is Overlooked, Overdue, or Missing

My ...

leonjld

I know there are Free Surface OBC,M2 OBC,M3 OBC and Tracer OBC, but I do not know what to specify. So do I basically choose one for every type of OBC (FS,M2,M3 and T?). I don't have any information at OBC, but many OBC need an input file ocean_bry.nc, how can I circumvent this? Is it possible to ...

leonjld

thanks Deborah. I managed to make it partially work. However, there is another problem. When I modified the cnt.in and tried to output my test run using upwelling case (predefined in ROMS), it generated the following error:

GET_NC2DAT - error while reading variable: temp
NetCDF: Index exceeds ...

leonjld

I have finished compilation and there are several executable files such as 'cnt' 'ccnt' 'csec', etc. But I don't know how to use these for plotting?

leonjld

From Utility/hbackground.F: #if defined NCARG430 || defined NCARG431 || defined NCARG441
CALL mdpchi (2,0,idsh)
#else
CALL mapchi (2,0,idsh)
#endif
We should probably change this to: #if defined NCARG410 || defined NCARG422
CALL mapchi (2,0,idsh)
#else
CALL mdpchi (2,0,idsh)
#endif

Thanks a ...

leonjld

If your NCARG used -fno-second-underscore, you will have to add it to the FFLAGS in the plotting code too. Perhaps start there after doing a "make clean". You can use the "nm" command to find out which way each piece was compiled:

nm /usr/local/lib/libnetcdf.a | grep nf_close

My version of the ...

leonjld

-fno-second-underscore
Try editing ncargf90 to remove this.

Actually, this could be trouble if NCARG was compiled with -fno-second-underscore. You will likely have to recompile Netcdf with this option too.

As for your mapcmx warnings, they are common blocks which changed from real to double at ...

leonjld

All those undefined references are to the NCAR Graphics package. This package comes with libraries and a script for linking to those libraries. You need a version of that script that will invoke gfortran with all the goodies it needs. Do you have the NCARG package? Does it have an ncargf77 script ...

leonjld

Oh, that. ncargf77 is a script that comes with NCARG. ncargf90 is a copy of it with the changes needed for linking with whatever fortran you are using. You can edit it to put gfortran instead of g77, for intance. You may or may not need to track down some libraries as well.

Thanks for the reply ...

leonjld

sorry, I mean the makefile of the roms plotting package, not roms itself.

I got the following error:

ar: creating libUTIL.a
ranlib libUTIL.a
ncargf90 -O3 -ffast-math \
cnt.o cpmpxy2d.o mapeod.o stumsl.o stumxy.o vvumxy.o -o /home/leonjld/bin/cnt \
libUTIL.a -L/usr/local/lib -lnetcdf
make ...

leonjld

I am using gfortran (in ubuntu syste) for the roms3.0. However, there is no makefile for the plotting toolbox associated with gfortran compiler under linux. Is there a solution to this? Say using the Linux-g95.mk and do some easy modifications? Thanks!

leonjld

I used to try the ROMS on the Sun workstations in the lab, but unfortunately ROMS does not work on it (and I still have no idea why so). Finally I formatted my labtop and installed ubuntu Linux on it. The system turned out to be quite good for ROMS :-)
How does it not work? Does it not compile ...

leonjld

otherwise the whole compiling and running experience is quite smooth.

I used to try the ROMS on the Sun workstations in the lab, but unfortunately ROMS does not work on it (and I still have no idea why so). Finally I formatted my labtop and installed ubuntu Linux on it. The system turned out to be ...

leonjld

there are some kind of option of "-ffree-line-length-none" which ought to be "ffixed-line-length-none'. I think it's a typo?

leonjld

I tried it without debug model also. with -O2 or -O3, both will generate segmentation fault during the compilation of pre_step3d.f90:

f95 -c -u -U -O3 pre_step3d.f90
"pre_step3d.f90", Line = 174, Column = 1: INTERNAL: Interrupt: Segmentation Fault

The code is:

integer :: IstrR, IendR, JstrR ...

leonjld

This is a serial run with just one thread, no?

Try increasing the number of threads: NI =1 and NJ=8 might be a good starting point. This reduces the amount of space required for temporary storage. On x86 processors it normally makes the model run faster, too.

Thank you but I'm not sure how to do ...

leonjld

Thanks Gerardo. I tried but still not work. In debug compiling mode I get:

ild: (Performing full relink) internal free space in output file exhausted (dynamic string table)

Then when I ran it, still the same segmentation fault.

The limits are now:

% limit
cputime unlimited
filesize unlimited ...

leonjld

That's a compiler bug, or optimizer bug to be precise. I'm using the Sun complier on Linux and have to use -O2 rather than -O3. You might try that, but I don't know why you're getting the error in the first post unless something in your limits is set impossibly low. Do you have the option of trying ...

leonjld

if I turn off the debug switch, then when I use 'make' I have errors as following:

"pre_step3d.f90", Line = 174, Column = 1: INTERNAL: Interrupt: Segmentation Fault
make: *** [pre_step3d.o] Error 2

Is it a machine issue or else? I'm using Solaris SPARC

leonjld

HI, I downloaded roms2.2c and sucessfully compiled it on a Sun system using f95. I didn't modify any files and tried to run the default settings. However when I execute the program it shows the following:

% ./oceanG < ocean_upw.in
Process Information:

Thread # 0 (pid= 16782) is active.

Model ...

Ocean Modeling Discussion

Search found 52 matches

Re: need help on compiling seagrid mexfiles for win64 (solve

about the usage of background brunt vasaila frequency

Re: A simple question about default obc in old version roms

A simple question about default obc in old version roms

Re: Is there any tools to output the "dia" at the time of "h

Re: Is there any tools to output the "dia" at the time of "h

how to set the contour interval in roms plotting package

Re: East-west tidal currents issue

different rx0, rx1 and totvolume for identical runs

Re: Seagrid Error

Re: how to make a forcing file with a different grid than RO

how to make a forcing file with a different grid than ROMS?

Re: Which heat fluxes to input when using bulk formulation?

Re: incorrect time label by roms plotting package?

Re: First Compiling Efforts

Re: Serial faster then openmp

incorrect time label by roms plotting package?

Re: Results and issues of barotropic tidal run

Re: Question about bathmetry data.mat file for seagrid

Re: model blow-up due to abnormal temperatures

Re: model blow-up due to abnormal temperatures

model blow-up due to abnormal temperatures

Re: need help on compiling seagrid mexfiles for win64

need help on compiling seagrid mexfiles for win64 (solved)

Re: Does seagrid give the correct boundary to ROMS grid file?

Re: Tidal forcing at the open boundary

Re: masking issue in seagrid

masking issue in seagrid

Faculty Positions available at National Taiwan University

Re: can I turn off the vertical turbulent closure model?

can I turn off the vertical turbulent closure model?

how to implement passive OBC in ROMS?

how to use roms plot package?

how to compile the released plotting toolbox using gfortran?

a bug(typo) in Linux-gfortran.mk

segmentation fault