Ocean Modeling Discussion

arango

You seem to be getting ahead of yourself on your modeling priorities. First, you need to learn how to use ROMS and become familiar with its I/O and how applications are set up. We offer plenty of idealized and realistic test cases. Then, you need to get proficient in the preprocessing software. Sinc...

arango

Never in the history of ROMS ocean_time had units of days, It is always seconds because ROMS state has MKS units. That said, the procedure netcdf_get_time in mod_netcdf.F is smart enough to make a conversion if the units attribute is correctly specified in the NetCDF file. The initial ROMS NetCDF fi...

arango

The observation error covariance, R, is assumed to be a diagonal matrix for simplicity. The whole R cannot be computed directly but is modeled. The cross-correlations are ignored. Basically, R has two terms: error of measurement (usually small) plus error of representation (tricky). This error of re...

arango

Yes, this capability has been available in ROMS for nine years! With a little curiosity, you can find the information that you seek in the ROMS trac system immediately instead of posting here in the Forum. We always recommend to the User to do that basic search first. See the :arrow: following trac ...

arango

Thanks, John, great catch. Weird, my aggressive compiling/linking flags didn't pick up those out-of-bounce indices in parallel. I will update the code.

arango

WOW, all the tracer advection CPP options were eliminated two years ago! You are using a very old code, please update. Check the following

track ticket for details. ROMS is a living entity, still evolving and improving.

arango

Hmm, the option WET_DRY is not supported in any of the adjoint-based algorithms! The reason is that their associated mask variables would become time-dependent, and we need the entire trajectory for stepping backward in time. However, we will need to change the TLM and ADM kernels to add the variati...

arango

Good catch. The provenance is primarily used in the observation sensitivity analysis. It is a minor typo. We need to have instead:

Code: Select all

provenance.Sargo     = 7;    % ARGO floats salinity from Met Office

arango

Nested grids resolve smaller scale physics that may or may not be associated with your wind accuracy in the open ocean. For example, high-resolution winds are required next to mountainous coastal areas to resolve thermal fronts, convention, and other physics. In addition, small-scale phenomena like ...

arango

I mentioned before that your WRF nested grid is ill-conceived. It is inside of ROMS grid. It would be best to think about physics here and what the nesting is doing. You have a solid tropical storm covering the entire area, and there is a horizontal gradient of the wind due to coarse and fine resolu...

arango

We recommended running without nesting, but still, you haven't reported that solution. Unfortunately, there is not much help that we can give you if the suggestions are not followed.

arango

Well, that is peculiar. If you are using a relative new version of ROMS, you will notice that in the Build_roms directory, the master.f90 file has: ! !----------------------------------------------------------------------- ! Terminate ocean model execution: flush and close all IO files. !-----------...

arango

What version of gfortran are you using? I don't have any memory leaks with gfortran and the upwelling test case. Anyway, you get what you pay for the compiler. I have to make some modifications to the YAML parser because gfortran does not support some features of Fortran-2003. It is ridiculous how b...

arango

These grids are badly designed. I suggest that you run without the nested grids first. You always have to start SIMPLE! Then, you add complexity. Tropical storms are large, so the resolution of the coarser grids is sufficient. WFR would need surface temperature everywhere (land/ocean). If the ROMS g...

arango

The problem that was fixed yesterday was for the makefile in the git repositories. The makefile in the svn repositories was fine. Yes, we always recommend to use build_roms.sh or build_roms.csh to compile ROMS. Alternatively, you can compile ROMS with CMake using cbuild_roms.sh and cbuild_roms.csh ....

arango

Please, update the repository. I forgot to make the required changes to the makefile during the static/share LibROMS update in the git repositories. This should fix the problem that you are having. Good luck.

arango

Did you update the code?

arango

Yes, set_vbc.F is the correct routine. You can code in the C-preprocessed set_vbc.f90 file if you are experimenting. Make sure the you save that .f90 file because it will be lost when you compile without the -noclean flag. In distributed routine, you just need CPP option and follow the design for ot...

arango

Why are you using time-cycling in 4D-Var and adjoint fields? Is this a forcing field? I don't see any reason to do so. There is a misunderstanding of the purposes of 4D-Var! You need to use actual observations and forcing. Get the appropriate forcing for your 4D-Var cycle.

arango

This an a issue with the gfortran compiler. I already took care of this issue. See the following

track ticket. It seems that you are ignoring track ROMS updates.

arango

Well, you have posted two bizarre errors messages due to compilation. It seems to us that you are using a very old gfortran compiler. Also, your NetCDF library is old. We are using NetCDF version 4.7.4. I think that you may need to update your compilers. If you have access to ifort , try to compile ...

arango

The most important information is missing? What compiler are you using and its version?

arango

Thank you, check my profile in ResearchGate:

https://www.researchgate.net/profile/He ... o/research

All the papers are there. Then, request access to the ones that you need.

arango

I know what is the problem. I will load a fix tomorrow. I am taking the day off to take my dogs to the lake.

arango

Thank you for reporting this issue. The problem is that the statement in mod_scalars.F

Code: Select all

      user=0.0_r8

needs to be removed. The other statements that you added are incorrect. The management of the user variable is now done in read_phypar.F.

arango

It seems that you created a grid and initial conditions NetCDF files for the UPWELLING test case. However, your grid is incorrect. Especially, the bathymetry. You are unavailable to understand the information that ROMS is providing you. You need to master the basics of the ROMS vertical grid to desi...

arango

Usually, I generate ensemble runs with more sophisticated ROMS algorithms. You can use the roms.in USER parameter to specify the desired wind speeds to be read from standard input: ! Generic User parameters, [1:NUSER]. NUSER = 2 USER = 2.0d0 5.0d0 In your customized ana_winds.h you can have: DO j=Js...

arango

There are 29 examples cases of idealized and realistic applications in the svn test repository of various complexity. Check

wikiROMS for how to access that repository. Then, start from one of the cases. It is what we recommend when you register as a user.

arango

There is no solution other than updating the gfortran compiler or using a different compiler. If you have access to another computer try to see what happens.

arango

A great percentage of the posts in this forum do not provide adequate information or do not read carefully the error. As a consequence messages are ignored since we are very busy. With a little curiosity, you will notice that routine ran1.F and module ran_state.F exclusively uses 32-bit integers in ...

arango

Hi Pierre, great catch! Thank you for reporting this problem. I updated the

repositories.

arango

Yes, I did notice those, thank you! As a matter of fact, I replaced varinfo.dat with a YAML file varinfo.yaml. It will released with ROMS 4.1. Stay tuned.

arango

Your best strategy is to start with the latest version of the code. I think that I updated the documentation Readme and PDF files in the test repository. Maybe we need to update some of the files in WikiROMS. Nowadays, we use I4DVAR and RBL4DVAR. Our preferred method is to use the dual formulation R...

arango

Yes, thank you for reporting this typo!

arango

We have a full-time position open at NASA’s Global Modeling and Assimilation Office (GMAO) to work on marine data assimilation, working with the SOCA system. I wondered if you could forward the info to anyone you think might be interested. It could be a good opportunity for a recent graduate. The po...

arango

Well, it seems that you missed the point that we make in that webpage that the SCORPIO library is much slower when compared to PIO. Use the PIO library instead. The SCORPIO library was forked from the PIO library several years ago and evolved separately. The generic interface for parallel I/O in ROM...

arango

Hi Kate, since ROMS now has a full-time management module ( dateclock.F ) that even includes a Fortran version of Matlab's datenum and datestr , it has been in my TODO list to add an option that includes some date format in the filename. Additionally, it also has day-of-the-year, ISO 8601 format, an...

arango

Yes, this is an easy change to make. However, making such a change will affect our nomenclature conventions for ensemble runs, 4D-Var forward solutions, operational set-ups, etc. I am reluctant to make such a change. You are the first user since ROMS was released more than 20 years ago that creates ...

arango

Yes, I updated c_initial.m, c_climatology.m, and c_biology.m to use the native Matlab interface to NetCDF. I have been removing slowly the old and obsolete interface to mexnc. Please update your repository. Thank for reporting this issue.

arango

Then, you need to check ROMS governing equations in the WikiROMS or the literature to understand it. I give you a clue: It is a quantity related to the vertically-integrated (barotropic) continuity equation and volume conservation. Does that rings any bells? Are you asking us to explain the basic ph...

arango

It is a the bottom of rho_eos.F. As always, you can check the C-preprocessed file rho_eos.f90 in the build directory for the case that NONLIN_EOS is not activated. It is a very simple equation and does not include any of the secant bulk modules terms.

arango

Yes, do not mess around with the averages in ROMS 4D-Var because they are used specifically to deal with time-averaged observations operators. If you need NLM time-averaged fields, you need to rerun the nonlinear model with the 4D-Var analysis initial conditions. Did you activate AD_AVERAGES ? It ma...

arango

Obviously, this is a compiler bug! We find such bugs in ifort and gfortran from time to time. They disappears when we update the compiler. I added a SOLVE3D conditional to mod_ncpararm.F since such variables are not needed/used in shallow-water configurations.

arango

Hmm, that is very weird because the variable isWvel is a scalar and well defined in mod_ncparam.F . It doesn't need an exception because SOLVE3D is not activated. It is used in read_phypar.F is inside a SOLVE3D conditional. I compiled and ran the SOLITON test. It works for me. If you have made chang...

arango

Yes, you need to update varinfo.dat. For more information about that specific update check the following

trac ticket.

arango

Very easily, such capability has been available in ROMS since ever. See the test repository directory test/upwelling . Notice that there is a copy of fennel.h that overwrites the one in the distributed master code. Also, notice the following variable in build_roms.sh : export MY_ANALYTICAL_DIR=${MY_...

arango

Also, you are using a very old version of ROMS. We no longer have CPP options for tracer advection. The tracer advection is selected in roms.in . There are more options for advection. You have the option to select one scheme for temperature and another scheme for salinity and positive-definite passi...

arango

John, I think that will be a simple change and a good idea. We can have other values for Dsrc. I assume that your strategy is to have some point sources doing LuvSrc and other doing LwSrc. We cannot have both methods for the same point source.

arango

Yes, thank you for reporting this typo!

arango

Yes. great catch. Thank you for reporting this problem. I missed those. It seems a little bit confusing to have two different indices. For example, idv3dD in the standard input file and idv3dH for the NetCDF variable metadata. This was introduced when I separated input tidal forcing and output detid...

arango

The tile partition in ROMS is computed with Lm and Mm , since everybody has the same number of ghost points. In my possibility values above for NtileI and NtileJ , I assume that the values provided were Lm and Mm . I always prefer less tiles in the I-direction to allow vectorization to accelerate co...

arango

That's not good. You need to estimate the tile partition by hand since we are dealing with some prime numbers. Try some of the options that I typed above.

arango

That's a very old version of the code. It doesn't have PIO. I released that capability this year. Then, what is your tile partition? It seems to me that it will run more efficiently with fewer processes. Are you activating an ecosystem model or nesting? The memory requirements increase as the tracer...

arango

What is the size of your grid? I assume that it is very large since you have been using 400 PETs. What type of I/O library are you using? Using 400 processes can add a substantial bottleneck to the simulation because of I/O. That's the reason I implemented the PIO library for these cases. What versi...

arango

The C-preprocessing option is CHECKSUM . It is there because I code it: ... ASSUMED_SHAPE Using assumed-shape arrays CHECKSUM Report order-invariant checksum (hash) when processing I/O BOUNDARY_ALLREDUCE Using mpi_allreduce in mp_boundary routine ... INITIAL: Configuring and initializing forward non...

arango

Yes, using checksum is a good idea. ROMS also has checksum for I/O processing. You need to activate the CPP option CHECKSUM.

arango

The order in the GlOSSARY is subject to the CPP options activated by the user. In the test repository, I show how to use the compact form of the standard input parameters for biology. See upwelling Test Case. It is always advantageous to check standard output since ROMS has lots of CPP options. Lots...

arango

Yes, the biology tracer numbering change according to the CPP options. When in doubt, I always recommend to everybody in this forum to check the standard output very carefully, and pipeline it to a log file instead of the screen. The information that you need is always there. For the upwelling test ...

arango

Thanks Gordon. I looked in the debugger yesterday and I didn't see anything wrong with it. However, you provided essential information that the problem occurs during restart. That piece of information was not provided before. I didn't check that. Let me see if I can reproduce the problem so I can fi...

arango

Yes, I updated the repository but I rejected the changes to read_phypar.F . As I mentioned above, the suggested change is not needed because the time-averaged NetCDF files activated with AVERAGES and DIAGNOSTICS options are special. The user Jianfei Ma didn't provide enough information as to why the...

arango

Notice that we use pden as potential density referenced to the surface. This quantity is not written in ROMS history files, but it can be computed using eos.m , which computes the different quantities from the ROMS equation of state. Notice that: pden = den1 - 1000 where den1 is the density at stand...

arango

Thank you for bringing this to my attention. I agree with the correction to mod_arrays.F . Now, I need to think about the issue with the AVERAGES files and also the DIAGNOSTICS files in read_phypar.F . They are special since the creation of the time-averaged files is delayed due to the time-averagin...

arango

Yes, there is a relative vorticity script rvorticty.m in the Matlab repository.

arango

Nope, the vorticity fields are only available in the AVERAGES output NetCDF file. You control the time-averaging window, NAVG > 1. It is not in the DIAGNOSTICS file because it only contains the various terms of the governing equations, and vorticity is not one of them. You will find vorticity in the...

arango

Yes, your learning process just started. To run over a particular number of processes you need to modify parameters NtileI and NtileJ in roms_upwelling.in. The number of process to use is determined by the product of those two parameters.

arango

Yes, I noticed that early today. It also in rp_get_data.F.

arango

Yes, thank you. It is weird why I didn't catch that one before.

arango

Okay, it seems that you are struggling to install the required libraries. The upwelling test case only requires the NetCDF library. You can either use the NetCDF-3 or NetCDF-4 library. The NetCDF-4 library has a lot of options to install. The HDF5 library is only needed for parallel I/O. One of the ...

arango

My understanding is that the nondimensional density scale (see rhoA and rhoS in rhos_eos.F ) enters only in the barotropic pressure gradient in step2d with VAR_RHO_2D . Notice that the paper's equation shows the density evaluated at the free surface, which is only obtained by vertically integrating ...

arango

Nope, I am taking about the first term: GRho0*z_w(i,j,N(ng)) . It needs to be g*z_w(i,j,N(ng)) , which also gives m2/s2 for kinematic pressure. I am sure that this term needs to be multiplied by gravity only and not scaled by density like it is done the step2d_LF_AM3.h for the barotropic pressure gr...

arango

Okay, I know that this is an old post, but I have been looking at the 3D and 2D pressure gradient terms and the various algorithms available. I implemented the astronomical tide generation forces ( TGF ) in terms of the equilibrium tide ( ζeq ), defined as the shape that the sea surface (m) would as...

arango

Sure, see LAB_CANYON analytical test case. Everything is already done for you. You just need to modify the analytical expressions.

arango

I think that it will be simple. You just need to replace the vertical semi-Lagrangian sinking algorithm in fennel.h with the sinking/ascending one in red_tides.h , which you can use for swimming/floating. However, these algorithms are very sophisticated, and you cannot make changes to them. I recall...

arango

Great, I think that we need to design a Matlab function that plots vectors correctly regardless if the grid is curvilinear or not.

arango

Great detective work! I also was starting to suspect about the quiver function or its usage. I am planning to draw the vectors with ROMS native NCAR graphics software next week to see what I get. I am wondering what kind of results we will the m_map ( m_quiver ) tool in Matlab will give. The vectors...

arango

Are you expecting flow to be everywhere along bathymetric contours? We can have bottom boundary layers, turbulence, pressure gradient differences, and friction that may force the flow across isobars and bathymetric contours. I think that what you need to plot are the barotropic currents at every gri...

arango

Hmm, the grid looks very orthogonal to me. It is hard to think that it is due to the averaging of the quiver plot. The angle between the red and green vectors is pretty much constant and around 30 degrees. It is weird. I wonder what do we get with uv_rotate.F when we output the vectors to geographic...

arango

Use Matlab script grid/roms_metrics.m to recompute the angle and other quantities to see what you get. You can download that script from the ROMS Matlab repository. Then, compare your rotation angle arrays. Interpolation is not a good idea!

arango

If you are using the latest version of the code, which I recommend using, you need to be sure that your roms.in is up to date. Compile with debugging flags so you get more information about the division by zero. We can get such errors when the arguments to MOD are zero or uninitialized. There are lo...

arango

I don't think that is an I/O error: Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO ERROR STOP Something is wrong in your configuration in roms.in that you get a division by zero . I updated the code yesterday to remove those confusing I/O errors when you have a con...

arango

We have not seen parallel bugs in the distributed ROMS code for years. In the past, such parallel bugs are associated with the user implementation of analytical functions. If there is an issue with the BENCHMARK application, we need to look at its analytical functions. I am very busy at the moment. ...

arango

I don't think so. This is because of the PIO library support changes to ROMS. For some reason, inp_type in roms.in is zero. It is weird because it is initialized to zero internally if the user doesn't specified a value.

arango

ROMS is telling you what it is wrong:

GET_GRID - Illegal output type, io_type = 0

Make sure that your roms.in is up to date.

arango

I don't know what is going on here, but NC_INDEPENDENT and NC_COLLECTIVE is for the NetCDF library and NOT for the PIO library. You cannot add things to the PIO interface without knowledge. The nf90_var_par_access function is for the native NetCDF library with parallel I/O (option PARALLEL_IO and HD...

arango

Your question is kind of weird. What do you mean by high-frequency tidal forcing? ROMS has its own tidal forcing file specified in TIDENAME . The tidal forcing file doesn't have a time coordinate but a tide angular period for each constituent. Therefore, a single file is required. This data is deriv...

arango

Yes, good catch. Thank you for reporting this issue. I will update the code.

arango

As mention previously, the information in the Wiki tells you how to inquire the build script about the libraries that your are using to compile ROMS without actually compiling: > build_roms.sh -p LIBS :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::...

arango

Check the debugging section of the

build_roms wiki page to learn how to inquire things about compiling variables and macros. There is lots of useful information in the wiki about the makefile, build scripts, libraries, and how to compile and link ROMS,

arango

I already updated the repositories.

arango

Yes, it is a typo, I will load the update later today.

arango

You also need the USE_PIO option in the build script. Both libraries are needed at running time since you may activate both in roms.in.

arango

Well, if you are going to use PIO , you need to follow the instructions provided in :arrow: WikiROMS or in the :arrow: trac ticket . Also, there is information available in the wiki for :arrow: roms.in . Please read the documentation carefully. PIO is too complicated to ignore the instructions. The ...

arango

Yes, thank you! Weird, my ifort compiler missed that one.

arango

Yes, in set_contat.F we need to have instead: ! ! Set the switch to compute vertical interpolation weights. Currently, ! they are only needed in non-coincident composite grids. ! IF (.not.ANY(Lcoincident).or.ANY(Lcomposite)) THEN get_Vweights=.TRUE. ELSE get_Vweights=.FALSE. END IF we need .or. inst...

arango

The arguments to load_r are correct. The 1 can be replaced by a colon ( : ) since this routine is called inside a module. The one argument is a valid F77 syntax since load_r will load Ngrids values, which is also an argument, starting from element 1 of the second dimension to BioUni .

arango

Hmm, I haven't seen this kind of problem in ROMS in a very long time. The squares clearly indicate a parallel partition bug in the code with the exchanges between tiles. Are you using distributed memory (MPI) or shared memory (OpenMP)? What version of the code are you using? And more importantly, di...

arango

Those two lines are identical. The code compiles fine for me when STATIONS is activated or not.

arango

Okay, thanks. I am getting annoyed with this routine. It needed to be modified because of PIO. I rarely use WET_DRY. Please update again.

arango

Okay, I see it now. It is fixed. Please update again. Thank you!

arango

Yes, thank you for reporting this bug. It is already fixed. Please check the following :arrow: trac ticket . Please update your code. I will have to check what your other error is. It looks weird. Those routines are private inside the get_grid_mod ( get_grid.F ). Have you made changes to get_grid.F ...

arango

Notice that the subdirectory plot/src/Bin have other conversion scripts like ncgm2cgm.sh, ncgm2gif.sh, and ncgm2png.sh. The call to ncgmwww can be replaced with ncgm2git.sh. Anyway, I am attaching the old ncgm2www.sh script.

arango

Yes, that's definitely a typo. Thank you for bringing that to our attention. Luckily, this logic is only used to detide ROMS fields (AVERAGES_DETIDE) via the

least-squares fit of time-averaged fields.

arango

I didn't know that IBM was using the NVIDIA compiler. It is unfortunate because the PGI compiler is one of the worse compilers that I have come across. We don't longer use it neither pay the license to maintain that compiler. The RSHIFT and SHIFTA intrinsic functions are part of the 2008 Fortran Sta...

arango

As you may have noticed, the nesting routines in nesting.F module were designed in a generic way to facilitate expansion and different schemes. The weighted area average is turned off in fine2coarse ( AreaAvg=.FALSE. ). One could try volume-weighted averaging (not coded). Right now, we use bilinear ...

arango

ROMS uses a horizontal, staggered Arakawa C-grid. You need to study and understand the following grid diagram in :arrow: WikiROMS . You need to look the grid spacing in terms of RHO -, PSI -, U -, and V -points. Then, you will answer your own questions. The code in roms.metrics.m is correct.

arango

Yes, this was fixed but that version is not ready for release. You have to wait. This is simply solved by deactivating the BALANCE_OPERATOR C-preprocessing option. We don't activate that option in the tutorials. The balance operator is an advanced feature for experienced users that know their applic...

arango

Yes, your Fortran compiler is too old and not supporting updates to the standard. The intrinsic function SHIFTR was introduced more than a decade ago in the Fortran 2008 Standard. What compiler are you using? It is highly recommended to keep Fortran compilers up-to-date. Models nowadays use Object O...

arango

You need to use any older or the latest versions of our distributed code. I checked the trac history for the mod_floats.F module and I cannot find the offending code in the last five years! Anyway, you need to read and understand the error message: forrtl: severe (194): Run-Time Check Failure. The v...

arango

Yes, I recall issues with the global attributes. In such cases, I manipulate the global attributes using my matlab/netcdf functions that are distributed in the ROMS Matlab repository: >> Imin=nc_getatt('my_file.nc', 'parent_Imin'); >> Imax=nc_getatt('my_file.nc', 'parent_Imax'); >> Jmin=nc_getatt('m...

arango

Yes, thank you!

arango

What software did you use to generate your original GRID NetCDF? Many users really miss the fact that although the application has a spherical grid, it is highly recommended to have the associated Cartesian coordinates to compute the metrics pm and pn since ROMS computational grid is in curvilinear ...

arango

Yes, that's the way to build complicated grids. One thing that you may consider is to avoid sudden bathymetry changes like seamount and ridges across the contact areas between coarse and fine grids. I have done telescoping grids in the Middle Atlantic Bight, which include the Gulf Stream, with tidal...

arango

Alternatively, you can copy Functionals/ana_grid.h to your application directory and make any desired change. Notice that the build_roms.csh or build_roms.sh script have the capability to use your customized analytical headed files ( ana_*.h ) and ignore the ones distributed in ROMS Functionals sub-...

arango

All the governing equations in ROMS are time-stepped differently. Recall that we have a three-time level predictor-corrector scheme. The tracer equations are kind of special. The t(:,:,:,3,itrc) are the intermediate tracer values ( n+1/2 ) assigned in the predictor step ( pre_step3d.F) for only hori...

arango

I think that this error has nothing to do with ROMS but communications between your computer processes with the MPI library. Sometimes, when you are using lots of processes one or more do not arrive at the collective MPI synchronization point and the system hangs out or gives this type of error. I g...

arango

Wow, are you really asking how Linux works? No wonder why you are having so many troubles at every step in your application. We have lots of posts in this forum from you. I am expecting users that select ocean modeling as a carrier or hobby to be more curious and familiar with computers. By the way...

arango

Hmm, the call to mp_scatter_state is correct. It is only used for the adjoint-based propagator analysis, which I doubt Users using those algorithms that compact the full ROMS state ( zeta , u , v , T , S ) into a 1D array for matrix operations with the ARPACK library. I think that the issue here is ...

arango

Obviously, you need to work on the libraries available on your computer. There is plenty of information about Compiling and Linking in WikiROMS. If you are using the latest version of ROMS, you may benefit from using CMake . Check cbuild_roms.csh or cbuild_roms.sh . CMake is a different philosophy f...

arango

Yes, good catch. Thank you. The stflx and btflx state variables are used in ROMS governing equations. Contrarily, the stflux and btflux are used exclusively to process data from NetCDF files or analytical functions. The problem here is that the assignment is missing in set_vbc.F : # if defined BIOLO...

arango

I don’t know what you are doing wrong. First, I highly recommend that you use the latest version of ROMS. Right now, we are in version 3.9. We have improved ROMS nesting. It is more efficient. The latest version of ROMS is consistent with all the files in the current test repository. That’s the reas...

arango

Thank you, Lars. Those are great references. I added them to my reading list. A couple of decades ago, I tried to derive an energy conservation equation for ROMS, so the only way to add energy to the system is from external forcing. I was unable to eliminate the pressure gradient term because of the...

arango

Nope, that bash script supports both SLURM (BATCH=1) and non SLURM (BATCH=0). You just need to change that flag. See the customizable section. I can run that script in my 14 CPUs Mac or in our SLURM supercomputer. The script is very generic, compact, and complex. It is well documented. You need to s...

arango

What is RPG? Did you mean RPCG option for RBL4D-Var minimization algorithm? I have never turned on the STATIONS option with the 4D-Var algorithms. I suppose that we can use the split 4D-Var algorithms that I released yesterday to only run the STATIONS in the background and analysis 4D-Varphases. And...

arango

I think that there is a confusion here with the forcing terminology. The surface and bottom heat ( Q ) and freshwater fluxes ( E-P ) are the boundary conditions to the vertical tracer (temperature and salinity, respectively) diffusion terms in the governing equations. We need to provide boundary con...

arango

The lake Jersey test case works for me. What you did is not LAKE_JERSEY :!: You changed the grid, land/sea mask, and added big and small islands. Stop calling it Lake Jersey because it is a different application and will confuse other users with misinformation! If doing nesting, it will require diff...

arango

Yes, thank you. It just need:

Code: Select all

#ifdef NESTING
      USE mod_nesting
#endif

Please, update.

arango

What do you mean by the same results? profiling time or state solution?

Usually, it is much efficient to do less partition in the I-direction (NtileI) and more in the J-direction (NtileJ) because of vectorization. Also, it depends on the computer architecture.

arango

Yes, thank you!

arango

Everybody has their own procedure for updating code from repositories. I have several research repositories, and I usually do the following steps: Copy the version that I want to update to a temporary one. So, I have a version of the code that works in case something goes wrong with the updating. I ...

arango

Well, you cannot pick and choose what routines you need to update. It doesn't work that way. Every change done to ROMS is well documented in the trac system, and the changes sometimes depend on previous changes and may be modified in future changes. The last major update to the Parallel I/O was done...

arango

I can believe that this is done :shock: We are not responsible for corrections to the code by a third party. Your solution is straightforward. Update your code from the official ROMS repositories. The agreement to receive a freely distributed version of the ROMS framework from us is that Users need ...

arango

Well, the error is telling your problem, if you think carefully about it. I assume that you previously defined SOLVE3D . Now, it is undefined , and you are solving the shallow-water equations of ROMS where you must have NDTFAST =1 for all nested grids, and you have NDTFAST = 30 :!: If you don't und...

arango

The varinfo.dat is an user-changeable file. In the beginning, we were thinking of writing omega in the restart NetCDF file as m 3 /s, and true vertical velocity in history files. But that's no longer the case. Nowadays, omega is recomputed internally. I rarely activate the switch for writing omega i...

arango

Well, the omega vertical velocity in ROMS is special and its orthogonality changes at each grid point because it depends on the bathymetry. It does not have a physical interpretation since it is only related to ROMS descrete, terrain-following coordinates, 3D continuity equation. Internally in ROMS,...

arango

I also have been using this capability for years and frequently and I never have any problems. Our group at Rutgers uses the same strategy on a daily basis in our operational system. Something is wrong in your files. When I do nesting, I only specify the forcing files for the first grid, and ROMS wi...

arango

The reason why nobody replayed to your post is that you didn't provide any concrete information about the ROMS or Fortran error. We are not magicians or have any potions to see the error written to your standard output. I have mentioned several times over the years in this forum to never never never...

arango

Are you trying to change ROMS equation of state? The definition of in situ density anomaly or potential density anomaly is that a 1000 kg m-3 value is subtracted to the density. The in situ density anomaly, as a field, is only used in ROMS in the pressure gradient algorithm where its value is not e...

arango

Yes, that's a small bug, thank you. I am running nowadays with the ROMS_STDOUT option that generates the output file log.roms instead of the standard Fortran output from unit 6. My bad, I forgot to run without the ROMS_STDOUT . Having this option activated is very convenient when running coupled sys...

arango

Oh my goodness, no. We cannot use WET_DRY in any of the adjoint-based algorithms including any of the 4D-Var drivers. That's the reason that you will find WET_DRY_NOT_YET in the code. Every time that you see a multiplication of a state variable with a mask array, we will need another term, which is ...

arango

Yes, gfortran is a stricter compiler. Other compilers relax the Fortran standard rule that we cannot have a module, subroutine, or variable with the same name. I missed this one. Thank you for reporting this issue. Please, update your code.

arango

In our experience, it is challenging for either the tangent linear ( TLM ) or adjoint models ( ADM ) to blow-up in the first iteration of the inner loops. Something must be wrong in your step-up. Both models are linearized from the nonlinear model ( NLM ) state trajectory (prior). The TLM and ADM st...

arango

Yes, thank you. Please update your code.

arango

Update your code again!

arango

I actually removing that parameter in an update that I am releasing today. Remove the couple of ocurrences of Ltracing in read_phypar.F. I have several reseach repositories and sometimes unwanted features leaks into the trunk. Sorry about that.

arango

Great work, Stefan. I concur with john about your telescoping approach into meter scales. It will take me some time to digest the changes that you make to the code. If you provide us the modifications that you have to do for the shallow-water nested applications to work, we can incorporate such chan...

arango

Okay, update your repository. It is now fixed. Here is the

trac ticket

arango

Of course, you need the observation error covariance (diagonal matrix) in the ROMS 4D-Var algorithm! The NetCDF variable is obs_error , which is read into ROMS variable ObsErr . You are searching for the wrong variable. Check ROMS/Modules/mod_fourdvar.F for the description of all variables.

arango

Yes, it will be easy to fix. I will update the repository tonight. Thank you for reporting this issue.

arango

Hi Koushik, great study, and thank you for the research that you continue doing about ROMS parallel I/O :!: Let me digest the information and come up with a strategy for more efficient parallel I/O. Are you aware that ROMS has the CPP option NO_WRITE_GRID , which suppresses the definition and writin...

arango

Yes, good catch :!: Thank you. I have been looking for a bug in the HSIMT scheme on and off. We fixed the issue that it needs three ghost points a few days ago, but forgot to make changes to the range of oHz . We need have an additional switch, Lhsimt : logical :: LapplySrc, Lhsimt, Lmpdata ... Lhsi...

arango

Yes, thank you for reporting this typo in the documentation. However, why do you want to set a different tracer advection scheme for temperature and salinity across nested grids? I will never do such a thing in any of my nesting applications. It doesn't make sense to me. You need to understand how t...

arango

Yes, I already knew about this one and included in a repository update that will be released today.

arango

Hmmm, I noticed that you activated both BULK_FLUXES and CCSM_FLUXES . I am not familiar with that version of ROMS. However, my understanding is that you should use a single formulation. You need to choose one and not both. If the sea ice model is activated, we need BOTH freshwater (E-P) and saltwate...

arango

I revised this logic recently. My assumption is that ndefAVG is an exact multiple (integer factor) of ntimes . If it is not the case, the file creation definition is changed. What values are you using that gives you OutFiles=0 ? The time averaged files are special because of its delayed creation. Th...

arango

I don't know if this behaviour will be related, but I would turn off SPLINES_VDIFF and SPLINES_VVISC and see what happens. I also noticed that you are using a different version of ROMS that has sea ice modeling. This will complicate your analysis.

arango

Well, u2dbc_im.F and v2dbc_im.F need to be modified to include code relevant to 2D shallow-water nesting applications. I guess that we never accounted for a User needing nesting in a 2D application. It will need an equation to impose the transport from the donor coarser grid. We will have to figure ...

arango

Notice that the indices told and tnew are local (dummy) time indices: ! ! Set time snapshot indices for the donor grid data. ! told=3-RollingIndex(cr) tnew=RollingIndex(cr) However, if you are running a 2D shallow-water application ( SOLVE3D is off), why are you dealing with state variables ( DU_avg...

arango

Hmm. I will have to think about it but maybe it will be needed. It will need to be tested. There are a set of those indices for RHO-, PSI-, U-, and V-points. It will be only relevant it coastlines are present in the contact points.

arango

Yes, Great catch

Thank you for reporting these two bugs. I updated the

repositories.

arango

It is all a matter of the assumed background error covariance hypothesis and its parameters. What do you trust more the model or the observations? HF radar velocity observations are very tricky since it is a very noisy data, and depends on the processing: averaging, detiding, super-observations, err...

arango

You need to make sure that the variables in your forcing NetCDF files have the _FillValue = 1.e+35 attribute or whatever other value you used. Otherwise, ROMS doesn't know how to process such data without the _FillValue that have land/sea masks. However, the fact the you have Min = 1.0E+35 and Max =...

arango

Check your standard input file, roms.in or your standard output log file, which contains lots of information. Notice that in roms.in we have: ! Logical switches (TRUE/FALSE) to nudge the desired climatology field(s). ! If not analytical climatology fields, users need to turn ON the logical ! switche...

arango

The nesting configuration is tricky since we support various types of grid connectivity. We only provide a Matlab interface to generate the nesting connectivity NetCDF file needed by ROMS. Unfortunately, we don't officially have any other software to create such a connectivity NetCDF file nor have t...

arango

The frozen versions of ROMS are available only on SVN. Usually, one checkout the tags SVN repository: svn checkout https://www.myroms.org/svn/src/tags tags svn checkout https://www.myroms.org/svn/src/tags/roms-3.7 roms-3.7 The GIT repository works in a different way. If you need the version that was...

arango

Yes, your first correction is fine. Thank you :!: I updated the repository. We didn't catch that one before because all our grids always have the ( XI , ETA ) coordinates even if the applications grid is spherical. It turns out that in curvilinear grids is better to do the interpolation in ( XI , ET...

arango

This is not a bug. It always has to be equal or greater than one by design. If no input forcing files are needed, ROMS will ignore those values on standard input. I don't understand what it is the Fuzz about it. There are a lot of parameters in ROMS standard input that will be only relevant for a sp...

arango

Look at Nonlinear/ini_fields.F instead. It is very clear how it is computed there. It is how the inital ubar anf vbar is computed in ROMS.

arango

I learned how to program and plot with the NCARG graphical library. I spent so much time reading the manuals and learning how to use that library. It was very satisfying plotting the results with computer-generated contours. I became a pro using that wonderful library. I still used it today. I wrote...

arango

Indeed, I took that class from John Klinck when I was a graduate student at Texas A&M. I learned a lot about coding and ocean numerical modeling in that first class. It was a great introduction to a world that it is now my professional life. I recall that we, the students, and John, enjoyed that...

arango

Hi Frank, great catch. Thank you! I updated the repository. See the following

trac ticket for more information.

arango

An application of size 899x629x40 is TOO small to be run in 1350 PEs :!: No wonder why is not scaling after 240 PEs. You are killing scalability with excessive MPI collective communications and exchanges. Your 20x20 tile size is too small, and it is killing vectorization. The good news is that you f...

arango

Great study. We are missing important information about your simulations. We need the grid size and the parallel domain decomposition. I have mentioned frequently in this forum that ROMS scalability is a function of the application and depends on the domain size and parallel partition. There is alwa...

arango

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...

arango

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...

arango

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...

arango

Indeed, thank you! I didn't test with LIMIT_STFLX_COOLING activated.

arango

Indeed. Thank you for reporting this issue. Please update.

arango

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 ...

arango

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...

arango

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. #-------------------...

arango

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...

arango

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...

arango

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 ...

arango

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 ...

arango

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 ...

arango

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.

arango

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...

arango

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...

arango

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...

arango

I updated the code to correct the bug in regrid.F. Check the following trac ticket

src

808 for more details. The parallel bug was corrected. Good luck.

arango

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...

arango

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 ...

arango

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...

arango

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 ...

arango

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.

arango

Just do it in Matlab.

arango

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...

arango

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. ...

arango

: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...

arango

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...

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