Ocean Modeling Discussion

pmaccc

Cheap at twice the price!

pmaccc

The image on the right looks like it is having problems getting open boundary information into the domain. Are you using exactly the same open boundary conditions in the dot-in, and the same values in the boundary file? Also if you are using nudging to climatology, is the climatology the same, and ...

pmaccc

Indeed. So much of what we are able to do in our field has relied on the ideas, tools, and persistent encouragement that he provided. Let us all grab a chair in the front row in his honor.

pmaccc

I think you can use: temp_rate = <d(temp*v)/dt>/<v> = <v>*<d(temp)/dt>/<v> + <temp>*<d(v)/dt>/<v> = <d(temp)/dt> + <temp>*<d(v)/dt>/<v> and then rearrange to find: <d(temp)/dt> = temp_rate - <temp>*<d(v)/dt>/<v> You can calculate the LHS using the difference of temp from two history files (the ones ...

pmaccc

One hack we have used is to modify the nudgcoef.nc array, adding a non-zero inverse timescale to places we want to slow down. This is a 3-D array so you can have variation in the vertical as well as horizontal. Then we set u, and v to zero in the ocean_clm.nc in the same regions, and turn on ...

pmaccc

Related to this, I found I had to make some edits to varinfo.yaml in order to get it to work with the fennel.h code. Specifically here is the diff between my edited version and the original version: (loenv) MacBook-Pro-6:varinfo pm8$ diff varinfo.yaml ORIG_varinfo.yaml 44c44 < #svn_repository: $URL ...

pmaccc

Dear ROMS folks, we are still having the problem Aurora describes above when using LwScr. She has tried many things to fix this: -carefully checking the forcing files -injecting the source at all levels, or at the top level, instead of the bottom level -trying different advection schemes (A4 instead ...

pmaccc

John, Parker here - I am part of the project that Aurora is writing about. We have tried running versions of our model with HSIMT for salt + temp (instead of MPDATA) and it has given really poor results, essentially eroding most of the stratification in a model of Hood Canal. Hence I am not excited ...

pmaccc

We generally calculate fluxes through sections using hourly saved output (for runs with tidal variability), and then calculating the transport at each time on the native u- or v-grid, interpolating h, zeta, salt, temp, etc. from neighboring rho-grid points onto the velocity grid. You can also do ...

pmaccc

Dear ROMS folk, does anyone have experience to share about running ROMS on any of the national supercomputers available through the NSF ACCESS (formerly XSEDE) system? The list of possible resources is here: https://allocations.access-ci.org/resources.

Thanks,

Parker

pmaccc

Come join our team investigating the carbon sequestration potential of Canada's coastal oceans! You'll need experience working with ROMS for coastal ocean downscaling, and enthusiasm for working in an interdisciplinary team. Please apply by September 30, 2022, though we will accept applications ...

pmaccc

I see in this ticket from Hernan: https://www.myroms.org/projects/src/ticket/736 that the ability to limit the eddy viscosity and diffusivity was introduced about 5 years ago (e.g. if LIMIT_VVISC is defined in your .h then the code will use AKV_LIMIT from your .in, and the default in ocean.in is 10 ...

pmaccc

Never mind this question - I figured out that I had inadvertently defined ANA_SRFLUX. Oops!

pmaccc

I am using fairly up-to-date ROMS code, including the new varinfo.yaml. It does not seem to be reading my swrad.nc atmospheric forcing file. I wonder if this is a problem with how I am interacting with the SWRAD alias in varinfo.yaml. It reads all the other atm forcing files just fine. Thanks, Parker

pmaccc

Excellent suggestion. You are a genius! It turned out that in my ROMS source folder the makefile was old (rev. 968). Notably, I had created that folder using git clone, and for some reason when I did git pull it did not update the makefile. Weird. In any case I have gone back to getting the source ...

pmaccc

Thanks for the tip. Unfortunately it did not change things. Even compiling with an exact copy of the latest Linux-ifort.mk produces the same error message: [pmacc@n3263 test0]$ ./build_roms.sh rm -f -r core *.ipo /gscratch/macc/parker/LO_roms_user/test0/Build_roms /mmfs1/home/pmacc/make_macros.mk cp ...

pmaccc

Dear all, I'm having trouble compiling after updating to the most recent version. I had been able to compile with a fairly recent version (after the introduction of the new varinfo.yaml file). Now when I run my build_roms.sh it fails quickly, with only this output: [pmacc@n3263 test0]$ ./build_roms ...

pmaccc

I think a couple of other river variables required by the Fennel code may also be missing from varinfo.dat. In fennel_var.h (release 1054) it asks for: CASE ('idRtrc(iPhyt)') idRtrc(iPhyt)=varid CASE ('idRtrc(iZoop)') idRtrc(iZoop)=varid but there are no phytoplankton or zooplankton river fields in ...

pmaccc

I think that the units of AttChl are still given incorrectly in the latest version of ROMS/External/bio_Fennel.in:

! Light attenuation by chlorophyll [1/(mg_Chl m2)], {0.02486d0}.

AttChl == 0.02486d0

Should be [m2 / (mg Chl)] right?

pmaccc

I am updating my system to use the most recent version of ROMS (my current version is from 2016, oops!). I am able to run the upwelling example on my cluster, but when I try to run using my realistic forcing ROMS appears to halt right after successfully reading the initial state from a history file ...

pmaccc

Hernan and John, thanks so much for your answers - very helpful!

pmaccc

Dear ROMS-ulans, I have some custom bio code based on fennel. In the past I have kept it all in ROMS/Nonlinear/Biology next to all the other bio code. However, I am updating everything to the latest ROMS revision, and would like to keep my edits out of the svn repo as much as possible. I have found ...

pmaccc

Sam,

I'm having a very similar problem to the one you describe, I think. When ROMS reads my boundary forcing for SSH the min values are zero (in the log) even though I can find no zeros in the bry.nc file. What was it you did to solve your problem?

Thanks,

Parker

pmaccc

Great opportunity to work on climate effects on coastal waters:

https://hansialice.github.io/posts/2021 ... rtunities/

pmaccc

I'll look into updating the version. What always holds my group back on this topic is that we have a custom NPZD model - mostly is it separate programs, but it requires a few edits to the ROMS source code as well. I'd like to design my system to absorb ROMS updates more easily. We are not using ...

pmaccc

Hernan, the grid size is (30, 1302, 663) (s_rho, eta_rho, xi_rho). ROMS version is revision 823, from 2016. I suppose I should try with a newer version! I don't know where to look for the I/O library but if you give me a clue I will find it. I am writing to NetCDF4 with compression: #define DEFLATE ...

pmaccc

Thanks, John. I did adjust NtileI and NtileJ accordingly, and did not change wrt_his. I'll see if I can find any more info.

pmaccc

I am having a curious problem on a cluster I use to run ROMS. I have 10 nodes with 40 cores each, and have routinely been running ROMS using mpi job on all 400 cores. However, when I try to run the same job with 200 or 40 cores I get an error like this: [pmacc@klone1 driver]$ cat slurm-1501920.out ...

pmaccc

The Coastal Modeling Group in the School of Oceanography at the University of Washington seeks a postdoctoral researcher to work on a new project “LiveOcean Model Enhancement and Transition to Operations,” funded through the NOAA Coastal and Ocean Modeling Testbed. If you are inspired to use reg ...

pmaccc

This is a great opportunity to get involved with ROMS-based climate downscaling:

https://hansialice.github.io/posts/2021 ... rtunities/

pmaccc

There is a postdoc available to work with and expand an ongoing ROMS modeling project:
https://ap.washington.edu/ahr/position- ... b_id=78220
Cheers, Parker

pmaccc

Siva, Budgets can be surprisingly difficult to calculate, and are easy to make coding errors in. When you make a budget term from the diagnostics, try to make the same budget term from scratch using the history files, and then plot the two on the same graph vs. time. In most cases they should be ...

pmaccc

Siva - that is a perplexing result. How do you know that KE decreases with time?

pmaccc

We give some details about using the ROMS diagnostics to calculate terms in energy budgets in this paper. Email me if you want a copy. pmacc@uw.edu MacCready, P., and S. N. Giddings, 2016: The Mechanical Energy Budget of a Regional Ocean Model. J. Phys. Oceanogr., 46, JPO-D-16-0086.1, doi:10.1175 ...

pmaccc

Peida,

The shared folder just had things like mexcdf and the seawater routines, which are publicly available. However, I am not supporting that code at all any more and I strongly urge you to write your own from scratch.

Cheers,

Parker

pmaccc

I have an idealized simulation in which I am adding a complex river source condition. The goal is to make a boundary source/sink pattern that is like the mouth of an estuary with the usual tidally averaged two layer exchange flow. I am using preprocessing tools and a recent version or ROMS that I ...

pmaccc

Thanks very much for the clarification, Kate. It was unclear to me in the wiki which restriction was removed. And now I see in ROMS/Utility/set_scoord.F where this is implemented (lines 176-178 in the version I have):

ELSE IF (Vtransform(ng).eq.2) THEN
hc(ng)=Tcline(ng)
END IF

pmaccc

Kate, thanks for your helpful response. I agree that what I want to use for hc is the Tcline I specify in the .in file. What is still unclear to me is if "hmin" is used anywhere in the calculation of z. From the "warning" paragraph here: https://www.myroms.org/wiki/Vertical_S-coordinate one way of ...

pmaccc

I have a related question. I have a grid where the min value of h is 4 m, and I specify Tcline = 10 m in the .in file. So if I am understanding things right ROMS should use hc = 4 m when calculating the z coordinates (I use Transform function 2 and Stretching function 4). Yet in my history files the ...

pmaccc

I am having a related problem. I have a daily model run I do, which has worked fine the past 2 weeks. This morning it did not work because for some reason ROMS was looking for a bry file starting 1 second earlier than the one I made. This is the error message in the log file: CHECK_MULTIFILE - Error ...

pmaccc

Thanks for the suggestions. I stopped using ramp_tides because (1) it seemed to handle the "rude awakening" without blowing up, and (2) it meant that I always had to make 2 versions of the executable. If I were always doing long "cold start" runs I could just have the ramp_tides version, but my ...

pmaccc

I am adding to all 8 tidal frequencies, and doing so in degrees in my "tides.nc" forcing file. My varinfo.dat implies to me that the input should be in degrees and that ROMS (rev. 823) converts it internally to radians: 'tide_Ephase' ! Input 'tidal elevation phase angle' 'degrees' ! [radians] 'SSH ...

pmaccc

I have a realistic run that uses tidal forcing from TPXO7.2 at the boundaries, both SSH and UV. The tidal forcing runs perfectly in general. I make some hand adjustments the the tidal amplitude when I make the forcing, to better match observations. This also works fine. However when I try to make ...

pmaccc

Kate - thanks for the tip. I realize that our choices about the vertical coordinate transform and stretching have not been updated for some time. I tried experimenting with VTRANSFORM = 2 and VSTRETCHING = 4, and can see that the results might be smoother than what I am using, but they won't be ...

pmaccc

I am using what I think are fairly common vertical stretching parameters: THETA_S,4 THETA_B,0.8 TCLINE,0 N,30 VTRANSFORM,1 VSTRETCHING,1 and when I have a river source with 10 m depth the upper layer is rather thin, like 5 cm. So when I have very high river flow, and a Vshape that varied linearly ...

pmaccc

John, I like all the ideas you mention to solve this problem. I favor the more physical solution (add of subtract freshwater) but understand that this will need modifications to the volume conservation. My reason for replying is more basic. I use bulk fluxes and provide a rain field in my forcing ...

pmaccc

Related to this thread, I have a model run which uses quadratic bottom drag. Since there is a wide range of bathymetric depth over the domain, the height above the bottom of the deepest velocity varies from a few cm (shallow water) to tens of meters (deep water). I would like to estimate the ...

pmaccc

In this paper: MacCready, P., and S. N. Giddings, 2016: The Mechanical Energy Budget of a Regional Ocean Model. J. Phys. Oceanogr., 46, JPO-D-16-0086.1, doi:10.1175/JPO-D-16-0086.1 (available by open access) we calculated the "geostrophic wind work" in Fig 10, and the method of calculation is ...

pmaccc

Very interesting. What was AKT_BAK for your simulations?

pmaccc

John, Here are the time reports from the log file. What stands out is that most of the total time is devoted to message passing between the two grids (I'm not sure why the numbers don't all add up to 100%). Nonlinear model elapsed time profile, Grid: 01 Allocation and array initialization ...

pmaccc

Thanks to everyone for your help. I did succeed in getting my realistic run to work with 2-way nesting. The problem is that the performance is poor. I'm running on 144 cores using the Intel compiler and mpi. The parent grid alone runs at faster than 1 minute per hour, and the child grid alone in 3 ...

pmaccc

When I create a new grid using coarse2fine.m what is the correct number of rows and columns to put in the .in file for the refined grid? For a regular grid I just look at the size of a field on the rho-grid and subtract 2 from both dimensions to get the right number. Is it the same for the ...

pmaccc

I'm trying 2-way nesting in an existing run. I made the refined grid and contacts files using the matlab tools. Then I recompiled the executable using the NESTING flag. When I try to run it with mpirun I get a segmentation fault right away. I'm running on 144 cores across 6 nodes. One question is ...

pmaccc

Reiner, We recently published a paper which gives a method for complete energy budgets in ROMS: MacCready, P., and S. N. Giddings (2016) The Mechanical Energy Budget of a Regional Ocean Model. J. Phys. Oceanogr., 46, 2719–2733, doi:10.1175/JPO-D-16-0086.1. http://journals.ametsoc.org/doi/10.1175/JPO- ...

pmaccc

Kate and John,

I added the time attribute to the bio climatology variables in their NetCDF file and this appears to have fixed the problem. Hooray and thanks so much for your help!!

PM

pmaccc

Kate, related to your comment about the time variable, in our _clm input file here are what salt (whose climatology is read) and NO3 (whose climatology is not read) look like: In [8]: print(ds['salt']) <class 'netCDF4._netCDF4.Variable'> float64 salt(salt_time, s_rho, eta_rho, xi_rho) long_name ...

pmaccc

Kate, Here is the complete debugging error message (actually one of many identical ones, presumably because I am running on 72 cores): forrtl: severe (408): fort: (3): Subscript #1 of the array TVAL has value 0 which is less than the lower bound of 1 Image PC Routine Line Source oceanG ...

pmaccc

Thanks very much, John and Kate. Running with USE_DEBUG=on I get errors like: forrtl: severe (408): fort: (3): Subscript #1 of the array TVAL has value 0 which is less than the lower bound of 1 I have turned on the flags for processing of bio tracer climatology in my bio.in file, as well as the ...

pmaccc

I am having a similar problem to John's. I am trying to read climatology fields (in this case from a NetCDF file instead of specifying them analytically) and use them for nudging to climatology in a strip near the open boundaries. This works fine for the velocities, and for salt and temp, but the ...

pmaccc

A Post-doctoral research position in ocean modeling is available in the School of Oceanography at the University of Washington. The successful candidate will join the UW Coastal Modeling Group to work on development and testing of a daily forecast model of coastal-estuarine circulation and ...

pmaccc

I figured out the problem with my salt_rate test. salt_rate is NOT <ds/dt>, where <> denotes averaging over the time period for which diagnostics are collected. Instead (I think) salt_rate = <d(s*v)/dt>/<v> where v is the (changing) volume of a given grid cell. When I use this interpretation to ...

pmaccc

I just tried adding up the momentum diagnostics in one of my runs and couldn't find any obvious error, or any difference between u and v momentum budgets. Are you using "nudging to climatology" in your domain? I believe this would add an extra term to the momentum budgets that would not be in the ...

pmaccc

I wonder if the problem might arise in the two different versions of the calculation of DiaTwrk(i,j,k,itrc,iTrate) taken from step3d_t.F. I assume the first, active, version forces the salt_rate diagnostic to equal the sum of all the other terms. Then the second, commented out, version appears to ...

pmaccc

I did some more analysis on the problem of the salt_rate diagnostic. The plot shows the evolution of temperature and salt at a surface model location, both from history and average files. They look very similar. Then I calculate the time derivative of both and plot it on the bottom row, comparing it ...

pmaccc

I'm using the diagnostic feature for some budgets. In the course of some error checking I compared the field from salt_rate to the difference between salt fields from the history files saved at the beginning and end of the diagnostic averaging period. The shapes and magnitudes, e.g. of a vertical ...

pmaccc

It appears to me that the flag ZCLM_NUDGING is missing from ROMS/Include/cppdefs.h, yet it still seems to have an active role to play in parts of the code, e.g. ana_nudgcoef.h and mod_clima.F (I am using version number 629 of the code). Any thoughts?

Parker

pmaccc

I am trying to get the latest ROMS using svn onto a linux machine. This has worked many times in the past but today it chokes halfway through with the error message: svn: Can't read file 'ROMS_620/Lib/ARPACK/LAPACK/.svn/log': Permission denied A possible clue is that today for the first time I got ...

pmaccc

In my experience you can help with this problem by making your rivers longer, so that non-zero salinity doesn't penetrate up to the river source cells. This naturally avoids the problem of having very sharp gradients which can lead to numerical inaccuracy.

pmaccc

We seek applications for a postdoctoral research associate at the University of Washington School of Oceanography. The postdoc will work in new Department of Energy-funded team exploring how circulation and mixing in estuaries and on the continental shelf might change under future climate scenarios ...

pmaccc

Postdoctoral Position: Harmful Algal Blooms & the Columbia River Plume The interdisciplinary PNWTOX project, jointly funded by NOAA and NSF, will use existing data in parallel with state of the art physical and bio-physical models to advance our understanding of HAB development/dissipation and ...

pmaccc

Following the suggestions of Andreas and Rob, I got ROMS3.# running on my relatively new MacBook Pro. For reference I have written up the exact steps I used, at:
http://www.ocean.washington.edu/people/ ... notes.html

Cheers, Parker

pmaccc

The University of Washington, School of Oceanography invites applications for a postdoctoral position. The position requires a PhD in Physical Oceanography, or related field, and expertise in numerical circulation modeling. The successful applicant will work closely with a Physical Oceanographer, Dr ...

pmaccc

The University of Washington, School of Oceanography invites applications for a postdoctoral position. The position requires a PhD in Biological or Physical Oceanography, or related field, and expertise in numerical ecosystem modeling. The successful applicant will work on the Columbia River Plume ...

pmaccc

I would like to amplify some of Bob Chant's thoughts. Estuaries take a little bit of river flow, pull in a LOT of ocean water, mix the two, and spit out the mixture, which is usually only slightly fresher than oceanic. Two points then are worth noticing when formulating a "river" BC: (i) the outflow ...

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