Search found 1082 matches

by arango
Fri Nov 15, 2019 9:55 pm
Forum: ROMS Installation
Topic: Compiling error - undefined reference to ice routines
Replies: 7
Views: 454

Re: Compiling error - undefined reference to ice routines

The version of the code that we distribute doesn't have a native sea ice model yet. I am sure that it will be included in the future. It has to be located in a subdirectory inside of the Nonlinear directory, like the biology and sediment models. The reason for it is quite logical and straightforward...
by arango
Sun Aug 04, 2019 4:21 pm
Forum: ROMS Installation
Topic: upwelling: - Configuration error ..... exit_flag: 5
Replies: 3
Views: 228

Re: upwelling: - Configuration error ..... exit_flag: 5

The default upwelling example in ROMS test repository has UV_QDRAG activated in the build script. If you notice, there are various options in build_roms.sh : # can be used to write time-averaged fields. Notice that you can have as # many definitions as you want by appending values. setenv MY_CPP_FLA...
by arango
Thu Jul 25, 2019 4:00 pm
Forum: ROMS Releases
Topic: ROMS 3.7 Released
Replies: 0
Views: 515

ROMS 3.7 Released

ROMS/TOMS 3.7 Released The latest version of the :arrow: ROMS/TOMS svn repository , revision 974 , was frozen and tagged as ROMS 3.7 . We haven't tagged a frozen version of ROMS in several years. This version is quite stable, and it is the one to be used at the upcoming 2019 ROMS 4D-Var Workshop to...
by arango
Mon Jul 22, 2019 3:03 pm
Forum: ROMS Bugs
Topic: Typo in ad_set_vbc.F line 1165 rev 973
Replies: 1
Views: 129

Re: Typo in ad_set_vbc.F line 1165 rev 973

Indeed, thank you! I didn't test with LIMIT_STFLX_COOLING activated.
by arango
Tue Jul 09, 2019 8:33 pm
Forum: ROMS Bugs
Topic: Error regarding variable dP in prsgrd44.h or prsgrd42.h
Replies: 1
Views: 146

Re: Error regarding variable dP in prsgrd44.h or prsgrd42.h

Indeed. Thank you for reporting this issue. Please update.
by arango
Thu Jun 27, 2019 7:48 pm
Forum: ROMS Problems
Topic: ROMS different src version leading to unalike results
Replies: 7
Views: 660

Re: ROMS different src version leading to unalike results

The ROMS basic numerical kernel has not changed much in a few years. However, configuration, CPP options, and parameters in the standard input have been modified and enhanced. You need to be sure that your header file ( application.h ) and standard input script ( roms.in ) is equivalent between the ...
by arango
Wed Jun 12, 2019 1:06 am
Forum: ROMS Discussion
Topic: Time type in nc file
Replies: 5
Views: 363

Re: Time type in nc file

ROMS has nothing to do with the time convention and elapsed time. The user selects how the time is managed in an application. There is nothing that we can do about it. It is up to the person(s) that set-up that application to use a consistent time zone in all the input NetCDF files (initial conditio...
by arango
Wed May 15, 2019 6:51 pm
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 6
Views: 976

Re: compile ROMS error

Your problem is that you haven't configured the build_roms.sh and build_roms.bash correctly. For example, notice that in the build_roms.sh script we have: #-------------------------------------------------------------------------- # If applicable, use my specified library paths. #-------------------...
by arango
Sun May 12, 2019 1:44 pm
Forum: ROMS Problems
Topic: Segmentation fault with floats
Replies: 6
Views: 489

Re: Segmentation fault with floats

Segmentation violations (SIGSEGV) are usually a sign of memory problems on the computer and available stack for the run. Perhaps, your computer doesn't have too much memory for your application, and you are deploying too many floats for it. I will try to run without floats to see if it works. Then a...
by arango
Wed May 08, 2019 10:35 pm
Forum: ROMS Installation
Topic: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT type
Replies: 4
Views: 288

Re: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT

You didn't understand at all what I was saying to you, or what WET_DRY does. The wetting and drying option ( WET_DRY ) is modeled in ROMS by changing the associated land/sea masking arrays at every barotropic time-step in step2d , which affect the ocean state variables. The wet/dry mask is a new arr...
by arango
Wed May 08, 2019 6:31 pm
Forum: ROMS Installation
Topic: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT type
Replies: 4
Views: 288

Re: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT

The WET_DRY option is not adjointed because it not fully differentiable, and because of every time-step of the forward trajectory need to be saved to have a consistent linearization of the tangent linear (TLM) and adjoint (ADM) models. You cannot use such time-depending land/sea masking in any ROMS ...
by arango
Wed May 01, 2019 4:22 pm
Forum: ROMS Discussion
Topic: cppdefs for BULK_FLUX
Replies: 11
Views: 1038

Re: cppdefs for BULK_FLUX

My current strategy is to activate LONGWAVE_OUT and provide downward longwave radiation so bulk_flux will subtract the outgoing IR by using ROMS surface temperature ( K ), infrared emissivity, and Stefan-Boltzmann constant. I also use downward shortwave radiation and I activate COOL_SKIN to correct ...
by arango
Tue Apr 16, 2019 9:50 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 728

Re: CF compliant units attributes in Varinfo.dat

ROMS has nowadays a very robust calendar. See the routine ROMS/Utility/dateclock.F for more details. It is consistently internally and can handle different reference date ( epoch ) for each forcing field from NetCDF files regardless of what we choose in the ROMS input parameter TIME_REF . I have to ...
by arango
Tue Apr 16, 2019 2:23 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 728

Re: CF compliant units attributes in Varinfo.dat

I agree with John. This part is not desirable. We and others have been using this standard for years. There are lots of datasets out there that follow this nomenclature. I am sympathetic with the issue of the links but some of the changes suggested are radical.
by arango
Thu Apr 11, 2019 9:33 pm
Forum: ROMS Information
Topic: units of specific humidity
Replies: 10
Views: 5115

Re: units of specific humidity

Indeed, I believe that unsavory piece of code was in the original COARE code. It is quite clever if you ask me. I recall putting enough comments in the code when I did some research about this threshold value many years ago. There is not a standardized unit for specific humidity in the atmospheric d...
by arango
Thu Mar 21, 2019 9:55 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 728

Re: CF compliant units attributes in Varinfo.dat

Thank you. The ROMS metadata file varinfo.dat is a user file and can be edited in any way that the user feels is necessary. You can even change the language. Some users in France wanted some of the attribute values to be in French. I haven't read the documentation about the UDUNITS-2 package. I look...
by arango
Wed Mar 13, 2019 2:28 am
Forum: ROMS Bugs
Topic: A small bug in ana_srflux.h
Replies: 12
Views: 3701

Re: A small bug in ana_srflux.h

Finally, I have time to browse the literature, Googling, and write a Matlab script to check the issue mentioned above. Indeed, the 15.0 factor used to compute the zenith is incorrect :!: We need to have instead:  zenith=cff1+cff2*COS(Hangle-lonr(i,j)*deg2rad) In my Matlab script, I compared against...
by arango
Sun Mar 10, 2019 10:38 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 878

Re: Pair and MPI version has problem with regridding

I updated the code to correct the bug in regrid.F. Check the following trac ticket :arrow: src:ticket:808 for more details. The parallel bug was corrected. Good luck.
by arango
Sat Mar 09, 2019 5:53 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 878

Re: Pair and MPI version has problem with regridding

It doesn't make sense to me. MyXout is a state, tiled variable and it is allocated as the others, and the pointer is passed correctly. It is the only way that this can be done. I bet that the problem is not in regrid . It seems like a memory leakage somewhere else. Yes, you can put the application i...
by arango
Fri Mar 08, 2019 9:04 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 878

Re: Pair and MPI version has problem with regridding

I took a look in the debugger on our US East Coast application and I cannot find anything wrong. I activated both ATM_PRESS and PRESS_COMPENSATE . I am also using BULK_FLUXES , which also need Pair . I don't see a parallel bug. Pair.png shflux.png The Pair is kind of jagged but it is because of the ...
by arango
Fri Mar 08, 2019 5:16 am
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 878

Re: Pair and MPI version has problem with regridding

Yes, the Dmem is a diagnostic quantity to estimate the memory requirement for an application. It has nothing to do with the numerical kernel. It is in my TODO list to look at your problem in the debugger. The issues that you are talking about sound like a parallel bug. However, the regrid subroutine...
by arango
Thu Mar 07, 2019 5:27 am
Forum: ROMS Bugs
Topic: A small bug in ana_srflux.h
Replies: 12
Views: 3701

Re: A small bug in ana_srflux.h

Both ana_srflux.h and ana_specir.h were coded longtime ago when we were testing the EcoSim bio-optical model in the late 90's. It was like twenty years ago. So I don't remember the details. At that time, both routines were intended for idealized toy problems for debugging purposes. The EcoSim model ...
by arango
Thu Feb 28, 2019 3:36 am
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 3242

Re: My ROMS

Thank you, Mark. Your logic is correct. We don't need to add processing logic since it needs ATM_PRESS anyway. I loaded your request ticket to the repository.
by arango
Mon Feb 11, 2019 10:34 pm
Forum: ROMS Tools and Techniques
Topic: Soundspeed for ROMS output
Replies: 4
Views: 616

Re: Soundspeed for ROMS output

Just do it in Matlab.
by arango
Mon Feb 11, 2019 5:12 am
Forum: ROMS Tools and Techniques
Topic: Soundspeed for ROMS output
Replies: 4
Views: 616

Re: Soundspeed for ROMS output

It has been in ROMS plotting package that uses the NCAR's GKS library since the beginning. Check the file src/Utility/svel.F in the plot repository. It uses the Che and Millero (1976) formula. Chen, C.T. and F.J. Millero, 1976: re-evaluation of Willson sound-speed measurements in pure water. J. Acou...
by arango
Sun Feb 10, 2019 1:14 am
Forum: Ocean News
Topic: Walter Munk (1917-2019)
Replies: 0
Views: 855

Walter Munk (1917-2019)

The oceanography community and the world lost one of its most renowned scientists. Walter Munk was 101. I met Walter in the mid-'80s when I was a graduate student at Texas A&M University. He visited and gave us an excellent Seminar/Lecture. My thesis advisor Robert O. Reid introduced me to him. It w...
by arango
Fri Feb 01, 2019 6:51 pm
Forum: ROMS Results
Topic: ROMS Granular model result in all variables
Replies: 8
Views: 1397

Re: ROMS Granular model result in all variables

:shock: Well, that's your problem. You are using biharmonic diffusivity (m4/s), which scales as 1/12 * ABS(U) * (dx ** 3) . A value for TS_DIF4 of 2 m4/s is too small :!: You need values of the order of 2.0d+8 m4/s . That is, you are using a value that is eight orders of magnitude too small :!: No w...
by arango
Thu Jan 31, 2019 9:09 pm
Forum: ROMS Results
Topic: ROMS Granular model result in all variables
Replies: 8
Views: 1397

Re: ROMS Granular model result in all variables

I guess that the more fundamental question is what type of horizontal advection are you using? Are you specifying explicit diffusion and viscosity? What do you specify for vertical diffusion/viscosity parameterization closure? You should compute your Reynolds Number (U dx/nu), where U is the maximum...
by arango
Tue Jan 22, 2019 10:35 pm
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 3242

Re: My ROMS

Hi Mark, Are you ready to submit the changes due to the PRESS_COMPENSATE?

Thank you.
by arango
Tue Jan 22, 2019 9:22 pm
Forum: ROMS Bugs
Topic: Issue restarting solutions in fraction of a day
Replies: 1
Views: 463

Re: Issue restarting solutions in fraction of a day

Indeed, good catch :!: Thank you for reporting this bug. I will update the code soon.
by arango
Tue Jan 22, 2019 7:24 pm
Forum: ROMS Bugs
Topic: tiny bugs? in metrics.F and nesting.F
Replies: 1
Views: 475

Re: tiny bugs? in metrics.F and nesting.F

Thank you for reporting this problem. I forgot to take care of the roundoff issues with the interpolation weights when I implemented the single precision ( SINGLE_PRECISION option) simulations. Your suggested solutions are incorrect :!: We cannot take the ABS value when computing the interpolation w...
by arango
Sat Dec 15, 2018 8:53 pm
Forum: ROMS Bugs
Topic: Equation error in GLS model coded into gls_corstep.F
Replies: 5
Views: 983

Re: Equation error in GLS model coded into gls_corstep.F

I haven't updated the code yet. I think that Ramsey Harcourt is correct. The shape functions used in mostly all vertical mixing parameterization should be smooth and continuous. We should stay away from sharp discontinuities that lead to eye bullet values in vertical diffusion and vertical viscosity...
by arango
Fri Dec 14, 2018 8:32 pm
Forum: ROMS Bugs
Topic: Equation error in GLS model coded into gls_corstep.F
Replies: 5
Views: 983

Re: Equation error in GLS model coded into gls_corstep.F

Thank you for looking this carefully and for providing a Matlab script to show the difference between the formulation currently coded in ROMS and the correction to the limiter (green curve). Obviously, the coded formulation has a discontinuity spike just before it remains constant. It is clearly wro...
by arango
Mon Dec 03, 2018 2:14 am
Forum: ROMS Problems
Topic: 'nfast' and 'ndtfast' on Barotropic time step
Replies: 5
Views: 940

Re: 'nfast' and 'ndtfast' on Barotropic time step

Again, Nope :!: The governing equations are timestep from n (right-hand-side terms) to n+1 (left-hand-side term: time rate of change). The vertically-integrated equations are integrated with smaller timestep to resolve fast dynamics due to gravity wave phenomena. For 3D total momentum coupling, the ...
by arango
Sun Dec 02, 2018 4:19 pm
Forum: ROMS Problems
Topic: 'nfast' and 'ndtfast' on Barotropic time step
Replies: 5
Views: 940

Re: 'nfast' and 'ndtfast' on Barotropic time step

Nope , there are actually M* barotropic timesteps :!: The reason for it is that the cosine-square shape filter needs to provide time-averaged values of ubar , vbar , and zeta centered at the n+1 baroclinic timestep, which gives us second-order temporal accuracy for time-averaged barotropic motions....
by arango
Wed Nov 14, 2018 5:00 pm
Forum: ROMS Bugs
Topic: tiny little bug in get_state.F for time evolving bathymetry
Replies: 2
Views: 566

Re: tiny little bug in get_state.F for time evolving bathyme

Done. Thank you for reporting this typo.
by arango
Fri Nov 09, 2018 2:43 pm
Forum: ROMS Bugs
Topic: Error compiling ROMS with new flag SINGLE_PRECISION (svn928)
Replies: 7
Views: 1320

Re: Error compiling ROMS with new flag SINGLE_PRECISION (svn

Nope. What I said above is correct :!: If the last argument to the mp_bcastf routine is single- precision it will use mp_bcast_1d , and if it is double-precision it will use mp_bcastf_1dp . Just look the subroutines in distribute.F :idea: If you don't understard, you need to check a Fortran 1990, 19...
by arango
Wed Nov 07, 2018 9:16 pm
Forum: ROMS Bugs
Topic: Error compiling ROMS with new flag SINGLE_PRECISION (svn928)
Replies: 7
Views: 1320

Re: Error compiling ROMS with new flag SINGLE_PRECISION (svn

You are doing something wrong or something is weird with the compiler. You need to read carefully the following :arrow: trac ticket . Notice that even if SINGLE_PRECISION is activated, there are several variables that are still in double precision ( dp 64-bit kind parameter) and the r8 kind paramete...
by arango
Mon Oct 01, 2018 4:10 pm
Forum: ROMS Discussion
Topic: missing temp_time
Replies: 2
Views: 467

Re: missing temp_time

You don't need to do that. One of the great things about NetCDF is that it is self-described. I have mentioned in the past that we need to follow CF convections to guarantee the functionality of metadata and avoid missinterpretation issues in ROMS. I highly recommend users to add the units , time , ...
by arango
Fri Sep 28, 2018 7:50 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 1608

Re: severe (174): SIGSEGV, segmentation fault occurred. libp

I am going to try again for the last time. Read carefully :arrow: trac ticket 747 . In the older version of the code, we choose either lower- or higher-level MPI function for exchanges. We no longer do that in the newer versions, you need to experiment and select which options are more efficient in ...
by arango
Thu Sep 27, 2018 1:53 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 1608

Re: severe (174): SIGSEGV, segmentation fault occurred. libp

I think that you need to read the following :arrow: trac ticket and choose the MPI communication options that are more efficient in the computer environment that you are running. You should check the profiling information that ROMS reports to standard output to see in what region of the code are slo...
by arango
Wed Sep 26, 2018 10:08 pm
Forum: ROMS Discussion
Topic: ROMS history file has suddenly included restart record
Replies: 7
Views: 913

Re: ROMS history file has suddenly included restart record

Hmmm, I haven't had the time to examine the issue that you are having. I haven't modified this part of the code in years. I use the split of history files frequently and I have never observed the behavior that you are reporting. I wonder if it is a matter of configuration. Are you changing DSTART ev...
by arango
Wed Sep 26, 2018 10:00 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 1608

Re: severe (174): SIGSEGV, segmentation fault occurred. libp

Yes, your problem is the stack size per CPU and it seems to be associated with the automatic arrays used in distributed-memory for I/O operations. This is not a direct ROMS problem, but a computer problem because of not enough memory to handle automatic arrays that are either allocated on stack or h...
by arango
Tue Sep 25, 2018 1:48 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 1608

Re: severe (174): SIGSEGV, segmentation fault occurred. libp

It is very simple as I have mentioned several times before. You just need to edit your login script and add one of the lines below:

Code: Select all

.cshrc, .tcshrc, etc.

limit stacksize unlimited

or  .bashrc

ulimit -s unlimited 
I wrote lots of information in previous :arrow: trac ticket.
by arango
Sat Sep 22, 2018 6:18 am
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 1608

Re: severe (174): SIGSEGV, segmentation fault occurred. libp

Nowadays, severe segmentation errors are associated with stack size, which is used for allocating automatic arrays. They are allocated on stack or heap according to you choice of compiler options. I mentioned this in the last trac ticket.
by arango
Thu Sep 13, 2018 9:12 pm
Forum: ROMS Bugs
Topic: Small bugs in CPP BIO_FENNEL with DIAG and DIAGNOSTICS_BIO
Replies: 2
Views: 751

Re: Small bugs in CPP BIO_FENNEL with DIAG and DIAGNOSTICS_

Nope. That's not what I have in the repository for def_diags.F : # ifdef DIAGNOSTICS_BIO # if defined BIO_FENNEL || defined HYPOXIA_SRM DO ivar=1,NDbio2d ifield=iDbio2(ivar) IF (TRIM(var_name(i)).eq.TRIM(Vname(1,ifield))) THEN got_var(ifield)=.TRUE. DIA(ng)%Vid(ifield)=var_id(i) END IF END DO # endi...
by arango
Tue Sep 11, 2018 9:23 pm
Forum: ROMS Bugs
Topic: bug in mod_tides.F
Replies: 1
Views: 613

Re: bug in mod_tides.F

Indeed, thank you. I have more stuff to update in the computation of ROMS memory requirements. I am missing arrays to account for. I am trying to come up with the best estimate.
by arango
Mon Sep 10, 2018 7:25 pm
Forum: ROMS Discussion
Topic: ROMS prestep3d , Crack-Nicolson method, lambda
Replies: 1
Views: 487

Re: ROMS prestep3d , Crack-Nicolson method, lambda

Yes, we need to update the documentation.
by arango
Fri Aug 31, 2018 9:00 pm
Forum: ROMS Discussion
Topic: Cannot find "coordinates" attribute for variable: Uwind
Replies: 15
Views: 1776

Re: Cannot find "coordinates" attribute for variable: Uwind

The ECMWF data has a minimal interval of 3 hours; you can easily create annual files instead monthly. It will be more efficient in ROMS to avoid inquiring and open so many NetCDF files. The time units for forcing file is usually days since the reference date ( epoch ). However, you can have any time...
by arango
Sun Aug 26, 2018 3:44 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 3434

Re: forrtl: severe (151): allocatable array is already alloc

Okay, that will do it. I put safeguards to the code when processing standard input file ocean.in . I made a couple of updates recently for it. It looks that your grid is not for a regional application, but it is a global grid. Is that correct? If that's the case, you have a problem with the design o...
by arango
Wed Aug 22, 2018 2:07 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 3434

Re: forrtl: severe (151): allocatable array is already alloc

It is a weird error if you didn't repeat the NtileJ parameter in ocean.in , which triggers the allocation of several modules. In yesterday update, I put safeguards for this to never happen. I don't know what to make of your case. I don't think that a corrupted ocean.in should trigger to process the ...
by arango
Mon Aug 20, 2018 4:58 pm
Forum: ROMS Discussion
Topic: How to setup for rotating frame
Replies: 10
Views: 1465

Re: How to setup for rotating frame

It is weird that you are not activating periodic boundary conditions in the south and northern boundaries :!: It is the perfect and appropriate case for it because your grid is an annulus :roll: You can set the desired flow in the initial condition instead of using Flather boundary conditions. If yo...
by arango
Mon Aug 13, 2018 6:08 pm
Forum: ROMS Discussion
Topic: blowing up on nested grid
Replies: 4
Views: 931

Re: blowing up on nested grid

That can be also a problem. However, the main issue here is that there are one or more grid cells with a value of 1E+40 1/km for both inverse metric factors pm and pn . We cannot multiply those variables with the mask because of division by zero in ROMS. The grid spacing ( DX=1/pm and DY=1/pn ) is a...
by arango
Sun Aug 12, 2018 3:36 pm
Forum: ROMS Discussion
Topic: blowing up on nested grid
Replies: 4
Views: 931

Re: blowing up on nested grid

The information is in the front of you. If you don't understand that information, you have homework to do before running ROMS. Look the large and a small numbers. Check your grid files. ( DXmin , DYmin ) cannot be zero!!! It is a trillion times smaller than the scales of electrons... I am sure that ...
by arango
Sun Jul 29, 2018 4:38 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 1935

Re: huge memory per node when up scaling application

I usually put lots of information in trac when I update the code. We have noticed that this information is generally ignored and our emails are treated as spam. There is nothing that we can do about it, and we cannot force users to update and or read the detailed information provided. We have thousa...
by arango
Fri Jul 27, 2018 8:00 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 1935

Re: huge memory per node when up scaling application

PARALLEL_IO works for me. You need to use a recent version of the code. Also, make sure that all your input NetCDF files are NetCDF-4 format. You can check which format you have using ncdump : % ncdump -k filename.nc netCDF-4 To convert from NetCDF-3 to Netcdf-4 try: % nccopy -k netCDF-4 nc3name.nc...
by arango
Wed Jul 25, 2018 4:30 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 1935

Re: huge memory per node when up scaling application

First, I don't think that ROMS will run with the PNETCDF library. It will need special function calls in ROMS. I never tried that library, it is a third party library. If you use PARALLEL_IO, you need to compile with the NetCDF-4 library with parallel MPI I/O and HDF5 support and your computer need ...
by arango
Wed Jul 18, 2018 9:43 pm
Forum: ROMS Problems
Topic: Problem generating contact file with three refined grids
Replies: 5
Views: 1120

Re: Problem generating contact file with three refined grids

Hi Marc and John,

I removed the restriction of having the noncoincident grid points in the indirect connectivity between grids for telescoping applications. See the following :arrow: trac ticket for more information.

Please update. Your particular set-up should work now.
by arango
Tue May 22, 2018 7:05 am
Forum: ROMS Bugs
Topic: ifort compile (make) error
Replies: 4
Views: 1152

Re: ifort compile (make) error

Yes, it is Darwin configuration that needs it. As Kate said, just comment the line in the Linux-ifort configuration file. Linux will take the unlimited value from the environmental variable. It is the loader LD that it is having the problem. It depends on what you have in your computer.
by arango
Thu Apr 26, 2018 7:04 pm
Forum: ROMS Problems
Topic: unable to open existing NetCDF file GET GRID
Replies: 10
Views: 1195

Re: unable to open existing NetCDF file GET GRID

By the way, you don't need to modify that routine. ROMS prints out the NetCDF error code at the end of the standard output file when it closes all the files. Notice that there are NetCDF-3 and NetCDF-4 input files for this application. You may be using the wrong one for the compiled code.
by arango
Fri Mar 30, 2018 5:54 pm
Forum: ROMS Problems
Topic: Could not read in multiple boundary files correctly
Replies: 2
Views: 741

Re: Could not read in multiple boundary files correctly

You need to provide more information. The new inquiry.F was modified to provide the correct transition between annual files.
by arango
Wed Feb 28, 2018 5:30 pm
Forum: ROMS Problems
Topic: Contact point problem with salinity in Two Way Nesting run
Replies: 6
Views: 1711

Re: Contact point problem with salinity in Two Way Nesting r

I haven't noticed this in my applications that have run stable for years. Are you using those three refinement grids? If so, one of the refined grids is touching the boundary of the other. That will affect the order of the contact points between them. It is the chicken and egg question, what came fi...
by arango
Tue Feb 20, 2018 3:54 pm
Forum: ROMS Bugs
Topic: List of analytical header files
Replies: 3
Views: 901

Re: List of analytical header files

It cannot be done during initialization because the CPP include syntax <*****.h> allows to use the header files from user's directories other than ROMS/Functionals . Notice that in analytical.F , we have # ifdef SOLVE3D # if defined ANA_BIOLOGY && defined BIOLOGY # include <ana_biology.h> # endif # ...
by arango
Tue Feb 20, 2018 5:30 am
Forum: ROMS Bugs
Topic: List of analytical header files
Replies: 3
Views: 901

Re: List of analytical header files

There is a reason for it that I need to remember exactly. It is not a bug, but why does it matter? I think that it has to do with with the global attributes of output NetCDF files and the fact that the user can overwrite the location of the code header files instead of using the ones distributed by ...
by arango
Tue Dec 12, 2017 6:35 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 5187

Re: CPU time and MPI issues with nested grids

Yes, you need to select a better option for MPI communications as I mentioned yesterday. Check the information on the svn trac ticket. If you are using too many processes for this application, the data exchanges due to nesting is a bottleneck. See the number for point data gathering . It explains th...
by arango
Tue Dec 12, 2017 1:24 am
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 5187

Re: CPU time and MPI issues with nested grids

Maybe your application is not big enough to justify 144 nodes, and your application is slowing down because of excessive MPI communications. It is a critical issue that some users ignore always. There is always an optimal parallel partition for each ROMS application. Now if you are using a recent ve...
by arango
Sat Dec 09, 2017 5:27 pm
Forum: ROMS Bugs
Topic: A little bug in get_cycle.F of src 884 and the fixing
Replies: 5
Views: 1991

Re: A little bug in get_cycle.F of src 884 and the fixing

Do you have the cycle_length attribute in the time variable? For the forward time-stepping, we can also have the following logic in get_cycle.F: IF (job.gt.0) THEN ! forward: Tval(i) =< mday =< Tval(i+1) IF (Linside) THEN tstart=Tmin DO i=2,ntime IF ((tstart.le.mday).and.(mday.le.Tval(i))) THEN Tstr...
by arango
Fri Dec 08, 2017 5:07 pm
Forum: ROMS Bugs
Topic: A little bug in get_cycle.F of src 884 and the fixing
Replies: 5
Views: 1991

Re: A little bug in get_cycle.F of src 884 and the fixing

Something is weird here. It doesn't make sense to me. Notice that the logic in get_cycle.F that set the switches is: ! ! Is the model time inside the data time range? If not, check if the ! data just has the LOWER- or the UPPER-snapshot interpolant. ! IF ((Tmin.le.mday).and.(mday.le.Tmax)) THEN Lins...
by arango
Tue Nov 21, 2017 6:32 pm
Forum: ROMS Bugs
Topic: Bug in output time step in DEF_DIAGS after restart
Replies: 5
Views: 2652

Re: Bug in output time step in DEF_DIAGS after restart

Smaller values of NDIA are possible but its value needs to be an exact factor of NRST, say NDIA=NRST/2 should give you an integer. The time window (in seconds) should be exactly divided by DT.
by arango
Fri Nov 17, 2017 6:26 pm
Forum: ROMS Bugs
Topic: Bug in output time step in DEF_DIAGS after restart
Replies: 5
Views: 2652

Re: Bug in output time step in DEF_DIAGS after restart

Well, this logic has worked for us for years. Your problem is that NAVG and NDIA are inconsistent with NRST . If you have AVERAGES and DIAGNOSTICS_TS and/or DIAGNOSTICS_UV activated, you need to set NAVG=NDIA . It doesn't make any sense to have different values because if you are going to compute ba...
by arango
Tue Sep 26, 2017 1:24 am
Forum: ROMS Problems
Topic: mp_collect bug when compiling with define PARALLEL_IO
Replies: 8
Views: 3821

Re: mp_collect bug when compiling with define PARALLEL_IO

The PARALLEL_IO is slower than serial I/O, and it won't help you to improve I/O performance. The last time that I checked that option, it was not working well, and I haven't checked if the NetCDF4 library has made progress on it. I can fix the issue with nf_read2d.F but it will not help you much. Th...
by arango
Tue Aug 29, 2017 4:27 pm
Forum: ROMS Problems
Topic: Error in ROMS execution
Replies: 7
Views: 1351

Re: Error in ROMS execution

You cannot change those values capriciously. They have to be exactly the same values used by the person that generated the initial conditions, boundary conditions, atmospheric forcing, and observations for data assimilation. The time clock has to be the same in all those files for consistency. The t...
by arango
Mon Aug 28, 2017 7:35 pm
Forum: ROMS Problems
Topic: Error in ROMS execution
Replies: 7
Views: 1351

Re: Error in ROMS execution

There is a weird set-up of the ROMS time clock here. You need to ask the person that set-up this application. First, the input parameters: 13295.000 dstart Time-stamp assigned to model initialization (days). 19000101.00 time_ref Reference time for units attribute (yyyymmdd.dd) It implies that the RO...
by arango
Mon Aug 28, 2017 4:36 pm
Forum: ROMS Problems
Topic: Error in ROMS execution
Replies: 7
Views: 1351

Re: Error in ROMS execution

Provide more information from the log file, not just the end. If you are using the latest version of ROMS, there is detailed information in the log file with source code and line number where the error occurred.
by arango
Tue Jul 11, 2017 10:10 pm
Forum: ROMS Benchmarks
Topic: Understanding ROMS output
Replies: 5
Views: 2145

Re: Understanding ROMS output

Yes, the primal formulation I4DVAR is very expensive because the minimization is done in the physical space (i.e. full application grid for the state vector, 10^5 to 10^7 points) so we need to do a lot of I/O manipulations in cgradient to compute and orthogonalize the Lanczos vectors. We need to rea...
by arango
Mon Jul 10, 2017 2:27 pm
Forum: ROMS Benchmarks
Topic: Understanding ROMS output
Replies: 5
Views: 2145

Re: Understanding ROMS output

What do you mean by the Lanczos algorithm? Are you talking about the minimization routine, rpcg_lanzos (RPCG)? The Lanczos vectors are stored in a NetCDF and use the adjoint model iterations over all outer and inner loops. I recently profiled WC13 with W4DPSAS : Nouter=2 and Ninner=50 on 4 CPUs on m...
by arango
Wed Jun 07, 2017 6:14 pm
Forum: Job Opportunities
Topic: Postdoctoral Research Position at UCLA
Replies: 0
Views: 1674

Postdoctoral Research Position at UCLA

Postdoctoral Researcher Position in Continental Shelf Currents and Their Surface Wave Interactions Departments of Atmospheric and Oceanic Sciences University of California, Los Angeles (UCLA) We are seeking a researcher to work on problems of oceanic circulation dynamics using the Regional Oceanic ...
by arango
Fri May 26, 2017 8:17 pm
Forum: ROMS Bugs
Topic: A new Y2K bug!
Replies: 2
Views: 1495

Re: A new Y2K bug!

Fixed the bug. It was not a Y2K bug. I coded datevec incorrectly in module dateclock.F . I was able to reproduce your problem with a simple test. Now, I get: 1 2000-02-28 00:02:30.00 9.193018E-09 1.954312E+04 1.954312E+04 1.659839E+17 (001,32,30) 1.799562E-05 8.159871E-10 0.000000E+00 4.667957E-03 2...
by arango
Thu May 25, 2017 11:04 pm
Forum: ROMS Bugs
Topic: A new Y2K bug!
Replies: 2
Views: 1495

Re: A new Y2K bug!

Weird. What calendar are you using? The behavior of your time reporting indicates to me that you are using the Proleptic Gregorian Calendar ( time_ref=0 or time_ref>0 ). The datenum and datevec routines in ROMS starts in in March 1, 0000 to facilitate the management of leap years: MyMonth=MOD(month+...
by arango
Sat Apr 29, 2017 2:00 pm
Forum: ROMS Installation
Topic: ran_state compilation error in ROMS
Replies: 5
Views: 1773

Re: ran_state compilation error in ROMS

Weird, I compiled with ifort , gfortran , and pgi and didn't get those errors. It turns out that I missed to transfer the updated files gasdev.F , nrutil.F , and ran1.F when I committed the ticket in another computer. We need these files to have i8b instead i4b . This is the reason why you are havin...
by arango
Wed Apr 26, 2017 8:22 pm
Forum: ROMS Ecosystem
Topic: Compiling error: dateclock?
Replies: 5
Views: 1775

Re: Compiling error: dateclock?

Yes, thank you for reporting this one. The weird thing is that I ran and debugged ( TotalView ) this version several times with the ifort compiler and didn't report any errors or warnings. It seems to be happy with the dot syntax. Of course, the correct syntax in Fortran is to use Rclock % . This ha...
by arango
Fri Apr 14, 2017 8:29 pm
Forum: ROMS Adjoint
Topic: nonlinear cost function not calculated in PSAS
Replies: 1
Views: 1156

Re: nonlinear cost function not calculated in PSAS

What are you reporting does not make sense to me. The NL_iDataPenalty and NL_fDataPenalty is computed and any of the 4D-Var drivers; w4dpsas_ocean.h in your case. In none of those drivers the VERIFICATION option is used. You just need to use the grep command to confirn this. The definition of these ...
by arango
Fri Apr 14, 2017 6:46 pm
Forum: ROMS Discussion
Topic: ROMS not bit-reproducible: northern boundary?
Replies: 32
Views: 7360

Re: ROMS not bit-reproducible: northern boundary?

Well, it seems that there is a problem with the latest version of OpenMPI . I wonder what did they change. This kind of problem is difficult to track and frustrating. Compilers and libraries are known to have bugs. One thing to check is if the OpenMPI library was compiled correctly with the same com...
by arango
Wed Jan 25, 2017 11:17 pm
Forum: ROMS Bugs
Topic: History file output fails using WRITE_WATER and river inflow
Replies: 2
Views: 2199

Re: History file output fails using WRITE_WATER and river in

Good catch, thank you :!: I updated the repository. Check the following :arrow: trac ticket for more information.
by arango
Tue Jan 24, 2017 3:18 am
Forum: ROMS Bugs
Topic: Error in Flux Integrals in Correct_Tracer - two-way nesting
Replies: 1
Views: 5399

Re: Error in Flux Integrals in Correct_Tracer - two-way nest

Yes, thank you very much for reporting this problem with great detail and providing a solution :!: I know that this kind of problems are kind of frustrating and takes a lot of patience to find them. It is refreshing when users get deep into the code and try to understand and find solutions to the pr...
by arango
Tue Jan 24, 2017 2:51 am
Forum: ROMS Bugs
Topic: Error with Multifiles
Replies: 9
Views: 6744

Re: Error with Multifiles

Yes, thank you for reporting this. It is difficult to guess the length of that string. I set it to 4096. See the following :arrow: trac ticket for more information.
by arango
Tue Jan 24, 2017 2:44 am
Forum: ROMS Bugs
Topic: Quicksave bug
Replies: 1
Views: 1322

Re: Quicksave bug

Yes, thank you. It is always a good strategy to initialize all the switches and variables. I updated the repository. For more information check the following :arrow: trac ticket.
by arango
Tue Jan 24, 2017 1:50 am
Forum: ROMS Bugs
Topic: A possible bug in get_data.F
Replies: 1
Views: 6944

Re: A possible bug in get_data.F

Yes, I can see why some compilers may have problems with this type of syntax. Thank you for reporting this issue. This is now fixed. See following :arrow: trac ticket.
by arango
Mon Oct 10, 2016 7:48 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, 4D-Var Tutorial Slides
Replies: 0
Views: 6966

2016 ROMS Asia-Pacific Workshop, 4D-Var Tutorial Slides

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 20, 2016 Andrew M. Moore will be giving a half day tutorial on ROMS 4D-Var. We are posting the slides for this presentation :arrow: here ahead of time so attendees can...
by arango
Tue Oct 04, 2016 5:03 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - Final Notice
Replies: 0
Views: 4730

2016 ROMS Asia-Pacific Workshop, Tasmania - Final Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 20, 2016 We have had several cancellations, making it necessary to rework the agenda. If you are presenting , please check :arrow: the agenda again as your presentatio...
by arango
Fri Sep 23, 2016 4:41 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS/TOMS Workshop T-shirt
Replies: 0
Views: 5005

2016 ROMS/TOMS Workshop T-shirt

This is our design for the ROMS T-shirt for the upcoming Asia-Pacific Workshop. The front is the an artistic rendition of the Hobart skyline with Mt. Wellington as a backdrop.
front.png
front.png (197.79 KiB) Viewed 5005 times
back.png
back.png (179.06 KiB) Viewed 5005 times
sleeve.png
sleeve.png (135.73 KiB) Viewed 5005 times
front_detail.png
front_detail.png (17.64 KiB) Viewed 5005 times
back_detail.png
sleeve_detail.png
sleeve_detail.png (2.24 KiB) Viewed 5005 times
by arango
Fri Sep 23, 2016 3:00 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 5th Notice
Replies: 0
Views: 4565

2016 ROMS Asia-Pacific Workshop, Tasmania - 5th Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 20, 2016 :!: NOTE: :!: Due to scheduling conflicts with other meetings the workshop has been compressed into 4 days. We apologize for the late notice on this. Please r...
by arango
Wed Aug 17, 2016 2:11 am
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 4th Notice
Replies: 0
Views: 5754

2016 ROMS Asia-Pacific Workshop, Tasmania - 4th Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 21, 2016 This is a reminder that the abstract deadline has passed. Please check the :arrow: participants list to confirm that your abstract has been submitted. If your...
by arango
Wed Aug 10, 2016 2:11 pm
Forum: ROMS Bugs
Topic: ROMS attempts to close un-named files
Replies: 3
Views: 3613

Re: ROMS attempts to close un-named files

Yes, please update. The error is due to the lack of the QCKNAME keyword in ocean.in . Notice that in :arrow: ticket 706 the field for NetCDF file ID, XXX%ncid=-1 , is initialized to close state in all the I/O structure arrays. This will allow to run newest ROMS version with old input ocean.in scripts.
by arango
Wed Jul 27, 2016 3:56 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 3rd Notice
Replies: 0
Views: 6379

2016 ROMS Asia-Pacific Workshop, Tasmania - 3rd Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 21, 2016 The extended registration deadline for the 2016 ROMS/TOMS Asia-Pacific Workshop is less than a week away. This is a reminder that registration deadline was ex...
by arango
Fri Jul 15, 2016 2:12 pm
Forum: ROMS Tools and Techniques
Topic: standard_name for U,V current components
Replies: 6
Views: 3969

Re: standard_name for U,V current components

Nope. It is not a vertical sum divided by the number of levels. It is a matter of semantics here. Perhaps, depth-averaged will be more appropriate. The shallow water equations are obtained by vertically integrating momentum and continuity equations in flux form. In curvilinear coordinates (xi, eta) ...
by arango
Thu Jul 14, 2016 5:06 pm
Forum: ROMS Tools and Techniques
Topic: standard_name for U,V current components
Replies: 6
Views: 3969

Re: standard_name for U,V current components

Nope, this cannot be done in varinfo.dat . I have thought about this in the past but we have so many variables. However, I can see how this is important for velocity components and third-party potting tools. It is very easy to add the standard_name to the variables in def_avg.F and def_his.F . We ju...
by arango
Thu Jun 09, 2016 5:55 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 2nd Notice
Replies: 0
Views: 7470

2016 ROMS Asia-Pacific Workshop, Tasmania - 2nd Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 21, 2016 The registration deadline for the 2016 ROMS/TOMS Asia-Pacific Workshop is approaching. This is a reminder that registration is open until June 30, 2016 . The ...
by arango
Thu Apr 21, 2016 3:38 pm
Forum: ROMS Bugs
Topic: Bug with grid coordinates for station file
Replies: 2
Views: 2078

Re: Bug with grid coordinates for station file

Thank you. I have to think about this. I need to reproduce your problem so I can look in the debugger.
by arango
Fri Feb 19, 2016 10:15 pm
Forum: ROMS Problems
Topic: Unrealisitic thickness of mixed layer
Replies: 15
Views: 10459

Re: Unrealisitic thickness of mixed layer

The MY2.5 scheme is coded correctly in ROMS and has several corrections that are not available in the original published formulation of the Mellor-Yamada 2.5. There are several papers in the literature about this. Also some people argue that the MY2.5 was not originally formulated correctly and the ...
by arango
Fri Feb 19, 2016 3:38 am
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 1st Notice
Replies: 0
Views: 4311

2016 ROMS Asia-Pacific Workshop, Tasmania - 1st Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 21, 2016 We are inviting you to participate at the 2016 ROMS Asia-Pacific Workshop to be held at the Institute for Marine and Antarctic Studies building on the Hobart ...
by arango
Thu Oct 29, 2015 2:54 pm
Forum: ROMS Problems
Topic: MP_EXCHANGE2D - communication buffer too small
Replies: 6
Views: 3386

Re: MP_EXCHANGE2D - communication buffer too small

This is not related to earlier posts in this forum thread. Anyway, this is weird. If you added biology, only mp_exchange4d is used in just two routines: pre_step3d.F: # ifdef DISTRIBUTE CALL mp_exchange4d (ng, tile, iNLM, 1, & & LBi, UBi, LBj, UBj, 1, N(ng), 1, NT(ng), & & NghostPoints, & & EWperiod...
by arango
Fri Oct 02, 2015 4:19 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 5187

Re: CPU time and MPI issues with nested grids

That's good that you guys use the full stencil at the interface to compute the mass fluxes entering the refined grid. I haven't observed smoothness problems in my testing applications with one-way nesting and 1:5 ratios. Anyway, we should always use two-way nesting since the one-way interaction has ...
by arango
Mon Sep 21, 2015 6:53 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 5187

Re: CPU time and MPI issues with nested grids

We need to take into account that ROMS_AGRIF has a reduced and simpler barotropic stepping engine ( step2d.F ), so it is more efficient. Therefore, we are not comparing apples with apples. Rutgers version of step2d.F includes additional terms so it is slower. In ROMS_AGRIF, all of those terms are in...
by arango
Fri Sep 18, 2015 1:15 pm
Forum: ROMS Problems
Topic: Online Nesting slow
Replies: 5
Views: 2584

Re: Online Nesting slow

What is the size of your grids? Also, what are the partitions that you are using? I want to be sure that you are not using excessive parallel nodes. There is always an optimal partition in ROMS. This is computer engineering and we should abstain to put a lot of processes just because they are availa...
by arango
Wed Sep 16, 2015 2:15 am
Forum: ROMS Installation
Topic: Can ROMS run just in Matlab?
Replies: 2
Views: 2301

Re: Can ROMS run just in Matlab?

Absolutely not. Why do you want to do such a thing? ROMS has over a million lines of code. There are ways to run simple and small Fortran programs in Matlab but the capability is very limited and you need to write an interface.
by arango
Fri Sep 11, 2015 10:47 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 4169

Re: two-way nesting only in the first refined grid

Please update. I fixed the problem that you were having. See the following :arrow: trac ticket for details. Thank you for reporting this problem :!:
by arango
Thu Sep 10, 2015 7:57 pm
Forum: ROMS Problems
Topic: Online Nesting slow
Replies: 5
Views: 2584

Re: Online Nesting slow

Yes, we are aware of this and it is in our TO-DO list. The issue here is that in two-way nesting (default) we are currently making global gathering of data (full 2D and 3D arrays) between all the MPI nodes to compute easily the fine-to-coarse averaging. This causes a bottle neck because of the exces...
by arango
Wed Sep 09, 2015 2:59 pm
Forum: ROMS Problems
Topic: Bug in large spherical nested run?
Replies: 5
Views: 2154

Re: Bug in large spherical nested run?

I have a new version of the Matlab scripts that I haven't released yet. I am still thinking about them. They are experimental and I will send them to your e-mail latter today. It provides alternatives to computing the metrics via interpolation instead of the great circle formula. Please sent me an e...
by arango
Tue Sep 08, 2015 5:09 pm
Forum: ROMS Problems
Topic: Bug in large spherical nested run?
Replies: 5
Views: 2154

Re: Bug in large spherical nested run?

Thanks Jamie for the detailed information. I have to think about this one. Obviously, the spherical grid is doing something to it. It makes me suspicious of the area/volume conservation. I wonder if the grid spacing (area) between coarse and fine grids is conserved in the sherical case. I assume tha...
by arango
Sat Sep 05, 2015 3:17 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 4169

Re: two-way nesting only in the first refined grid

I will have to reproduce this problem with a test case to see what it is going on. Your fix to main3d.F is not correct.
by arango
Fri Sep 04, 2015 10:10 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 4169

Re: two-way nesting only in the first refined grid

Refined grid by a factor of 4 is illegal. I don't know why contact.m allowed you to work by such a factor. You should get an error warning and stop. You only can have refimnement ratios of 3 , 5 , 7 , 9 , etc in ROMS because it is discritized on a C-grid . As a matter of dynamics and because of nume...
by arango
Fri Sep 04, 2015 5:47 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 4169

Re: two-way nesting only in the first refined grid

Perhaps, you should show us a diagram (plot) of all grids and their refinement ratio with respect the donor grid to check if you are setting the grids correctly.
by arango
Fri Sep 04, 2015 4:24 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 4169

Re: two-way nesting only in the first refined grid

Nope, this is not a good idea! because of the internal manipulations in several routine inside module nesting . It seems to me that you didn't specified the parameters correctly. The order of the grids are crucial. You need to think about the logical order when generating the contact NetCDF file wi...
by arango
Fri Sep 04, 2015 1:31 am
Forum: ROMS Bugs
Topic: bug in check_massflux in nesting.F
Replies: 2
Views: 2135

Re: bug in check_massflux in nesting.F

Yes, I did moved this code after I tested. Thank you for report this. I updated the repository. Nope, the values of BOUNDARY_CONTACT(:,:)%Mflux(:) are only used during debugging and testing to write several diagnostics to Fortran fort.100 , fort.200 , and fort.300 output files. Yes, they are loaded ...
by arango
Wed Aug 19, 2015 5:09 pm
Forum: ROMS Bugs
Topic: Bug in nesting when MASKING not defined
Replies: 1
Views: 1487

Re: Bug in nesting when MASKING not defined

Yep, good catch. Thank yTo be precise we need instead:

Code: Select all

# if defined MASKING || defined WET_DRY
      PRIVATE :: mask_hweights
# endif
I will update the code today.
by arango
Tue Jul 21, 2015 8:41 pm
Forum: ROMS Bugs
Topic: Bug in fine2coarse.m for nesting
Replies: 6
Views: 2417

Re: Bug in fine2coarse.m for nesting

There are two ways to construct refined nested grids: (1) coarse to fine grid refinement or (2) fine to coarse grid extraction. I prefer to do option (2) since all the quantities needed in the contact area are already available in the donor grid. If you don't see this, think about refinement and com...
by arango
Tue Jul 21, 2015 12:12 am
Forum: ROMS Usage
Topic: How to generate and use composite grids?
Replies: 16
Views: 5911

Re: How to generate and use composite grids?

Yes, it needs that information from the global attributes. Otherwise, contact.m will not work. These scripts are complex and there is a lot of internal details. They need to be used as a full package. I won't guarantee that a mixture of third party scripts will work together. There is a lot of subtl...
by arango
Mon Jul 20, 2015 7:06 pm
Forum: ROMS Usage
Topic: How to generate and use composite grids?
Replies: 16
Views: 5911

Re: How to generate and use composite grids?

That's your problem! You need to use Lmask=false when generating the contact points with the Matlab script. Please read the instructions! Notice that the default value is false . :idea: I have said several times in this forum that if we don't have experience in nesting applications for a particular ...
by arango
Thu Jul 16, 2015 7:02 pm
Forum: ROMS Bugs
Topic: Possible IO bug in close_io.F
Replies: 1
Views: 1591

Re: Possible IO bug in close_io.F

This is weird because close_inp is used in the adjoint-based algorithms to facilitate the iterations in the propagators and 4D-Var algorithms. This means that these files were already processed when reading input forcing fields. In the example that you provide above, which is exactly what I wrote in...
by arango
Thu Jul 16, 2015 6:29 pm
Forum: ROMS Bugs
Topic: Small bug in ad_v2dbc_im.F
Replies: 4
Views: 2180

Re: Small bug in ad_v2dbc_im.F

I don't know what are you talking about. I checked the code and it already have that correction! I think that you need to update. As you see below, ad_v2dbc_im.F already have the change as shown on :arrow: trac for Revision 767:
by arango
Thu Jul 16, 2015 5:15 pm
Forum: ROMS Problems
Topic: Create a sponge layer
Replies: 5
Views: 2667

Re: Create a sponge layer

I did a major overhaul of the sponge areas in ROMS sometime ago. We can have now visc_factor and diff_factor in the Grid NetCDF file. This is the way all application (simple or complex) that require areas of enhanced viscosity and diffusion. See the following :arrow: trac ticket for details. Notice ...
by arango
Thu Jul 16, 2015 4:35 pm
Forum: ROMS Wish List
Topic: Wish list
Replies: 2
Views: 1818

Re: Wish list

The nesting in ROMS (one- or two-way) is designed for all tracers active and passive. The nesting interface is generic for all tracers. The only constraint is that the bio-geochemical or sediment model needs to be activated in all grids in order to compute the contact point data between all grids (d...
by arango
Wed Apr 01, 2015 12:36 am
Forum: ROMS Bugs
Topic: Possible Issue with White_noise
Replies: 4
Views: 2113

Re: Possible Issue with White_noise

The routines in the white noise module white_noise.F are specific to the adjoint algorithms and we pass the Imin , Imax , Jmin , Jmax dummy variables as arguments. These are tiled parallel routines and need to be used by passing the appropriate values for these I- and J-range parameters. Using the a...
by arango
Thu Mar 12, 2015 5:10 pm
Forum: ROMS Bugs
Topic: Small bug in ad_v2dbc_im.F
Replies: 4
Views: 2180

Re: Small bug in ad_v2dbc_im.F

Yes, thank you.
by arango
Tue Mar 10, 2015 6:26 pm
Forum: ROMS Tools and Techniques
Topic: the depth of rho points for ROMS
Replies: 2
Views: 57811

Re: the depth of rho points for ROMS

The function zlevs is not part of our official distribution code and we are not responsible for third party functions coded by others. In the ROMS Matlab repository we offer: set_depth.m . This is the official Matlab version of such a function for computing depths at any C-grid location, if you use ...
by arango
Thu Mar 05, 2015 1:50 am
Forum: ROMS Discussion
Topic: DISCUSSION: Parallel Global Reduction & Volume Conservation
Replies: 0
Views: 1080

DISCUSSION: Parallel Global Reduction & Volume Conservation

Users can use the following thread to discuss the :arrow: Parallel Global Reduction and Volume Conservation post from the ROMS Messages forum.
by arango
Thu Mar 05, 2015 1:28 am
Forum: ROMS Messages
Topic: IMPORTANT: Parallel Global Reduction and Volume Conservation
Replies: 0
Views: 2156

IMPORTANT: Parallel Global Reduction and Volume Conservation

WARNING: You cannot replay or post comments in this forum thread. If you have any comments, use the following :arrow: post instead. In ROMS, we have the option to impose a volume conservation in applications with open boundaries if tidal forcing is not anabled: ! Set lateral open boundary edge volu...
by arango
Wed Mar 04, 2015 1:13 am
Forum: ROMS Usage
Topic: How to generate and use composite grids?
Replies: 16
Views: 5911

Re: How to generate and use composite grids?

I already fixed this problem in contact.m . I pretty much rewrote this logic so it is more robust. However, I am not ready to release it yet. There are other changes that we need to think carefully about and discuss between us before we can release the updated scripts. I don't have the time to check...
by arango
Fri Feb 27, 2015 6:26 pm
Forum: ROMS Usage
Topic: Is OUT_DOUBLE strictly necessary when using PERFECT_RESTART?
Replies: 2
Views: 1409

Re: Is OUT_DOUBLE strictly necessary when using PERFECT_REST

Yes, the ROMS restart file is always, by default, in double precision since all the computations in ROMS are in double precision. The option RST_SINGLE was added because some users were complaining that the restart file was getting too big in very large applications. The restart file has only two ro...
by arango
Mon Feb 16, 2015 6:40 pm
Forum: ROMS Problems
Topic: Assimilating SSH – high res model blowup! Stability issue?
Replies: 5
Views: 2668

Re: Assimilating SSH – high res model blowup! Stability issu

The error covariance balanced operator is kind of tricky. It is based on Weaver et al. (2005) method. It imposes a multivariate constraint on the background error covariance such that the unobserved variable(s) information is extracted from the observed (assimilated) data using T-S empirical relatio...
by arango
Mon Feb 16, 2015 5:29 pm
Forum: ROMS Ecosystem
Topic: light units for ec_Fobar
Replies: 1
Views: 1681

Re: light units for ec_Fobar

I don't know what are the units. This is used in the downwelling spectral irradiance routine ana_specir.h . This was adapted from a routine provided by Paul Bissett for the EcoSim model. That routine says that it is based on Gregg and Carder (1990) model and few units were provided. It is used to co...
by arango
Wed Feb 11, 2015 6:15 pm
Forum: ROMS Discussion
Topic: How can i get the depth from sima coordinate to Z- ??
Replies: 2
Views: 1026

Re: How can i get the depth from sima coordinate to Z- ??

In the ROMS Matlab repository you can find the function depths.m or set_depth.m . More importantly, the above plot was produced with scoord.m , which outputs the quantity that you seek: [z,s,C]=scoord(h, x, y, Vtransform, Vstretching, theta_s, theta_b, ... hc, N, kgrid, column, index, plt, Zzoom) Yo...
by arango
Wed Feb 11, 2015 6:02 pm
Forum: ROMS Bugs
Topic: Bug in wet_dry- the lake_jersey case has the same issue
Replies: 8
Views: 2465

Re: Bug in wet_dry- the lake_jersey case has the same issue

You need to start paying more attention to the updates to the code, specially if you are using nesting. You need to read carefully the following :arrow: post . It contains information about the quadratic interpolation. It is not ready yet :!: Also, the information about the wet/dry update was provid...
by arango
Fri Feb 06, 2015 4:09 pm
Forum: ROMS Problems
Topic: Assimilating SSH – high res model blowup! Stability issue?
Replies: 5
Views: 2668

Re: Assimilating SSH – high res model blowup! Stability issu

I hope that you are plotting the cost function to see if 4D-Var is converging. It is not clear to me if you are using 5 or 30 inner loops. If you are using 5 inner loops, I doubt that the 4D-Var algorithm converged and this may explain your blow-up when running the nonlinear model. If your prior SSH...
by arango
Thu Jan 29, 2015 5:49 pm
Forum: ROMS Tools and Techniques
Topic: Coastline file for the ROMS Plotting Package
Replies: 4
Views: 3785

Re: Coastline file for the ROMS Plotting Package

I pretty much doubt that you will be able to do this. These coastlines files are very special and extremely difficult to reproduce. We need closed polygons and the order of values matters to distinguish between continents, islands, and lakes. The filling algorithm in the plotting package requires th...
by arango
Wed Jan 28, 2015 4:18 pm
Forum: ROMS Tools and Techniques
Topic: Coastline file for the ROMS Plotting Package
Replies: 4
Views: 3785

Re: Coastline file for the ROMS Plotting Package

Yes, that's correct. There are several coastline files at various resolutions including global datasets: global_low.cst, global_crude.cst, and global_inter.cst. Western longitudes and southern latitudes are negative with ranges -180 to 180 and -90 to 90, respectively.
by arango
Thu Jan 22, 2015 5:14 pm
Forum: ROMS Usage
Topic: How to generate and use composite grids?
Replies: 16
Views: 5911

Re: How to generate and use composite grids?

Although I have not tried passive tracers yet in nesting, the algorithm is designed to work on all tracers (active and passive). We operate on the full 5D tracer array. If works on temperature and salinity, it will work also on passive tracers. As designed, you need passive tracers (like biology) in...
by arango
Wed Jan 21, 2015 6:00 pm
Forum: ROMS Bugs
Topic: bug report in BIO_fennel module
Replies: 3
Views: 1819

Re: bug report in BIO_fennel module

Nope, what I am saying is that in a model like BIO_FENNEL with so many options for additional biological components, you need to know what the order of biological tracer is in idbio(:) and that's the order that you need follow in LBC(isTvar) . If you don't know what that order is, you need to look a...
by arango
Wed Jan 21, 2015 5:21 pm
Forum: ROMS Usage
Topic: How to generate and use composite grids?
Replies: 16
Views: 5911

Re: How to generate and use composite grids?

Okay, I need to track this problem in contact.m . I was able to reproduce you error. I will look at this soon to see what is the solution for this out-of-range values when computing the interpolation weights. I also have in my to do list to have a realistic application with composite grids. However,...
by arango
Wed Jan 21, 2015 5:12 pm
Forum: ROMS Bugs
Topic: bug report in BIO_fennel module
Replies: 3
Views: 1819

Re: bug report in BIO_fennel module

Your first panel is completely illegal and a numerical absurdity; the western boundary is periodic and the eastern boundary closed for zooplankton and others. You better understand what periodicity is. Periodic boundary conditions works in pairs: west/east boundaries and south/north boundaries. ROMS...
by arango
Thu Jan 15, 2015 2:07 pm
Forum: ROMS Problems
Topic: 4DVAR observation impact driver problem WC13
Replies: 3
Views: 1745

Re: 4DVAR observation impact driver problem WC13

Yes, that fixed the problem.
by arango
Wed Jan 14, 2015 4:32 pm
Forum: ROMS Problems
Topic: make_ clim error
Replies: 5
Views: 2884

Re: make_ clim error

The only Matlab scripts that we support for processing our version of ROMS are located in the Matlab svn repository: https://www.myroms.org/svn/src/matlab :!: These are the official version of these scripts containing the correct functions to process vertical coordinate schemes, nesting, land/sea ma...
by arango
Thu Jan 08, 2015 2:55 pm
Forum: ROMS Problems
Topic: TS_MPDATA and TS_U3HADVECTION_TL... Dsrc not found? I4DVAR
Replies: 4
Views: 2139

Re: TS_MPDATA and TS_U3HADVECTION_TL... Dsrc not found? I4DV

I changed the TS_MPDATA to TS_MPDATA_NOT_YET in several TLM , RPM , and ADM routines. It think that this will solve your compilation problem. See :arrow: trac ticket for more information. You need to update. By the way, your header file angola_3km_4dvar.h needs some cleaning, specially when you use ...
by arango
Tue Jan 06, 2015 5:23 pm
Forum: ROMS Problems
Topic: TS_MPDATA and TS_U3HADVECTION_TL... Dsrc not found? I4DVAR
Replies: 4
Views: 2139

Re: TS_MPDATA and TS_U3HADVECTION_TL... Dsrc not found? I4DV

Yes, it needs to be SOURCES(ng)%Dsrc(is) , thank you :!: That's was easy an obvious. The ARPACK library is needed in the propagators drivers for Generalized Stability Analysis that uses the tangent linear and adjoint models. What are the undefined references in ad_step3d_t ? We don't need the ARPACK...
by arango
Wed Dec 17, 2014 2:49 pm
Forum: ROMS Bugs
Topic: nesting_bug
Replies: 3
Views: 1835

Re: nesting_bug

I have checked the new released codes carefully for the last two months (countless hours in the debugger) with idealized and a realistic applications in the South China Sea and the US East Coast and they work fine. The one that you were using before have several serious bugs. I don't know what is wr...
by arango
Tue Dec 16, 2014 2:26 pm
Forum: ROMS Installation
Topic: Compiling with TS_MPDATA and I4DVAR... Dsrc not found?
Replies: 3
Views: 2100

Re: Compiling with TS_MPDATA and I4DVAR... Dsrc not found?

The option TS_MPDATA is not adjointed. It is highly nonlinear. You can still use the TS_MPDATA for the forward nonlinear model and any other option for the adjoint and tangent linear models. In cppdefs.h , we have: ** The flags below are optional. By default, the same options chosen ** ** for the no...
by arango
Tue Dec 16, 2014 12:02 pm
Forum: ROMS Releases
Topic: Major update to the Nesting Algorithms
Replies: 0
Views: 10853

Major update to the Nesting Algorithms

Recommendations: :idea: This post has lots of detailed information. Please carefully read and study the provided information before loading this forum with lots of questions that are probably answered below. The nesting algorithms are complex and require experience and patience. I highly recommend ...
by arango
Mon Dec 15, 2014 5:18 pm
Forum: ROMS Information
Topic: Question about Sea level
Replies: 5
Views: 2935

Re: Question about Sea level

This is very simple. You are gaining volume and this is due to the open boundaries. You may plot the domain volume for your solution as a function of time. It seems that using climatology at the boundary is not working for you. Nowadays, we get boundary condition from global models. Imposing climato...
by arango
Tue Dec 09, 2014 3:59 am
Forum: ROMS Bugs
Topic: WET_DRY and NESTING (refined) possible bug
Replies: 6
Views: 2447

Re: WET_DRY and NESTING (refined) possible bug

I changed the logic how is this done. Please be patient. An upgrade to the nesting algorithms will be released in the next two days. I am working on the documentation.
by arango
Wed Dec 03, 2014 2:14 am
Forum: ROMS Discussion
Topic: one problem in run time
Replies: 7
Views: 1285

Re: one problem in run time

One person reported much better performance from the ROMS_Agrif code over both the Rutgers ROMS and the COAWST ROMS when using the nesting. You might try that. Actually, this has a good explanation that mostly everybody is not aware. The barotropic engine in either the UCLA ROMS or ROMS_Agrid (I be...
by arango
Tue Nov 25, 2014 2:49 pm
Forum: ROMS Discussion
Topic: Latent Heat Flux Problem with ROMS 741
Replies: 3
Views: 2556

Re: Latent Heat Flux Problem with ROMS 741

It is up to you what values to use according to the dataset that you have. Notice that in ocean.in you need to specify the height (m) of the atmospheric fluxes: ! Height (m) of atmospheric measurements for Bulk fluxes parameterization. BLK_ZQ == 10.0d0 ! air humidity BLK_ZT == 10.0d0 ! air temperatu...
by arango
Thu Nov 20, 2014 12:07 am
Forum: ROMS Discussion
Topic: inert passive tracer boundary not being read
Replies: 8
Views: 1730

Re: inert passive tracer boundary not being read

Please update your codes. I corrected this bug in the repository. See following :arrow: trac ticket for details.
by arango
Wed Nov 19, 2014 11:03 pm
Forum: ROMS Tools and Techniques
Topic: TNU2 and VISC2 values
Replies: 4
Views: 2319

Re: TNU2 and VISC2 values

Your question cannot be answered in this forum because pretty much you need to be aware of the full history of Physical Oceanography and Ocean Modeling. There are decades of excellent literature about the subject starting with Henry Stommel, Walter Munk, and others. Any Physical Oceanographer or Oce...
by arango
Fri Nov 14, 2014 9:54 pm
Forum: ROMS Discussion
Topic: inert passive tracer boundary not being read
Replies: 8
Views: 1730

Re: inert passive tracer boundary not being read

Yes, I know. I has an update for it. Mark Hadfield put a post about this and the solution.
by arango
Thu Nov 13, 2014 6:39 pm
Forum: ROMS Discussion
Topic: way of reducing vertical mixing ...
Replies: 3
Views: 1239

Re: way of reducing vertical mixing ...

The turbulent schemes like MY-2.5 or GLS tend to give high vertical mixing coefficients if you have strong winds and buoyancy forcing. Try the KPP scheme to see what you get. The mixing is more controlled in LMD_MIXING.
by arango
Fri Nov 07, 2014 7:33 pm
Forum: ROMS Problems
Topic: tidal forcing file: inconsistent restart and harmonic time
Replies: 2
Views: 1551

Re: tidal forcing file: inconsistent restart and harmonic ti

I don't know why you have to do this. I far as recall, we don't need to change the input script except for the restart flag and the initial conditions NetCDF: NRREC == -1 ... ININAME == ocean_rst.nc You shouldn't change: DSTART = xxxxx ! days TIDE_START = xxxxx ! days TIME_REF = xxxxx ! yyyymmdd.dd ...
by arango
Thu Nov 06, 2014 4:04 pm
Forum: ROMS Discussion
Topic: Compiling 'AVERAGES_TIDE'
Replies: 13
Views: 3274

Re: Compiling 'AVERAGES_TIDE'

Come on people... With a little of curiosity and using " grep -r Hcount * | grep -v .svn " in the top of the ROMS tree directory you will find where Hcount is used. You will noticed that it is defined in def_tides.F and written in wrt_tides.F . If you do another search for def_tides you will find th...
by arango
Thu Nov 06, 2014 3:42 pm
Forum: ROMS Bugs
Topic: PROFILE report
Replies: 4
Views: 2579

Re: PROFILE report

This is in my to do list. I had noticed it too. The logic is delicate because of shared-memory. I am busy with other codes now.
by arango
Sat Nov 01, 2014 4:55 pm
Forum: ROMS Bugs
Topic: Problem with compact tracer Rad + Nud boundaries
Replies: 2
Views: 2093

Re: Problem with compact tracer Rad + Nud boundaries

Yes Mark, good catch :!: Thank you.
by arango
Wed Oct 29, 2014 2:30 am
Forum: ROMS Discussion
Topic: how to active ADJUST_BOUNDARY
Replies: 2
Views: 623

Re: how to active ADJUST_BOUNDARY

This is only used in the 4D-Var algorithms to include the boundary conditions in the control vector. You just need to activate ADJUST_BOUNDARY. Additional input files are required for this option. See tutorials.
by arango
Wed Oct 29, 2014 2:25 am
Forum: ROMS Discussion
Topic: ROMS Boundary Condition: Clamped vs. Flather
Replies: 4
Views: 1178

Re: ROMS Boundary Condition: Clamped vs. Flather

Apparently, you are using a very old version the ROMS. All the CPP for open boundary conditions were removed and replaced with logical switches in ocean.in to facilitate nesting.
by arango
Wed Oct 29, 2014 2:22 am
Forum: ROMS Bugs
Topic: a small bug in inp_par.F
Replies: 2
Views: 1730

Re: a small bug in inp_par.F

Yes, good catch. Thank you.
by arango
Sat Oct 25, 2014 11:51 pm
Forum: ROMS Problems
Topic: Unexpected(?) blow up
Replies: 7
Views: 3055

Re: Unexpected(?) blow up

My experience with blows-up of this type after several years running is due to atmospheric forcing, specially wind stress due to strong storms. By the way, this happen to us in the Mediterranean part of our grids too. In the Aegean, there are strong winds sometimes. What we usually do is restart wit...
by arango
Wed Oct 22, 2014 4:35 pm
Forum: ROMS Problems
Topic: wetting and drying problem
Replies: 22
Views: 10229

Re: wetting and drying problem

Applying the wetting and drying mask in step_t or to any tracer anywhere is really bad :!: Lyon, this was actually the problem that you were having with the perfect restart in your Cook Inlet application. We were multiplying with such mask during I/O. I mentioned this before. If a particular cell is...
by arango
Mon Oct 20, 2014 4:57 pm
Forum: ROMS Bugs
Topic: WET_DRY and NESTING (refined) possible bug
Replies: 6
Views: 2447

Re: WET_DRY and NESTING (refined) possible bug

Well, this is a hard problem. The interpolation weights need to be adjusted if you get wet and dry cells at every time step because of the masking. I need to look for a solution for this case. Bringing refinement grids all the way to the coast with wetting and drying requires special considerations....
by arango
Mon Oct 20, 2014 4:46 pm
Forum: ROMS Tools and Techniques
Topic: nested grid layer and min depth
Replies: 7
Views: 3249

Re: nested grid layer and min depth

It has been mentioned several times in this forum that more than two nesting layers for refinement grids still need some debugging for NestLayers > 2 . Your configuration with four grids is very poor and ill-posed in my opinion. Obviously, you need to gain more experience with nested grids and ocean...
by arango
Mon Oct 20, 2014 4:30 pm
Forum: ROMS Bugs
Topic: latest ROMS version problem
Replies: 6
Views: 3225

Re: latest ROMS version problem

You are getting this error because you are using an older version of the metadata file varinfo.dat . You need to use the updated file from the latest version of the code. Notice that I added to varinfo.dat the metadata for the wetting and drying mask at PSi-points that it is needed for restart: 'wet...
by arango
Mon Oct 20, 2014 4:22 pm
Forum: ROMS Bugs
Topic: tiny nesting/mp_aggregate2d bug
Replies: 1
Views: 1229

Re: tiny nesting/mp_aggregate2d bug

Yes, good catch. Thank you. I am still debugging this routines for various configurations.
by arango
Mon Oct 13, 2014 5:35 pm
Forum: ROMS Bugs
Topic: WET_DRY and Dcrit
Replies: 13
Views: 6682

Re: WET_DRY and Dcrit

I can see how the rotated tensor for tracer diffusion can go unstable near wetting and drying areas. We cannot numerically develop a wetting and drying algorithm from first principles in a model like ROMS, but we can use an engineering approach. I think that if you need horizontal diffusion in your ...
by arango
Mon Oct 13, 2014 4:50 pm
Forum: ROMS Problems
Topic: wetting and drying problem
Replies: 22
Views: 10229

Re: wetting and drying problem

Hi Kate, I think that my big update to the wetting and drying will be released this week and the restart problem is now solved :D I am still running NOAA's Cook Inlet application but very slowly :( The grid is huge ( 1044x724x30 ) and I am running in my 8-CPUs desktop in case that I need to examine ...
by arango
Wed Oct 08, 2014 8:58 pm
Forum: ROMS Discussion
Topic: initial-nest
Replies: 13
Views: 3374

Re: initial-nest

The answer for both questions is that you need separate files. Nesting is complex and users need to explore first with the larger grid before trying to run with nested grid. It requires expertise to set the nested grids correctly. Users need lots of experience with ROMS, ocean modeling, and the ocea...
by arango
Tue Oct 07, 2014 1:09 am
Forum: ROMS Installation
Topic: How can I write concise global attributes into netcdf files
Replies: 2
Views: 1777

Re: How can I write concise global attributes into netcdf fi

This is absurd. In never heard anything like it. The buffer for the global attributes is extremely smaaaaaaall compared with the data. Obviously, you need to read more about the NetCDF files and its unique format. You cannot remove the global attributes in any of the ROMS history file because the mo...
by arango
Mon Sep 01, 2014 5:34 pm
Forum: ROMS Problems
Topic: 4DVAR observation impact driver problem WC13
Replies: 3
Views: 1745

Re: 4DVAR observation impact driver problem WC13

I don't know what it is the problem here. The CLIMA(:) structure has a -1 index. That's is kind of weird. I will need to reproduce the problem. I added it to my to-do list.
by arango
Tue Aug 19, 2014 5:59 pm
Forum: ROMS Bugs
Topic: Test cases failing to compile in ROMS 3.7
Replies: 2
Views: 1667

Re: Test cases failing to compile in ROMS 3.7

Indeed, thank you for reporting this.
by arango
Mon Jun 30, 2014 4:17 pm
Forum: ROMS Discussion
Topic: tidal analysis of large output files
Replies: 22
Views: 6486

Re: tidal analysis of large output files

It is possible that your solution is not long enough to separate all the 9 tidal frequencies in your application. Recall that we have in ROMS the nonlinear interaction between all the frequencies and resonance. If you have an application with just M 2 and S 2 , it will take around 30 days of solutio...
by arango
Fri May 16, 2014 3:54 pm
Forum: Meetings/Workshops
Topic: 2014 ROMS/TOMS User Workshop, Rovinj, Croatia - Final Notice
Replies: 0
Views: 1465

2014 ROMS/TOMS User Workshop, Rovinj, Croatia - Final Notice

2014 ROMS/TOMS User Workshop Island Hotel Istra, Rovinj, Croatia, May 26 - 29, 2014 Please check the following link for the workshop agenda: http://www.myroms.org/index.php?page=ROMS_2014_agenda Notice that it includes oral talks, lectures, and poster sessions. The oral presentations are 30 minutes...
by arango
Tue May 06, 2014 3:25 pm
Forum: ROMS Discussion
Topic: 3-level nesting
Replies: 3
Views: 1055

Re: 3-level nesting

Yes, thank you. It is in my list of things to do. I am updating the script contact.m . In the mean time, you may experiment with the two-level nesting. It takes awhile to get the grids just right. So you need to run and play with the configuration that works the best. The placement of nested grids i...
by arango
Tue May 06, 2014 12:29 pm
Forum: Meetings/Workshops
Topic: 2014 ROMS/TOMS Workshop T-shirt
Replies: 0
Views: 1475

2014 ROMS/TOMS Workshop T-shirt

This is out current design of the ROMS T-shirt for the upcoming User Workshop. The symbol on the front is the letter M (mislite) from the Glagolitic alphabet and means thought or think. The alternating red and white symbolizes the well-known red and white checkerboard from the Croatian coat of arms ...
by arango
Tue Apr 29, 2014 2:32 pm
Forum: ROMS Discussion
Topic: different restart files
Replies: 7
Views: 1685

Re: different restart files

You have LcycleRST = F . This implies that you will have a single restart file with multiple time records (in your case, each record is written every 1920 time-steps). The restart records are not recycled to have the latest two records in the restart file. Therefore, the restart file will grow with ...
by arango
Fri Apr 18, 2014 10:22 pm
Forum: ROMS Bugs
Topic: Potential bug in ROMS perfect restart
Replies: 16
Views: 4889

Re: Potential bug in ROMS perfect restart

I don't know. I will need to reproduce the problem to check if this is the case.
by arango
Fri Apr 18, 2014 8:00 pm
Forum: ROMS Bugs
Topic: Potential bug in ROMS perfect restart
Replies: 16
Views: 4889

Re: Potential bug in ROMS perfect restart

The correction suggested by Kate above is incorrect. We ALWAYS need to use the rmask_io, umask_io, and vmask_io in the output NetCDF files :!: This is even more crucial when we have rivers and wetting and drying...
by arango
Fri Apr 11, 2014 4:08 pm
Forum: ROMS Usage
Topic: Construction of forcing file (stationary forcing)
Replies: 5
Views: 2534

Re: Construction of forcing file (stationary forcing)

The cycle_length attribute is for other purposes. There is even a better solution for perpetual forcing. You don't need two-time records and avoid all that unnecessary time interpolation at every time-step :!: You guys really need to read the information that I put in the ticket changes to the repos...
by arango
Thu Apr 10, 2014 10:33 pm
Forum: ROMS Bugs
Topic: Possibly 3 nesting-related bugs
Replies: 16
Views: 5389

Re: Possibly 3 nesting-related bugs

Of course, this makes a lot of sense to me. We cannot apply volume conservation in a regional tidally forced application :!: Tides do not conserve volume in such applications. If you do so, you will alter the tidal signal. Therefore, this explains very well your pink curve. So now you know what happ...
by arango
Thu Apr 03, 2014 9:01 pm
Forum: ROMS Bugs
Topic: Beware of netCDF STRINGs
Replies: 6
Views: 4225

Re: Beware of netCDF STRINGs

Yes, I read your postings in the NetCDF forum. This is an annoying one. I always use the CHAR flags. Characters and strings are awkward in NetCDF. I am pretty conservative about the new features in the NetCDF library. I struggled a lot with them when designing the NetCDF file for the nesting contact...
by arango
Thu Apr 03, 2014 6:35 pm
Forum: ROMS Discussion
Topic: 3-level nesting
Replies: 3
Views: 1055

Re: 3-level nesting

Okey, I haven't tried the three-level case yet. I did tried 3-grids and two-levels. I will need to reproduce this problem. I will put in my list of things to do. I hope that it is simple to fix. The order of how you specify the grid file names is extremely important (coarser to finer). Thank you for...
by arango
Thu Apr 03, 2014 5:48 pm
Forum: ROMS Bugs
Topic: Possibly 3 nesting-related bugs
Replies: 16
Views: 5389

Re: Possibly 3 nesting-related bugs

Yes, the calls to the exchange routines exchange_v2d_tile and mp_exchange3d need to be corrected as you mentioned above. However, your corrections to get_data and set_data are incorrect :!: We still can use climatology fields in refined grids for other purposes :!: Notice that the processing of clim...
by arango
Thu Apr 03, 2014 5:15 pm
Forum: ROMS Bugs
Topic: missing routine
Replies: 7
Views: 2152

Re: missing routine

Okey, all my refinement test cases have a ratio of 1:3 . I will need to have a test case with a 1:5 ratio to reproduce this problem and check in the debugger for a fix to the out-of-bounds error. It shouldn't that difficult to fix. This is only used in coupled routines. I think that something is wro...
by arango
Thu Apr 03, 2014 5:05 pm
Forum: ROMS Bugs
Topic: missing routine
Replies: 7
Views: 2152

Re: missing routine

Yes, the uniform field in the grid structure was added recently. The fix in coarse2fine.m and fine2coarse.m is very simple. ITS value should be available and inherited from the donor grid.

Thank you for bringing this to my attention. Please update.
by arango
Tue Apr 01, 2014 12:13 pm
Forum: ROMS Discussion
Topic: How to define the input forcing files when having many?
Replies: 2
Views: 1625

Re: How to define the input forcing files when having many?

:idea: The instructions are very clear in all input scripts. You just have to read :!: ! Input parameters can be entered in ANY order, provided that the parameter ! ! KEYWORD (usually, upper case) is typed correctly followed by "=" or "==" ! ! symbols. Any comment lines are allowed and must begin wi...
by arango
Tue Apr 01, 2014 2:55 am
Forum: ROMS Bugs
Topic: missing routine
Replies: 7
Views: 2152

Re: missing routine

The gcircle.m script is in the matlab/utility directory. The G.uniform should be set-up in get_roms_grid.m . Do you have the latest version of this script? or perhaps it is shadowed by an old version in another disrectory in your path. If not, it missed something about this. I always get the uniform...
by arango
Fri Mar 28, 2014 10:03 pm
Forum: ROMS Bugs
Topic: 2 possible bugs in Shc boundary conditions
Replies: 6
Views: 3388

Re: 2 possible bugs in Shc boundary conditions

Indeed, I fixed those bugs. Please update. Thank you for bringing this to my attention. I also corrected the tangent linear, representer, and adjoint versions of u2dbc_im.F and v2dbc_im.F.
by arango
Fri Mar 28, 2014 6:26 pm
Forum: Meetings/Workshops
Topic: 2014 ROMS/TOMS User Workshop, Rovinj, Croatia - 4th Notice
Replies: 0
Views: 1221

2014 ROMS/TOMS User Workshop, Rovinj, Croatia - 4th Notice

2014 ROMS/TOMS User Workshop Island Hotel Istra, Rovinj, Croatia, May 26 - 29, 2014 The deadline to submit abstracts for oral presentations and posters is only a week away on April 4, 2014 . Please submit your abstract by that date. The registration deadline for the 2014 ROMS/TOMS User Workshop was...
by arango
Wed Mar 19, 2014 7:42 pm
Forum: ROMS Bugs
Topic: ini_hmixcoef.F
Replies: 1
Views: 1149

Re: ini_hmixcoef.F

Yes, indeed. Thank you for reporting this problem. Please check the following :arrow: trac ticket and update.
by arango
Wed Mar 19, 2014 7:39 pm
Forum: ROMS Bugs
Topic: Possible bug with check_multifile.F changeset 713
Replies: 5
Views: 2571

Re: Possible bug with check_multifile.F changeset 713

OK, I improved the decoding of the units attribute. Please check the following :arrow: trac ticket. Please update. Thank you for providing enough information for tracking this.
by arango
Wed Mar 19, 2014 12:09 am
Forum: ROMS Bugs
Topic: Possible bug with check_multifile.F changeset 713
Replies: 5
Views: 2571

Re: Possible bug with check_multifile.F changeset 713

Around line 117, we have the following code: IF (Lcheck) THEN Tmax=Tscale*BRY(ng)%time_max(Nfiles) IF (Tfinal.gt.Tmax) THEN CALL time_string(Tmax, Tmax_code) IF (Master) THEN WRITE (stdout,30) 'Lateral Boundary', & & TRIM(BRY(ng)%files(Nfiles)), & & Tmax_code, F_code END IF exit_flag=4 END IF END IF...
by arango
Mon Mar 17, 2014 2:11 pm
Forum: ROMS Problems
Topic: Inconsistent timestep reporting after restart under OpenMP?
Replies: 4
Views: 1883

Re: Inconsistent timestep reporting after restart under Open

This bug was corrected. Please check the following :arrow: ticket for details. Thank you for reporting this problem. Please update.
by arango
Mon Mar 17, 2014 2:09 pm
Forum: ROMS Bugs
Topic: OpenMP problem with restart from file
Replies: 4
Views: 2332

Re: OpenMP problem with restart from file

Yes, I was able to reproduce this bug. I finally have time to check it in the debugger. I corrected the bug. See :arrow: ticket for details. Thank you for bringing this to my attention. Please update.
by arango
Wed Mar 12, 2014 3:40 pm
Forum: ROMS Problems
Topic: restart file vs. grid file
Replies: 2
Views: 1154

Re: restart file vs. grid file

No. It still reads the grid NetCDF file. You just need to change the file that it reads for initial conditions. In this case, it need to read the restart file for the specified input time record.
by arango
Wed Mar 12, 2014 3:35 pm
Forum: ROMS Installation
Topic: problem when first running upwelling test
Replies: 13
Views: 7529

Re: problem when first running upwelling test

ROMS/Include/cppdefs.h:625:0: fatal error: /Projects/upwelling/upwelling.h: No such file or directory compilation terminated. make: *** [/Projects/upwelling/Build/abort.f90] Error 1 The compiler is telling you what the error is. It cannot find the ROMS header file for this application: /Projects/up...
by arango
Wed Feb 12, 2014 7:20 pm
Forum: Meetings/Workshops
Topic: 2014 ROMS/TOMS User Workshop, Rovinj, Croatia - 3rd Notice
Replies: 0
Views: 1227

2014 ROMS/TOMS User Workshop, Rovinj, Croatia - 3rd Notice

2014 ROMS/TOMS User Workshop Island Hotel Istra, Rovinj, Croatia, May 26 - 29, 2014 The reduced rate hotel booking deadline of is only a few days away. Please book your hotel reservations using :arrow: this link by February 15, 2014 because prices will be significantly higher after that date. For e...
by arango
Tue Feb 11, 2014 3:02 am
Forum: ROMS Bugs
Topic: possible bug with TCLIMATOLOGY
Replies: 4
Views: 2499

Re: possible bug with TCLIMATOLOGY

Nope, that it is your homework. I just give you a clue CLIMA_TS_MIX
by arango
Tue Feb 11, 2014 2:59 am
Forum: ROMS Bugs
Topic: Possible bug with check_multifile.F changeset 713
Replies: 5
Views: 2571

Re: Possible bug with check_multifile.F changeset 713

Yes, good catch :!: We need to use dstart instead:

Code: Select all

!
!  Get final time string for simulation.
!
      Tfinal=dstart*day2sec+ntimes(ng)*dt(ng)
      CALL time_string(tfinal, F_code)
Thank you for reporting this problem. Please update.
by arango
Tue Feb 11, 2014 1:56 am
Forum: ROMS Bugs
Topic: possible bug with TCLIMATOLOGY
Replies: 4
Views: 2499

Re: possible bug with TCLIMATOLOGY

Well, I have been reviewing all this logic lately. I need to remove all the CPP options for climatology and substituting them with logical switches because of nesting. We need to control if a nested grid needs climatology or not. The code is correct as it is. This is done intentionally. The switches...
by arango
Tue Feb 11, 2014 1:09 am
Forum: ROMS Bugs
Topic: small bug in ad_npzd_iron.h
Replies: 1
Views: 1077

Re: small bug in ad_npzd_iron.h

Good catch :!: Indeed, we need to initializing both to zero in the adjoint code. Thank you for reporting this bug.
by arango
Sat Feb 01, 2014 2:00 am
Forum: ROMS Bugs
Topic: Possible bug with stations in a nested grid configuration
Replies: 1
Views: 1806

Re: Possible bug with stations in a nested grid configuratio

Indeed, this should be: IF (ABS(Apos(np)).eq.0.0_r8) Apos(np)=0.0_r8 ! positive ! zero This is done to impose positive zero . It is harmless except when you have only one station and ng > 1 , so you get the out-of-bounds error. It occurs in several places in extract_sta.F . Starting F95 zero values ...
by arango
Wed Jan 29, 2014 3:18 pm
Forum: ROMS Usage
Topic: river points
Replies: 6
Views: 3142

Re: river points

The river_flag is obsolete and not longer used it :!: Read the documentation: LtracerSrc Logical switches (T/F) to activate tracer variables point Sources/Sinks. Only NAT active tracers (temperature, salinity) and NPT inert tracers are activated here: LtracerSrc(itemp,ng) for temperature (itemp=1) L...
by arango
Wed Jan 29, 2014 3:11 pm
Forum: ROMS Problems
Topic: run problem
Replies: 4
Views: 1921

Re: run problem

We are very busy people to start downloading everybody files for us to plot them and then tell you what it is wrong. It is for you to investigate and learn what maybe happening. The fact that model is blowing-up right away is possibly due to wrong configuration files and/or CFL violation. The learni...
by arango
Tue Jan 28, 2014 2:12 am
Forum: ROMS Discussion
Topic: Problem with large size initial files
Replies: 10
Views: 2145

Re: Problem with large size initial files

It is possible that either the input nesting parameter NestLayers or GridsInLayer were set to zero in the ocean.in script. That may explain the out-of-bounds in GridNumber . I updated the code today to overwrite such zero value in non-nesting applications. In non-nesting applications, we need to hav...
by arango
Thu Jan 16, 2014 5:21 pm
Forum: ROMS Bugs
Topic: Subscript out of range for array a (extract_obs.f90)
Replies: 1
Views: 1698

Re: Subscript out of range for array a (extract_obs.f90)

This is usually a problem of how the observations are processed. However, it is wise to add this constraint to extract_obs.F and ad_extract_obs.F. Thank you for bringing this to my attention.
by arango
Wed Jan 15, 2014 10:52 pm
Forum: Meetings/Workshops
Topic: 2014 ROMS/TOMS User Workshop, Rovinj, Croatia - 2nd Notice
Replies: 0
Views: 1417

2014 ROMS/TOMS User Workshop, Rovinj, Croatia - 2nd Notice

2014 ROMS/TOMS User Workshop Island Hotel Istra, Rovinj, Croatia, May 26 - 29, 2014 The registration deadline for the 2014 ROMS/TOMS User Workshop is approaching. This is a reminder that registration is open until March 7, 2014 . The abstracts for oral presentations and posters are due by April 4, ...
by arango
Thu Jan 09, 2014 3:17 pm
Forum: ROMS Bugs
Topic: hour or day
Replies: 5
Views: 3332

Re: hour or day

What are you talking about? The Matlab script to process ECMWF ERA data for ROMS is d_ecmwf2roms.m and it is in the Matlab repository :!: Some of ERA surface fluxes are time-averaged cumulative sums. So you have to process them first, before they can be used in ROMS. You cannot use the ERA data dir...
by arango
Tue Jan 07, 2014 5:30 pm
Forum: ROMS Bugs
Topic: how to call the function get_3dfld
Replies: 4
Views: 2313

Re: how to call the function get_3dfld

Nope, it has to be a 4D-array to store the two time snapshots that are used to linearly interpolate input data at each time-step: # ifdef WAVE_MIXING allocate ( FORCES(ng) % bv(LBi:UBi,LBj:UBj,0:N(ng)) ) allocate ( FORCES(ng) % bvG(LBi:UBi,LBj:UBj,0:N(ng),2) ) # endif Then, you need to pass array bv...
by arango
Tue Jan 07, 2014 2:05 pm
Forum: ROMS Bugs
Topic: how to call the function get_3dfld
Replies: 4
Views: 2313

Re: how to call the function get_3dfld

The routine get_3dfld can read any 3D field. You just need to specify the correct range for the vertical dimension: 0, N(ng) #if defined SOLVE3D && defined WAVE_MIXING CALL get_3dfld (ng, iNLM, idWbv, ncFRCid(idWbv,ng), & & nFfiles(ng), FRC(1,ng), update(1), & & LBi, UBi, LBj, UBj, 0, N(ng), 2, 1, &...
by arango
Fri Jan 03, 2014 7:12 pm
Forum: ROMS Discussion
Topic: Strange Oscillation
Replies: 7
Views: 2114

Re: Strange Oscillation

What do you mean by unstable? I don't see nothing unstable in your solution :!: There are two types of instability: physical and numerical. For physical instabilities, you need to carry a more specific analysis that just plotting. There are various types of physical instabilities (barotropic, baroc...
by arango
Thu Jan 02, 2014 4:58 pm
Forum: ROMS Bugs
Topic: hour or day
Replies: 5
Views: 3332

Re: hour or day

Nope . The time variable ( sms_time , srf_time , shf_time , or swf_time ) in the NetCDF file created by the script d_ecmwf2roms.m is in days :!: The number of time records in a NetCDF file is independent of the units of the time coordinate. In ROMS, the default is to provide the units for the forci...
by arango
Wed Dec 18, 2013 5:27 pm
Forum: Meetings/Workshops
Topic: 2014 ROMS/TOMS User Workshop, Rovinj, Croatia - First Notice
Replies: 1
Views: 2658

Re: 2014 ROMS/TOMS User Workshop, Rovinj, Croatia - First No

The :arrow: Istria region is well known for its :arrow: cuisine, :arrow: wines, :arrow: olives, and specially :arrow: white truffles.
Istria_Croatian_Adriatic.png
Istria_Croatian_Adriatic.png (83.62 KiB) Viewed 2604 times
Istria.png
Istria.png (361.35 KiB) Viewed 2601 times
by arango
Wed Dec 18, 2013 1:57 pm
Forum: ROMS Bugs
Topic: forcing the ROMS with ERA interim
Replies: 17
Views: 16731

Re: forcing the ROMS with ERA interim

We are busy people and sometimes don't have time to answer everybody's questions. The ECMWF website has a lot of documentation for this dataset including :arrow: FAQ page . You can spend some time reading that information. No, you cannot do that change in the d_ecmwf2roms.m script. The ERA dataset f...
by arango
Tue Dec 17, 2013 7:45 pm
Forum: Meetings/Workshops
Topic: 2014 ROMS/TOMS User Workshop, Rovinj, Croatia - First Notice
Replies: 1
Views: 2658

2014 ROMS/TOMS User Workshop, Rovinj, Croatia - First Notice

2014 ROMS/TOMS User Workshop Island Hotel Istra, Rovinj, Croatia, May 26 - 29, 2014 We are inviting you to participate in the next ROMS/TOMS User Workshop to be held at the Island Hotel Istra (Otok Sv. Andrije), Rovinj, Croatia. The Red Island (Crveni otok) is one of the most renowned tourist locat...
by arango
Thu Dec 12, 2013 2:08 pm
Forum: ROMS Discussion
Topic: QCORRECTION Function
Replies: 1
Views: 925

Re: QCORRECTION Function

We have talked about this here in the past. You just need to search the scientific literature on the subject. For example, you can read Bernard et al. (1995) paper. Everything is explained really well there. It also provides some bibliography. Barnier_ThermalForcingECMWF_JMS1995.pdf Barnier, B., L. ...
by arango
Wed Dec 04, 2013 5:06 pm
Forum: ROMS Problems
Topic: Stormsurge simulation problem
Replies: 7
Views: 3216

Re: Stormsurge simulation problem

Check your initial conditions for temperature and salinity at every level to see if you have a bad value like an NaN, Inf, or a very large number. The model is blowing up in the equation of state for seawater when computing density. This computation involves polynomial expansions of various powers, ...
by arango
Mon Nov 25, 2013 9:35 pm
Forum: ROMS Bugs
Topic: Initialisation of ANANAME
Replies: 3
Views: 1950

Re: Initialisation of ANANAME

I updated the svn repository. See following :arrow: ticket for more information.
by arango
Thu Nov 21, 2013 2:06 pm
Forum: ROMS Discussion
Topic: error while writing variable: zeta
Replies: 2
Views: 1362

Re: error while writing variable: zeta

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME C => (i,j,k) Cu Cv Cw Max Speed 0 0 00:00:01 1.567195E-06 2.153599E+04 2.153599E+04 3.828818E+17 (166,001,05) 0.000000E+00 3.603793E-03 0.000000E+00 9.407347E-01 DEF_HIS - creating history file: ocean_his.nc WRT_HIS - wrote history fie...
by arango
Wed Nov 20, 2013 1:49 pm
Forum: ROMS Bugs
Topic: Initialisation of ANANAME
Replies: 3
Views: 1950

Re: Initialisation of ANANAME

Yes, thank you. The reason is that when a character assignment involves an expression or constant (on the RHS) that is shorter in length than the variable (on the LHS) then the RHS value is padded with blanks. Indeed but various compilers behave not the same in different computers. Therefore, I init...
by arango
Fri Nov 15, 2013 12:46 am
Forum: ROMS Bugs
Topic: two errors in npzd_iron_inp.h
Replies: 2
Views: 1463

Re: two errors in npzd_iron_inp.h

The load_lbc arguments in the current version of npzd_iron_inp.h in the repository were correct. Perhaps, you are using an older version of this routine. However, I have to correct the END SELECT statement to END IF. Thank you for bringing this to my attention.
by arango
Tue Nov 05, 2013 7:21 pm
Forum: Job Opportunities
Topic: Postdoctoral Researcher Position at UCLA
Replies: 0
Views: 2140

Postdoctoral Researcher Position at UCLA

Postdoctoral Researcher Position in Oceanic Circulation Modeling Department of Atmospheric and Oceanic Sciences Institute of Geophysics and Planetary Physics University of California, Los Angeles We are seeking a researcher to work on problems of oceanic circulation dynamics using the Regional Ocea...
by arango
Mon Nov 04, 2013 7:08 pm
Forum: ROMS Usage
Topic: NTSAVG and NTSDIAG
Replies: 3
Views: 3184

Re: NTSAVG and NTSDIAG

I will check when I get the chance the logic for NTSAVG and NTSDIA to see if I can reproduce this behavior. I have done this before during spin-up simulations. For example, you can run ROMS for two years without activating AVERAGES or DIAGNOSTICS_* . Make sure that you are saving the restart file at...
by arango
Mon Nov 04, 2013 6:49 pm
Forum: ROMS Discussion
Topic: Surface heat flux. Double the count?
Replies: 18
Views: 8468

Re: Surface heat flux. Double the count?

Recently, I was playing with the surface heat flux correction in the Gulf of Mexico (GOM). I even :arrow: added an analytical functional ana_dqdsst.h in ROMS to set up the net heat flux sensitivity to SST, d(Q)/d(SST) . However, I didn't have the stamina to code Barnier et al. (1995) equation. Notic...
by arango
Mon Nov 04, 2013 6:09 pm
Forum: ROMS Bugs
Topic: wrong file name in inquire.F error message
Replies: 1
Views: 1435

Re: wrong file name in inquire.F error message

Yeah, inquire.F is a very tricky routine. It is very difficult to write this type of routine to check out for an application that is not set-up correctly. There are so many possibilities. In 4D-Var we need to save all the state variables. Otherwise, we will be in a lot of trouble. I will take a look...
by arango
Mon Nov 04, 2013 5:36 pm
Forum: ROMS Bugs
Topic: Compilation errors in check_multifile
Replies: 3
Views: 2503

Re: Compilation errors in check_multifile

Yes, this was fixed. Actually, there were a parallel bug in distributed memory that took me couple of hours to find. See following :arrow: ticket for more information. Please update.
by arango
Tue Oct 29, 2013 9:27 pm
Forum: ROMS Problems
Topic: Potential Vorticity
Replies: 8
Views: 3773

Re: Potential Vorticity

Yes, good catch. Every time that I computed potential vorticity I have one of those CPP activated. I correct this and now the potential density, pden , is always computed. I removed CPP directive. We will use this field in the future for other algorithms. Thank you for finding the cause of this prob...
by arango
Thu Oct 24, 2013 2:02 pm
Forum: ROMS Discussion
Topic: TIMELESS_DATA
Replies: 1
Views: 711

Re: TIMELESS_DATA

Yes, that would work for your particular set-up. However, the correct way is to modify the internal definition for FRC_FILE in globaldefs.h to: /* ** Define internal flag indicating processing of input forcing ** NetCDF file. */ #ifdef SOLVE3D # ifdef BULK_FLUXES # ifdef ANA_SMFLUX # undef ANA_SMFLU...
by arango
Wed Oct 23, 2013 1:47 am
Forum: ROMS Discussion
Topic: GET_VARCOORDS - Cannot find "coordinates" attribute
Replies: 4
Views: 2719

Re: GET_VARCOORDS - Cannot find "coordinates" attribute

You cannot use this file as it is in ROMS. It needs the coordinates attribute as mentioned in the error message. ROMS needs this attribute to process your data. It is very simple to fix. Use the provided nc_attadd from ROMS Matlab reposiotry: nc_attadd('u_10_zero.nc', 'coordinates', 'lon lat wind_ti...
by arango
Wed Oct 16, 2013 2:59 pm
Forum: ROMS Discussion
Topic: Boundary error
Replies: 10
Views: 2087

Re: Boundary error

Like I said, you have a huge misunderstanding about periodic boundary conditions. Periodic boundary conditions are applied in boundary pairs. If you want the eastern boundary to be periodic, the western boundary must be periodic also and vice versa. It you want the southern boundary to be periodic, ...
by arango
Mon Oct 07, 2013 2:31 pm
Forum: ROMS Installation
Topic: inlet
Replies: 3
Views: 1858

Re: inlet

You are using an old version of the analytical files with your version of ROMS. Compare your modified ana_*.h with those in the ROMS/Functionals directory. The boundary conditions (periodic) were changed two years ago.
by arango
Sun Oct 06, 2013 4:08 pm
Forum: ROMS Discussion
Topic: spatially varying Jwtype in a forcing file
Replies: 5
Views: 1534

Re: spatially varying Jwtype in a forcing file

That will be a little too much, I think. Where are you going to get the data for that? River runoff to the ocean is usually via estuaries and they are shallow. It will be sufficient to set a fix Jerlow water type. Having spatially varying Jerlow water type makes sense because you can correlate their...
by arango
Sat Oct 05, 2013 6:03 pm
Forum: ROMS Discussion
Topic: spatially varying Jwtype in a forcing file
Replies: 5
Views: 1534

Re: spatially varying Jwtype in a forcing file

No that option is not available in the Rutgers version of ROMS. This is probably a good idea. Such field can be added to the grid NetCDF file. The only routine that needs to be changed is get_grid.F plus the metadata for the new variable. See the logic for option UV_DRAG_GRID . I put this option in ...
by arango
Sat Oct 05, 2013 5:58 pm
Forum: ROMS Discussion
Topic: Boundary error
Replies: 10
Views: 2087

Re: Boundary error

This is a problem in your configuration and not in ROMS. All the versions of ROMS are tested with periodic boundary conditions before they are released. Obviously, you are doing something wrong here. Your previous posts indicate that you have a misunderstanding about periodic boundary conditions. It...
by arango
Sat Oct 05, 2013 5:35 pm
Forum: ROMS Discussion
Topic: my test problem
Replies: 4
Views: 1103

Re: my test problem

Very simple. You need to pay attention to the statistics that are dumped to standard output when plotting. Also, see the minimum and maximum values in the bottom left corner of the plot. Notice also the at the bottom of the colorbar there is a scale x10^38. The maximum value in the plot is around 1E...
by arango
Tue Oct 01, 2013 1:43 am
Forum: ROMS Bugs
Topic: Possible Bugs in Radiation OBC in t3dbc_im.F
Replies: 2
Views: 1872

Re: Possible Bugs in Radiation OBC in t3dbc_im.F

Wow, great catch :!: You should get the award for the most significant bug discovered by a regular ROMS user . I updated the code. See the following :arrow: trac ticket for details. Thank you for reporting this important bug. It is possible that it has very little impact in some applications. It ju...
by arango
Sun Sep 29, 2013 4:51 pm
Forum: ROMS Problems
Topic: Problem with Bulk_flux
Replies: 2
Views: 1753

Re: Problem with Bulk_flux

Why are you masking the surface air pressure?
by arango
Wed Sep 18, 2013 2:29 am
Forum: ROMS Discussion
Topic: srun:error:
Replies: 4
Views: 1862

Re: srun:error:

That's your problem. The 4D-Var algorithms are primarily for 3D applications using SOLVE3D. I won't guarantee the shallow-water (only 2D) equations are running with 4D-Var nowadays. We have that working in the early years for debugging purposes only. When I get this kind of error, I always compile a...
by arango
Fri Sep 13, 2013 4:08 pm
Forum: ROMS Tools and Techniques
Topic: is ncinfo a native function of matlab?
Replies: 5
Views: 3101

Re: is ncinfo a native function of matlab?

Of course not. The text above implies that you can read NetCDF-4 files with versions 2010b or higher. Similarly, you can read OpenDAP NetCDF files with native Matlab version 2012a or higher. You can read NetCDF-3 files with version 2008b or higher. This is information is available everywhere. You ju...
by arango
Fri Sep 13, 2013 2:38 pm
Forum: ROMS Problems
Topic: About Tile Decomposition
Replies: 1
Views: 1204

Re: About Tile Decomposition

But why do you want to run such a small application 229x146x40 in 576 (24x24) processors?

Think about it...
by arango
Thu Sep 12, 2013 4:05 pm
Forum: ROMS Tools and Techniques
Topic: is ncinfo a native function of matlab?
Replies: 5
Views: 3101

Re: is ncinfo a native function of matlab?

Yes, ncinfo is native to Matlab. The native interface was introduced in Matlab version 2008b for NetCDF-3 type files. The NetCDF-4 support was introduced in version 2010b . The support for HDF5 files was completed in version 2011a . The OpenDAP support started in version 2012a . Mostly all of the sc...
by arango
Wed Sep 11, 2013 9:20 pm
Forum: ROMS Discussion
Topic: ROMS restart and floats
Replies: 25
Views: 7280

Re: ROMS restart and floats

We discovered a problem with the floats restart. See the following :arrow: ticket for more information. Many thanks to Diego Narvaez for providing excellent clues.
by arango
Mon Sep 09, 2013 2:11 am
Forum: ROMS Adjoint
Topic: WC13\Normalization-error!
Replies: 4
Views: 2984

Re: WC13\Normalization-error!

The BULK_FLUXES option is not supported in the tangent linear and adjoint models. This is what the error says :!: The bulk fluxes routine is not continuously differentiable and not easy to adjoint. We did it anyways and the solution is very unstable because of nonlinearities. The same goes for verti...
by arango
Wed Sep 04, 2013 5:17 pm
Forum: ROMS Problems
Topic: How to interplate observations to model grids
Replies: 5
Views: 2578

Re: How to interplate observations to model grids

The 4D-Var observation NetCDF file for ROMS is very special since it needs several observations variables and a particular metadata design. Check tutorial 13 in :arrow: WikiROMS . If you are doing 4D-Var data assimilation, you need to study and master all these tutorials. Otherwise, you will not be ...
by arango
Wed Aug 28, 2013 12:57 pm
Forum: ROMS Adjoint
Topic: WC13 compiling error
Replies: 6
Views: 2922

Re: WC13 compiling error

I don't see how you can possible tested these adjoint-based data assimilation algorithms. You always need the ARPACK/PARPACK library to compile before you run. We are using few routines from these libraries in the minimization algorithm (conjugate gradient).
by arango
Tue Aug 27, 2013 4:46 pm
Forum: ROMS Adjoint
Topic: WC13 compiling error
Replies: 6
Views: 2922

Re: WC13 compiling error

The 4D-Var tutorials in :arrow: WikiROMS has an Instructions section to run each of these adjoint-based algorithms. It says that we need the ARPACK library to compile. If running in parallel with distributed-memory ( MPI ), you also need the PARPACK library. :idea: If running ROMS complex adjoint-ba...