Ocean Modeling Discussion

stef

Yes, now I can see them! Thanks for converting!

stef

Yes! Thanks, I would probably never have found those! Unfortunatly I can't play the flash movies, but the .ppt file looks fine in LibreOffice.

stef

Fascinating, thanks!

Also, I saw the Tutorial 11 pdf explains how to derive an adjoint operator, and I also should read the Giering-Kaminski paper.

stef

Regarding the negative ad_Hz, I now don't think it's an error. It just arises from the adjoint model in the incremental method. Is this right? If yes, the diagnostic energy outputs are just relevant in terms of magnitude, e.g. to detect blowups. Is this correct?

stef

Regarding the negative ad_Hz, I now don't think it's an error. It just arises from the adjoint model in the incremental method. Is this right?

stef

Hi, In the forward models the bottom velocity can flip signs due to the bottom stress parameterizations, hence there is LIMIT_BSTRESS. Do you know if there is an analogous problem in the adjoint model, or is this of no concern there? I'm seeing negative ad_Hz in some of my runs. So far I have no ...

stef

Hi, In the diagnostic output of the adjoint run I get negative total kinetic energy. I looked at ad_diag.F and found that ad_Hz(i,j,k) is negative in my runs. Do you know where this comes from, or what I should do about this? I just saw it this afternoon and tried to debug, but grepping for ad_Hz ...

stef

This is a more general question about modelling background error covariance close to the slope. Looking at the figures below, I'm guessing that the diffusion approach for correlation modeling diffuses along s-coordinates. Do you find this problematic in realistic applications? Now I discovered ...

stef

I'm a beginner in 4D-Var and I'm wondering how to get the accumulated TLM increments at observation locations/times for I4DVAR (I know it's deprecated, but I use it for learning). According to [1] (their section 4.4), this is required to test the tangent linear hypothesis. Maybe I'm misunderstanding ...

stef

In tutorial slide Tutorial_10_2019.pdf slide it says If deeper than z_r(:,:,1), observations are rejected. Is it *strictly* deeper? In the condition above it says ... Zobs(iobs).le.1.0_r8 ... I have no experience with "clustering due shallowing of bathymetry during smoothing and coarse level half ...

stef

I'm aware that I4DVAR is deprecated, but I still use it for learning and working through the tutorial. Is there a bug in I4DVAR in case an observation lies exactly on the bottom-most rho point? In the vetting logic, there seems to be a logic bug around the cancellation of the background-extracted ...

stef

Hmm, that patch I suggested is incorrect, leads to this error: <<<< Conjugate Gradient Algorithm >>>> At line 496 of file cgradient.f90 Fortran runtime error: Index '0' of dimension 1 of array 'cg_zu' below lower bound of 1 Would this one work?: diff --git a/ROMS/Utility/cgradient.F b/ROMS/Utility ...

stef

In I4DVAR (I know it's deprecated, but I'm using it to learn), it is possible to obtain negative values for the cost function. This happend to me after I did not #define BGQC and thus accidentally included a bad datapoint in the computation. In the first inner loop, the cost function is computed as ...

stef

I'm using strong constraint I4DVAR along with RBL4DVAR+RPCG, although I know I4DVAR is deprecated, but I'm using it to learn because it's easier to understand. I have only tried to understand the I4DVAR code so far, but will start with RBL4DVAR soon. I just noticed that I always forgot to #define ...

stef

I know I4DVAR is deprecated, but I'm still trying to find out what the algorithm does, because it's the most simple version of 4dvar. Could it be that there is a bug in cgradient.F, specifically in the computation of the reduction of the gradient norm? In cgradientF, the tridiagonal system is solved ...

stef

Hmm, now I saw the tl_new_state() function. Is this an implementation of getting x^k from z^k according to Eqs. 21-22 of [1]? So new_direction() is just to store the gradients in the d_* arrays? With the lanczos method, the actual cg search directions are never explicitly computed? However, the ...

stef

I just noticed that in cgradient.F, the function ! ! Compute new direction, d(k+1). ! CALL new_direction (ng, tile, model, & ... is called right after the the (normalized) gradient vector has been computed with CALL lanczos (ng, tile, model, & But in new_direction, the code is like d_zeta(i,j)=ad ...

stef

Oh, I just saw the comment in lapack_mod.F. That explains it, so it seems more a question of code style and easier future maintenance. ! This module includes modernized versions of the selected routines ! ! from thw Linear Algebra Package (LAPACK) library, which are used ! ! in ROMS 4D-Var ...

stef

Good to know, it was not clear from the trac ticket (at least for me) that NCEP was complaining about the GOTO's. Do you mean their code doesn't compile due to the GOTOs?

stef

I should add that in the successful run, the next lines are (001,007): New Ritz eigenvalues and their accuracy, RitzMaxErr = 1.00000E-01 001 3.6293220E+00 3.6446995E-03 converged (Good=001) 002 8.5684099E+00 9.1391967E-03 converged (Good=002) 003 2.1050775E+01 2.1416478E-03 converged (Good=003) 004 ...

stef

I have a toy test case using RBL4DVAR & RPCG with 1 outer loop and 7 inner loops. The run hangs at inner loop 6 at the computation of the Lanczos vectors. This occurs when using the 'develop' branch at git commit b7a47408ba22 ([1]), which uses the internal lapack routines in lapack_mod.F ([2]). When ...

stef

Oh, I did not see the roms_test repository on github! On the 4dvar tutorial page still mentions svn: https://www.myroms.org/wiki/4DVar_Tutorial_Introduction (accessed 2024/02/14) I might have missed some announcements... As long as you keep both repositories (roms and roms_test) updated the ...

stef

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. Hmm, not sure if I understand. Which ROMS version on github, the 'develop' branch or the 'main' branch? Which revision should we use with the currently ...

stef

Sorry may I ask a question about the Tutorial in this thread (it may be related to my problem discussed here): I noticed that the tutorial does not seem to work with git branch 'main'. Currently 'main' is at 21d8ab47ad4b (from June 2023). The debugger complains about what looks like related to the ...

stef

But I suggest staying in the strong-constraint regime since modeling the model error, Q, is not trivial. Yes, I'm trying to look at the simplest case possible. NADJ should be the same size as ntimes. That's what I thought after I first tried to change it. Because if the input is lower than that, it ...

stef

Thanks for the reply! I used RBL4DVAR with RPCG, as in Exercise 3 of the tutorial. It worked in some cases, but then I got blow-ups and didn't now how to investigate the causes. That's when I switched to I4DVAR and modified the NADJ to write out the adjoint solutions more frequently (I'm aware that ...

stef

Hmm, regarding what I wrote above about preconditioning: In i4dvar.f90 (as noted in the first post I use I4DVAR for debugging), there is a segment ! Convert observation cost function gradient, GRADx(Jo), from model ! space (x-space) to minimization space (v-space) which is executed after the first ...

stef

Hi Ivica, Thanks for the suggestions! Yes I haven't provided enough details about the run, I will try to write it up in a blog post. My present set up is more of a test case for learning 4dvar than a realistic application, i.e. an addition to the tutorial excercises. Alongside I am reading the ...

stef

I am making simple experiments with 4dvar and sometimes I get blow-ups in the first iteration of the adjoint model (it doesn't actually terminate during the adjoint, but the output is clearly nonsensical). In one experiment I use: * ARGO profiles from a single float, with one profile every 3 days ...

stef

I think there is a bug at the following line in obs_k2z.F: https://github.com/myroms/roms/blob/5ca8b9d0559233eaa40e7fc1d04607b5aa8d579e/ROMS/Utility/obs_k2z.F#L187 (src:trac:960, git branch develop at 5ca8b9d05592) Should this r2=REAL(k2-k1,r8)*(Zobs(iobs)-REAL(k1,r8)) be instead r2=REAL(k2-k1,r8 ...

stef

Thanks for clarifying!

Makes sense to me, because you are probably resolving some diurnal signal in the top layer.

Thanks again for all the help, it is all much clearer now.

stef

Thanks, great resource!! Hmm, I've skimmed through the paper and there is a sentence: PWR SST is consistent with in situ data during both day and night and thus may be viewed as an estimate of ‘depth’ in situ SST. The PWR SST is expected to be a useful input into L4 SST analyses, especially for fou ...

stef

Thanks for the information! Wow, that's cool! So it probably means you assimilate the ascending and descending passes individually, and maybe the subskin temperature directly as opposed to converting it to a foundation temperature.

stef

Am a beginner in data assimilation and a question came up relating assimilation of microwave SST data, specifically from AMSR2. In Lecture 6 of the 4D-VAR tutorial, it says that the sampling frequency for AMSR2 and WindSat is daily (Table 21.1). According to [1], AMSR2 is near-polar orbiting and ...

stef

After reading the manuals I guess this is incorrect, with a balance operator one would see both and adjustment of the surface, and an adjustment of dynamic/steric height via tracers. I couldn't test it so far using a balance operator (see below), but looking at the definition of the matrix it seems ...

stef

Do I assume correctly that for gridded altimetry, the domain-averaged steric signals should have no effect on the tracer increments (even if not removed), because the model is Boussinesq? After reading the manuals I guess this is incorrect, with a balance operator one would see both and adjustment ...

stef

I'm asking because I think in the BoB,the steric seasonal mean sea-level fluctuation can be like 5 cm amplitude. In [1] it seems to be much less, their Fig. 3 suggests roughly 4 cm range (2 cm amplitude) of the seasonal steric component. That's domain-averaged over the northern Bay of Bengal ...

stef

Hi, Is there a common practice of how to remove seasonal thermo/halosteric signals from along-track altimetry in data assimilation? Do these have to be removed from gridded altimetry? Do I assume correctly that for gridded altimetry, the domain-averaged steric signals should have no effect on the ...

stef

Have you tried logarithmic drag? In [1], it says Because the vertical elevation of the velocity in the bottom computational cell will vary spatially and temporally, the inclusion of the elevation provides a more consistent formulation. For testing purposes, it may be possible to disable LIMIT ...

stef

Looking at the code in extract_obs.F, what I wrote above "obs_depth" in ROMS is "depth of observations below the sea surface" is not true, is it? Do I understand correctly that the varinfo.yaml is out of date, because it says there: variable: obs_depth standard_name: depth_of_observation_below_sea ...

stef

I'm trying out data assimilation and a question regarding in-situ profiles came up. Do we have to consider dynamic height anomalies when assimilating CTD profiles into ROMS, i.e. do you adjust the "depth" axis with each individual salinity and temperature profile from the cast? In the past week I've ...

stef

I'm trying to learn 4dvar and noticed that some observations got rejected, even though the observation locations and time looked fine. Am I doing the time conversion for observations with the wrong numerical precision, or is there a minor bug in the binning of observations to baroclinic time steps ...

stef

It's been about a week since I asked at the rda.ucar helpdesk, no answer yet. They seem to re-organize their website, maybe the ticket got lost. It may also be possible that the helpdesk tickets I lodge have lower priority than others (due to my non-institutional email address, no affiliation with ...

stef

The individual files, e.g., https://rda.ucar.edu/thredds/dodsC/file ... grib2.html (one every 3 hours) have variable Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average Well, I guess not all of them. The +09 file you linked above https://rda.ucar.edu/thredds/dodsC/files/g/ds083.3/2021/202101 ...

stef

Or, since the folks at NCAR are usually super helpful, perhaps log a ticket with their helpdesk asking for clarification.

Ok, I'll log a ticket! I'll update this post once I get a response.

stef

You are plotting values extracted from individual files Well I'm plotting the files that are accessed by the scripts you mention above, where you wrote roms_{get,write}_gfs_NCARds083_bulkflux.m for accessing the NCAR archive of GFS data to my tools https://github.com/johnwilkin/roms_wilkin ...

stef

and if you plot them together you get a nice diurnal cycle resolved at 3-hour intervals? So I'm comparing this with ERA5 data, and also what I would get from applying a (hypothetically necessary) conversion from the 6-hour averages to 3-hour averages of the RDA aggregation/Best fluxes. Below figure ...

stef

It's my understanding that variables denoted "average" are just that ... they are averages over the 3-hour interval as opposed to snapshots at a time instant. So the question is whether they are 3-hour averages, or mixed 3-hour averages and 6-hour averages, right? Earlier you wrote The codes return ...

stef

Wow, great! The codes return everything at 3-hour intervals because NCAR have unpacked those 6-hour accumulated variables before adding to the aggregation. That's interesting, may I ask how you found this? I didn't see it in the manuals. Do you ask at their helpdesk for this type of information? Hmm ...

stef

Hmm, I guess one could easily compute the 3-hourly resolution from the available data: F_a: average flux from +00 to +03 (available from the resources) F_b: average flux from +03 to +06 (missing in the resources) F_c: average flux from +00 to +06 (available from the resources) Can't one compute F_b ...

stef

Thanks for your reply! I have seen the ERA5 scripts, thanks! However, my question was specific to GDAS/FNL and GFS. In that repository you linked to, do you have scripts that extract hourly data from those as well? The question was whether 1) the radiative fluxes for GDAS/FNL and GFS really are (as ...

stef

Hi, I am comparing a simulations forced with ERA5, GDAS/FNL and GFS fields using bulk fluxes (I know it can be problematic [1]). ERA5 has radiation fluxes at the same time steps as wind, albeit temporally staggered because it's an averaged quantity, but effectively all fields have the same ...

stef

regarding the 'h' variable, in set_vbc.F there is # ifdef UV_QDRAG real(r8), intent(in) :: rdrag2(LBi:UBi,LBj:UBj) real(r8), intent(in) :: zeta(LBi:UBi,LBj:UBj,3) real(r8), intent(in) :: h(LBi:UBi,LBj:UBj) # endif and you could write # ifdef UV_QDRAG real(r8), intent(in) :: rdrag2(LBi:UBi,LBj:UBj ...

stef

I never actually used the code snippet above. I'm lazy, what I actually did is "abuse" the existing field "rdrag2" (which is actually the quadratic bottom drag coefficient) in set_vbc.F and initialized it with manning_n values. This is dangerous and can go very wrong, because the "rdrag2" variable ...

stef

Ok, thanks for taking the time to explain it! I will test the various options soon. I just started the thread because I was worried that 1/0.5=2 was mistakenly coded as 0.5, but in hindsight I learned a lot.

stef

The distance between zeta(west,j) and zeta(Istr,j) is always a full pm. Now I'm confused. Isn't this inconsistent with set_tides.F? Isn't zeta(west,j) already set to be centered at u-points: 322 ! If appropriate, load tidal forcing into boundary arrays. The "zeta" 323 ! boundary arrays are ...

stef

Thanks for the tip, yes, I have not looked into the time stepping. I will write into my note that I don't fully understand it yet. Maybe I can figure it out in spring or summer when it's less busy. But for the record: I didn't see your first code block in the Flather condition, only in the reduced ...

stef

Thanks for the reply! Ok, I'll test it. Along with testing this, I should test prescribing the barotropic velocity. First I wanted to document carefully what I have been doing up to now (reduced physics). I attached an excerpt from a note I'm writing, in case anybody is interested in this topic. The ...

stef

I had the same thought about the staggering of zeta_west, i.e. that it's centered on u-points. This is supported by the comments/code in set_tides.F, see below. zeta_w+=0.5(zeta_{i-1}+zeta_i). But assuming that's right, a forward difference would be (zeta_i-zeta_w)/(0.5*dx) = 2*pm*(zeta_i-zeta_w ...

stef

I'm trying to write up the boundary condition I use and I wanted to confirm whether the following is correct: ! ! Western edge, Flather boundary condition. ! ELSE IF (LBC(iwest,isUbar,ng)%Flather) THEN DO j=Jstr,Jend IF (LBC_apply(ng)%west(j)) THEN #if defined SSH_TIDES && !defined UV_TIDES IF (LBC ...

stef

Just a quick callout to a past post of mine viewtopic.php?t=4665 on performance versus memory bandwidth. Thanks, I haven't seen this! ROMS scales well with increasing number of MPI processes (eg. NtileI*NtileJ) until the number of processes exceeds twice or three times the number of memory channels ...

stef

After reading the thread [1] I am wondering if it wouldn't be nice to have a reference operating system for benchmarking. I don't know much about computers, so I'm not sure if this makes sense. Argument for using clearlinux [2] to produce reproducible OS images for benchmarking x86-64 hardware ...

stef

Ok, thanks for the tip! Here is a tomshardware article about the AMD threadripper strategy [1], if I understand correctly the prices for the workstation CPUs with quad- and octacore memory do not differ much from server CPUs nowadays. There used to be an "enthusiast" line which they don't offer ...

stef

Wow, the information on the thread you link to is all new to me! I looked at your figure in this thread and wondered why there are so many tiles. Now I see it's explained in the thread. My hopes are up that I can get a significant speedup by configuring everything properly. Hernan is right in the ...

stef

Good to know, thanks for all the great advice!

stef

Get a high-level gaming mother board. Quad-channel memory system in a MUST. Do not settle with dual-channel memory. Ok! In AMD land that would imply a Ryzen Threadripper I think. They have 4 or 8 channels. In terms of price difference to a server: Doing a quick search, Lenovo offers a ThinkStation ...

stef

Good point, and even with a flat internet rate, I guess the compute nodes should be close to wherever the large data archive is. I guess the largest data set is the output data, assuming one wants to keep it all. There is a blog post saying it's ok to run 24/7, except the fans deteriorate easily ...

stef

Thanks for sharing your experience! Yes, SWAN takes up lots of resources. I guess I'll try to run everything on my existing workstation for now.

stef

I am running a toy "operational" model and consider buying a dedicated consumer-grade desktop for it. The plan is to pick some number of cores (arbitrary, say 6 or 12 cores) and adjust the model configuration and data processing pipeline such that the desktop runs continuously under full load, doing ...

stef

Indeed, thanks! Sorry, I thought I had the current release before reporting.

Edit: I take it back, apparently it was fixed after I reported it

:
https://www.myroms.org/projects/src/ticket/919

Anyway, thanks for the update!!

stef

So this is intended behaviour: The units of ocean_time in the ini files can be 'days' when doing forward runs, but *must* be 'seconds' when doing 4dvar runs, otherwise the program will error at runtime (after multiple timesteps have already been performed).

Okay, thanks for the clarification!

stef

I have been using ocean_time units of 'days since 1970...' for some time now in the initial conditions netcdf. This worked (even though in varinfo.yaml the units are s). However it does not seem to work when using 4dvar, because the updated initial conditions are always written in seconds (I think ...

stef

Following the 4dvar tutorial there was a runtime error: AD_WRT_HIS_NF90 - wrote adjoint fields (Index=1,1) in record = 5 Found Error: ** Line: 525 Source: ROMS/Utility/time_corr.F, time_corr_nf90 TIME_CORR_NF90 - error while writing variable: ubar at time record = 5 into NetCDF file: wc13_tlf.nc ...

stef

Thanks for the information! Searching for references to Desroziers et al., I found Fig. 12a) of [1] where I think the 2 cm error for the 30km experiment are justified. [1] The Regional Ocean Modeling System (ROMS) 4-dimensional variational data assimilation systems. Part II – Performance and a ...

stef

I was wondering if the observation error covariances in the tutorial represent instrument errors or the actual spread of the data around a valid model. In the tutorial excerise 1, WC13 is described as: While 30 km resolution is inadequate for capturing much of the energetic meso-scale circulation ...

stef

For tutorial exercise 3 I tried to compile a RBL4DVAR application without RPCG. It fails with cd xxx; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch -O3 -ffast-math -fallow-argument-mismatch convolve.f90 convolve.f90:299:37: 299 | CALL wrt_ini (ng, Rnew(ng)) | 1 Error: Missing actual ...

stef

Thanks for taking the time to provide so much background! I will switch it off, work through more of the tutorials/lectures you provide and at some point revisit your post when I understand more about assimilation (I'll admit I don't yet understand much of what you are saying about the math). I get ...

stef

Sorry Hernan I think it's a WET_DRY bug (you mentioned in a previous post that maintaining the option is a burden). No urgency, I can do it myself, but still wanted to report it. Using WET_DRY in a 4dvar results in: cd xxx; /usr/bin/mpif90 -c -frepack-arrays -O3 -ffast-math -fallow-argument-mismatch ...

stef

I am tinkering with the assimilation tutorial, and this looks like a typo: provenance.Targo = 6; % ARGO floats temperature from Met Office provenance.Targo = 7; % ARGO floats salinity from Met Office The same lines are in d_sst_obs.m. The .Targo/.Sargo properties are also used in d_ts_metoffice.m ...

stef

Last week I asked a question to ncep.webmaster@noaa.gov about the GFS forcing, but haven't received an answer yet. I was wondering if someone on this forum could help, it might be of interest to many beginners here. I do not understand the difference between the analysis fields and forecast data ...

stef

Apparently they may open enough data for WRF downscaling in 2023: For open data, the next plan is to open a 'CAMS Support set' in 2023 which contains more parameters - this would be with a view that users could run WRF. This is their entire answer: Hi Stefan, Apologies that the answer was not ...

stef

Recently ([1]), ECMWF opened access to some of their data. Forecasts are available globally at 0.4 degrees resolution (i.e reduced spatial resolution), in steps of 3h for at least 90 hours. The available fields are listed in [2]. Unfortunately, the list is incomplete for a bulk flux parametrization ...

stef

I use data from a global model without tides for my u/v/T/S boundary, and (as noted above) use ADD_FSOBC, so the SSH of the global model is used too. I want to make a sensitivity study quantifying the effect of tidal forcing on the circulation with ROMS, and I don't use UV_TIDES. I have Chapman ...

stef

Great, thanks for your help!

stef

I'm comparing 2d vs 3d tide simulations with ROMS, and many studies with 2d tide models use a Manning-Strickler formula. If I wanted to use a Manning-Strickler type formulation for bottom friction into ROMS in a quick-and-dirty fashion, would I insert something like cff1=0.25_r8*(vbar(i ,j ,krhs ...

stef

Thanks for your reply, I went to researchgate and made a request.

stef

I was trying to download one of the earlier papers on data assimilation [1] from the myroms.org page: https://www.myroms.org/index.php?page=papers Could it be that there is a "bug" on that website: list items 3. and 5. point to the same pdf, which is the excerpt on the Mercator Ocean Quarterly ...

stef

I confirm that the first excercise ran without error, with the wc13.h and varinfo.dat provided in the test repository, and the latest src version commit 3b74341007c1b2312f091fed3758655d8f2e485f (HEAD -> master, origin/master, origin/HEAD) Author: Hernan G. Arango <arango@marine.rutgers.edu> Date ...

stef

Your best strategy is to start with the latest version of the code.

I see! Thanks!

stef

I had trouble running the first exercise in the 4DVar tutorial. I checked out svn checkout --username joe_roms https://www.myroms.org/svn/src/test my_test as described in [1]. I checked out revision 974 as described in [2]. But they seem to be incompatible, the files in the project directories do ...

stef

Fantastic! Thanks! I'm sure a lot of us appreciate the work you put into this. It seems to be a very widely used data set, and having the options for direct momenum/heat/salt fluxes and BULK_FLUXES is great. However, something we have noticed in tests is that near the coast, in regions where the ...

stef

Thanks for the WMO paper, I should read it! These are great. Yes we should look at the rda.ucar documentation. Unfortunately I did not realize that rda.ucar offers the ERA5 data set until it was too late. I like to download the netcdfs via thredds/opendap on rda.ucar. But I had already invested some ...

stef

I just saw in [1] it says In HRES atmospheric (hourly steps), mean rate precipitation at time=06:00, step=3 represents the average precipitation rate in the 1-hour period from 08:00 to 09:00, so that's clear now. I'm downloading from "cds.climate.copernicus.eu". Not sure which time axis "rda.ucar ...

stef

I'm trying to learn how to use atmospheric forcing. Thanks for the matlab scripts on github! They are great. I saw in [1] that e.g. the mean evaporation rate in the era5 reanalysis is This parameter is a mean over a particular time period (the processing period) which depends on the data extracted ...

stef

You integrate for 5 days 2400 ntimes Number of timesteps for 3-D equations. 180.000 dt Timestep size (s) for 3-D equations. I would check if the cotide/corange plots are sensitive to the integration period. Depending on how many constituents you are solving for in the LSQR routine, 5 days may be too ...

stef

Turns out I probably took the wrong turn here. Most of the difference does not appear to be due to the splitting itself, but due to the fact that that bottom stress was artificially limited in the 3d application. In set_vbc.F, there is: # ifdef LIMIT_BSTRESS cff3=cff*0.5_r8*(Hz(i-1,j,1)+Hz(i,j,1 ...

stef

I think the difference is mostly due to the differences in bottom stress application between 2d vs. 3d. From main3d.f90 it seems that the bottom stress is computed at the beginning of the baroclinic time step (set_vbc) and held constant throughout the barotropic stepping, whereas in 2d applications ...

stef

A run with ndtfast=4 is much similar to the 2d solution. Could it be that the "slow forcing" terms in the 2d momentum equations are the reason? In my case, these are * vertically integrated 3d "rhs" terms (rhs3d.f90) * bottom/surface stress plus (rhs3d.f90) * 3d horizontal viscosity (uv3dmix.f90 ...

stef

I'm running tide simulations and want to compare the results of 2d simulations to 3d barotropic simulations (no tracers, homegeneous density). Vertical viscosity is constant and prescribed by AKV_BAK. Should I expect the 3d solution to converge to the 2d solution for very large AKV, e.g. AKV=1e5? I ...

stef

I have the following error: Found Error: ** Line: 311 Source: ROMS/Utility/wrt_tides.F, wrt_tides_nf90 WRT_TIDES_NF90 - error while writing variable: v_tide into detide harmonics NetCDF file: ... I tried to fix it as follows, but don't have a run long enough to validate the detided output, so I'm ...

stef

Again, as I said before, for ocean tides the seasonal effects (tropical year) dominate over the gravitational effects (anomalistic year) so it makes sense to use the tropical year, whereas for earth tides, presumably the opposite is true. Thanks for pointing this out again, I had not fully ...

stef

Wow, I just saw that appendix A of [1] explains it very well, and it's open access!

[1] Ray, R.D., Loomis, B.D. & Zlotnicki, V. The mean seasonal cycle in relative sea level from satellite altimetry and gravimetry.
https://link.springer.com/article/10.10 ... 21-01529-1

stef

I'm modelling tides with 2d configuration in the north-eastern Bay of Bengal, as a precursor to a storm-surge modelling exercise. A figure of the northern part of the domain (Ganges-Brahmaputra-Meghna Delta): https://sriha.net/articles/assets/harmAnaBoBPart1/images/map_closeup_overview.png The white ...

stef

Very good, thanks for the advice. The question came up indirectly because [1] don't seem to distinguish between "H1" (aka "alpha_2")in the Foreman software, with Cartwright number (2 0 -1 0 0 1), and the "MA_2" constituent proposed by [2], which IMHO should have Cartwright number (2 0 -1 0 0 0). So ...

stef

I have a general oceanography question about the tidal constituent SA. Does it have the period of a tropical or anomalistic year? I know it's not directly related to ROMS. Sorry, but currently I don't know where else to ask. In the harmonic analysis packages [1] and [2], SA is defined as inverse of ...

stef

I'm trying to do harmonic analysis and detiding, and get weird results for a child grid when nesting. The results for the parent grid seem ok. Searching for a possible bug in ROMS, I noticed in set_tides.F ! ! If nested grids and detiding, load period and harmonics to other ! grids. ! IF ...

stef

But I do not think that is the cause because that issue seems to affect the input of information from coarse to fine grid and thus the artifacts seen in my results would be present in both one-way and two-way nesting. Please let me know if you agree. Yes, agreed! I have yet to try out one-way ...

stef

If you aren't using identical bathymetry in the contact regions, the following may be interesting too: viewtopic.php?f=14&t=5438&p=21072#p21072 I haven't updated my ROMS code in a while, so I'm not sure if this is still relevant. I thinkt the problem was that the barotropic volume flux through the ...

stef

Ok today I searched for 'Dynamic Atmospheric Correction' and there are a lot of resources! Thanks.

stef

I'm interested in storm surges and I'm trying to understand how to use satellite altimetry. The ROMS 4DVar tutorial [1] mentions 'satellite SSH in the form of a gridded product from Aviso'. I'm wondering if one has to do any preprocessing (filtering?) on that data? I read about how datasets like [2 ...

stef

But if there is a problem with the grid topology, how come the experiment with the same timestepping does run fine. Hmm, it's surprising, isn't it?

stef

[edit: deleted]

stef

There is approximately 5km between the stripes and the barotropic wave speed is 166m/s, so there is a period of 30s, which is in sync with the baroclinic time step? So assuming the signal is generated at the nesting boundary and propagating into the fine domain, maybe check the effect of the cpp ...

stef

I was thinking that the masking could be done in the preprocessing step that generates the contact zone input file (e.g., 'roms_ngc.nc') so that the model can be tricked to think that there is an island where the coarse grid is supplanted by the fine grid so that the fine2coarse interpolation ...

stef

(In case this is directed to me, not the original poster...)

For me everything seems to work using the flag mentioned above! Let me know if you still want the output. Thanks!

stef

If the parent grid discrete stencil for advection and/or diffusion spans, say, 3 parent grid cells then do we need to match bathymetry precisely over this range, which would be refine_factor times the 3 parent cell stencil width. Yes, any insight into this would be great! If I recall correctly, my ...

stef

[Edit: just saw you replied while I was posting...the following is intended as reply to wilkin's comment..] To test this, what do you think about the following: Mask all coarse grid points in the interior of the fine2coarse contact region, except the ones adjacent to the nest boundary, i.e. the ...

stef

I don't understand much of this, but for the record I'm posting error messages when compiling the following version of Roms Rutgers on a recently updated Arch Linux distribution: >>git log commit 697c77dc4836919704033f970a1b051f24c595d0 (grafted, HEAD -> master, origin/master, origin/HEAD) Author ...

stef

I had a similar error, using gcc 10. Adding the '-fallow-argument-mismatch' to FFLAGS solved it for me. See also here: https://www.myroms.org/forum/viewtopic.php?f=17&t=5696&p=22037&hilit=fallow+argument+mismatch#p22037 https://github.com/Unidata/netcdf-fortran/issues/212 But then I had other errors ...

stef

Probably not relevant for your 3 vs 5 refinement, but perhaps interesting to look into if you have very shallow regions or very steep bathymetry gradients along the grid: https://www.myroms.org/forum/viewtopic.php?f=14&t=5438&p=21072#p21072 I haven't updated my ROMS code in a while, so I'm not sure ...

stef

I noticed this thread just a couple of days ago (when agpc posted), and after reading wilkin's first post from 4 years ago, I'm not sure if I'm doing it right. I'm using the source https://www.ncei.noaa.gov/data/north-american-mesoscale-model/access/historical/analysis/201210/20121027/namanl_218 ...

stef

think of the beach, and the tide (or surge) coming in and out. what is the horizontal distance from the high tide line to the low tide line - that is the what you should think about.

Good point, thanks again for your help!

stef

I think at 12km your spacial scales are probably not resolving those wet-dry processes. Thanks for the reply, that makes sense. I have a nested toy setup and tried to keep the processing of the grids identical as far as possible. So I have not used a minimum depth at all, even in the coarsest grids ...

stef

I have a grid with 12km resolution and dcrit=0.1. Is this reasonable? I have been looking at a specific blowup and I'm wondering if there is an instability caused by the combination of wet-dry flux-inhibitor and the multiple time levels used in the predictor-corrector scheme. The "three-time" Adams ...

stef

Update: note that there is a problem with the patch in that the wet/dry flux limiter (i.e. suppress outflow from a dry cell) does not work at the boundary. An already dry cell adjacent to the boundary may still export water out of the domain, depending on the boundary condition. It could be fixed ...

stef

I should say that the "mod_stef.F" is very messy. Sorry.

The only variables needed are the ones used in step2d.

stef

Hi, Thanks for your email, I'll respond tomorrow, meanwhile I attached the patch. Please note: *) Some (much?) of this may be incorrect. I'm a beginner. My approach was "if I get a reasonable result, it's good enough for now". *) I have not really understood MPI yet, in particular, in the end of ...

stef

I wrote a blog post [1] about my experience using ROMS in 2d setups with grid nesting and wetting/drying. Very early stage, but if anybody is interested in this, I appreciate comments/suggestions, in particular if you are working on new code that is being pushed to the repository in the near future ...

stef

In the first post of this thread it says: u(XI,ETA)=u(LON,LAT)*cos(angle(i,j))+v(LON,LAT)*sin(angle(i,j)) v(XI,ETA)=u(LON,LAT)*sin(angle(i,j))-v(LON,LAT)*cos(angle(i,j)) shouldn't this instead be u(XI,ETA)=u(LON,LAT)*cos(angle(i,j))+v(LON,LAT)*sin(angle(i,j)) v(XI,ETA)=-u(LON,LAT)*sin(angle(i,j))+v ...

stef

Another question about the boundary condition for barotropic flow for nested grids. This applies to 3d setups. In 'u/v2dbc_im.F', there are lines like: cff=0.5_r8*GRID(ng)%on_u(Istr,j)* & & (GRID(ng)%h(Istr-1,j)+zeta(Istr-1,j,kout)+ & & GRID(ng)%h(Istr ,j)+zeta(Istr ,j,kout)) cff1=GRID(ng)%on_u(Istr ...

stef

So maybe in a 2d setup, one could store the volume flux of the donor after each barotropic corrector step, and impose that during the 3 (or 5 etc...) time steps made in the receiver grid? Hmm, I guess one should store two time levels of the donor volume flux along the boundary, and then do a ...

stef

I guess that we never accounted for a User needing nesting in a 2D application. The motivation would be to do storm surge modelling, in a way that is roughly consistent with other storm surge models such as SLOSH or ADCIRC (both mostly 2d, at least until a couple of years ago...I'm not sure about ...

stef

I see, thanks. That DU_Avg field is actually appearing in u2dbc_im.F, for the "nested" type boundary conditions (in a 2D application). I substituted it there by a dummy value to test, and then the dummy value appears in my history file. Unfortunately I can only continue testing on Monday. Anyways ...

stef

Thanks for your replies! I work on a 2d application, and another potentially relevant thing I just noticed is that the nesting boundary conditions for the refined grid use fields called e.g. REFINED(cr)%DU_avg2(1,m,tnew) I think this is the case even in 2d applications. However, I think that this ...

stef

Hi,

I read wetdry.F, and was wondering if the index boundaries should account for the contact regions in nested applications? Currently, there are ranges like "JstrR,JendR" etc., but shouldn't they be "JstrT,JendT" instead?

Thanks!

Regards, Stefan

stef

I wonder if in 2d applications, the multi-valued mask can just be converted to a binary mask like so

I mean only in fine2coarse2d(), not elsewhere....

stef

Hi, This is unrelated to the incorrect netcdf header reproduced in the wiki (as reported earlier in https://www.myroms.org/forum/viewtopic.php?f=17&t=5425 ), but it's related to nesting in general. In 2-d applications with wetting/drying, the u/vmasks supplied to fine2coarse2d() are in their multi ...

stef

I think that we, as ROMS developers, have freely provided a very sophisticated modeling framework to the ocean community without asking anything in return. I highly appreciate your effort and that of your team, and the appreciation and admiration grows every day I work with the software you provide ...

stef

Hi, I was able to do a refinement using 2 grids, using a self-written python script to generate the contact file. It's a 2d application and although I hit a bug with the wet masks using wetting/drying, I was able to patch it and proceed. However, now I want to use 3 refined nests (i.e. one ...

stef

Thanks, that sounds perfect! I have never heard about this!

This way I don't have to set up the server, plus it occurred to me I would have needed to set up a VPN too. Much simpler!

stef

Wow, thanks for this! Looks great! I like the zooming with the mouse wheel and the panning.

I'm not sure if I need a time axis with calendar units, but maybe I can tweak it. I'll read the docs! Thanks!

stef

Also, I just found a paper on "Accessing HDF5 Files via SSHFS".

https://support.hdfgroup.org/pubs/paper ... -final.pdf

They say it's comparable to NFS, and useful for subsetting remote files. So it may be comparable to using the THREDDS server anyways.

stef

Thanks for your response! Yes that would be great, but does THREDDS have an option to deliver a UI to the clients so they can browse data, in the sense that they can specify e.g. which x-y slice at fixed z and t they want to look at? This way only the figure would be sent over the internet, not the ...

stef

I was wondering if anybody has experience with visualtization tools for remote work over the internet (WWW, not LAN). I used to mount remote directories on my local machine via sshfs, so any netcdf browser will work. However, now I sometimes make larger simulations, and the UI of the browser becomes ...

stef

Also, there is a typo in the computation of the radiation stress component derivative for the vbar forcing: >> git diff master mybranch ROMS/Nonlinear/nearshore_mellor08.h ... @@ -1116,9 +1116,9 @@ DO j=JstrV,Jend DO i=Istr,Iend cff=(Syyl(i,j )- & - & Syyl(i,j-1))*on_v(i,j)+ & - & (Sxy_psi(i+1,j ...

stef

I tested the spurious wetting of high elevation grid points now with the 3d version of COAWST. No spurious wetting occurred in my test, neither using WEC_VF nor WEC_MELLOR. Browsing through the source code and Warner et al. (2013) I currently think the following (unverified/untested hypothesis): In ...

stef

Thanks for your reply! Yes, I should have mentioned it's a 2d application. I'm trying to simulate storm surges. At some point I want to have at least a bottom boundary layer, but having 2d simulations for reference and comparison is interesting. (also I just noticed that I have the WET_DRY_LIMIT ...

stef

I have tried ROMS+SWAN coupling with wetting/drying and the model blew up. jcwarner already had told me to use the COAWST version for ROMS+SWAN coupling, but I wasn't able to compile it (see below for the error. Also, I'm not sure where to report errors.). So I kept working with the Rutgers version ...

stef

I'm interested in modeling storm surges in the context of probabilistic risk assessment, e.g. using the Joint Probability Method as described e.g. in [1]. See also ROMS forum post [3]. I just found a paper [2] describing an efficient alternative to SWAN. The authors of [2] note that, as opposed to ...

stef

Thanks John, I sent the email! Sooner or later I wanted to learn about COAWST anyways, so that's great. For the near future, I have to keep it simple as I'm still learning nearshore processes, wind waves and small scales in general. I looked for the most simple method to compute wave setup. SWAN has ...

stef

I'm trying to set up a minimal storm surge model and hit the same bug. It seems to affect any 2d application using both NEARSHORE_MELLOR0*. I don't know much about wind waves yet, still reading literature. But this is still a bug, isn't it?

stef

I should add that an example for the 1D transects can e.g. be found on page 25 in: Federal Emergency Management Agency, 2013: Flood Insurance Study (preliminary). City of New York, New York. https://hazards.fema.gov/femaportal/prelimdownload/prelim/ProductsDownLoadServlet?pfiProdId=16353 This ...

stef

Hi, May I kindly ask for your opinions on using ROMS for storm surge modelling? I'm particularly interested in risk assessment, similar to what has been done by FEMA for coastal flood hazard studies. Here is a link to the New York - New Jersey region: http://www.region2coastal.com/ They are using ...

stef

Just a quick warning in case anybody (like me) considers making oblique Mercator projections with Proj version (4.9.3): be careful

stef

It turns out that "oblique Mercator projection" is exactly what I need, I think. It lets you define two points in lat,lon coordinates through which the central line for the cylindrical projection goes (that's the line at which the projection cylinder touches the sphereoid), and this can be tilted ...

stef

Wow, Lambert conformal conic! On Wikipedia it says: By scaling the resulting map, two parallels can be assigned unit scale, with scale decreasing between the two parallels and increasing outside them. This gives the map two standard parallels. In this way, deviation from unit scale can be minimized ...

stef

figure_grid_rotation_tutorial_mercator.png I'd like to show off a figure about one way to correctly (?) rotate the grid, where I'm trying to follow the steps from above post: For pm, pn, I have an initial value based on the flat projection space. Then I later remap to the sphere so that I can ...

stef

Very good, thanks for your patience and the information, it helped a lot. I will try to process all of this during the next couple of weeks

stef

Ok, but ROMS doesn't care whether it's orthogonal on the sphere, right? What it wants is orthogonality in the plane. And this cannot be fulfilled if we measure pm and pn on the sphere and then use it on the plane. Is this right? Or is there a conformal projection that can do that? The way I see it ...

stef

Thanks for the help! Now I also found a presentation , where you explain this on page 4 (may be helpful for other readers). However, strictly speaking, when we measure pm, pn on the sphere and use it in the horizontal plane, we don't get an orthogonal grid, right? So if we computed the ds quantities ...

stef

Ok thanks a lot for your time Kate. Let me see if I understand correctly: The real question to ask is what to use for pm and pn in the first place. This reflects how the projection is made from the sphere to the plane. It already involves a trade off: If one chooses Mercator, one doesn't conserve ...

stef

After spending some time today browsing through the SCRIP manual, I think I should better explain the motivation of my initial question. If I understand correctly :? none of the bilinear and bicubic methods take into account the sphericity, neither in SCRIP nor in ROMS. What they do is interpolate ...

stef

Very good, thanks! Meanwhile I also found some Python code, specific to ROMS: https://github.com/ESMG/pyroms/blob/master/pyroms/pyroms/remapping/remap.py with "conservative" and "bicubic" remapping. It seems they use the "SCRIP" library you linked to, so that starts to make sense to me :) Cheers ...

stef

I'm trying to configure a model to practice data assimilation, but stumbled across a very basic question about interpolation (maybe embarrassing for a geophysicist :oops: , but I never had to do with that problem before.). When I interpolate data on an equidistant lat/lon grid, do I need to do some ...

stef

met_c48xlarge.png Hi, I'm tinkering with benchmarks on Amazon Web Services (AWS). The attached figure shows time (in seconds) spent per process for the ROMS ”large” benchmark test (benchmark3.in), as function of the number of processes. Axes are logarithmic with base 2. Computations are performed on ...

stef

Yes I'm trying AWS. At the moment I'm doing some benchmark testing, see https://github.com/poidl/awsroms and https://poidl.github.io/awsroms/ . I still have few results, and they are not interpreted properly. I'd like to become an independent (sub-) contractor, so I'm also very interested in ...

stef

That's it, thanks. Setting the right path in the platform dependent file solves it!

On a side note, this still leaves me wondering why the line after the prerequisites is executed (sfmakedepend), if the prerequisites are not fulfilled? Not urgent, though.

stef

I'm trying to run the upwelling example, and make gets caught in an infinite loop. To reproduce: I change the compiler and netcdf paths in the makefile: >> diff makefile path/to/original/makefile 142c142 < FORT ?= gfortran --- > FORT ?= pgi 312,313c312,313 < NETCDF_MODFILE := ../../include/netcdf ...

stef

Thanks for the guidance! I'll try that.
--stefan

stef

Hello! We use a grid generated with 'Roms Tools', and we changed the code in the m-files to have constant, user defined coriolis acceleration. Everytime we make a run with different f we have to generate a new grid, although the rest is the same as before. Is there an easy way to analytically define ...

stef

Relating to this discussion I want to point to a different post. The following is *very* instructive:
viewtopic.php?t=622
Thanks!

stef

Thank you for the replies! Ok, we will try to isolate the user-modified parts of the code and avoid using svn for anything else than checking out a working copy from the roms/toms-group repository for every user. This seems to be easy and gives every user a chance to learn how to use svn. When we ...

stef

We are in the process of switching to the new ROMS version and I have some questions concerning administration: Imagine that on a cluster of our university, there are three people using ROMS and making setups, all working on the same project, but all going into a slightly different direction (one is ...

stef

Hi Zhou Wei!
If it's because of the blank, mybe you can try type your username 'Zhou\ Wei'. the backslash is use in linux (and I guess unix) to mark a blank.
good luck
--Stefan

stef

Hi Mark! Yes, I will read the manual for ifort to see what kind of options it has. I also will ask our sysadmin to install g95 and idb. SALINITY is undefined. I think the error was caused by my altering the files over and over again and making some copy-paste error with emacs, because the error ...

stef

Hi!
The post I was referring to is the one from Mon May 28, 2007 10:34 pm in:
viewtopic.php?t=538

There seem to be a lot of other posts on this topic, but I haven't read them yet...

stef

Hi! I recently ran into troubles with segmentation faults and it was the first time that I tried the debug option. I'm using ifort on Linux. As m.hadfield suggested in another post, I also added a '-traceback' option the the '-g -check bounds' in the Linux-ifort makefile. Now when I start oceanG ...

stef

Concerning the pressure gradient: I'm looking at prsgrd31.h (probably not good, but maybe for flat ocean bottom it's ok) and there is a term called fac2 that is multiplied by a gradient of z_w(i,j,N). It looks like the shallow-water-part of the prsgrd. z_w(i,j,N) is set in set_depth (called at the ...

stef

I see. So the baroclinic mode is effectively doing nothing. I'm not sure, but my guess is that is has to do with the time-filtering of the barotropic mode in the coupled system. I don't know if time-filtering is used in the standalone 2d-code, but I guess not, since it serves to remove instabilities ...

stef

Hi!
Sorry, I don't know the answer, but I wonder how the vertical velocity-profile looks like? Is v z-independent, like it's supposed to be?

stef

I think that what I wrote above only makes sense for 2nd order centered advection, both for velocity and tracers.

stef

Hi! I still use version 2.2, and don't know if anything has changed in the new version. In mod_grid.F there are some variables defined, three of them are: Hz: Thickness of vertical rho-Points Huon: Total u-Momentum Flux term: interpolated(Hz)*u*dy (dy is the same as 1/pn, at least for a rectilinear ...

stef

I just reread the scrum manual and there it just says "finite diffences", not finite volume. I looked at the 2d-momentum equation and if I did everything right, then for a rectilinear grid the finite-volume and centered finite difference formulation is the same thing. But for a curvilinear grid you ...

stef

Hello! Thanks for the reply! I am also searching for information on ROMS finite volume formulations on the c-grid. Specifically, I have troubles understanding how the variables on the boundary of the gridcells are reconstructed to do the integration of the fluxes. It seems like there are many ways ...

stef

Hi! I was wondering if someone could give me hints about where to find documentation of the 3d momentum time-stepping (Adams-Bashforth 3) used in version 2.2. I tried to understand the Shchepetkin-McWilliams paper, and could extract some info about the barotropic LF-AM3, but I think they don't cover ...

stef

I'm going to try that as soon as I can. My most stable setup so far is: Everything clamped in north, m3, m2 and tracer clamped in south, with free surface radiation.

stef

Hi! Hmm, that's interesting. When I define m2 to be zero and define a m3 profile, e.g. u=w=0 and v=v(z), with all values negative from zeta down to the bottom (so vbar should be negative), the entry in the history files for the first calculated baroclinic timestep (NHIS=2) containes a vertical v ...

stef

Thanks Kate, In my version (2.2) there is only one possibility to define 3d velocity initial conditions analytically: ANA_INITIAL. If I define it, I have to insert analytical initial fields for BOTH m2 and m3 velocities (and tracers). That's why I don't think that there is a call to any routine that ...

stef

My configuration is a flow-channel with open boundaries in north/south and closed walles in the east and west. I want to have velocity boundary conditions identical to velocity initial conditions. All of these conditions are analytically defined. If I want inflow from the north with u=w=0 and a ...

stef

I see. Thanks. Another question: In my mathematical model, I will have water flowing in a channel from north to south, with u=w=0 and a vertical shear in v (just like in the paper above). This implies a horizontal density gradient wich I want to impose by using a linear equation of state. A tilted ...

stef

In the vertical boundary conditions for z=zeta there should be the total time derivative of zeta for the w condition. If I understand correctly, the advective terms are missing.

stef

I would like to set up a thermal wind balanced channel flow. The channel will have flat bottom for now, later I will put a cylinder or an island into the domain. I basically follow the setup in the article "Island Wakes in Deep Water" by Changming Dong. http://www.atmos.ucla.edu/~cdong/papers/iswake ...

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