Ocean Modeling Discussion

arango

I don't know what bit-reproduction means in this context. In the past, I have checked all ecosystem kernels in ROMS to produce identical solutions in serial, serial with partitions, shared-memory, and distributed memory with tiles partitioning 1x1 , 2x2 , and 3x3 with the upwelling test case. Of ...

arango

Thanks, Pierre. Good catch. Yes, the stress components due to waves and currents are computed at RHO -points. We also need to correct the metadata for those variables in varinfo.yaml . I will include that correction in a branch I am working on for the ECB model. By the way, excellent work ...

arango

The (i,j,k) are the 3D state array indices of where the maximum value of the velocities occurs. It is an indication of possible trouble spots if the model blows up. In our experience, ROMS typically fails due to vertical CFL violations in shallow regions with extremely thin vertical level ...

arango

Check your bathymetry. It cannot be zero, since the governing equations involve division by it. There is an issue with your configuration or grid.

arango

The NestedGrids environmental variable was abandoned several years ago. We used to have it in ROMS versions 3.3 and 3.4 . We used to have:

integer, parameter :: Ngrids = NestedGrids

This awkward strategy was abandoned, and the code was modified to use the value Ngrids provided in roms.in ...

arango

A significant percentage of the messages in this Forum would be unnecessary if the user takes into account the following recommendations.

Recomendations:

Many users avoid reading the emails sent to everyone after the ROMS code and support repositories are updated. They contain helpful ...

arango

That's weird. I never got that error when I tested that update of the code — the mystery of compilers during linking. The compiler is telling you that it cannot find a module association to FUNCTION find_string . Indeed, in line 159 of ROMS/Drivers/rbl4dvar.F , we need to add such a function:
USE ...

arango

Yes, use the branch feature/sediment , which is up to date with the develop branch.

> git pull
> git checkout feature/sediment
> git pull

Then, compile your application. It should work.

I'm finishing a couple of branches: wec and sediment , which I will merge into the develop branch soon.

arango

That was coded years ago, and processing ERA-5 data has evolved. The script d_ecmwf2roms.m was provided as pseudo-code for the user to modify and adapt. I don't have the time to look at it now. It depends on whether you are extracting instantaneous or accumulated fields, where the time interval is ...

arango

In addition, nudging 2D momentum is very tricky because it will affect the barotropic transport, which depends on the source and destination bathymetries. I won't recommend it since you can spend months tuning realistic applications. In such cases, I recommend examining the application grid and its ...

arango

I think you need to abandon your idealized application. ROMS's analytical interface is for toy problems that usually include simple periodic boundary conditions in the x- or y-directions to avoid the issues with ill-conditioned boundary conditions in an idealized test. Otherwise, you have to specify ...

arango

Wow, you don't understand how ROMS boundary conditions and parallelism work. Then, you start modifying the code wrongly without any knowledge. Your issues will be solved quickly if you pay attention to ROMS's standard input file section, where the lateral boundary conditions are specified. I assume ...

arango

Hi Pierre, I am glad to hear that. I must return to that branch and check what I need to do to merge it into the develop branch. In the ROMS GitHub version, we can switch branches in the build script very quickly by the command:

build_roms.sh -j 10 -b feature/kernel

It creates the src ...

arango

Yes, thank you! It happens after ROMS_finalize when all the model variables are deallocated before the run is completed. Hmm, I didn't get any error when I tested it. Sometimes, compilers ignore errors.

arango

Something is wrong here. I don't know what version of ROMS you are using, but:

There is not limitation to the variable GRID(ng) % rdrag since it is always defined because of the new 2D kernel in the feature/kernel branch uses implicit linear drag. It is always declared in ROMS/Modules/mod_grid.F ...

arango

The current svn trunk revision ( -r 1225 ) is the last version we will distribute through the Subversion control system. Starting January 1, 2025 , ROMS code and associated software will be distributed exclusively via GitHub: https://github.com/myroms.

ROMS Version 4.2 is now frozen and starts ...

arango

As homework, look at routines u2dbc_im.F and v2dbc_im.F , read the papers, and think! We all do that, including professors, scientists, and seasoned ocean model developers. What is the fun of giving you a couple of sentences for an explanation? This is how we all learn in this profession, and it is ...

arango

The Oceanography (OC) Department in the Naval Postgraduate School (NPS) invites applications for the faculty position in the broadly defined area of Physical Oceanography. We anticipate an appointment at the Assistant Professor level, but exceptional candidates at the Associate Professor or Full ...

arango

The NOT_YET suffix in the CPP option means that such an algorithm is only available/executed in the nonlinear (NLM) kernel in applications that also activate the tangent linear (TLM) and adjoint (ADM) kernels. In such cases, we don't have the respective TLM and ADM transformations.

arango

Yes, that routine is the full-time-stepping kernel. You can also check interp_floats.F , vwalk_floats.F , and Biology/biology_floats.F . There are other packages to compute offline tracking lagrangian particles that you may examine. I am not aware of tracking done with Python. We experience that ...

arango

Have you examined the Rutgers ROMS Nonlinear/step_floats.F module? It has its 4th -order predictor/corrector time-stepping kernel for every Lagrangian particle (in the order of millions) to determine their trajectory, which is independent of the vertical coordinate system and ocean model. The ...

arango

The stretching vertical terrain-following coordinate functions C(σ) are non-dimensional, ranging from 0 to -1 . Their values are a function of the bathymetry h(lon, lat) at every grid point and the number of application vertical levels. Your question doesn't make sense to me. Please check the ...

arango

Perhaps, you would like to check the following posts:

viewtopic.php?t=162
viewtopic.php?t=268

arango

The tangent linear and adjoint time-evolving fields are perturbations and can be positive or negative. For example, check salinity, a positive definite quantity in the ocean (nonlinear model physical space), represents the dissolved matter content in seawater. A negatively valued salinity is a ...

arango

This must be a first in this forum . You must read about ocean observations' history, geophysical fluid dynamics, and their governing equations. We cannot measure the density of seawater accurately. So, our classical physical oceanographer's ingenuity was to design and build instruments that ...

arango

What version of ROMS are you using? You can compare the logic of LBC allocation value in the latest https://github.com/myroms/roms develop branch.

arango

Please stop sending me personal emails. They will go directly to the trash bin. I don't have the time to reply to specific emails from users when something doesn't work. ROMS has thousands of users, and our policy is not to answer such particular inquiries. All the communications about ROMS should ...

arango

I answered your question precisely. ROMS uses a coarse-grained horizontal parallelization. Thus, NtileI(ig)*Ntile(ig) = ncpus , where ig is the nested grid number. You can have different combinations provided that the product is always ncpus . This is why it is always desirable that the number of ...

arango

Yes, it is possible to append the initial conditions of the biological model constituents to the restart NetCDF file. Another possibility is to activate ANA_BIOLOGY but using the restart NetCDF file as initial conditions ( NRREC = 0 ) and not as a restart ( NRREC ≠ 0 ) because restating check the ...

arango

The nested grid algorithms run sequentially, so we are not using split MPI communicators to run concurrently because of the nature of two-way telescoping grid time-stepping. Thus, the NtileI * NtileJ must be the same for each nested grid.

arango

Yes, those MPI warnings are typical from gfortran . The MPI libraries are written in C and C++, allowing generic calls to enable polymorphism and type-bound objects in the argument type, calling the parallel communications function. There are specific compiling flags in gfortran for surprising such ...

arango

Hi, you are using the old user customizable ana_initial.h . Compare with the released one. We must have:

IF (first) THEN
first=.FALSE.
DO i=1,SIZE(Stats,1)
Stats(i) % checksum=0_i8b
Stats(i) % count=0
Stats(i) % min=Large
Stats(i) % max=-Large
Stats(i) % avg=0.0_r8
Stats(i) % rms=0.0_r8 ...

arango

Yes, thank you for reporting this issue. Please update your branch. For details, see

github.com/myroms/roms PR #36.

arango

Your information is very minimal and incomplete. If it was working before, the error is due to your changes. You need to deep into your changes and make sense of what is happening. If you have more tracers than the usual temperature and salinity, it is very likely that you activated the biology and ...

arango

Yes, we call that field surface potential temperature representing the finite volume integral of the top model-level grid cube. ROMS has no formal governing equation for the actual SST or skin SST. It requires the physics of the ocean-atmosphere turbulent boundary layer. In the past, we have ...

arango

To me, the behavior of vertical velocity near the open boundary is the byproduct of the lateral boundary conditions. Recall that in ROMS, the vertical velocity ( omega ) is an expression of the 3D continuity equation computed by the horizontal divergence. There must be some vertical biases in your ...

arango

Well, the compiler is telling what is wrong. To use the GRID(ng) structure, you need to include its module association in ana_pair.h:

Code: Select all

          USE mod_grid

Your application also needs to have spherical coordinates (lat, lat). Most idealized applications in ROMS use Cartesian coordinates.

arango

John, did your post get deleted? That's weird. Only a couple of us have the permission privileges to do so. We have been having power failures recently, and it is possible that your post was lost because of it. I always use Firefox with history control to recover lost messages and text. It happened ...

arango

Why do you think that it is a ROMS bug? You didn't configure your application correctly! ROMS internal time is in seconds. Any input NetCDF data into ROMS needs to have the correct units attribute to the time variable to make the proper conversion. This is my first time hearing such a message about ...

arango

You are using a very new version of gfortran. This seems like a compiler bug, which I will not be surprised by. If you check the

trac ticket, you will notice that we are trying to modernize the routines used from this legacy library since NCEP is complaining about the GOTOs.

arango

Except periodic boundary conditions, all the open boundary conditions in ROMS are ill-conditioned from the purest mathematician point of view. The only thing that we can do is minimize its errors. There are several strategies that are available, as you found out. In my experience, we need to first ...

arango

Nope, there is no limitation. The filename is limited to 256 characters, and the number of files in the sequence files(:) is allocated internally to the number of files that it finds. This is the first time we have heard of a user providing files for 30 years. If I want to do such a long simulation ...

arango

I updated the tutorial information in WikiROMS. Thank you! We are usually swamped and will take time to update the information. We also have minimal information and instructions in the GitHub repositories wiki. Some users are unfamiliar with Git and GitHub, and we are given plenty of time to learn.

arango

I updated all the versions of ROMS in the svn and git repositories, but I recommend the GitHub version since it has branches of other developments that we are working on and will be merged to the default develop branch in the future. We will stop updating the other repositories on January 1, 2025 ...

arango

Yes, use the ROMS version on GitHub. We will no longer update all the SVN versions after January 1, 2025. I fixed all the indices in the code.

arango

You cannot change NADJ in I4DVAR since the primal formulation is only a strong constraint algorithm (the model is assumed to be perfect). However, RBL4DVAR is both strong- and weak-constraint. But I suggest staying in the strong-constraint regime since modeling the model error, Q , is not trivial ...

arango

Why do you use the primal formulation I4DVAR ? That algorithm works, but it is deprecated. Please use the dual formulation RBL4DVAR . It is faster! Check the WC13 test cases for RBL4DVAR . The dual formulation works on the space span by the observations and allows impacts and sensitivities. We also ...

arango

We never coded 3D-Var in ROMS native variational data assimilation algorithms. But, if you check the literature, 4D-Var performs better than any 3D-Var algorithm. In 3D-Var, we assume that the linearized model (tangent linear kernel) is the identity matrix! It doesn't use the adjoint model. Anyway ...

arango

It is working again. We don't know what the issue was, but it started to work again when we restarted the server.

arango

WARNING:

Starting January 1, 2025 , ROMS will be exclusively distributed from its GitHub repository at :arrow: https://github.com/myroms . Please get familiar with GitHub repository management. The updating of the svn repositories at :arrow: https://www.myroms.org will be discontinued but kept ...

arango

A little bit of fun trivia . If we use the Sloc Cloc and Code ( SCC ) program (https://github.com/boyter/scc), it gives us an estimate of the cost in US dollars of developing ROMS, which we give you for free. The number will be much higher if we put the actual salaries of the people involved. So ...

arango

In ROMS, we have the GAMMA2 parameter to set the slip and no-slip boundary conditions. In the no-slip, the velocity is zero at the wall.

Code: Select all

! Slipperiness parameter: 1.0 (free slip) or -1.0 (no slip)

      GAMMA2 == 1.0d0

arango

We started interfacing ROMS with the UFS-coastal framework. The basic connectivity is working well. We still have to develop the testing applications. So far, the DATA-ROMS coupled components are working as the first step to couple with ESMF/NUOPC -based CDEPS/CMEPS. We use Hurricane Irene to test ...

arango

John will be missed, RIP. Chatting with him was always interesting. I remember visiting his office at OSU when we took the summer IOMS course with Andrew Bennett. I don't know how he was able to work at his desk. He had mountains of papers, journals, and books on it, blocking the view of who was ...

arango

Nowadays, we distribute ROMS in

github.com/myroms. Please follow the instructions on https://github.com/myroms/roms/wiki

arango

Yes, those summaries take time, which I don't have. My list of priorities is too long. However, every change made to ROMS is well documented on trac. See

https://www.myroms.org/projects/src/report/4

arango

We completed the transition of ROMS to GitHub. We have been working on this for the last couple of months.

The GitHub ROMS repositories are at :arrow: https://github.com/myroms . For more information and instructions on ROMS framework source code, please visit :arrow: https://github.com/myroms/roms ...

arango

I updated the code last week. I think that I fixed the issue of the state vector variables' indices order. Please update and try again.

arango

Great. The versioning of the ifort is weird. I used 2023.0.0 in our Spack-Stack for ROMS-JEDI:

pontus % which ifort
/opt/sw/apps/intel/oneapi/compiler/2023.0.0/linux/bin/intel64/ifort
pontus % ifort --version
ifort (IFORT) 2021.8.0 20221119
Copyright (C) 1985-2022 Intel Corporation. All rights ...

arango

Try again, it is fixed. The problem was due to changes in the DNS server at Rutgers. Thank you for bringing this issue to our attention.

arango

Please read the preamble and glossary instructions in ROMS standard input file. If you check ROMS/Utility/read_phypar.F , ROMS will only read and process the parameters that it needs and ignore the rest. Several test cases in the ROMS test repository for beginners users show how ROMS is configured ...

arango

Did you specified the correct location of varinfo.yaml? We recommend Users download the ROMS test repository. Everything is set up and isolated for you.

arango

All the modern operational forecasting systems for the atmosphere and ocean do not do spinup. They require initial ocean analysis conditions that combine the model with the observations. They use data assimilation, which is a pretty advanced subject. The limitation of true ocean prediction is the ...

arango

The comments in the YAML file within the brackets indicate the internal ROMS code values after multiplying by the scale factor. It is the units that ROMS needs in the governing equations. It has been like that for decades.

arango

It is telling you the problem! Please, read and understand the error that ROMS is giving you:

YAML_TREE_CREATE - Unable to open input YAML file: ~/roms_project/test/varinfo.yaml
ERROR: Cannot open file '~/roms_project/test/varinfo.yaml': No such file or directory

Do you have varinfo.yaml in you ...

arango

Weird. How was it able to find the location of varinfo.yaml when you got the error in the first posting above?

The error is telling you that it cannot find varinfo.yaml . Mostly all the time, you need to specify the full path for that file in roms.in:

! Input variable information file name. This ...

arango

Yes, there is some garbage in varinfo.yaml. Search for mnbvc43 and remove that line. I will update that file code latter.

arango

In our version of ROMS, we no longer distribute the metadata file varinfo.dat but its equivalent YAML file varinfo.yaml.

arango

The candidate will study the ocean, ice, and coupled data assimilation strategies within the NASA GEOS coupled forecast system. This researcher will help to design novel techniques to assimilate new NASA observations such as laser altimetry from ICESAT-2, high-resolution altimetry from the Surface ...

arango

We haven't released the Nested 4D-Var algorithms yet for you to activate the NESTING flag in any of the adjoint-based data assimilation algorithms. Nesting has nothing to do with the computation of the error covariance normalization coefficients. They are computed from the coarser nested grid ...

arango

I don't have time to look at this now. However, as a guideline, the indexing in the I-direction for the U - and PSI -points are identical. Similarly, the indexing in the J-direction for the V - and PSI -points are identical. Thus, if you look at interpolating at PSI -points are a combination of both ...

arango

That's a classic parallel collision bug of state variables computing horizontal operators. They are tough to find and usually take much TotalView debugging time. It implies that the ice state variable illegally accesses global data belonging to another parallel tile somewhere in the DO-loops. We use ...

arango

There is no replacement CPP option. Use the switches LuvSrc, LwSrc or LtracerSrc from standard input file roms.in. It was done years ago to facilitate nesting.

arango

Yes, that's a possibility. But it is a bug in the gfortan compiler! It works for me. I'm using gfortran versions Red Hat 11.3.1-2 and MacPorts gcc11 11.3.0_5. It is telling us how crappy is the gfortran compiler, and the folks at GNU have not read or misinterpreted correctly Fortran 2003 standard ...

arango

Nope, if SOLVE3D is undefined, you are solving the vertically integrated shallow-water equations. There are no vertical levels in such an application. Neither vertical mixing parameterization like GLS_MIXING or others. The state variables are only zeta , ubar , and vbar .

I updated the repositories ...

arango

Okay, I will check it out later. I think that in mod_ncparam.F , we need to have instead:

!
! Set generic lateral boundary indices for LBC structure. Use the same
! values of the state variables at the same C-grid location. Generic
! indices are used for testing periodicity. The PSI-variables and ...

arango

Your compiler is too old and does not support 2003 and 2008 updates to the Fortran standard. Need to use a newer version of the ifort compiler or a recent version of gfortran.

arango

For the 2D test case, you need to undefine SOLV3D. Check ROMS test repository

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

arango

On behave of Bernard Jean Barnier:

I first met dale during the first summer school on space oceanography organized by CNES in Grasse in 1985. I was still a Ph.D. student at FSU, and Dale was teaching numerical modeling techniques applied to oceanography. Great class, and no surprise that I decided ...

arango

I haven't had the time to check this issue. We need to analyze the caping of the values. It is probably in the wrong place and needs to be postponed after all the terms are computed. ROMS equations and conservation statements are written in flux form, so things change between horizontal and vertical ...

arango

I met Dale when I was a PostDoc at Harvard University. He came to our group and gave an excellent presentation about ocean modeling. We also met in my office to discuss SPEM, which I had been learning. When I was ready to leave Harvard, I emailed him about my chances for me to get a modeling ...

arango

Okay, you don't understand how the multifile option works in ROMS. You CANNOT whatsoever change the values of NTIMES or DSTART to run correctly on your supercomputer with a queue time limits that don't finish your simulation. Then, you have to restart. I suspected this was your problem, so I wrote ...

arango

I added information in

wikiROMS to be used as a guideline when designing the multi-file strategy for a ROMS application. Unfortunately, this is all I can do now in my free time.

arango

What will happen if you do a single run without restarting? If ROMS creates the multifile correctly, the issue will be the restart mechanism, which is even more complicated in this case. The issue is no longer in output.F but in g et_state.F , def_his.F , and check_multifile.F . I think that the ...

arango

Well, that is weird because when single precision is activated in ROMS, there are still several important variables that are declared in double precision, and time management is one of them. That is, ROMS is compiled in hybrid precision. You can check that easily by typing the following command at ...

arango

You can compile with gfortran ; I do it all the time. However, you need to use a newer version of the compiler. Notice that in the :arrow: message that you referred to, the user solved the memory leak and bug in the compiler by using a newer version. To use ifort, you need to customize the proper ...

arango

It is difficult to diagnose your problem because you are using a version of ROMS that we don't support, and we are blind to how your version departs from the code we release. In addition, there is not enough information here to diagnose the problem, nor do I have the time for it. It is not only the ...

arango

I will look at it when I get the chance. The ROMS parallel tile indices are shown below and include the interior ( red points) and nesting contact points ( blue ) in the purple area. Things get complicated when dealing with nested grids. The diagram shows the southwestern and northeastern parallel ...

arango

Thank you for the detailed information. Yes, this logic is tricky. First, what version of ROMSare you using, We have corrected issues for this logic in the past. It is very subtle and requires lots of time in the TotalView debugger. We need to be sure that you are using the latest version of ROMS ...

arango

If you are a new user of ROMS, get the latest version of the code as you are supposed to. The code that you are using is eight years old! A lot of updates and corrections have been done since then. Nobody here is going or has the time to answer questions about an old version of ROMS. It is the ...

arango

I don't have a shallow water (2D kernel) application to test this term. But, yes, a cyclone rotates counterclockwise around a center of low atmospheric pressure in the northern hemisphere. Consequently, the inverted barometer effect causes the water level to rise to form a dome around the low ...

arango

Hi Parker, we have a new 2D kernel for ROMS that is more accurate and efficient. It is based on Shchepetkin and McWilliams (2005, 2009) formulation for the Generalized Forward-Backward 3rd-order Adams-Bashword 4th-order Adams-Moulton (FB AB3-AM4) time-stepping algorithm. It does a barotropic ...

arango

It seems to me that your surface flux transport is too strong and violates the CFL condition. You can compute the CFL, given your horizontal resolution and timestep size. Then, you need to lower your timestep or reduce your point source transport. It is a basic numerical modeling strategy. The LwSRC ...

arango

Ensure the time in the initial conditions NetCDF file is 2017-08-09. ROMS sets the initial time when reading the initial conditions NetCDF file. You can check that time easily if your NetCDF file has the correct units attribute for time:

Code: Select all

ncdump -t -v ocean_time my_roms_ini.nc

arango

Indeed, how you design your nested grid application and locate the telescoping domains is essential. That's where experience comes to play a role in successful nested applications. We want a smooth transition of bathymetry and dynamics. For example, a canyon or a significant ocean current a the ...

arango

Yes, this makes a lot of sense to me. In such an active region, the nesting should always be two-way! The issue is that the finer, high-resolution nested grid resolves the smaller-scale processes, and there is no feedback from fine-to-coarse, so the two coarser and finer grid solutions are diverging ...

arango

I always recommend Users to keep the ROMS code up to date. Every time that the code is changed to correct bugs or improvements, detailed information is provided in the trac tickets. Users should never ignore that information, even if they are not updating the code. For example, the surface fluxes ...

arango

Yes, there is an inconsistency in my explanation above. I am trying to show you that 0.5 is associated with x-spacing and not a time-step factor. If the zeta_west is averaged at the u-point, its usage in the zetabc routine for the boundary conditions for zeta is halfway in, but it won't be much ...

arango

The 0.5 factor is associated with the dx when we evaluate d(zeta)/dx and noting to do with time stepping. The C-grid stencil is:

.--------- .-------- vbar(Istr,j+1)-------.
+ | |
+ | |
zeta(west,j) ubar(Istr,j) zeta(Istr,j) ubar(Istr+1,j)
+ | |
+ | |
.--------- .-------- vbar(Istr,j ...

arango

It can go both ways, but we need to test. The section of the code in question is rarely used since we specify both tidal elevation and tidal currents. For the case that only tidal elevation is activated, we need to approximate the tidal currents with reduced-physics terms evaluated at the open ...

arango

Yes, I fixed main2d.F some time ago in my research repositories, but I forgot to do it in the distributed svn and git repositories. Please update for code. Here is that

trac ticket.

arango

It would help if you interpolated spatially. In Matlab, there are various native functions to perform the interpolation. Notice that ROMS can also output any of the time-varying depths in the history file:

Hout(idpthR) == F ! z_rho time-varying depths of RHO-points
Hout(idpthU) == F ! z_u time ...

arango

We have all the terms for balance studies in the average and diagnostic output files. You need to make sure the time-averaging window is the same ( NAVG=NDIA ). Also, it would help if you considered that ROMS is a finite volume model, and the governing equations are written in flux form (transport ...

arango

ROMS will run much faster if the code is optimized (executable romsM) than with debugging flags (executable romsG).

arango

Your model is blowing up right away. I think that it is blowing up in the barotropic kernel ( step2d) because I suspect that your currents are becoming very high. That may be a CFL violation due to surface forcing or, more likely, to lateral boundary conditions data. You should compare that forcing ...

arango

I think that the issue here is that something is missing in the configuration. Did you update varinfo.yaml ? Mostly all users ignore trac updates to ROMS. We provide precise information in trac tickets with instructions on using new features. We usually see postings here that we need to reconstruct ...

arango

Yes, thank you. We need to put the NetCDF file in define mode. I missed that call. I updated the repository.

arango

Yes, please update.

arango

You need proper treatment for all the tracers and momentum values if you have open boundary conditions. Any suspicious values along the boundaries are an artifact of the ill-posed open boundary conditions. In addition, it is possible to create artificial upwelling/downwelling along the domain edges ...

arango

Why do you want to do a radical thing like that if you are a beginner? The Fennel model is tightly coupled with highly nonlinear terms that depend on phytoplankton and a balance between prey and predactor The 3D time-stepping kernel for tracers is quite complex to start hacking and removing pieces ...

arango

Perhaps, you didn't add the appropriate metadata and logic for the new variables. Nowadays, our version of ROMS uses varinfo.yaml instead of varinfo.dat. I don't know if that change was incorporated into COAWST or the version you are using. But it may explain the issues that you are having.

arango

This application does not make sense to me. You specified a land mask around all four edges of the grid. However, you are setting East-West periodic with the LBC parameter in roms.in . You will get an unphysical solution closing all four boundaries. It would help if you had a strategy for open ...

arango

ROMS is telling what is wrong:

GET_GRID - Illegal output type, io_type = 0

I believe that your roms.in is old and missing several parameters. For Example, you need to have logic for I/O:

! Input and Output files processing library to use:
!
! [1] Standard NetCDF-3 or NetCDF-4 library
! [2 ...

arango

You didn't post enough information to diagnose the problem. Does ROMS standard output write more specific information?

The abort error is internal to the PIO library routine pio_nc.c , so we don't know what ROMS call triggered a such error in the PIO C-routine:

Abort with message NetCDF ...

arango

By the way, there are a couple of obscure native Matlab functions in its maputils that can be used to reset the longitude range to [0 360] or [-180 180] :

> lon = wrapTo360(lon);
> lon = wrapTo180(lon);

These functions are helpful when setting ROMS grids and datasets in Matlab. I bet that they ...

arango

I added the useful bitcount.m and other helpful Matlab scripts to the Matlab repository. Please update.

arango

Your log file doesn't give us useful information about the segmentation fault. In cases like this, it is useful to compile with the debug option ( -g ) in the build script:
export USE_DEBUG=on
which usually gives better information than the optimized code. Try a different compiler if gfortran ...

arango

It is in our TODO list to update the COARE algorithm to newer version in bulk_flux.F to facilitate stronger wind regimes. However, we don't know when it will be available.

arango

Throughout the years, there has been excellent discussions and different point of view about benchmarking ROMS on various hardware. Perhaps, it is time to summarize that information in

wikiROMS for easy and centralized access in the future. Thus, I am adding this task to our TODO list.

arango

We updated the code last week to use the NAGFOR compiler directly with Apple Silicon. See Darwin-nag.mk. David Robertson is benchmarking ROMS on the new Macs and comparing it with ifort.

arango

Yes, indeed. Thank you! I will have to check if the boundary values of Akt are used in the numerical kernel. I think that this was done for output purposes.

arango

ROMS will not generate the floats NetCDF file without activating the FLOATS option. You MUST have activated it. Check the ROMS standard output and look at the report of the activated options. There is a test for the 2D and 3D Lagrangian floats in the test repository. We even provide the plt_floats.m ...

arango

Gosh, you need to pay attention to what ROMS tells you in the standard output. Where in the ocean can we have velocities of 93 m/s , and what does that mean? Your application is blowing-up because of a violation of the CFL condition. If you don't know what a CFL condition is and how to remediate it ...

arango

Great, that's the way to do it. One needs to get deeper into debugging to solve the problems. Also, users learn the code more intimately and don't get scared of making changes.

arango

The ITLNAME and IADNAME initialization NetCDF files are needed for specific algorithms like adjoint sensitivities, observation impacts and observation sensitivities. To generate those files you will need to know how to write the adjoint for the specific functional in ADSNAME . They are very advanced ...

arango

It has a problem reporting to standard output. Put a print statement to check was is the value of ng and ncname. You can modify the def_his.f90 in the Build_romsG directory and recompile it with the -noclean option. You need a little debugging to figure out what is going on.

arango

We have many issues with gfortran in the GSW-Fortran (TEOS-10 equation of state) in JEDI. The problem is with various versions of gfortran implementing basic Fortran2003 functionality weirdly or incompletely. For example, the fact that you get memory leaks is a symptom of the problem and bug in the ...

arango

I bet that you are using gfortran? What version of the compiler? The YAML parser use features of Fortran2003 that gfortran has issues with them. I update the parser because of it. Have you updated your code to the latest version of ROMS?

arango

The temperature or salinity is getting very high in those places. That is, the model is blowing up. You must check the bathymetry, minimum depth allowed (cannot be zero), and r-factors. Recall that ROMS has terrain-following coordinates and needs to stack N-levels between bathymetry and the free ...

arango

Hmm, you must be doing something wrong. We always need the RPCG solver for the RBL4DVAR data assimilation algorithm. I don't understand the nature of the error because ROMS 4D-Var algorithms need the nonlinear ( NLM ), tangent linear ( TLM ), and adjoint ( ADM ) kernels, and all those variable are ...

arango

Yep, good catch! We need an underscore here.

Code: Select all

      &                 COS(S2%omega*t_time_sec+                         &
      &                     deg2rad*(2.0_r8*lonr(i,j)+S2%chi+S2%nu))+    &

arango

It seems that you are using an older version of ROMS. All the I/O routines were modified when the PIO library was added. Such a routine has additional arguments. I think that you need to update.

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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