Search found 52 matches

by leonjld
Tue Sep 24, 2013 4:49 pm
Forum: ROMS Tools and Techniques
Topic: need help on compiling seagrid mexfiles for win64 (solved)
Replies: 3
Views: 1902

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

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 your...
by leonjld
Thu Nov 17, 2011 3:07 pm
Forum: ROMS Discussion
Topic: about the usage of background brunt vasaila frequency
Replies: 2
Views: 961

about the usage of background brunt vasaila frequency

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 ...
by leonjld
Thu Nov 17, 2011 2:55 pm
Forum: ROMS Discussion
Topic: A simple question about default obc in old version roms
Replies: 9
Views: 3736

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

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?
by leonjld
Thu Nov 10, 2011 2:02 pm
Forum: ROMS Discussion
Topic: A simple question about default obc in old version roms
Replies: 9
Views: 3736

A simple question about default obc in old version roms

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 are...
by leonjld
Thu Sep 08, 2011 4:05 am
Forum: ROMS Tools and Techniques
Topic: Is there any tools to output the "dia" at the time of "his"
Replies: 7
Views: 4175

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

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 and k...
by leonjld
Wed Sep 07, 2011 4:37 pm
Forum: ROMS Tools and Techniques
Topic: Is there any tools to output the "dia" at the time of "his"
Replies: 7
Views: 4175

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

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.
by leonjld
Wed Sep 07, 2011 4:30 pm
Forum: ROMS Tools and Techniques
Topic: how to set the contour interval in roms plotting package
Replies: 0
Views: 1148

how to set the contour interval in roms plotting package

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 temp...
by leonjld
Tue Mar 15, 2011 4:17 pm
Forum: ROMS Problems
Topic: East-west tidal currents issue
Replies: 7
Views: 2344

Re: East-west tidal currents issue

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 you...
by leonjld
Tue Mar 08, 2011 5:42 pm
Forum: ROMS Bugs
Topic: different rx0, rx1 and totvolume for identical runs
Replies: 1
Views: 1840

different rx0, rx1 and totvolume for identical runs

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 roms3.out...
by leonjld
Sat Jan 01, 2011 4:41 am
Forum: ROMS Problems
Topic: Seagrid Error
Replies: 26
Views: 8478

Re: Seagrid Error

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 d...
by leonjld
Mon Dec 13, 2010 8:53 pm
Forum: ROMS Discussion
Topic: how to make a forcing file with a different grid than ROMS?
Replies: 3
Views: 1199

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

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) and lat(lat,...
by leonjld
Mon Dec 13, 2010 6:42 pm
Forum: ROMS Discussion
Topic: how to make a forcing file with a different grid than ROMS?
Replies: 3
Views: 1199

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

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 if it ...
by leonjld
Sun Dec 12, 2010 4:13 am
Forum: ROMS Discussion
Topic: Which heat fluxes to input when using bulk formulation?
Replies: 24
Views: 6589

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

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 assu...
by leonjld
Tue Oct 05, 2010 2:29 am
Forum: ROMS Tools and Techniques
Topic: incorrect time label by roms plotting package?
Replies: 1
Views: 1014

Re: incorrect time label by roms plotting package?

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 ...
by leonjld
Wed Sep 29, 2010 1:43 am
Forum: ROMS Installation
Topic: First Compiling Efforts
Replies: 2
Views: 1247

Re: First Compiling Efforts

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/w...
by leonjld
Wed Sep 29, 2010 1:30 am
Forum: ROMS Benchmarks
Topic: Serial faster then openmp
Replies: 6
Views: 5989

Re: Serial faster then openmp

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 s...
by leonjld
Fri Sep 24, 2010 7:29 pm
Forum: ROMS Tools and Techniques
Topic: incorrect time label by roms plotting package?
Replies: 1
Views: 1014

incorrect time label by roms plotting package?

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?
by leonjld
Mon Sep 06, 2010 3:05 am
Forum: ROMS Problems
Topic: Results and issues of barotropic tidal run
Replies: 14
Views: 5049

Re: Results and issues of barotropic tidal run

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 e...
by leonjld
Thu Mar 04, 2010 1:59 am
Forum: ROMS Discussion
Topic: Question about bathmetry data.mat file for seagrid
Replies: 1
Views: 706

Re: Question about bathmetry data.mat file for seagrid

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.
by leonjld
Wed Nov 25, 2009 4:10 pm
Forum: ROMS Discussion
Topic: model blow-up due to abnormal temperatures
Replies: 5
Views: 1374

Re: model blow-up due to abnormal temperatures

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 t...
by leonjld
Wed Nov 25, 2009 2:29 pm
Forum: ROMS Discussion
Topic: model blow-up due to abnormal temperatures
Replies: 5
Views: 1374

Re: model blow-up due to abnormal temperatures

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 va...
by leonjld
Tue Nov 24, 2009 10:04 pm
Forum: ROMS Discussion
Topic: model blow-up due to abnormal temperatures
Replies: 5
Views: 1374

model blow-up due to abnormal temperatures

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...
by leonjld
Tue Mar 24, 2009 4:16 pm
Forum: ROMS Tools and Techniques
Topic: need help on compiling seagrid mexfiles for win64 (solved)
Replies: 3
Views: 1902

Re: need help on compiling seagrid mexfiles for win64

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 s...
by leonjld
Mon Mar 23, 2009 3:58 pm
Forum: ROMS Tools and Techniques
Topic: need help on compiling seagrid mexfiles for win64 (solved)
Replies: 3
Views: 1902

need help on compiling seagrid mexfiles for win64 (solved)

Anyone made seagrid run successfully on matlab 2008b (64bit) on a 64bit windows vista?
by leonjld
Mon Mar 23, 2009 3:57 pm
Forum: ROMS Tools and Techniques
Topic: Does seagrid give the correct boundary to ROMS grid file?
Replies: 2
Views: 1154

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

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, b...
by leonjld
Thu Feb 26, 2009 7:13 pm
Forum: ROMS FAQ
Topic: Tidal forcing at the open boundary
Replies: 23
Views: 42532

Re: Tidal forcing at the open boundary

[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 th...
by leonjld
Thu Feb 19, 2009 12:11 am
Forum: ROMS Tools and Techniques
Topic: masking issue in seagrid
Replies: 3
Views: 1081

Re: masking issue in seagrid

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. 8)

Zafer
wow~~it works perfectly. Thanks!
by leonjld
Wed Feb 11, 2009 5:00 pm
Forum: ROMS Tools and Techniques
Topic: masking issue in seagrid
Replies: 3
Views: 1081

masking issue in seagrid

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 ...
by leonjld
Fri Oct 17, 2008 2:43 pm
Forum: Job Opportunities
Topic: Faculty Positions available at National Taiwan University
Replies: 0
Views: 1144

Faculty Positions available at National Taiwan University

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 do...
by leonjld
Mon Aug 04, 2008 5:03 pm
Forum: ROMS Problems
Topic: can I turn off the vertical turbulent closure model?
Replies: 2
Views: 1096

can I turn off the vertical turbulent closure model?

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 ?
by leonjld
Wed Jun 04, 2008 6:22 pm
Forum: ROMS Problems
Topic: how to implement passive OBC in ROMS?
Replies: 7
Views: 4038

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.
by leonjld
Tue Jun 03, 2008 6:35 pm
Forum: ROMS Problems
Topic: how to implement passive OBC in ROMS?
Replies: 7
Views: 4038

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 main ...
by leonjld
Mon Jun 02, 2008 8:16 pm
Forum: ROMS Problems
Topic: how to implement passive OBC in ROMS?
Replies: 7
Views: 4038

how to implement passive OBC in ROMS?

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 spe...
by leonjld
Mon Nov 26, 2007 4:01 pm
Forum: ROMS Tools and Techniques
Topic: how to use roms plot package?
Replies: 19
Views: 5663

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 dimens...
by leonjld
Sun Nov 25, 2007 6:03 pm
Forum: ROMS Tools and Techniques
Topic: how to use roms plot package?
Replies: 19
Views: 5663

how to use roms plot package?

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?
by leonjld
Tue Aug 14, 2007 8:39 pm
Forum: ROMS Discussion
Topic: how to compile the released plotting toolbox using gfortran?
Replies: 12
Views: 4342

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 lot, Ka...
by leonjld
Tue Aug 14, 2007 7:38 pm
Forum: ROMS Discussion
Topic: how to compile the released plotting toolbox using gfortran?
Replies: 12
Views: 4342

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 plot...
by leonjld
Mon Aug 13, 2007 6:37 pm
Forum: ROMS Discussion
Topic: how to compile the released plotting toolbox using gfortran?
Replies: 12
Views: 4342

-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 some...
by leonjld
Mon Aug 13, 2007 2:50 pm
Forum: ROMS Discussion
Topic: how to compile the released plotting toolbox using gfortran?
Replies: 12
Views: 4342

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? ...
by leonjld
Thu Aug 09, 2007 8:05 pm
Forum: ROMS Discussion
Topic: how to compile the released plotting toolbox using gfortran?
Replies: 12
Views: 4342

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,Kat...
by leonjld
Fri Jul 27, 2007 4:35 am
Forum: ROMS Discussion
Topic: how to compile the released plotting toolbox using gfortran?
Replies: 12
Views: 4342

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: ncargf90: ...
by leonjld
Thu Jul 26, 2007 6:30 pm
Forum: ROMS Discussion
Topic: how to compile the released plotting toolbox using gfortran?
Replies: 12
Views: 4342

how to compile the released plotting toolbox using gfortran?

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!
by leonjld
Thu Jul 19, 2007 8:50 pm
Forum: ROMS Bugs
Topic: a bug(typo) in Linux-gfortran.mk
Replies: 4
Views: 1955

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? Not...
by leonjld
Thu Jul 19, 2007 3:18 am
Forum: ROMS Bugs
Topic: a bug(typo) in Linux-gfortran.mk
Replies: 4
Views: 1955

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 q...
by leonjld
Thu Jul 19, 2007 3:12 am
Forum: ROMS Bugs
Topic: a bug(typo) in Linux-gfortran.mk
Replies: 4
Views: 1955

a bug(typo) in Linux-gfortran.mk

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?
by leonjld
Wed Feb 07, 2007 10:52 pm
Forum: ROMS Installation
Topic: segmentation fault
Replies: 11
Views: 4685

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, JendR, ...
by leonjld
Wed Feb 07, 2007 8:52 pm
Forum: ROMS Installation
Topic: segmentation fault
Replies: 11
Views: 4685

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 th...
by leonjld
Wed Feb 07, 2007 3:16 pm
Forum: ROMS Installation
Topic: segmentation fault
Replies: 11
Views: 4685

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 datasiz...
by leonjld
Tue Feb 06, 2007 9:37 pm
Forum: ROMS Installation
Topic: segmentation fault
Replies: 11
Views: 4685

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...
by leonjld
Tue Feb 06, 2007 6:27 pm
Forum: ROMS Installation
Topic: segmentation fault
Replies: 11
Views: 4685

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
by leonjld
Tue Feb 06, 2007 5:14 pm
Forum: ROMS Installation
Topic: segmentation fault
Replies: 11
Views: 4685

segmentation fault

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 Input P...