Ocean Modeling Discussion

jivica

I am using the open-source drift model OpenDrift, it has the native reader for ROMS outputs and many "modules", written in Python with the Xarray engine. https://opendrift.github.io/ or for example radionuclides: https://opendrift.github.io/gallery/example_radionuclides.html Cheers, Ivica

jivica

You are close, think your river_direction and/or transport is wrong. Read about the rivers, John wrote a nice tutorial.

jivica

what about temperature? Is it correct or do you have a strange result? Are you sure about the inflow direction you set (inflow not outflow from the domain)?

jivica

Hi Mark, having a look into your stations.in I can see the problem is that you put stations only for GRID 1: NSTATION == 1 2 ! you want to have 1 station in grid 1 (parent) and 2 stations inside a nested grid 2 (child) POS = GRID FLAG X-POS Y-POS COMMENT 1 1 120.5750 33.7917 ! this is station inside ...

jivica

Hi Stef, we need more info about your experiment (do you alter your boundary conditions, forcing, how frequently, and/or only the inital state, how you computed your model error cov, obs erros?) to help you more. Do you start your application from a balanced run (i.e. some restart of already spun ...

jivica

It is not the problem of running on the different nodes on the cluster. They are working or crashing the model in case memory problem etc. You need to recompile your model with less aggressive optimization flags (i.e. do not use -O3) and then try again with the exactly the same inputs. Different ...

jivica

There is Crocco (Brest version) that has the most advanced non-hydro options with even coupled 3D waves.
Have a look in the Ocean Modelling for papers.

Cheers
Ivica

jivica

Hi Colette, as Julia pointed out in her email, you should look at the ./ROMS/Utility/obs_read.F and ./ROMS/Adjoint/ad_extract_obs.F (this one in particular) There you can see what is going on. I remember Hernan updated the logic behind reading/extracting obs to prevent rejecting of the bottom (and ...

jivica

A long time ago Rich Signell wrote very useful Matlab function called "map_rivers.m" (I can see you are using Matlab). If you can't find it in the ROMS matlab repo or somewhere on the net, I will try to dig it out. Hope this example (you are showing on the figures) is not something you want to use ...

jivica

Dear all, General question to ROMS users regarding CMIP5 (and/or CMPI6 ) regional downscaling; Have you done some of the studies for a) short-range (i.e. 2030 - 2050) scenarios with 4.5 or 8.5 emissions, and if you did what you used for b) atmospheric forcing as well as c) ocean boundary conditions ...

jivica

Had the same issue:

viewtopic.php?t=5592

and the only way to make it right is to use splitting, which needs more effort and scripting.

Cheers,
ivica

jivica

There are many variables in the play; a) what about your surface model layer thickness? SST is usually referenced to 0.5m and if your model cell is ~3m then you are comparing different things. b) if you are using WRF winds then possibly BULK_FLUX is not good (Cd is more complex than it is coded ...

jivica

I had a similar problem a long time ago when I was (re)starting the model from the "slightly" vertically unbalanced initial state. If you have a mismatch btw your initial state and boundary then it might happen. If you grep in the roms source you'll see it is acting as a limiter. Cheers, Ivica

jivica

Possibly it is along the line

https://www.myroms.org/projects/src/ticket/865

jivica

Dear all, when I am running the latest version (1084) of ROMS for longer simulations I got an error after/before writing the last avg file. I am outputting 10 records per single avg file (10 daily records / file), model crash just when it needs to create the very last avg file. Have anyone else ...

jivica

I think you can't escape from using tides in your domain, it is well known on internal tides/waves and I am not surprised with your NLM - baseline solution w/o tides, mixing and errors at the end. Whenever I encounter errors in SST - model comparison larger than 2C then there is something wrong with ...

jivica

There is no problem in using 4D-Var with tidal forcing, and all the info is in the papers. We are doing that quite often, where, for example, internal tides are important. However, you have to be careful when you compute model error cov (!) not to allow for too much variability. We usually don't ...

jivica

There are a few options you could explore; (a) offline BIO ROMS (think Kate managed to build the code a long time ago) with your (pre)saved history file and then play with passive tracer(s), or (b) use some other advection diffusion reaction code with ROMS currents and diffusion (doesn't matter is ...

jivica

in recent versions of ROMS we have tracer advection scheme defined inside ocean.in file.
the best is to have a look at the example in the Include folder

cheers
Ivica

jivica

What I would do in your place is:
a) spinup your NLM mode to some physical state (i.e. 1 week and save all you need into history or restart file) and use that for your DA init
b) if you don't want to spinup then start from 0 - no mixing state, it will mix quite fast

Cheers
I

jivica

jivica

As you know time stepping in ROMS is a elaborated and complex beast and exchanging info between grids for fast varying variables is a nighmare. If you are modelling non-tidal, slowly evolving dynamics you are most likely OK. However, if you are in the space of high frequency motions then, I think ...

jivica

I just checked effect of the different options in the contact.m for interpolation (akima, linear, cubic) and results are the same -- parallel stipe pattern still exist in grad zeta (differences are super small for different interp options). I am doing diffs after 7 days in simulation after ...

jivica

Really good detection of any problems with nesting is to compute free surface gradient, for both parent and child and then plot them together. I did that for my 2-way case using simple python script, here is snip of the most important part: .... def roms_fs_grad(zeta, pm, pn): dphi_y, dphi_x = np ...

jivica

Possibly you don't have to change the code, only your contact netcdf file and its flags coincident and mosaic 0/1, as they should be used to IF branch the nesting code.

Ivica

jivica

Gents, you are running the latest ROMS version with one/two-way nesting constelations so possibly have the answer from the head; I read long time ago about speedup of nesting algorith in ROMS by excluding some vertical interpolation, masking etc. My question is what are the steps and how to use ...

jivica

Mate, you should familiarize with ROMS and python if you want to use pyNGL (and on top of that some knowledge of NCL would help). My scripts, as I wrote you before, are elaborated version with multi model config files etc. and are not easily transferable to your (or any) system without effort. For ...

jivica

add on;
In that way (standard tile parallelization) memory allocation could be even more efficient.
MASTER node shouldn't allocate all obs into memory and do all the liftings, instead each worker should know only about observations falling into it's specific tile and make calcs. Does it make sense?

jivica

Just click on the link I've sent you in the previous email?!

jivica

If you really want to stick to NCL, still you can. Getting on the NCL web site and going on Models/ROMS: https://www.ncl.ucar.edu/Applications/roms.shtml You can have basic scripts (and roms_utils.ncl) that Kate and myself contributed long time ago. PyNGL is advertised as future development of NCL ...

jivica

Just wondering about minimization problem (for example ad_rpcg_lanczos.F) in ROMS and would like to hear your opinion. For example, if we are using (think the trend is mostly true) weak formulation, then all is done in obs space. For that case rpcg is working only on single MASTER node with, and in ...

jivica

Thanks Hernan for your swift response. Yes, I am thinking about rbl4dvar . I thought there is easier way to handle/call station file output (If statement last NLM sweep then activate station output). However, if ROMS is going into SPLIT architecture then I'll spend some time to familiarize. Saying ...

jivica

Dear Hernan, just wondering if you changed IO for station files within RPG? I am using almost ;) latest version and saw that there are multiple time series with outer loops outputs (?) inside station file (actually only missing values are written). Is there cpp option or whatever switch to turn that ...

jivica

The first post is showing you problem with finding NCARG libs during the linking phase. You have to specify -L path_to_libs
On the other topic, why don't use NCL (this is NCARG based software and you have it for free), or python version (pyNGL)?
Cheers
I

jivica

Dear Hernan and the rest of DA community, I've noticed that in the latest ROMS build (updated today to 1037) we have output of the ADJ model in the "average file" output (avg_outer0.nc and then for new outer loops in avg_outer1.nc etc). Is there a way to get average output from the NLM model ...

jivica

You have cdl example file in your ROMS/Data/ROMS/CDL/ and this is my ncdump -h forcing.nc netcdf forcing { dimensions: time = UNLIMITED ; // (56 currently) dim1 = 221 ; dim2 = 341 ; variables: double time(time) ; time:long_name = "time" ; time:field = "time, scalar, series" ; time:units = "days ...

jivica

ROMS should interpolate atmo fields for you (unless you have exactly the same dimensions as your grid). I am using the approach but have defined lon/lat as 2d fileds. This is simple, just repmat and it cost nothing as doesn't change in time. Problem I had was if you are in the south hemisphere then ...

jivica

Hi Hernan, thanks for the swift reply! Actually, what I am doing is running ROMS in super tidal region with tidal sea level variations due to tides having strong impact on stability and quality of results. In regions that I am interested in I have > 50% internal tidal energy (of total) and running ...

jivica

Does anybody run or even have been able to compile the latest ROMS 4DVar for application with WET_DRY option switched on? I fixed some easy picks in tl_zeta.F, ad_zeta.F where we need to define eps (missing definition as local variable). Then in ad_initial.F and tl_initial.F when calling initrc or ...

jivica

Looks to me that you made and used wrong tidal forcing file. There could be a few things, from time definitions to wrong tidal periods (saving in wrong order) in the file. To nail down the error I would pick a few points from your tidal forcing file and plot "synthesized" sea level (simple stuff ...

jivica

I've done similar test with nesting and eddy propagating through the domain (in addition to sea-mount). Have a look at the:
Janekovic, I., Powell, B. 2012, 'Analysis of imposing tidal dynamics to nested numerical models', Continental Shelf Research, 34, pp. 30-40.

Cheers
Ivica

jivica

You can use faster approach if you are starting new simulation and doing offline down-scaling i.e. 1-way nesting by using "stations" in the parent grid with exact locations of the boundary cells for your nested domain. That way you can save more frequently needed info (i.e. not loosing energy if for ...

jivica

Dear Colleagues, Numerical ocean models have proved to be useful, modern tools, used daily to analyse, predict and advance our knowledge of ocean dynamics. Novel techniques of solving model equations on high-resolution unstructured grids, or multiple nesting inside finite difference models, make ...

jivica

I was waiting for someone else to response, but none did, so here it goes. What I think is happening is that you have defined too loose model forcing standard deviations (i.e. std file you use in your s4var.in STDnameF). The "easy" way for model to get closer to your obs (in your case surface ...

jivica

I wonder if it is related to the post submitted long time ago:

viewtopic.php?f=19&t=4864&p=18889&hilit=MPDATA#p18887

Regards,
Ivica

jivica

UWA Integrated Marine Observing System (IMOS) PhD Scholarship : Physical oceanographic processes off North West Cape, Australia Coastal observations include a variety of tools, both traditional and novel, such as satellites, moored instruments, shore-based systems, and remotely operated vehicles ...

jivica

As a new user you should definitely read your log file (!) and pay some attention on the stuff inside. There you can find all options that you activated (and which are used in ROMS, note that you can miss spell or use unsupported options during compilation, but they will not be in the log and not ...

jivica

First of all you should read your log file (at the end) where you have profiling of your run. There you can see what portion of time is spent in IO and what in real computing kernel etc. In some cases when I need often IO I get bad ratio but this is to be expected. Remember Sasa once told he had ...

jivica

I'm using CRAY XC40 and must admit, quite happy with performance (dragonfly net topology), 24 core nodes. Made some benchmarking and it really depends on your application and grid size. Note that depending on users load on scratch you can have totally different results (and you can tweak parallel ...

jivica

Hernan and the rest, are there any plans to make nesting scripts (contact.m) capable of ingesting rotated grids? Have feeling that all the bits of the engine are already available to make more general contacts between the grids. I am currently doing 1 way downscaling of arbitrary nested grids which ...

jivica

ROMS is not black box model, and it is very well documented. In that sense you should dig into the source and, for example, have a look at the Utility/extract_obs.F There you will find relevant part of the code: p2=REAL(i2-i1,r8)*(Xobs(iobs)-REAL(i1,r8)) q2=REAL(j2-j1,r8)*(Yobs(iobs)-REAL(j1,r8)) p1 ...

jivica

Just to add on top of that, ERA-5 is amazing source of atmo forcing. From 1979 -> recent at 0.25 deg with HOURLY (!) fields. It was couled with ocean and used advanced data assimilation. Even for strong tropical cyclones it gets decent results, think it is better than JRA55 and definitely better ...

jivica

Just adding comment when Sasa is not going to ;) I find extremely useful Alex's tool for generating curvlinear orthogonality error free grids and suggest you to have a look at the older posts: https://www.myroms.org/forum/viewtopic.php?f=23&t=3878&p=14908 and https://www.myroms.org/forum/viewtopic ...

jivica

I've sent you the link privately on the email..

Ivica

jivica

Not sure if I am right, but think the problem is in new version of regrid and new variable "myxout" After compiling in debug mode (with mpi) I managed to trap it for 6x6 tile configuration (4x4 and 8x8 works?!): At line 155 of file regrid.f90 At line 155 of file regrid.f90 At line 155 of file regrid ...

jivica

It is getting even more interesting; it is working for certain tile (2x2, 3x2) configuration and crashing for 6x4, and then working for 32, 36, 48 but having wrong pressure as I wrote. I recompiled roms with debug option and gfortran + openmpi and bomb turns to be in inp_par.f90 which in line 77 is ...

jivica

John, tried mpirun -np 1 and it is working OK, gives identical result as serial run. It is southern hemisphere system, NO BULK_FLUX, only storm surge case with surface wind stress and pressure. Reading of original data is OK as well (in all ceases, MPI or serial), reasonable values within range ...

jivica

Hernan, I know you are quite busy and that this bug is on your todo list, this post was more to have others aware of the problem in the latest version of ROMS code (if they use MPI and Pair as I am). Using in addition (to ATM_PRESS) option for bry pressure correction --> PRESS_COMPENSATE doesn't ...

jivica

Having problem with application where I am using Pair on atmo model native grid and *ONLY* MPI-parallel version of the latest code. In serial version is regridding and working OK, but parallel version still has problem.. Trying to nail that, and by digging I think I've found bug in ./Modules/mod ...

jivica

If you are using SINGLE_PRECISION and wet-dry option then you can't compile the latest version of ROMS. There is DSIGN problem (at least with gfortran), so after changing DSIGN -> SIGN for Build/u2dbc_im.f90 Build/v2dbc_im.f90 Build/wetdry.f90 Build/step2d.f90 and ./build_roms.bash -noclean you can ...

jivica

I suggest you first to read a few papers related to the wind stress formulations in extreme events like TC, many of them are John's papers using COAWST and many Hurricane cases etc. Not to just blindly run ROMS model and then expect to get result that is perfect. For example: Bryant & Akbar in JMSE ...

jivica

Dear Sasha, really like you answers, always getting to the bottom of the problem. Regarding mesh, I can see that many wants to nest inside global models (Hycom or NEMO) and do not want/need to download the whole grid domain just to get stripes along boundary. In other words, getting stripe along ...

jivica

Actually the best option would be to dig a uniform depth/width channel inland (a few pixels should be enough) and have mixing processes happening "over the land", so once entering the ocean it is as should be.

Cheers,
Ivica

jivica

Adding my 2c to the topic; I am running "many rivers scenario" without specifying temperature (only salinity) of the river sources and all is working fine (this option is using ambient ocean temperature for river sources as I don't know exactly temperature and it is shallow and really similar to the ...

jivica

Thanks for all responses! Farhid in which version of ROMS you've implemented it? Looking in Rutger's version and lmd_vmix.F there is only diffusivity due to the internal waves and not because of surface wind induced waves? lmd_vmix.F ! Compute interior diffusivity due to wave breaking (Gargett and ...

jivica

Dear ROMS users, before duplicating already done job I am wondering if someone already did it? I am looking into the additional mixing (via k-e turbulence) with NONBREAKING(!) waves as additional term in the shear production term (along with shear and bouy2) as a function of depth, Hs and frequency ...

jivica

Have you checked your initial condition's file values? This line looks really suspicious: 1 2018-01-01 12:15:00.00 NaN NaN NaN NaN Do you have missing values in the ini.nc? What about bry.nc? atmo.nc? you have to check all those files to be sure you are not giving NaN to ROMS model... Cheers I.

jivica

I think that gregorian_proleptic is not a standard name according to https://www.unidata.ucar.edu/software/thredds/current/netcdf-java/CDM/CalendarDateTime.html Should be proleptic_gregorian Seems semantic but ncview is picky and some other software as well. Easy fix in Utility: dateclock.F:809 ...

jivica

I think I've fixed it. It is working now as I would expect (MP_DATA) and the problem was in step3d_t.F and pre_step3d.F (note that "_original" is current version in roms trunk) Shortly, indexing was (I think) wrong in the step3d_t.F and in pre_step3d.F part with source direction == 1 was missing etc ...

jivica

Hi Kate
I am using MPDATA in old 3.4 and the latest code
And with old all is as should be... looking into the code
to figure what/when went wrong
Cheers Ivica

jivica

Think there is a "feature" introduced in the recent ROMS related to river source temperature set to 0C even you chose not the alter ocean ambient temperature. What I am doing is simulating only fresh water inflow using river forcing and setting source salinity but do not want to change ocean ...

jivica

Regarding cores; I've made some benchmark for CRAY XC40 machine (dragonfly topology, ~70G/s infiniband), which agrees well with what long time ago Kate wrote, it is close to up to 20x20 tiles. In other words, you get reasonable speedup/CPU_cost if your tiles are up to 20x20. For your 600x400 that ...

jivica

Hi Ivan, I think that nothing is wrong, it just takes time. Your grid is not that small (and depending on your de-correlation scales) and given small number of cores it takes quite a lot. My recipe is to make exact solution only (!) for zeta (2D so should be faster) and then compare that with ...

jivica

Actually, you might be able to run your child grid with time step the same as in your parent grid (large time step, efficient, as for example I have the case in coastal nested domain where is quite shallow region). If your child grid is in shallow region and parent has some deep parts then interplay ...

jivica

This is really not enough info to give you any decent help. Checking ROMS output at the boundary and comparing it with tidal boundary forcing is just to make sure you haven't messed with creating forcing. What does your grid looks like, how big domain? do you resolve shelf and consequently resonance ...

jivica

I think there was already a quite a lot discussion about HPGE and smoothing techniques in the forum. In short, I would make pure HPGE simulation using only vertical profile of T and S (using ANA_INITIAL), and no forcing, closed brys (or clamp to the same profile of T,S using again ANA_). You can ...

jivica

Seems to me that tidal forcing doesn't match :?: :!: at your northern region either, this is where your BC are. You can have amplification in the the bays, like resonance, and if you are having say 10% wrong BC than that can result with large errors elsewhere, even more in bays like that, sensitive ...

jivica

Hey both Johns,

Actually it is ivica

and not ivicia

and if you remember we met at Canberra last year at IMOS/ACOMO when I showed you some ROMS data assimilation for WA...

Cheers,
Ivica@UWA

jivica

Just to update you, I've managed to trap and fix it .. not nice and full fix but working on it. John's script to plot weights helped in a way to see that wav2atm and ocn2atm differ at the narrow strip along the coast i.e. landmask. I just plotted diffs btw them and then you can see the region ...

jivica

Well it is strange, ROMS is crashing at the first step, or better to say between init and 1 step while as it didn't saved 1st his record. WRF is happily running till next coupling exchange even after ROMS died. I've put WRF output every time step and fields looks OK. So, I am confident that problem ...

jivica

I don't think it is the cause, as I wrote in my initial email WRF is bigger and encompassing ROMS (and SWAN) grids; My feeling is that mapping btw WRF and ROMS is the problem (scrip/weights), as they are not defined on the same grid (WRF is on 10km grid and ROMS 2km, so I have to use #define MCT ...

jivica

Dear all, I'm having problem with setting/using COAWST (rev 1169) for 2-way WRF and ROMS. The problem is with WRF sending unrealistic forcing fields to ROMS which is crashing at the 1st ROMS time step (can't save his as not ending 1st step). Possibly someone had similar problem and could shed some ...

jivica

Just a hint you can try saving variables as short using add_offset and scale_factor.
This is useful if you have already created netCDF files but want to make them smaller.
With nco you have already ncpdq doing that for you...
I.

jivica

It is exactly telling you what is missing! In your .in file, at the top, you have line where you define location of varinfo.dat So, you can put right link or even copy varinfo.dat into the folder where you run your model, but it has to be correct. example: my ocean.in file has line with ...

jivica

If you are into bulk flux then you probably need heat flux etc. Here is mine forcing file ncdump -h to give you idea about structure (and you could see that in the $ROMS_SOURCE/Data/ROMS/CDL as well) ncdump -h forcing.nc netcdf forcing { dimensions: time = UNLIMITED ; // (56 currently) dim1 = 220 ...

jivica

not sure if you made typo but when running with MPI you do not use "<" to feed in .in file
this is wrong: mpirun -np 8 ./oceanM<tidebasinforcing.in
and should be: mpirun -np 8 ./oceanM tidebasinforcing.in > log &

Cheers
I.

jivica

This is because of your meteo data are flipped up-down, and lower left coordinate is not correct. You have to make sure that lower left coordinate is (1,1), because of search/interpolate algorithm within ROMS. Easy to check this is to make your lat coords (or lon, depending where you model and ...

jivica

Should be easy if you are using git.
What speedup you got when compared to "standard" version?
I am interested into making benchmark for my application on my cluster (using intel compilers + openmpi 1.8.6)

Cheers,
Ivica

jivica

do you interpolate atmo forcing (i.e. T2) before run or you leave that to ROMS linear interpolation? If you use ROMS then it might use atmo values over the land :!: and interpolate them as they were above the channel, hence used as forcing. To test that you have to interpolate atmo forcing before ...

jivica

Well you can get better interconnection btw nodes to get better efficiency; For example I setup cluster last week (4 x Dell r620 E5 with 40 cores) using infiniband Mellanox FDR 56G/s (!!) and I have really nice low latency and high speed communication. So, in short you hit the wall, you have to ...

jivica

This is not a problem in forward nonlinear model setup because you can radiate outside, however if using adjoint back in time then you are in trouble. That is basically what it is, so use clamped boundary and then you can get boundary increments from data assimilation fixing that if needed... Have a ...

jivica

Just wondering would it be possible to use one if statement in a way if cell is dry then use tracer old state (from the previous time step) without applying anything i.e. heatflux etc?
And keep doing that until it get wet again.
probably it is like that already in new version

Ivica

jivica

I had problem with data assimilation and shocks when applying all increments to the initial state at t0.
As far as I know Andy is working on it and in the near? future it should be available.
This is "normal" approach to use in the atmospheric DA.
Ivica

jivica

Create 1 file using obs_merge.m or something similar. This will give you idea what to do.
$ROMS/matlab/4dvar/obs_merge.m

Ivica

jivica

viewtopic.php?f=17&t=1080#p12021

see at the bottom -> my last response, hope it helps.
cheers
I.

jivica

If you decide to go the way of python or matlab then you can use pp (parallel python) or parallel toolbox in matlab and distribute the node_loop along the cluster (cores); doing that you are minimizing memory footprint and speedup calcs. Note that MPI is reducing memory footprint and not openmp ...

jivica

glad it helped
the best option is to use ana_ if you can, it is then, during compilation, included directly into the code, so no reading at all.
Cheers,
Ivica

jivica

OK, looking into .h more deeply I can notice that you use central 2nd order for advection, why not standard upwind 3rd order is there some specific reason for C2? you can add diffusion and/or viscosity within ocean.in... If you want more/less temp/salt conservative then use MPDATA, I do not use ...

jivica

I believe it is too simple to have it ;) You can setup it easily without any grid or forcing, just using ana_* For example use ana_grid.h to make rectangular basin, in that case you can increase resolution within ocean.in file where you specify number of cells, no need for recompile (specify some ...

jivica

If you have static field you can create forcing file with actually 2 time steps sms_time 0 and 1000000 because ROMS is linearly interpolating to your model time. Having those limits encompassing your model run period you are sure to have it correct within the model interval. You can use ROMS CDL ...

jivica

From your .h file I can see that you do not have realistic atmo forcing, you do not have river forcing, etc ... It is hard to expect model to reproduce physical features if not using physical assumptions. To get correct dynamics in the Adriatic I use 39 river sources, realistic as possible atmo ...

jivica

You can use http://www.teos-10.org/software.htm which is "official"
There is matlab suite of routines and is easy to follow.
Cheers,
Ivica

jivica

What I did for one test case of LNG (temp) impact to the environment was: run the model with source but neutral with respect to temp (as suggested switch F for temp). Before that switch option, many years ago :), I had to run model without point source and saved station file with temp at the ...

jivica

This topic is recycled over and over, many posts about river forcing, position, etc have been answered and all you need is to look *search* and scratch a bit under the forum, after all this is the main goal of the forum. Rich Signell wrote matlab function to plot you river sources for a given grid ...

jivica

From my point of view it is waste of CPU time to have CFL 0.1, but should look at the dynamics and make a few tests to be sure how far with dt you can go. I believe Kate once wrote that for Rutgers version CFL should be less than 0.85. Quick and dirty way you can compute it by yourself, for ...

jivica

This was asked before

so have a look at the
viewtopic.php?f=17&t=2238

basically you do not put number of forcing files == 0 but leave it empty

Ivica

jivica

Use the source Luke

ROMS/Nonlinear/set_depth.F

there is all you need, you can invent even new function

Cheers,
Ivica

jivica

Got some spare time and quickly fixed it; so the steps were: 1) for your problem you can use 2D, no need to mess with 3D and is by far faster stromsurge.h: /* Momemtun equation */ #define UV_VIS2 #define UV_ADV #define UV_COR #undef UV_QDRAG #define UV_LDRAG #define CURVGRID #define AVERAGES #define ...

jivica

I have looked at your files and there are many things you should reconsider; you want to get storm surge but configure application to be nor full atmo driven nor only storm surge which is a bad idea. You want bulk flux but put constant swrad and lwrad through the whole simulation. Make up your mind ...

jivica

It is hard to debug your application from the info you gave.
If you can put your grid file and forcing so I can grab it (when got time)
and see what is going on.
Ivica

jivica

If you care only about storm surge possibly you are happy with 2D barotropic case which has only N=! !! What is killing you (blowup) is not rx0 but rx1, this is important to notice (i.e. density fields, number of vertical nodes, theta_b, ... all of them play a role). For wet_dry one have to be ...

jivica

Dear community,
does any of you have experience with new Intel Xeon Phi arch and ROMS performance?

Thanks in advance for your time,
cheers
Ivica

jivica

I think tidal ellipses, to be more precise inclination, is not rotated to the ROMS grid within forcing file. It is rotated during applying BC see angler(i,j) in the last line of code , in Nonlinear/set_tides.F: # if defined UV_TIDES ...

jivica

You are right, you do not need obs file just to compute norms, they depend only on the grid. Whenever you change something with the grid you have to recompute norms. They are expensive, so be sure the grid is final before kick. To be more precise you need to define in addition error decorrelation ...

jivica

You want to have as real as possible bathy (tides sensitive) so smooth as less as possible. In one of my real applications, there are many big and small passages for tides and currents to in and out which usually with big slope on depth. The problem is i can not smooth these deep-narrow patches as ...

jivica

I am afraid I do not follow you; If you for example copy your original roms grid to say new_grid.nc (in order to have original to compare with) and than smooth variable h and put it back inside that new file. Than in ocean.in you have to change GRDNAME to point to the new_grid.nc; run roms and check ...

jivica

Well it is really important topic, so here is my 2c. All is your grid, problem to solve related question. For example if you want to do internal tides or tides only than you will look at the some spectral lines and currents that are generated because of HPGE (horizontal pressure gradient errors) are ...

jivica

just hit search for SWAN in the forum and got

+371 posts

related to it

jivica

Well that is one of the " many time commented/discussed topic " so I really do not get it why not to look what other people wrote; strongly would suggest to search at the forum posts first. With really small effort, if you look at the roms source folder then you will find src/User/Functionals/ana ...

jivica

Dear developers,
is there working version of Utility/interpolation.F that is using options CUBIC_MASKED along with LIMTR capable of taking care LANDMASK?

Thanks,
Ivica

jivica

Well I have to say that I do not use the latest version :oops: of ROMS (using version 3.4 from Aug 2011)so I am doing all in a classical 1-way nesting. For that I found the easiest and by far fastest and memory efficient is to use "station file" approach. I create child grids (as much as I want) and ...

jivica

Dear all, in the past months there was never-ending story about tides, tidal dynamics BC inside ROMS model, hence think that some of you could benefit from paper we have recently published. Analysis of tidal dynamics as a function of BC that you use in a constellation of parent-child (or even only ...

jivica

OK figured it out, It is in the degrees and during the loading phase it is converted into radians (varinfo.dat, the last line) 'Dwave' ! Input 'wind-induced wave direction' 'degrees' ! [radians] 'Dwave, scalar, series' 'wave_time' 'idWdir' 'r2dvar' 0.017453292519943295 ! pi/180 This resolves ...

jivica

Thanks John on swift replay! Nevertheless, I am not using SWAN but other wave model (WWM), the most important is to have the same convention DEGREES not RADIANS (Nautical SWAN convention) calculating direction from the North clockwise and that direction, as you said, is pointing direction "from ...

jivica

Dear users, I have question regarding NEARSHORE_MELLOR05 . In the varinfo.dat I have found that Dwave (Direction for waves) should be in degrees, so I have used forcing file where I defined Dwave in degrees from North CW. Should I rotate the values into grid coordinate, I mean to rotate for -angler ...

jivica

in the old matlab "finite" was OK but in new version it is replaced with "isfinite"
so go into the code and find/replace "finite" with "isfinite"

Cheers,
Ivica

jivica

You can do landmasking by a) using landmask utility in roms matlab toolbox or b) if you have coastal line in polyline (closed lines stored in matlab struct ie poly(1).lon poly(1).lat and so on for other islands like poly(n).lon poly(n).lat ...) you can do it easy in matlab by checking roms grid ...

jivica

It is simply not true that MASKED points are not used in computations! They are just zeroed out at the end of time step (!) we have been through that zillion times. ROMS is different animal than say SWAN which excludes those points from calculations. Navidad if you are still struggling with your ...

jivica

ncdump is a application that is "made" when you installed netcdf library and is located inside netcdf bin folder, so in your case should be: /opt/netcdf/3.5.1-intel/bin/ncdump It is veeeery useful command and you will use it a lot. So if you can show us how does this grid file looks like: /opt ...

jivica

give us:
ncdump -h your_grid_file.nc

hope you used seagrid2roms.m because seagrid is giving you .mat file
cheers,
Ivica

jivica

If you do not want to use any forcing file than simply leave it clear:

NFFILES == ! number of forcing files

FRCNAME ==

And that should do, do not put any number like 0.
This means that all needed forcing should be done through ANA_

Cheers,
Ivica

jivica

Think UCLA group has offline float tracking code for ROMS that is capable of going back in time. So, basically you feed it with ROMS precomputed history files and use similar input file for initial float positions. There is a option for going frwd or back in time.. Capet and Sasa did that long time ...

jivica

Think that there is a possible bug :?: in routines for applying boundary conditions for tracers and velocity when used NUDGING option. Issue is regarding time step in the last term t(Istr-1,j,k, nstp ,itrc) should be t(Istr-1,j,k, nout ,itrc) to be consistent. # ifdef WEST_TNUDGING t(Istr-1,j,k,nout ...

jivica

You should check your setup, think there is a problem 1. we need more info to help you out - do you use "tide.nc" file with tidal info for zeta and tidal ellipses or pure ANA? (if so you have specified ANA_FSOBC as well, hope you know what you are doing) 2. you used ndtfast==1 ?! if not in 2D does ...

jivica

As Hernan suggested run the case with some zero forcing and vertical (stable) density profile to see HPGE (Horizontal Pressure Gradient Error) effect. Just 10cents :idea: to the topic; you can afford higher rx0 in shallow region than in deeper (I do smoothing with different rx0 target in different ...

jivica

I should say that this is really good to do at the begining :wink: , just to make sure you have all setup right (!) and can explain "ghost currents" if you have them :roll: What I do is run model similar like you but with analitical (for my region specific) vertical T & S; just to be sure that there ...

jivica

if you are adding tides to the open boundaries then you have to do something like: /* if you are adding tides on turn on SSH_TIDES and UV_TIDES */ # define SSH_TIDES # define UV_TIDES # ifdef SSH_TIDES # define ADD_FSOBC # define WEST_FSCHAPMAN # else # define WEST_FSCHAPMAN # endif # if defined UV ...

jivica

Are you sure that you are using the last version of ROMS? This was corrected recently, we had the problem with atmo forcing scaled to short int (to save diskspace)! Think there are still some issues if trying to read boundary files using scales (short int), but those files are small anyway and we ...

jivica

Well be sure that you know what are the limits of the model that you use... In your example you have vertical velocities order of m/s which is comparable with horizontal ones.... hydrostatic/non-hydrostatic models? From my experience I use "near-field model" for close to the source dynamics and ...

jivica

Be careful, the last time I used it was not working properly. Application was: Q_SOURCE with sediments and after when all sediment was on the bottom there was no mass conservation. On the other hand while using UV_ there it was exactly. Do some tests to see if it is working OK, the code was running ...

jivica

Well I would not be happy with that phrase "... a few cells inside things in velocity field is OK." We have seen this in our application for the Adriatic Sea when one can get strong along boundary current that is due only to boundary conditions; like yours.. Imagine that you have some tracer like T ...

jivica

Well I have trouble with restarting from history file, think the problem could be when reading initial fields like zeta, temp, ubar ,.... then mask is not applied like it should be... restarting his file that I am using have for example zeta (ncdump output:) like this: zeta ...

jivica

Well for fully coupling I can not help you :( , but if you need info for preparing WRF forcing for ROMS (variables, and so on) I can.. :wink: One thing that you can do is run ROMS forced with WRF (1 way) and than save in time SST from ROMS and then feed it into next loop for WRF... in a few ...

jivica

Jacopo, sure I do agree that hybrid vertical could be thing that improve many thinks, BUT you should know how rx* looks like (for the ALL POINTS of your domain!) not just max value. So you can pcolor it and see where it is 'insane' and believe me, at the regions HPGE is devel! you'll get your real ...

jivica

Jacopo, have you checked your sigma layer angle with the respect to "z", and hydrostatic stability among rx0 and rx1 at the region? We have made some experiments with regions that have big slope of sigmas and result was plaque by HPG a lot, giving unrealistic velocity which after some time went to ...

jivica

Dear users, I have to talk to the "non physical oceanographers" in our ministry of env. protection (decision makers and possible funding source) and make intro to the ROMS. Idea is ti show them quality of the model, capabilities in as many aspects as possible, from bio, sediment, chem to the pure ...

jivica

Safe bet is if you get binary for NCL (compiled with g77 ... gcc) and compile roms_plotting package as well with g77 see if that is working *get netcdf compiled with g77 as well*.. compilation of ncl with ifort take some time and can be tricky.. Just one quick question for plotting; say temp field ...

jivica

TIDE_START is used in the code for tidal phase lag (check it by tour self) in simple manner. so If you have tidal phase lags calculated (using say t_tide or some other tools) for specific day say 20080610 and you MODEL TIME is for current time (say 20080620) thanyou have to specify the two times in ...

jivica

From my point of view of building small linux cluster for ROMS + WRF I have to say that I am not happy with performance on quad cores connected with 1Gb switch... I have HP Blade 460c (2x quad cores 2.8G) with 4G of RAM and HP procurve switch.. well it turns out that running on 2 blades (2x8CPUs) is ...

jivica

What have you used for optimization of compiler?
We had problems when using too aggressive -03 option (default) and had to put -O2
just idea...
Ivica

jivica

I am just posting my comment on the WRF and ROMS; Discussing with J. Wilkin I got to quite happy usage of WRF and ROMS without messy cloud fraction at all. I am using net shortwave at surf., only incoming longwave and the rest for bulk (T2, mslp, U10,V10, Rh) and let ROMS compute longwave outgoing ...

jivica

Or just simply specify startdate in the first line of .in file (second variable) for ccnt?

jivica

I have problem using plotting package when I use TIMEREF=-2,
so I have offset of datenum(1968,23,5) which is state in @units and not in the add_offset ....
Should I change opencdf.F where are attributes checked to get right offset?
Thanks
Ivica

jivica

Thanks Kate; I find Hernan's ploting stuff very usefull and have installed it without a problem. More over, I would like to change vector's color and so on, play little bit with contour @res and other options, add something and put it to run via cron (without DISPLAY which matlab req.).. so I think ...

jivica

Thanks for the reply, I have installed week ago :wink: , plotting stuff from roms svn, I am using it but seems to me it's easier to use scripts like .ncl where one can change more options like res@ and so on on the fly... At think that on the wiki you should put ncargwww and ncarg2gif commented that ...

jivica

Dear users,
I am thinking to move on NCL to get ROMS figures instead of Matlab
so I am collecting scripts .ncl for vecplots and other fields..
If you are willing to share you'll save me a lot of time
Thanks in advance!
Cheers, Ivica

jivica

Well I can confirm that model blows up is one have quite large values (or low) for forcing.. What I do is I find nans and replace them with nanmean(field) rather than putting just 0 or some missing_value
... After that all is working oky..
Cheers,
Ivica

jivica

Hej guys have any of you tried to load ROMS on that structure? I have build 6 HP blades 460c with dual quads so at the end 6x8=48 cores, 2G ram / blade... I have tried ROMS with ifort_10.1.x and pgi_7.0.7 as well mich1-27 and mpich2 latest one, have GB net with HP procurve switch 1800 G24... at the ...

jivica

Hej Kate (If you do not recall I'm the one with funny shirt at Gordon RC :D ), I am not able to run the same grids for WRF and ROMS, I use NCEP GFS 0.5deg for init of WRF at 20km and than I use nest to my domain at 5km and this is CPU disaster (on my hand made cluster) ... I can not afford it to run ...

jivica

Dear community, I am running WRF as forcing counterpart for ROMS and I am wondering what are impressions of any of you in the same business... I have question about forcing variables for ROMS, what do you use (some .m scripts?) for computing (or better saying preparing) forcing fields like relative ...

jivica

Thnks Rich, I have found it and test it as well. It is working the way I wanted :D this bug is fixed. (we were talking about that at the GRC; in old way with Q_PSOURCE I got negative sand_01 and/or mud_01 (it used UV_PSOURCE) and because I put it on the top of the column and in the middle of domain ...

jivica

In which version is that? official roms with svn or SED_CODE? and BTW what is policy of that now, is there merging of SED stuff done occasionally as before, and we should look for the last SEC CODE or is it done in no time & we can find it in the last official roms version? Thanks for the info! Ivica

jivica

Dear all, I am wondering if some of you have used option in model for sediments by specifying vertical flux like: #undef UV_PSOURCE #define Q_PSOURCE (Q_PSOURCE should allow a vertical flux tracer instead of a horizontal flux) I have made test grid of 60x30x20 (grid cell size is about 50m in both ...

jivica

It is exactly what I needed ... John please if you can provide little bit of info about Q_PSOURCE option .... Like what direction notation is used (1 -1 downward or upward), and if it is specified at the surface like sand storm (just for testing how it works) at some rho points, than it actually ...

jivica

Well, I had the same situation when I played with sand storms applying sediment flux at the surface in the middle of the basin :D .... Point is that I (and think you) want to have VERTICA L flux downward like rainfall and not horizontal like is implemented in the ROMS code... If using horizontal ...

jivica

Hej, just wondering if there is any gain in compiling MCT using mpicc?! (What do you use for netcdf lib compilation?) We are using SWAN+ROMS but using for fortran mpif90 and for preprocessor cpp. One more thing, if using ifort and -O3 we got blowups quite often, and by reducing so aggressive ...

jivica

Well think that you are using symbolic toolbox in matlab where you have defined sub function...
what do you get by typing in matlab prompt: which sub
you can disable it by rmpath /your_matlab_path_to_symbolic_toolbox

Hope it helps
Ivica

jivica

Well I just wonder
what to #def and #undef for specifying only TIDE_SSH
and not TIDE_UV?? but to be able to use FLATER OBC?
Thnks!
ivica

jivica

Well, For my application (Adriatic Sea in spherical) it is not working, your patch I ment. Still hindices does not find corresponding I,J in tiles. The simplest solution for me is to run serial code for 1 iteration with stations defined in station.in like 1 1 lon,lat then get from out_sta.nc Ipos ...

jivica

Yip, there is a problem when using more than 1 tile (*MPI*) at the connecting nodes with Lon,Lat , so you have to find locations in I and J before (*NOT LON,LAT) and put them in the station file. You can test this with serial run and then grab i,j model coordinates and feed them into station file ...

jivica

You can use LM_LIBRARY_PATH variable to specify directory which should be incluced in search path.
like (bash):
export LM_LIBRARY_PATH=$LM_LIBRARY_PATH:/usr/your_path_to_spec_lib

should work..
Cheers, Ivica

jivica

Well. I saw the example where you used ADCIRC tidal fields but you have prescribed tidal fields at all grid points instead only at the open boundaries. If I only want to have tidal forcing open boundary, how do I specify this in the NetCDF file? Do I need to set it at all other interior points to a ...

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