Search found 4014 matches

by kate
Mon Jul 25, 2022 4:55 pm
Forum: ROMS Tools and Techniques
Topic: Pyroms installation error
Replies: 6
Views: 207

Re: Pyroms installation error

I don't know what to say. Perhaps we should disable the building of scrip? It's not like
I use it anymore, as I've said here in these forums before. For me it builds, but doesn't load.
by kate
Sat Jul 23, 2022 3:00 pm
Forum: ROMS Tools and Techniques
Topic: Pyroms installation error
Replies: 6
Views: 207

Re: Pyroms installation error

netcdf.inc comes with the NetCDF-Fortran prerequisite. The first question is do you have it? Where is it? The second question is how do you get scrip to find it? There's a makefile in pyroms/pyroms/external/scrip/source using the NETCDF_INCDIR environment variable. Mine is currently pointing to: /us...
by kate
Fri Jul 22, 2022 5:21 pm
Forum: ROMS Tools and Techniques
Topic: Pyroms installation error
Replies: 6
Views: 207

Re: Pyroms installation error

It says it can't find pyroms/src/iso.f. Do you have pyroms/pyroms/pyroms/src/iso.f? I have seven Fortran files in that directory, including iso.f.
by kate
Tue Jul 19, 2022 3:18 pm
Forum: ROMS Discussion
Topic: Creating initial field, boundary field files from grid files
Replies: 3
Views: 335

Re: Creating initial field, boundary field files from grid files

You haven't told us which tools you are using to generate initial and boundary files. Impossible to say from here what's wrong.
by kate
Fri Jul 01, 2022 4:09 pm
Forum: ROMS Discussion
Topic: I want to use HYCOM GLB v0.08 as the initial / boundary data of ROMS.
Replies: 16
Views: 965

Re: I want to use HYCOM GLB v0.08 as the initial / boundary data of ROMS.

I should explain the pyroms status: * It's a package written by people who are long gone from Rutgers, no longer using ROMS. * It is only my github repo because I got into git early, I am not a major contributor. * It is no longer representing best modern Python practices. I suggest you dig into som...
by kate
Tue Jun 28, 2022 4:52 pm
Forum: ROMS Discussion
Topic: I want to use HYCOM GLB v0.08 as the initial / boundary data of ROMS.
Replies: 16
Views: 965

Re: I want to use HYCOM GLB v0.08 as the initial / boundary data of ROMS.

If you are missing one day of SSH, can you go to their server and download it directly?
by kate
Sun Jun 05, 2022 9:45 pm
Forum: ROMS Discussion
Topic: problem to use trondkr python codes(era5)-Kate
Replies: 2
Views: 291

Re: problem to use trondkr python codes(era5)-Kate

Have you considered asking on github? Or asking Trond? For ERA5, I am using the tools in https://github.com/jsimkins2/nwa25. The README in setup/forcing has a link to how to download files. Once they are downloaded, we do several operations on them before using them to force the model. All the codes...
by kate
Mon May 09, 2022 5:06 pm
Forum: ROMS Bugs
Topic: Pyroms scrip Fortran runtime error: Bad FORM parameter in OPEN statement
Replies: 2
Views: 272

Re: Pyroms scrip Fortran runtime error: Bad FORM parameter in OPEN statement

You are getting further with scrip than I have in years! My advice is to switch to xesmf. I know, it has its own issues, best to make it its own conda environment.
by kate
Wed Apr 20, 2022 5:24 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 4780

Re: PYROMS error

No, sorry, packing for a trip, not able to help right now.
by kate
Wed Apr 20, 2022 4:58 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 4780

Re: PYROMS error

remap_bdry.py should not be run stand-alone, but rather is called by make_bdry_file.py.
by kate
Wed Apr 20, 2022 12:45 am
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 4780

Re: PYROMS error

It's not working correctly and my husband has no idea why either. mask_t should have three dimensions, just like var. He says the "~" should be returning valid entries. We want to know which points are masked out. For me, ncview looking at the temp variable shows some white patches where i...
by kate
Tue Apr 19, 2022 9:36 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 4780

Re: PYROMS error

So the shape of mask_t is wrong for some reason. What does that "~" do?
by kate
Tue Apr 19, 2022 9:22 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 4780

Re: PYROMS error

I meant inside Python, print out the shapes of the objects in Python.
by kate
Tue Apr 19, 2022 8:28 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 4780

Re: PYROMS error

I don't know. What are the shapes of all the things?
by kate
Tue Apr 19, 2022 4:39 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 575

Re: error:different horizontal mixing scheme

It is easy to code up and it makes sense over a flat bottom.
by kate
Thu Apr 14, 2022 5:31 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 575

Re: error:different horizontal mixing scheme

No, no, no MIX_S_TS! It's a terrible thing to do with a sigma coordinate. Why wouldn't MIX_GEO work? My biggest problems with it involve wetting and drying and realistic bathymetry. I don't know what you are trying. I'm just suggesting trying a shorter timestep so that you can rule out CFL troubles....
by kate
Wed Apr 13, 2022 4:05 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 575

Re: error:different horizontal mixing scheme

Yes, there's a CFL condition. There's also the timescale of damping on the scales you want to damp (2 dx) and the timescale of damping on scales you don't want to damp. A CFL of 1.0 will be unstable. What are you shooting for?
by kate
Tue Apr 12, 2022 4:58 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS: SCRIP installation error
Replies: 9
Views: 2851

Re: PYROMS: SCRIP installation error

It has been a while since I could get scrip to work. The solution is to give up on it, switch to remapping with ESMPy. There's an example using xesmf in examples/Arctic_HYCOM_GLBy.
by kate
Tue Apr 12, 2022 4:39 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 575

Re: error:different horizontal mixing scheme

They have different timestep constraints, depending on dx. You could try a shorter timestep to see if it runs.
by kate
Mon Apr 11, 2022 4:51 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 575

Re: error:different horizontal mixing scheme

Does it run with TNU2? Is this a new domain? Are you sure you have a small enough timestep?
by kate
Tue Apr 05, 2022 3:35 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 4780

Re: PYROMS error

What exactly are you running? It has been a few years since I got scrip to work for me, so I'm switching over to ESMPy. There's one HYCOM example of it.
by kate
Thu Mar 10, 2022 6:25 pm
Forum: ROMS Discussion
Topic: Different boundary scenarios
Replies: 15
Views: 1799

Re: Different boundary scenarios

For what it's worth, this is what I'm using: LBC(isFsur) == Che Che Che Che ! free-surface LBC(isUbar) == Shc Shc Shc Shc ! 2D U-momentum LBC(isVbar) == Shc Shc Shc Shc ! 2D V-momentum LBC(isUvel) == RadNud RadNud RadNud RadNud ! 3D U-momentum LBC(isVvel) == RadNud RadNud RadNud RadNud ! 3D V-moment...
by kate
Tue Mar 08, 2022 5:16 pm
Forum: ROMS Ice
Topic: Sea-Ice Output
Replies: 1
Views: 279

Re: Sea-Ice Output

You are using an unsupported code! I never ran with the ICESHELF, though there are those who did. Yes, the outputs will go from sea bottom to under the ice. There are diagnostics which should be zero where there's no ice that aren't zero. I wouldn't swear by diagnostics ever being right. I abandoned...
by kate
Thu Jan 20, 2022 8:21 pm
Forum: ROMS Discussion
Topic: Number of history files greater than 9999
Replies: 7
Views: 698

Re: Number of history files greater than 9999

Yes, someone in Enrique's lab wrote a Python code to rename files based on the date in there. Very useful!

MOM6 files all have names starting with the date, such as 20100101.ice_daily.nc
by kate
Thu Jan 20, 2022 7:45 pm
Forum: ROMS Discussion
Topic: Number of history files greater than 9999
Replies: 7
Views: 698

Re: Number of history files greater than 9999

He is at least the second person to run into this issue. I ran into it with daily output over 40 years, each day in its own file. Maybe it wouldn't happen with today's code, I don't know.
by kate
Wed Jan 19, 2022 6:54 pm
Forum: ROMS Discussion
Topic: Number of history files greater than 9999
Replies: 7
Views: 698

Re: Number of history files greater than 9999

It's quite easy. Just change output.F so that you have:

Code: Select all

  10          FORMAT (a,'_',i5.5,'.nc')
instead of

Code: Select all

  10          FORMAT (a,'_',i4.4,'.nc')
and similar for all the other format statements.
by kate
Wed Jan 19, 2022 5:18 pm
Forum: ROMS Ice
Topic: Sea ice in COAWST
Replies: 1
Views: 337

Re: Sea ice in COAWST

Sorry, I stopped supporting my ROMS branch, so John Warner opted to stop including the ice into COAWST.

You can use the metroms coupling to use CICE with ROMS, but CICE isn't on an Arakawa C-grid.
by kate
Fri Dec 24, 2021 6:57 pm
Forum: ROMS Installation
Topic: cmpiling error for roms-kate_svn
Replies: 1
Views: 284

Re: cmpiling error for roms-kate_svn

make: *** No rule to make target `/public/home/hufang/project/ecs922/Build_roms/round.f90', needed by `/public/home/hufang/project/ecs922/Build_roms/round.o'. Stop. I am not aware of any round.F or .f90 file. I haven't updated my code in quite some time, so I'm missing things from the main trunk. W...
by kate
Fri Nov 19, 2021 6:08 pm
Forum: ROMS Discussion
Topic: ROMS blowing up problem
Replies: 19
Views: 6366

Re: ROMS blowing up problem

Those NE boundary conditions look ghastly. Something is going on there, I don't know what.
by kate
Thu Nov 18, 2021 7:01 pm
Forum: ROMS Discussion
Topic: The model blows up in the first step
Replies: 4
Views: 628

Re: The model blows up in the first step

It is bad before taking the first timestep. I would look carefully at your initial conditions.
by kate
Thu Nov 18, 2021 6:58 pm
Forum: ROMS Discussion
Topic: ROMS blowing up problem
Replies: 19
Views: 6366

Re: ROMS blowing up problem

How long before the final blow-up is this snapshot? You are running COAWST? I have no experience with modes of blowing up for anything but the ocean component. For the ocean, it can go from fine to bad in the blink of an eye. A history snapshot some hours before the trouble can look great. I tend to...
by kate
Sun Oct 31, 2021 5:31 pm
Forum: ROMS Discussion
Topic: Problems with restarting the model
Replies: 11
Views: 1277

Re: Problems with restarting the model

The first thing to do is to track down the restart issue. You can run the model for two steps, restart it for two more, then compare that solution to a run that's four steps long. You have to restart after an even number of steps because the model doesn't save nstp, which alternates between 1 and 2....
by kate
Fri Oct 15, 2021 4:33 pm
Forum: ROMS Installation
Topic: Linking to shared library
Replies: 2
Views: 481

Re: Linking to shared library

You have already compiled your library externally? There is a mod_eco.mod file in that directory? If so, you need to tell the compiler how to find that file. Or you could copy it into the ROMS build directory, which is what is done with the netcdf.mod and friends files.
by kate
Sat Sep 18, 2021 5:58 pm
Forum: ROMS Usage
Topic: Clarification about ROMS/Utility/get_nudgcoef.F
Replies: 1
Views: 700

Re: Clarification about ROMS/Utility/get_nudgcoef.F

ROMS does read the varinfo.dat and scale things accordingly.
by kate
Fri Sep 10, 2021 5:43 pm
Forum: ROMS Discussion
Topic: Blow up when restart from history file
Replies: 5
Views: 682

Re: Blow up when restart from history file

I'm glad you got it to run. As for the restarts matching exactly, you do not have enough information stored in the history files to accomplish that. The nature of the ROMS timestepping requires information from more than one timelevel of some fields, plus some right-hand-side information to do perfe...
by kate
Thu Sep 09, 2021 6:50 pm
Forum: ROMS Discussion
Topic: Blow up when restart from history file
Replies: 5
Views: 682

Re: Blow up when restart from history file

I have run from an averages file, no problem. Do you have all the fields you need? Did you tell ROMS it was a new run with NRREC=0? If there's biology, did you really save everything you need in the history file? I've had runs die with COBALT when the averages file didn't have say the htotal field w...
by kate
Sat Sep 04, 2021 1:18 pm
Forum: ROMS Discussion
Topic: Change Output Frequency?
Replies: 3
Views: 680

Re: Change Output Frequency?

You can run for a bit with one output frequency, then restart with a different output frequency. Anything more fancy is going to take hacking the code.
by kate
Sat Sep 04, 2021 1:17 pm
Forum: ROMS Discussion
Topic: Open boundary condition set up
Replies: 3
Views: 707

Re: Open boundary condition set up

m2 is the barotropic velocity while m3 is the full barotropic plus baroclinic velocity.
by kate
Wed Sep 01, 2021 5:51 am
Forum: ROMS Discussion
Topic: ROMS/TOMS - Output error ............ exit_flag: 3
Replies: 3
Views: 570

Re: ROMS/TOMS - Output error ............ exit_flag: 3

Your error might not be in the input files at all. It says:
DEF_VAR - unable to define variable: Tobc_in
in NetCDF file: /scratch/gh9/mx3818/waom/output_1996_2015/
Do you have permission to write to this /scratch/gh9/mx3818/waom/ directory? Does it exist?
by kate
Mon Aug 30, 2021 3:35 pm
Forum: ROMS Discussion
Topic: Open boundary condition set up
Replies: 3
Views: 707

Re: Open boundary condition set up

You can do the OBC via the ana_ files too. Check out the ana_m2obc.h for example.
by kate
Fri Aug 13, 2021 10:12 pm
Forum: ROMS Discussion
Topic: Multiple Wind Field
Replies: 3
Views: 594

Re: Multiple Wind Field

Yes, it doesn't care if you have one file or five. The variable names and dimensions all have to be appropriate to their fields.
by kate
Thu Aug 12, 2021 6:54 pm
Forum: ROMS Discussion
Topic: Multiple Wind Field
Replies: 3
Views: 594

Re: Multiple Wind Field

You can merge them before having ROMS read them and regrid/rotate them if they are both on lat/lon grids of the same resolution. You can copy the ROMS code for reading then regrid/rotating winds to also read/rotate/regrid say Unwind2 and Vwind2. Then you can come up with some means of merging them i...
by kate
Wed Aug 11, 2021 5:49 pm
Forum: ROMS Discussion
Topic: MPI - tiling on POWER8
Replies: 6
Views: 1511

Re: MPI - tiling on POWER8

I would say that any time the answer changes for different tilings, you have a bug. To debug these things, run both tilings for just a timestep and plot the differences between solutions. Which field changes first? If you run 1x4 and 4x1, do you get a grid pattern in the diffs of three vertical stri...
by kate
Sun Aug 01, 2021 7:09 pm
Forum: ROMS Discussion
Topic: Introducing Eulerian tracer during a simulation - flushing time
Replies: 18
Views: 2454

Re: Introducing Eulerian tracer during a simulation - flushing time

I gave up on offline bio because it fought with wetting and drying and all my domains have wetting and drying. Sorry, I probably left it in some half-baked stage.
by kate
Sat Jul 31, 2021 1:27 pm
Forum: ROMS Discussion
Topic: How to save monthly data in average file?
Replies: 3
Views: 589

Re: How to save monthly data in average file?

There are models which know about the different months, but ROMS isn't one of them. You could add that feature with some effort. You could run for 31 days to average for January, then restart and run for x days for February.
by kate
Fri Jul 30, 2021 5:08 pm
Forum: ROMS Discussion
Topic: ERROR: Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Replies: 2
Views: 746

Re: ERROR: Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.

/home/markus/roms_project2/NORSJO2/Build_romsG/omega.f90:215
Can you show us what is on this line? Each person's omega.f90 can differ from the others due to differing cpp options.
by kate
Fri Jul 30, 2021 5:05 pm
Forum: ROMS Discussion
Topic: How to save monthly data in average file?
Replies: 3
Views: 589

Re: How to save monthly data in average file?

If you want thirty-day months, that is simple enough to do. Just figure out how many timesteps per month and ask for that.

I typically save daily, one record per file, rename the files to have the date in the filename, then average to get monthlies.
by kate
Thu Jul 29, 2021 6:22 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 1555

Re: ROMS grid for conservative remapping

You'd have to try a polar projection instead of Lambert conic. Is that supported by your software?
by kate
Thu Jul 29, 2021 5:31 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 1555

Re: ROMS grid for conservative remapping

I bet av2 is simply an average of the two arguments.

Your domain is similar but different from my Arctic domains. Mine cover all the Bering, but less of the Atlantic.
by kate
Wed Jul 28, 2021 11:01 pm
Forum: ROMS Discussion
Topic: Introducing Eulerian tracer during a simulation - flushing time
Replies: 18
Views: 2454

Re: Introducing Eulerian tracer during a simulation - flushing time

Yes, I think that should work. There are a few ana_trc_psource.h files in https://github.com/kshedstrom/Apps, mostly (all?) for steady tracer sources. They are meant to go with my ROMS fork so I have no idea how incompatible the trunk code is these days.
by kate
Wed Jul 28, 2021 5:10 pm
Forum: ROMS Adjoint
Topic: INP_PAR, PHYPAR: Problems finding input file.
Replies: 7
Views: 1273

Re: INP_PAR, PHYPAR: Problems finding input file.

Is it in the roms.in or in the grid file? My grid file has:

Code: Select all

// global attributes:
		:type = "ROMS grid file" ;
by kate
Tue Jul 27, 2021 10:48 pm
Forum: ROMS Discussion
Topic: Incorrect water velocity with open boundaries
Replies: 3
Views: 800

Re: Incorrect water velocity with open boundaries

Is this a time when there should be full pack ice preventing the gyre? I had to have really strong nudging on the ice fields to make things sort of behave.
by kate
Tue Jul 27, 2021 3:57 pm
Forum: ROMS Adjoint
Topic: INP_PAR, PHYPAR: Problems finding input file.
Replies: 7
Views: 1273

Re: INP_PAR, PHYPAR: Problems finding input file.

INP_PAR:FIND_FILE - empty file name string for standard input script KeyWord: SSFNAME
Do you have a line for SSFNAME? That is a newish requirement.
by kate
Tue Jul 27, 2021 3:55 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 1555

Re: ROMS grid for conservative remapping

Yes, gridpak on github. What do you want in an Arctic grid? I've got two you could try as well.
by kate
Tue Jul 27, 2021 3:52 pm
Forum: ROMS Discussion
Topic: Introducing Eulerian tracer during a simulation - flushing time
Replies: 18
Views: 2454

Re: Introducing Eulerian tracer during a simulation - flushing time

I'd think it would be easier to use a restart file. Would this be a problem for some reason?
by kate
Mon Jul 26, 2021 6:57 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 1555

Re: ROMS grid for conservative remapping

Rob Cermak has been working on https://github.com/ESMG/gridtools for making MOM6 grids, including handling polar grids. There's a ROMS-to-MOM6 grid tool and one could easily make the reverse. I make my Arctic grids using old, old grid tools which still work and still produce the psi fields along wit...
by kate
Mon Jul 26, 2021 5:41 pm
Forum: ROMS Discussion
Topic: Incorrect water velocity with open boundaries
Replies: 3
Views: 800

Re: Incorrect water velocity with open boundaries

I assume you know what I used for a regional Beaufort domain. I would go back to the RadNud option and also use nudging to climatology. If it's blowing up due to high speeds, where is that happening? Is that the usual vertical instability needing a short, short timestep or something else? As for you...
by kate
Fri Jul 23, 2021 6:14 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 1555

Re: ROMS grid for conservative remapping

How did you make your grid? Some grid generators add more points to the outside of the model domain than others. You can just extrapolate what you need from the interior. Or if all the lat_rho, lon_rho values are zero, then there's a problem in the generation phase.
by kate
Tue Jul 20, 2021 7:05 pm
Forum: ROMS Ice
Topic: blow-up in first time step, using glorys and ERA5
Replies: 8
Views: 2067

Re: blow-up in first time step, using glorys and ERA5

I'm sure I've said this a number of times before, but it's time to develop some debugging skills. Plot the results after one timestep, try a shorter timestep just in case. Look to see what is going bad and where. If you want ice, I'd keep it on since turning it off isn't helping. The ice-free troubl...
by kate
Tue Jul 20, 2021 6:43 pm
Forum: ROMS Discussion
Topic: tide-calibration
Replies: 7
Views: 1413

Re: tide-calibration

Another option for fussing is the bottom drag. You can make a spatially variable bottom drag and modify it to get a better match.
by kate
Tue Jul 20, 2021 6:42 pm
Forum: ROMS Discussion
Topic: DIURNAL_SRFLUX and cloud fraction
Replies: 3
Views: 878

Re: DIURNAL_SRFLUX and cloud fraction

The best place to search is the code itself. The file to look at is ROMS/Functionals/ana_srflux.h, which has options both including ALBEDO_CLOUD and not including it.
by kate
Fri Jul 16, 2021 7:01 pm
Forum: ROMS Problems
Topic: Boundary forcing error (t3dbc_im)
Replies: 8
Views: 1670

Re: Boundary forcing error (t3dbc_im)

If you can get xxgdb to work, wonderful! I would expect it to be fine as long as your job fits onto one core/process.
by kate
Wed Jul 14, 2021 6:28 pm
Forum: ROMS Problems
Topic: Boundary forcing error (t3dbc_im)
Replies: 8
Views: 1670

Re: Boundary forcing error (t3dbc_im)

I would look at this in a debugger, but lacking that, try print statements. You know it's something to do with dTdt or dTdx, so print them and the things that go into them. It's happening early enough in the run that this shouldn't be too insane. Print the i,j,k values so you know which point(s) are...
by kate
Mon Jul 12, 2021 9:49 pm
Forum: ROMS Ice
Topic: blow-up in first time step, using glorys and ERA5
Replies: 8
Views: 2067

Re: blow-up in first time step, using glorys and ERA5

GET_2DFLD - snow fall rate, 1998-01-15 03:00:00.00 (Grid=01, Rec=0000114, Index=1, File: final_snow_1998.nc) (Tmin= 18263.0000 Tmax= 18627.8750) t = 18277.1250 (Min = 1.00000000E+35 Max = -1.00000000E+35) regrid = T You've got some crazy snow fall rates here. The ice frazil thing can be triggered b...
by kate
Mon Jun 28, 2021 4:53 pm
Forum: ROMS Problems
Topic: cannot make bry file larger than 2g
Replies: 3
Views: 674

Re: cannot make bry file larger than 2g

Yes, old netcdf files had a 2 GB limit. You can make a bunch of under 2 GB files and ask ROMS to read from one, then the next, then the next. Or you can convert them to a newer netcdf format (possibly even with compression) and concatenate them into one file.
by kate
Mon Jun 21, 2021 4:28 pm
Forum: ROMS Discussion
Topic: Issue of exceptionally low velocity
Replies: 8
Views: 2175

Re: Issue of exceptionally low velocity

How large are your wind stresses?
by kate
Fri Jun 18, 2021 5:28 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

Why don't you look through the trunk code examples to see what they use?
#undef MIX_GEO_TS
#define MIX_S_TS
I would swap these.
# define LI_FOX_KEMPER
This is not in the trunk.
by kate
Fri Jun 18, 2021 4:47 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

The trunk code does not have CCSM_FLUX, nor does it have all those albedo options. You should use the .h file consistent with your code.
by kate
Thu Jun 10, 2021 3:58 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

TIME_REF = 2000101.0d0
I think it thinks you have year 200 instead of year 2000. Try adding another 0.
by kate
Wed Jun 09, 2021 8:40 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

Woah! Where did you get that DSTART? It should be the number of days between your time origin (2000) and your starting time (2013?). That would make 13*365 plus the number of leap days in there, so 4749 days.
by kate
Wed Jun 09, 2021 6:16 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

So, do you know what to do next? You need to change your TIME_REF to match that of your forcing files. I have: ! DSTART = 29226.5d0 ! days (1980) DSTART = 42003.5d0 ! days (2015) TIDE_START = -1.0d0 ! days TIME_REF = 19000101.0d0 ! yyyymmdd.dd
by kate
Wed Jun 09, 2021 5:36 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

What about trying "ncdump -h" on one of these things? I get: netcdf JRA55DO_1.5_rain_2020 { dimensions: lon = 640 ; lat = 320 ; time = UNLIMITED ; // (2928 currently) variables: double lon(lon) ; lon:units = "degrees_east" ; lon:valid_min = 0. ; lon:valid_max = 359.4375 ; lon:lon...
by kate
Wed Jun 09, 2021 5:06 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

What is the time variable like in one of these things? You need one common time origin for *everything*.
by kate
Wed Jun 09, 2021 4:33 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

You have only one month of forcing per file? You can string them together in the roms.in file. I have my forcing files with one year each and string them together from one year to the next: NFFILES == 14 ! number of forcing files FRCNAME == /center1/AKWATERS/kate/JRA55-do/JRA55DO_1.4_Pair_2015.nc | ...
by kate
Tue Jun 08, 2021 10:17 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

#define MIX_S_TS
This is OK if your bottom is flat, otherwise it leads to mixing along s-surfaces which can be unrealistic. I don't see anything else wrong, but I could be missing something, who knows.
by kate
Tue Jun 08, 2021 5:57 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

So how are you forcing it? You have:
#define ANA_STFLUX
#define ANA_SSFLUX
Are these set to zero or something reasonable?

Note that I have been using BULK_FLUXES (with CCSM_FLUXES) and atmospheric reanalysis fields for over a decade now.
by kate
Tue Jun 08, 2021 4:52 pm
Forum: ROMS Bugs
Topic: ROMS4 built with PIO, freeze on creating history file
Replies: 17
Views: 2538

Re: ROMS4 built with PIO, freeze on creating history file

get_idata.f90(73): error #6404: This name does not have a type, and must have an explicit type. [ING] & TIDE(ing)%pioFile, & -------------------------------^ compilation aborted for get_idata.f90 (code 1) make: *** [/nesi/project/mocean03294/NZB_3/build/get_idata.o] Error 1 Looks to me like...
by kate
Tue Jun 08, 2021 4:50 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 2861

Re: Wrong Temperature and salinity outputs

Your model is salty at the surface when it should be fresh. What are you using for fresh water forcing?
by kate
Sat May 29, 2021 2:36 pm
Forum: ROMS Discussion
Topic: Atmospheric forcing for child grid
Replies: 3
Views: 738

Re: Atmospheric forcing for child grid

It could be that ROMS only checks once when deciding whether to remap or not. The check happens at line 226 of nf_fread2d.F.
by kate
Thu May 27, 2021 5:17 pm
Forum: ROMS Discussion
Topic: Boundary Condition Choice
Replies: 4
Views: 937

Re: Boundary Condition Choice

Adding a strip of land-masked cells is fair amount of work.
This is why it is good to know your tools. We have landmask editing in both Matlab and Python. Also, it is worthwhile to learn to edit netcdf files in SOME programming language.
by kate
Thu May 27, 2021 1:05 am
Forum: ROMS Discussion
Topic: WET_DRY compilation problem
Replies: 10
Views: 6525

Re: WET_DRY compilation problem

Actually, it looks like some bugs have been introduced. This:

Code: Select all

INI(ng)Vid(idVwet)=Vindex
is not the proper syntax, as the compiler notes. Try

Code: Select all

INI(ng)%Vid(idVwet)=Vindex
instead.
by kate
Thu May 27, 2021 12:00 am
Forum: ROMS Discussion
Topic: WET_DRY compilation problem
Replies: 10
Views: 6525

Re: WET_DRY compilation problem

I would look for idRwet and friends in your varinfo.dat. They need to be there.
by kate
Wed May 26, 2021 5:56 pm
Forum: ROMS Discussion
Topic: Which tool is the stablest tools to create ROMS grid?
Replies: 45
Views: 13884

Re: Which tool is the stablest tools to create ROMS grid?

An Arakawa C-grid is supposed to be staggered, with different sizes of the different variables. I haven't used panoply, but you need to teach your plotting tools about the staggered C-grid.
by kate
Fri May 14, 2021 4:30 pm
Forum: ROMS Discussion
Topic: grid-tide blowup
Replies: 3
Views: 942

Re: grid-tide blowup

So the same configuration runs with 16 vertical levels and blows up with 30? This is not surprising. When you add more vertical levels, the vertical advection requires a shorter timestep. Your run ran long enough that it seems fine except for the timestep limitation. Try a smaller DT. Your vertical ...
by kate
Fri May 07, 2021 5:11 pm
Forum: ROMS Ice
Topic: Landfast ice
Replies: 2
Views: 2637

Re: Landfast ice

You may well be right, but as I said elsewhere, I'm no longer maintaining that code.
by kate
Fri May 07, 2021 5:08 pm
Forum: ROMS Ice
Topic: How to use SEAICE
Replies: 3
Views: 818

Re: How to use SEAICE

It is true that Paul Budgell put the ICE_SHOREFAST in there for the Caspian, but that was a long, long time ago. The ICE_LANDFAST is what I would use now, it's the Lemieux landfast ice parameterization which is also in CICE6. If you need it in CICE5, I can help with that. Why would you read the manu...
by kate
Fri May 07, 2021 4:36 pm
Forum: ROMS Ice
Topic: How to use SEAICE
Replies: 3
Views: 818

Re: How to use SEAICE

I'm sorry, I'm no longer supporting that ice code. I'm five years into a plan to switch to using MOM6 instead, finally getting somewhere.

For ice with ROMS, the Norwegians are supporting their metroms package (but don't try to learn git from their example).
by kate
Wed May 05, 2021 6:03 pm
Forum: ROMS Discussion
Topic: How to split the advection and diffusion term
Replies: 4
Views: 1178

Re: How to split the advection and diffusion term

The vertical diffusivity is in Akt, which is dimensioned by three spatial dimensions and the NT (number of tracers) dimension. You can set some to zero. There will still be implicit changes which I don't think you can do anything about other than try different advection schemes.
by kate
Tue May 04, 2021 6:28 pm
Forum: ROMS Discussion
Topic: How to split the advection and diffusion term
Replies: 4
Views: 1178

Re: How to split the advection and diffusion term

In modeling, there is always implicit diffusion from your advection operator. You can reduce this by going to a fourth-order advection scheme. I use the third-order one with its implicit diffusion, then turn off explicit diffusion by turning off the cppdefs for it. Vertical diffusion is trickier. Pe...
by kate
Mon May 03, 2021 12:23 am
Forum: ROMS Discussion
Topic: Blow up ( River run off)
Replies: 7
Views: 1842

Re: Blow up ( River run off)

Did you provide river tracer values?
by kate
Mon Apr 26, 2021 5:27 pm
Forum: ROMS Discussion
Topic: What's the difference between online and offline running?
Replies: 2
Views: 747

Re: What's the difference between online and offline running?

As I posted elsewhere, I've given up on offline biology. The point of it was that you run the physics once, saving daily outputs. Then you read those fields in as "climalotogy" for running the biology. The dream is that you can maybe take a longer timestep when you only have the biology go...
by kate
Mon Apr 26, 2021 5:21 pm
Forum: ROMS Bugs
Topic: main3d_offline.F and step3d_t.F in ROMS 3.9
Replies: 2
Views: 856

Re: main3d_offline.F and step3d_t.F in ROMS 3.9

If this is my code, I've given up on OFFLINE_BIOLOGY. I sort of had it working in the "main" branch, not the default "kate_svn" branch. But for me, I have wetting and drying and it wasn't doing the right thing in the dry parts, nor did it even know if it was wet or dry that day.
by kate
Sun Apr 25, 2021 7:03 pm
Forum: ROMS Discussion
Topic: Blow up
Replies: 2
Views: 580

Re: Blow up

This is when you need to become a detective. Which field is blowing up. You say it is in the land? Is that the only place going bad?
by kate
Sun Apr 25, 2021 7:01 pm
Forum: ROMS Discussion
Topic: A strange error while open the biological options
Replies: 5
Views: 1326

Re: A strange error while open the biological options

I haven't used BIO_UMAINE since Hernan changed the advection scheme choices. Good catch, John. As for my github code, I have stopped updating it because updates can be disruptive and I don't want to spend the time sorting them out. Mark Hadfield is keeping his github code up to date. If you find any...
by kate
Sat Apr 24, 2021 7:58 pm
Forum: ROMS Discussion
Topic: A strange error while open the biological options
Replies: 5
Views: 1326

Re: A strange error while open the biological options

The check you are running into is in diag.F: IF (maxbio(ibt,ng).gt.max_bio(ibt)) THEN It looks like you have max_bio set to 10000. Does that make sense for the units you are using? You can change it if 10000 is a valid number for your BGC model. I probably added the check for COSINE, but then kept i...
by kate
Fri Apr 23, 2021 10:19 pm
Forum: ROMS Discussion
Topic: problem in open boundary
Replies: 5
Views: 1123

Re: problem in open boundary

That's great that the model is running without any problems. You're all set, then, right? You need to look at your solution to see if you are happy with it. Are you happy with it? If not, there are steps you can take to possibly improve your boundary solution, but nothing is guaranteed when it comes...
by kate
Fri Apr 23, 2021 5:41 pm
Forum: ROMS Discussion
Topic: problem in open boundary
Replies: 5
Views: 1123

Re: problem in open boundary

How are you getting your ROMS information? There is both a manual and a wiki. The wiki page might help you. The manual has much the same information and also examples containing open boundaries.
by kate
Fri Apr 23, 2021 5:39 pm
Forum: ROMS Discussion
Topic: add passive tracer
Replies: 9
Views: 1755

Re: add passive tracer

I see the wiki page on FLOATS is still empty. There is probably something about floats in the manual, though.
by kate
Fri Apr 23, 2021 1:29 am
Forum: ROMS Discussion
Topic: add passive tracer
Replies: 9
Views: 1755

Re: add passive tracer

The FLOATS option is a whole different can of worms. Is that what you want? Online or offline?
by kate
Thu Apr 22, 2021 11:33 pm
Forum: ROMS Discussion
Topic: problem in open boundary
Replies: 5
Views: 1123

Re: problem in open boundary

What sort of open boundary do you want? In the UPWELLING case, the southern edge is in shallow water and typically has a wall. Are you changing the bathymetry? Are you providing fields on the open boundary? I never use a sponge in the ROMS sense of the word. I do use nudging to a climatology, which ...
by kate
Thu Apr 22, 2021 3:29 am
Forum: ROMS Discussion
Topic: add passive tracer
Replies: 9
Views: 1755

Re: add passive tracer

You need these as well:

Code: Select all

# define ANA_BPFLUX        /* analytical bottom passive tracers fluxes */
# define ANA_SPFLUX
unless you want the top and bottom tracer fluxes to be non-zero.
by kate
Wed Apr 21, 2021 5:27 pm
Forum: ROMS Discussion
Topic: add passive tracer
Replies: 9
Views: 1755

Re: add passive tracer

First, you turn on T_PASSIVE and set NPT in roms.in. For the initial conditions, ANA_PASSIVE can be used, otherwise you'll have to put the initial conditions into a netcdf file. I've usually initialized with zero via ANA_PASSIVE, then used sources to introduce the passive dye locally. What is your s...
by kate
Mon Apr 19, 2021 6:07 pm
Forum: Job Opportunities
Topic: Position in Colorado
Replies: 0
Views: 878

Position in Colorado

The University of Colorado Cooperative Institute for Environmental Sciences (CIRES) jointly with the NOAA/Physical Sciences Lab is hiring an associate scientist in the area of ocean data analysis/visualization. Here is a brief position description: The chosen candidate will assist in the development...
by kate
Mon Apr 19, 2021 5:50 pm
Forum: Job Opportunities
Topic: Postdoc at Princeton/GFDL
Replies: 1
Views: 1105

Re: Postdoc at Princeton/GFDL

This position is closing soon. If you intend to apply, get your application submitted now.
by kate
Fri Apr 16, 2021 4:53 pm
Forum: ROMS Discussion
Topic: Timestamp of ROMS diagnostic files
Replies: 1
Views: 483

Re: Timestamp of ROMS diagnostic files

Yes, the diagnostics are time-averaged.
by kate
Mon Apr 12, 2021 5:28 pm
Forum: ROMS Problems
Topic: segmentation fault when running the COAWST model
Replies: 16
Views: 2845

Re: segmentation fault when running the COAWST model

Make sure NBCFILES is defined. Some roms.in files have it, some do not. If using COAWST, you need to have it.
by kate
Sat Apr 10, 2021 7:39 pm
Forum: ROMS Discussion
Topic: Direction of Uwind and Vwind
Replies: 2
Views: 635

Re: Direction of Uwind and Vwind

For the incoming 2-D forcing, it depends. ROMS will check the dimensions of each field you provide. If they match that of your ROMS grid, it assumes Uwind and Vwind are aligned in the directions of the grid. If not, it assumes it needs to do the interpolation and the rotation to the ROMS grid.
by kate
Mon Apr 05, 2021 4:14 pm
Forum: ROMS Problems
Topic: How to solve the speed trouble on the open boundaries?
Replies: 3
Views: 1508

Re: How to solve the speed trouble on the open boundaries?

I use SODA as my initial condition, no spin-up period. You can try a spin-up and see how much drift you get.
by kate
Sun Apr 04, 2021 5:18 pm
Forum: ROMS Problems
Topic: How to solve the speed trouble on the open boundaries?
Replies: 3
Views: 1508

Re: How to solve the speed trouble on the open boundaries?

I typically add a nudging to a monthly climatology in a band around the edge of the domain, ramping to zero in the middle. Note that this will overwrite TNUDG and friends in the default ROMS code.
by kate
Tue Mar 30, 2021 5:07 pm
Forum: ROMS Discussion
Topic: Era5 data is not read by the ROMS
Replies: 7
Views: 1961

Re: Era5 data is not read by the ROMS

GET_2DFLD - surface u-wind component, 2013-01-01 00:00:00.00 (Grid=01, Rec=1, Index=1, File: era5_u10_year_2013_roms.nc) (Tmin= 0.0000 Tmax= 30.9583) t = 0.0000 (Min = 1.00000000E+35 Max = -1.00000000E+35) regrid = T GET_2DFLD - surface v-wind component, 2013-01-01 00:00:00.00 (Grid=01, Rec=1, Inde...
by kate
Mon Mar 29, 2021 8:11 pm
Forum: ROMS Discussion
Topic: Era5 data is not read by the ROMS
Replies: 7
Views: 1961

Re: Era5 data is not read by the ROMS

NETCDF_GET_TIME_1D - error while inquiring ID for variable: srf_time in input file: era5_msdwswrf_year_2013_roms.nc What does "ncdump -h era5_msdwswrf_year_2013_roms.nc" look like? Is there a time variable? What is it called? ROMS is looking for srf_time and it could have gotten this from...
by kate
Sat Mar 27, 2021 2:45 am
Forum: ROMS Discussion
Topic: ROMS blowing up problem
Replies: 19
Views: 6366

Re: ROMS blowing up problem

Same answer as above - use a shorter timestep and look more closely at your model output files.
by kate
Tue Mar 23, 2021 5:00 pm
Forum: ROMS Problems
Topic: Speeding up ROMS Model simulation
Replies: 6
Views: 1545

Re: Speeding up ROMS Model simulation

You know your DT and you should be able to figure out how many timesteps per day from that. Say DT=120 leads to 720 steps/day. Three days of steps is therefore 2160 steps.
by kate
Sun Mar 21, 2021 6:25 pm
Forum: ROMS Problems
Topic: Speeding up ROMS Model simulation
Replies: 6
Views: 1545

Re: Speeding up ROMS Model simulation

When going coarser, you can take longer timesteps. When going coarser, are you reducing the number of grid points?

Why not use MPI?
by kate
Sun Mar 21, 2021 6:22 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

The debugger I use is called totalview. There is also ddt. Both are quite expensive, but the supercomputer center I use pays for the license. For free, there is gdb, which works if you run on just one processor. There may be a gui (ddd?) that can make it easier to use, but using these things is stil...
by kate
Sat Mar 20, 2021 5:27 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

We know it's dying for some unknown reason. So maybe it didn't actually finish ana_initial. I would look in there. Did you change anything there?

Personally, I would run this in the debugger to watch it go bad.
by kate
Thu Mar 18, 2021 4:49 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

You know it got to ANA_INITIAL because it printed stuff from there. I think the next calls it would make from initial.F are these: CALL set_depth0 (ng, tile, iNLM) CALL set_depth (ng, tile, iNLM) CALL set_massflux (ng, tile, iNLM) I would add print statements before these, then after these, then aft...
by kate
Tue Mar 16, 2021 4:25 pm
Forum: ROMS Problems
Topic: Fatal erorr after update to ubuntu 20.04
Replies: 2
Views: 782

Re: Fatal erorr after update to ubuntu 20.04

What I would do is recompile netcdf-fortran. Did you compile it yourself before or use the one from "apt install"?
by kate
Tue Mar 16, 2021 6:41 am
Forum: ROMS Discussion
Topic: ROMS blowing up problem
Replies: 19
Views: 6366

Re: ROMS blowing up problem

I'll say what I always say: try a shorter timestep and look more closely at your solution to see where it is blowing up.
by kate
Sun Mar 14, 2021 3:04 pm
Forum: ROMS Installation
Topic: upwelling - linux-ifort.mk compilation error
Replies: 5
Views: 1247

Re: upwelling - linux-ifort.mk compilation error

Do you have USE_NETCDF4? Do you have netcdf installed properly?
by kate
Sun Mar 14, 2021 7:37 am
Forum: ROMS Installation
Topic: upwelling - linux-ifort.mk compilation error
Replies: 5
Views: 1247

Re: upwelling - linux-ifort.mk compilation error

I think you want to have USE_MPIF90 turned on.
by kate
Mon Mar 08, 2021 7:24 pm
Forum: ROMS Discussion
Topic: The defination of Hz
Replies: 2
Views: 645

Re: The defination of Hz

Hz is the height of the vertical grid box, which you could call Hz=∂z/∂σ.
For consistency between the baroclinic and barotropic solutions, you also need D=ΣHz.
by kate
Mon Mar 08, 2021 7:19 pm
Forum: Job Opportunities
Topic: Postdoc at Princeton/GFDL
Replies: 1
Views: 1105

Postdoc at Princeton/GFDL

I wanted to let everyone know that Princeton is now accepting applications for a Princeton/GFDL postdoc to further develop the regional capabilities of the MOM6 ocean model: https://puwebp.princeton.edu/AcadHire/apply/application.xhtml?listingId=19521 The position would include algorithmic developm...
by kate
Sun Mar 07, 2021 5:25 pm
Forum: ROMS Discussion
Topic: Modify UPWELLING case to a flat bottom, etc.
Replies: 3
Views: 882

Re: Modify UPWELLING case to a flat bottom, etc.

I would not edit UPWELLING, but rather create a new name for your case. Then search the whole code for UPWELLING so you know what files to look in. For the flat bathymetry, the "else" case on ana_grid.h should take care of that for you. For the wind stress, you should be able to find that ...
by kate
Fri Mar 05, 2021 5:44 pm
Forum: ROMS Discussion
Topic: various time indices in ROMS
Replies: 2
Views: 670

Re: various time indices in ROMS

There is some discussion of the timestepping in the roms manual . Most of them point to the old/new time which alternates between 1 and 2, while 3 is always a working time level for tracers. Note: on restart, the model doesn't save these things and always assumes whatever is true for the first step....
by kate
Tue Mar 02, 2021 7:19 pm
Forum: ROMS Discussion
Topic: MPI_ERR_TRUNCATE
Replies: 4
Views: 1288

Re: MPI_ERR_TRUNCATE

initial_ 219 initial.f90
What is on line 219 of your initial.f90? This would be in your scratch directory.
by kate
Tue Mar 02, 2021 6:03 pm
Forum: ROMS Discussion
Topic: nested grid with pyroms: tutorial and python routines
Replies: 15
Views: 3701

Re: nested grid with pyroms: tutorial and python routines

Yes, you got it.

I don't use Matlab if I can help it. You should get the script from the ROMS Matlab repository.
by kate
Tue Mar 02, 2021 8:20 am
Forum: ROMS Discussion
Topic: nested grid with pyroms: tutorial and python routines
Replies: 15
Views: 3701

Re: nested grid with pyroms: tutorial and python routines

Online nesting requires a special 1:3 or 1:5 relationship between the grids, as in Lake Jersey. Both models are run at the same time and the computer spends a lot of time communicating between the domains for you. That's what the contact stuff is for. I did this only once and it was pretty painfully...
by kate
Tue Mar 02, 2021 8:01 am
Forum: ROMS Discussion
Topic: nested grid with pyroms: tutorial and python routines
Replies: 15
Views: 3701

Re: nested grid with pyroms: tutorial and python routines

You are talking about doing online nesting in that case. I have a lot less experience with that than with offline nesting.
by kate
Tue Mar 02, 2021 7:19 am
Forum: ROMS Discussion
Topic: nested grid with pyroms: tutorial and python routines
Replies: 15
Views: 3701

Re: nested grid with pyroms: tutorial and python routines

When doing offline nesting, each domain is a fully independent domain. You run the larger, coarser one first, then use fields from that domain to create the initial/boundary files for the smaller domain. This creation of boundary files for the child grid happens offline, for instance with pyroms, bu...
by kate
Sun Feb 28, 2021 6:34 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

I always have USE_MPIF90 on so that it knows where to find mpif.h.
Are you using COAWST? It is recommended to use that code when coupling to SWAN. Not that I've done it with any of the versions.
by kate
Wed Feb 17, 2021 5:53 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

All those Dout flags control the output, not the tides. I have this section in my .h file: /* tides */ #define LTIDES #ifdef LTIDES # if defined AVERAGES && !defined USE_DEBUG # define FILTERED # endif # define SSH_TIDES # define UV_TIDES # define ADD_FSOBC # define ADD_M2OBC # undef RAMP_TI...
by kate
Wed Feb 17, 2021 5:48 pm
Forum: ROMS Discussion
Topic: Discharge a chemical substance
Replies: 3
Views: 973

Re: Discharge a chemical substance

There are people who study oil spills, maybe not on this forum though. What I know of it is that they simulate a spill for all those cases and see where it goes. For some hypothetical spill, you want to be prepared for all the cases, all the sea levels, all the wind directions. Is it from a leaky ba...
by kate
Sat Feb 13, 2021 2:29 pm
Forum: ROMS Tools and Techniques
Topic: Error to plot by the ROMS plotting package
Replies: 17
Views: 3487

Re: Error to plot by the ROMS plotting package

You need to clean out the old build and start fresh. Getting that error in debug mode should give you more useful information than that.
by kate
Fri Feb 12, 2021 7:39 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

Simply add statements such as these marked with the plus signs: diff --git a/ROMS/Nonlinear/initial.F b/ROMS/Nonlinear/initial.F index 6e20ae7d9..25fd9c4e6 100644 --- a/ROMS/Nonlinear/initial.F +++ b/ROMS/Nonlinear/initial.F @@ -677,6 +677,7 @@ END DO END IF #endif + print, *, "after get_state&...
by kate
Thu Feb 11, 2021 6:36 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

Once the model gets the initial conditions, it should start reading in your surface forcing fields. I see you have BULK_FLUXES, so it should read in shortwave, longwave, winds, etc. There's no mention of that in your output so I have no idea what went wrong. There is a listing of your input forcing ...
by kate
Wed Feb 10, 2021 7:13 pm
Forum: ROMS Discussion
Topic: How to setup the river discharges with only salinity but no temperature?
Replies: 6
Views: 1478

Re: How to setup the river discharges with only salinity but no temperature?

For numerical stability you must give it something other than the water temperature at that grid point. Using the water temperature there is an unconditionally unstable numerical scheme - downwind advection. In MOM6, the default is to use air temperature instead, something you'd have anyway if you w...
by kate
Wed Feb 10, 2021 6:35 pm
Forum: ROMS Discussion
Topic: How to setup the river discharges with only salinity but no temperature?
Replies: 6
Views: 1478

Re: How to setup the river discharges with only salinity but no temperature?

It doesn't make sense numerically to do what you want. As you see, the thing will become unstable. Lacking river temperatures, some have used air temperature instead.
by kate
Mon Feb 08, 2021 7:14 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

I would use the NCO package for this job, specifically the "ncatted" command. Something like:

Code: Select all

ncatted -a time,,m,c,'time'
Note that the missing value between two commas means apply to all variables.
by kate
Mon Feb 08, 2021 5:20 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

You just need to change some attributes in your frc file. You now have: double time(time) ; time:long_name = "time since intialization" ; time:units = "days since 2011-01-01 00:00:00" ; time:calendar = "gregorian" ; float Uwind(time, lat, lon) ; Uwind:long_name = "...
by kate
Sun Feb 07, 2021 10:48 pm
Forum: ROMS Installation
Topic: Compilation error for plotting package
Replies: 10
Views: 2441

Re: Compilation error for plotting package

make: /opt/gfortransoft/serial/netcdf4/bin/nc-config: Command not found
If you have a modern netcdf-c and netcdf-fortran correctly installed, nc-config should be on your search path. Did you install them? What operating system is this? Your laptop or a major computing platform?
by kate
Thu Feb 04, 2021 6:01 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

From your frc file:

Code: Select all

	double time(time) ;
		time:long_name = "time since intialization" ;
		time:units = "days since 2011-01-01 00:00:00" ;
		time:calendar = "gregorian" ;
Can you use 20110101 as your time origin for everything else?
by kate
Tue Feb 02, 2021 6:09 am
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

I always have a TIME_REF of 19000101, which is year 1900, day 1. What year is your time origin? My DSTART is the offset in days from that time, 29225 for 1980, something larger for more recent times. Again, how does the time look in the forcing and what are its attributes?
by kate
Tue Feb 02, 2021 4:00 am
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

The forcing times need to be along the same time axis as everything else. What are the times in your files? It might be easier to make ROMS consistent with them rather than vice versa.
by kate
Sat Jan 30, 2021 3:48 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6375

Re: Error while executing ROMS for a self created grid region

NFFILES == 1 ! number of unique forcing files FRCNAME == frc_TPXO9_alderneyrace_09Dec2068.nc | ! forcing file 1, grid 1 (tidal forcing) frc_watl_ERA5_bulkflux_new_201805.nc !(wind forcing) This should instead be: NFFILES == 2 ! number of unique forcing files FRCNAME == frc_TPXO9_alderneyrace_09Dec2...
by kate
Thu Jan 28, 2021 5:11 pm
Forum: ROMS Discussion
Topic: How to run COAWST model with real-time data
Replies: 6
Views: 1352

Re: How to run COAWST model with real-time data

I went through this exercise in pyroms, now in the pyroms/examples/Arctic_HYCOM_GLBy directory.
by kate
Wed Jan 27, 2021 4:59 pm
Forum: ROMS Discussion
Topic: Use Bulk Formula or Net Flux Form
Replies: 4
Views: 1142

Re: Use Bulk Formula or Net Flux Form

I personally always use bulk_fluxes, in part because the sea ice model requires it.

If you don't use bulk_fluxes, it is advised to also use the dQdSST term to account for your SST differing from that used to compute the fluxes.
by kate
Tue Jan 26, 2021 5:54 pm
Forum: ROMS Discussion
Topic: Use Bulk Formula or Net Flux Form
Replies: 4
Views: 1142

Re: Use Bulk Formula or Net Flux Form

Think about say the Gulf Stream or the Kuroshio. If your fluxes were computed when it was wobbling south, colder water would be present and the fluxes would reflect that. If your Gulf Stream was instead wobbling north, the fluxes would therefore be off. Instead, using BULK_FLUXES, you get the fluxes...
by kate
Mon Jan 25, 2021 6:29 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 2213

Re: problem in svn and nf_config

Code: Select all

NETCDF_CREATE - unable to create output NetCDF file:
roms_his.nc
call from: ROMS/Utility/def_his.F
NetCDF: Malformed URL
Found Error: 03 Line: 105 Source: ROMS/Utility/def_his.F
I don't think your problem is in varinfo.dat.
by kate
Mon Jan 25, 2021 5:29 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 2213

Re: problem in svn and nf_config

Wow, I've never seen that one before. I would check for hidden characters in the ocean.in file where you provide the file names. Or is that file somehow in DOS mode?
by kate
Sun Jan 24, 2021 8:25 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 2213

Re: problem in svn and nf_config

Code: Select all

chinook02.rcs.alaska.edu 203% grep id3dPVI var*
varinfo.dat:  'id3dPVI'
varinfo.dat.cobalt:  'id3dPVI'
varinfo_jra.dat:  'id3dPVI'
I ran this in the Apps directory.
by kate
Sun Jan 24, 2021 7:32 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 2213

Re: problem in svn and nf_config

This is due to a change in the varinfo.dat file. Search through mine for that string idStr and you'll find it.
by kate
Sun Jan 24, 2021 7:42 am
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 2213

Re: problem in svn and nf_config

Just change that path to my nf-config to your path to your nf-config.
by kate
Sat Jan 23, 2021 7:21 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 2213

Re: problem in svn and nf_config

The version of netcdf-fortran doesn't matter, but it has to be compiled with the same version of gfortran as you are using. Just search for "netcdf-fortran download" and you find it. Then you need to follow the instructions for compiling it. Or if you have control of the computer, somethin...
by kate
Sat Jan 23, 2021 7:03 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 2213

Re: problem in svn and nf_config

I don't know that the svn error matters.
/import/home/kshedstrom/bin/nf-config
This is a hard-coded path on a computer here to my home-built netcdf-fortran. You'll have to change it.
by kate
Wed Jan 20, 2021 6:13 pm
Forum: ROMS Discussion
Topic: cmpiling error when using roms-kate_svn
Replies: 3
Views: 881

Re: cmpiling error when using roms-kate_svn

It is failing to find the netcdf library, part of the build system. Since I don't use Hernan's build script, you'll have to figure out what's different between the two and do the appropriate thing.
by kate
Tue Jan 19, 2021 4:53 pm
Forum: ROMS Ecosystem
Topic: Problems with river input forcing when using NEMURO
Replies: 11
Views: 2832

Re: Problems with river input forcing when using NEMURO

Do you have coastal river sources? Are you providing values of the BGC tracers on them? They can easy go unstable if you don't provide values for all incoming tracers. Look at the global NEWS product for nutrient values. Don't worry about varinfo.dat. Best practice is to have the name of the time va...
by kate
Mon Jan 18, 2021 6:03 pm
Forum: ROMS Ice
Topic: How add ice
Replies: 6
Views: 1811

Re: How add ice

You should read the manual. It has sections on the ice and also on how to use git.
by kate
Sun Jan 17, 2021 10:30 pm
Forum: ROMS Ice
Topic: How add ice
Replies: 6
Views: 1811

Re: How add ice

My code is at: https://github.com/kshedstrom/roms. I'm not now finding an svn option, but you can download a tarball of it from that site. It has been over ten years since I've used svn...
by kate
Sun Jan 17, 2021 7:50 pm
Forum: ROMS Ice
Topic: How add ice
Replies: 6
Views: 1811

Re: How add ice

There is no ice in the ROMS trunk code. There is ice in my code on github, also in COAWST from John Warner. There is also ice in the metroms code on github, where they couple to a more complete ice model (CICE). As for forcing, if you are reading winds, air temp, etc. and using BULK_FLUXES, you are ...
by kate
Thu Jan 14, 2021 5:55 pm
Forum: ROMS Discussion
Topic: Curvilinear grid for ROMS
Replies: 4
Views: 1438

Re: Curvilinear grid for ROMS

Yes, I can make a grid like that. However, you want your corners to be right angles. Also, a boundary across the pack ice will be hard to make well-behaved. We had a grid with a boundary at Bering Strait and we didn't like how that behaved either. I guess it depends on what your goals are. How to do...
by kate
Wed Jan 13, 2021 6:06 pm
Forum: ROMS Ecosystem
Topic: Problems with river input forcing when using NEMURO
Replies: 11
Views: 2832

Re: Problems with river input forcing when using NEMURO

This is when you need to build up some debugging skills. You need to find out if the bio fields are sensible in the model, getting corrupted on output, or if they're just nuts everywhere. Feel free to add print statements at will.
by kate
Tue Jan 12, 2021 5:18 pm
Forum: ROMS Ecosystem
Topic: Problems with river input forcing when using NEMURO
Replies: 11
Views: 2832

Re: Problems with river input forcing when using NEMURO

It has to be something in the varinfo.dat. I seem to have both: 'river_fed' 'fed river source' 'mol.m-2.s-1' 'river_fed, scalar, series' 'runoff_time' 'idriver_fed' 'r2dvar' 1.0d0 and 'river_fed' 'river runoff Dissolved Iron' 'mol/kg' 'fed, scalar, series' 'ocean_time' 'idRtrc(ifed)' 'r3dvar' 1.0d0 ...
by kate
Sat Jan 09, 2021 2:27 pm
Forum: ROMS Tools and Techniques
Topic: NCL
Replies: 16
Views: 9295

Re: NCL

This is not the time to start learning NCL. Support for NCL development has been dropped and the focus is now on developing Python tools instead. While we have some plotting capability in pyroms, it too is now out of date, what with the rapid development in new Python tools. I am hardly the expert o...
by kate
Sat Jan 09, 2021 2:17 pm
Forum: ROMS Tools and Techniques
Topic: plot package problem
Replies: 21
Views: 8090

Re: plot package problem

by kate
Fri Jan 08, 2021 5:09 pm
Forum: ROMS Tools and Techniques
Topic: plot package problem
Replies: 21
Views: 8090

Re: plot package problem

unknown option: --flib Usage: nc-config
Try --flibs instead of --flib
by kate
Fri Jan 08, 2021 5:36 am
Forum: ROMS Tools and Techniques
Topic: plot package problem
Replies: 21
Views: 8090

Re: plot package problem

There's a freetype library too, I would guess. Perhaps a quick web search is what you need.

The warnings are a little concerning too, like maybe there's a version inconsistency.
by kate
Thu Jan 07, 2021 5:51 pm
Forum: ROMS Tools and Techniques
Topic: plot package problem
Replies: 21
Views: 8090

Re: plot package problem

cairo is a library which you'll need to link to as well. Try adding -lcairo to your link command.
by kate
Wed Jan 06, 2021 6:46 pm
Forum: ROMS Discussion
Topic: Erorr when applying rivers
Replies: 8
Views: 1785

Re: Erorr when applying rivers

Here's what one of my rivers files looks like: netcdf JRA-1.4_Arctic_rivers_1980 { dimensions: river_time = UNLIMITED ; // (366 currently) river = 18430 ; s_rho = 50 ; variables: double river_time(river_time) ; river_time:units = "days since 1900-01-01 00:00:00" ; river_time:long_name = &q...
by kate
Tue Jan 05, 2021 9:23 pm
Forum: ROMS Discussion
Topic: Erorr when applying rivers
Replies: 8
Views: 1785

Re: Erorr when applying rivers

Yes, exactly. How much do you want shallow and how much deep? For the coastal Gulf of Alaska, I use a linear profile, max at the surface, zero at the very bottom.
by kate
Tue Jan 05, 2021 8:03 pm
Forum: ROMS Discussion
Topic: Erorr when applying rivers
Replies: 8
Views: 1785

Re: Erorr when applying rivers

You could well be dividing by zero because it doesn't have the Vshape. Yes, you need it to be non-zero.
by kate
Thu Dec 31, 2020 3:01 am
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 3183

Re: Issues when running ROMS coupled with bio_UMAINE15 model

If you don't have a working debugger, I would add print statements in there to make sure everything is as you expect it to be. You can add a print of min(pm), max(pm), min(pn), max(pn). Whatever it takes.
by kate
Wed Dec 30, 2020 7:17 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 3183

Re: Issues when running ROMS coupled with bio_UMAINE15 model

758 CALL mp_exchange2d (ng, tile, model, 2, & 759 & LBi, UBi, LBj, UBj, & 760 & NghostPoints, & 761 & EWperiodic(ng), NSperiodic(ng), & 762 & pm, pn) It is unhappy with your pm, pn values.
by kate
Tue Dec 29, 2020 5:45 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 3183

Re: Issues when running ROMS coupled with bio_UMAINE15 model

It means it's trying to pass a bad value in an MPI call. You need to look up a level to:
758 analytical.f90
by kate
Mon Dec 28, 2020 5:32 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 3183

Re: Issues when running ROMS coupled with bio_UMAINE15 model

Now you need to make sure idpthR is in your varinfo.dat.
by kate
Sun Dec 27, 2020 6:09 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 3183

Re: Issues when running ROMS coupled with bio_UMAINE15 model

So now what's on this line?
read_phypar_ 2611 read_phypar.f90
If you're getting your code from Professor Peng, shouldn't you be asking him how to get it to run?
by kate
Fri Dec 25, 2020 5:43 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 3183

Re: Issues when running ROMS coupled with bio_UMAINE15 model

I did run CoSine successfully, but it has been some years since I've tried. Claudine Hauri and I added an iron limitation to it.

As for your line 2002, you still need to make sure your varinfo.dat has everything you need in it. Did professor Peng give you a working one?
by kate
Thu Dec 24, 2020 7:44 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 3183

Re: Issues when running ROMS coupled with bio_UMAINE15 model

2002 mod_ncparam.f90 What is on line 2002 of your mod_ncparam.f90? Mine has: CASE ('idRtrc(icadet_calc)') You then need to see if your equivalent to idRtrc(icadet_calc) is in your varinfo.dat. The only varinfo.dat I have that might contain the CoSine stuff is this one: https://github.com/kshedstrom...
by kate
Wed Dec 23, 2020 6:58 pm
Forum: ROMS Discussion
Topic: blowing up error
Replies: 15
Views: 2977

Re: blowing up error

Do you want to have ice in the model? There are numerous options to do so, including my branch, COAWST, Metroms, and Scott Durski's branch. Metroms (on github) has a version coupled to the community CICE model, the most complete/mature of the ice models. On the other hand, before I had ice in the mo...
by kate
Wed Dec 23, 2020 5:45 pm
Forum: ROMS Discussion
Topic: Velocity is too large near open boundary
Replies: 8
Views: 1728

Re: Velocity is too large near open boundary

There are reanalyses out there at better than monthly, starting before 1979. You might have to contact the authors and mail them some harddrives to load it onto to get it, though. A colleague of mine has done that to get both SODA and Mercator.
by kate
Tue Dec 22, 2020 5:55 pm
Forum: ROMS Discussion
Topic: Velocity is too large near open boundary
Replies: 8
Views: 1728

Re: Velocity is too large near open boundary

You haven't told us anything about your boundary conditions except which options you have. What is the frequency of providing new information and what is the source of it? I remember seeing a vast improvement when going from monthly climatology of just T and S to 5-daily SODA fields. The climatology...
by kate
Tue Dec 22, 2020 5:34 pm
Forum: ROMS Discussion
Topic: blowing up error
Replies: 15
Views: 2977

Re: blowing up error

Yes, exactly. However, you know how you have the #ifdef GLS_MIXING... section? Here's what I have for LMD: # define LMD_MIXING # ifdef LMD_MIXING # define LMD_RIMIX # define LMD_CONVEC # define LMD_SKPP # define LI_FOX_KEMPER # undef LMD_BKPP # define LMD_NONLOCAL # define LMD_SHAPIRO # define LMD_D...
by kate
Tue Dec 22, 2020 7:48 am
Forum: ROMS Discussion
Topic: Zeta data in boundary files can't be read
Replies: 2
Views: 784

Re: Zeta data in boundary files can't be read

What is the exact error you are getting?
by kate
Tue Dec 22, 2020 7:44 am
Forum: ROMS Discussion
Topic: blowing up error
Replies: 15
Views: 2977

Re: blowing up error

I bet you have some vertically unstable T and S profiles. If they are what you want, you should turn on a vertical mixing scheme like GLS or LMD.
by kate
Sun Dec 20, 2020 9:55 pm
Forum: ROMS Discussion
Topic: blowing up error
Replies: 15
Views: 2977

Re: blowing up error

You don't have an open boundary. Where is the velocity always 1.4 m/s? Do you expect it to be less? Is that where the blow-up is happening or not? Actually, it reports: REASON: MaxSpeed = 6.2E+03 Rather a larger velocity. So where is that and why? I usually use U3H advection and some fourth-order ve...
by kate
Fri Dec 18, 2020 11:36 pm
Forum: ROMS Discussion
Topic: blowing up error
Replies: 15
Views: 2977

Re: blowing up error

This is when you need to start looking at the model's netCDF output as well as just the text. Where is the model blowing up and in what way? Is it a boundary problem or not?
by kate
Wed Dec 16, 2020 9:39 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 3139

Re: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred

3082 read_phypar.f90
What is on this line in your code? You say you are using COAWST, but where did you get your roms.in file? Does it have lines for how many boundary and climatology files you have? NCLMFILES and NBCFILES, also NSSFFILES. These need to be non-zero.
by kate
Wed Dec 16, 2020 9:35 pm
Forum: ROMS Installation
Topic: git clone
Replies: 11
Views: 2333

Re: git clone

Sorry, maybe Dave can answer? I only use git via github.
by kate
Tue Dec 15, 2020 5:50 pm
Forum: ROMS Installation
Topic: git clone
Replies: 11
Views: 2333

Re: git clone

Did you do a "git clone" first? You can checkout different branches/tags once you have the clone.
by kate
Mon Dec 14, 2020 12:41 am
Forum: ROMS Documentation
Topic: Abnormal in boundary
Replies: 2
Views: 1150

Re: Abnormal in boundary

The people who run climate models at one degree resolution have spent *years* working on their solutions. ROMS was designed to be run at more eddy-resolving scales while the climate models have parameterizations to try to take care of what the eddies would be doing. Is one of your ovals on the equat...
by kate
Fri Dec 11, 2020 6:09 pm
Forum: ROMS FAQ
Topic: Segmentation Faults
Replies: 10
Views: 7814

Re: Segmentation Faults

Oh gosh, that was two and a half years ago! I have no memory of it whatsoever.

As for metroms, I haven't played with that lately either. I might have to go back to it if I can't get this other monster (CESM) working on our supercomputer.
by kate
Fri Dec 11, 2020 5:57 pm
Forum: ROMS Discussion
Topic: Running error
Replies: 1
Views: 506

Re: Running error

All of your times have to be consistent, however you choose to do that. Pick a time origin and stick with it, in both your input files and ocean.in.
by kate
Thu Dec 10, 2020 5:08 pm
Forum: ROMS Discussion
Topic: Vertical eddy viscosity
Replies: 4
Views: 1068

Re: Vertical eddy viscosity

It is the vertical viscosity used by the model, the sum of all the bits that go into it. The details depend on which vertical mixing scheme you are using.
by kate
Wed Dec 09, 2020 4:49 pm
Forum: ROMS Discussion
Topic: Vertical eddy viscosity
Replies: 4
Views: 1068

Re: Vertical eddy viscosity

I believe it is called Akv in the ROMS output.
by kate
Tue Dec 08, 2020 6:06 pm
Forum: ROMS Discussion
Topic: Temperature blowing up near boundary while use nudge
Replies: 4
Views: 1105

Re: Temperature blowing up near boundary while use nudge

So this is only in the bottom temperature and salinity? What are the velocities doing? Rather than nudging to cover it up, it would be better to understand where it is coming from.
by kate
Mon Dec 07, 2020 12:08 am
Forum: ROMS Discussion
Topic: Temperature blowing up near boundary while use nudge
Replies: 4
Views: 1105

Re: Temperature blowing up near boundary while use nudge

If the boundary is at the edge of the plot, you want to mask out those two purple points. Otherwise you should unmask the point just north of them. At the boundary, the algorithm is using values a few gridpoints in from the boundary so they all have to be wet for it to be well-behaved.
by kate
Wed Dec 02, 2020 6:23 pm
Forum: ROMS Usage
Topic: Differences with CROCO
Replies: 6
Views: 2200

Re: Differences with CROCO

I don't know what the capabilities of PISCES is, but my ROMS "master" branch has the COBALT model. The person who put it into ROMS has moved on, taken a different job, and I'm hardly an expert. The files for a Gulf of Alaska domain are in my Apps_master repository (time to rename some of t...
by kate
Mon Nov 30, 2020 6:38 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 9
Views: 2330

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

When you get a seg fault, you can recompile with USE_DEBUG to get line numbers in the output. You then need to look at the relevant lines in *your* .f90 files.
by kate
Mon Nov 23, 2020 7:41 pm
Forum: ROMS Problems
Topic: upwelling case READ_PHYPAR - Variable index not yet loaded, idStr
Replies: 1
Views: 710

Re: upwelling case READ_PHYPAR - Variable index not yet loaded, idStr

You need to use a varinfo.dat file which is consistent with your ROMS version. idStr is in some varinfo.dat files: 'strain' ! Output 'strain' 'second-1' ! [1/s] 'strain, scalar, series' 'ocean_time' 'idStr' 'p3dvar' 1.0d0
by kate
Wed Nov 11, 2020 6:27 pm
Forum: ROMS Discussion
Topic: Compiling error
Replies: 1
Views: 591

Re: Compiling error

'use_mpif90=on' means that the executable name to use is mpif90. However, which: no mpif90 in (/root/.local/bin:/root/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/var/lib/snapd/snap/bin) On the supercomputer I use, openmpi is in a module. Loading the module adds mpif90 to my pat...
by kate
Wed Nov 11, 2020 3:24 am
Forum: ROMS Problems
Topic: ROMS<kshedstrom version> question about the "zeta <free surface elevation>"
Replies: 4
Views: 1167

Re: ROMS<kshedstrom version> question about the "zeta <free surface elevation>"

What is it that you hope to gain by switching from POM to ROMS? I haven't modeled such a small lake with ROMS, but I expect it can handle it. It smells like a setup problem or who knows what. Anyway, I am in the process of leaving ROMS for yet another model - MOM6. It too should be able to handle a ...
by kate
Tue Nov 10, 2020 10:56 pm
Forum: ROMS Problems
Topic: ROMS<kshedstrom version> question about the "zeta <free surface elevation>"
Replies: 4
Views: 1167

Re: ROMS<kshedstrom version> question about the "zeta <free surface elevation>"

Are the red areas elevated land, as in for wetting and drying? I too would have expected the currents to be more closely related to the ssh contours - it looks like they align right at the end?
by kate
Sat Nov 07, 2020 3:07 am
Forum: ROMS Problems
Topic: ROMS<kshedstrom version>blowing up problems with the "specific heat for seawater" "
Replies: 3
Views: 965

Re: ROMS<kshedstrom version>blowing up problems with the "specific heat for seawater" "

I meant you should #define LIMIT_BSTRESS, though I haven't tried it with LOGDRAG.
by kate
Fri Nov 06, 2020 3:52 pm
Forum: ROMS Problems
Topic: ROMS<kshedstrom version>blowing up problems with the "specific heat for seawater" "
Replies: 3
Views: 965

Re: ROMS<kshedstrom version>blowing up problems with the "specific heat for seawater" "

You have gone for many steps before it blows up. You might as well try a shorter step and see if that helps. You also know that it blew up on the bottom: point 28, 7, 1. What do you have for bottom drag options? Are you limiting the bottom drag?
by kate
Tue Nov 03, 2020 12:54 am
Forum: ROMS Discussion
Topic: Problem with ssh response to uniform winds.
Replies: 4
Views: 1064

Re: Problem with ssh response to uniform winds.

If you want a solution that is invariant along-channel, making it periodic that way is certainly the way to go. You can save some cycles by making the channel quite short, say only 3-4 points in that direction. Did you try a wall at the shallow side and open offshore?
by kate
Mon Nov 02, 2020 8:59 pm
Forum: ROMS Discussion
Topic: running error
Replies: 5
Views: 1084

Re: running error

You are fine, your builds are all clean. As for how to figure out what's going on, you say you are running in serial mode? Can you use the gdb debugger? I would run roms in a debugger to see exactly what is going on, but I know most don't have access to totalview or ddt (costly debuggers that work i...
by kate
Mon Nov 02, 2020 8:09 pm
Forum: ROMS Discussion
Topic: running error
Replies: 5
Views: 1084

Re: running error

I know the default with the build scripts is to always do clean builds - "make clean" before "make". It looks like you didn't change that.
by kate
Mon Nov 02, 2020 7:27 pm
Forum: ROMS Discussion
Topic: running error
Replies: 5
Views: 1084

Re: running error

To clarify, you changed to your grid file and it ran. Now you've changed so that ANA_INITIAL is no longer on and that's when it failed?
Did you do a clean build in debug mode? I would have expected more of a backtrace.
by kate
Sat Oct 31, 2020 9:54 pm
Forum: ROMS Discussion
Topic: run error when applying forcing file
Replies: 7
Views: 1545

Re: run error when applying forcing file

You can see my various .h and .in files here: https://github.com/kshedstrom/Apps Of course, they go with my ROMS branch, so you have to know what you are doing to pick and choose features. I've described things as best I can here: https://github.com/kshedstrom/roms_manual/blob/master/roms_manual.pdf
by kate
Sat Oct 31, 2020 8:53 pm
Forum: ROMS Discussion
Topic: run error when applying forcing file
Replies: 7
Views: 1545

Re: run error when applying forcing file

Maybe? I don't see BULK_FLUXES in your .h file, so without ANA_SMFLUX, the model will only read your sms_era file, not many of the rest of them. There may be other errors in your roms.in file though. The line: allocate ( FRC(max_Ffiles,Ngrids) ) happens once in read_phypar.F, so I assume that's what...
by kate
Sat Oct 31, 2020 8:01 pm
Forum: ROMS Discussion
Topic: run error when applying forcing file
Replies: 7
Views: 1545

Re: run error when applying forcing file

I see that you turned off ANA_SMFLUX. Did you turn on anything else to compensate? I use BULK_FLUXES with: # if defined BULK_FLUXES || defined CCSM_FLUXES # define LONGWAVE_OUT # undef DIURNAL_SRFLUX # define SOLAR_SOURCE # define EMINUSP # undef ALBEDO_CLOUD # define ALBEDO_CURVE /* for water */ # ...
by kate
Sat Oct 24, 2020 3:33 pm
Forum: User Applications
Topic: Forcing file
Replies: 1
Views: 876

Re: Forcing file

Once the forcing is on a regular lat, lon grid, ROMS should be able to interpolate correctly internally. Just make sure your winds are east (u) and north (v) and let ROMS rotate to its grid.
by kate
Tue Oct 20, 2020 7:33 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS MERRA-2 Example
Replies: 4
Views: 1359

Re: PYROMS MERRA-2 Example

I haven't run the MERRA scripts since we switched to using JRA55-do some time back. The "lat" on line 56 is creating the variable and setting it based on what's in the first file. The use on line 85 is using the existing "lat" to write it into a second file. You can search on the...
by kate
Wed Oct 07, 2020 5:16 pm
Forum: ROMS Problems
Topic: ROMS<kshedstrom version> blowing-up with ' REASON: KEchar = NaN, PEchar = NaN' report
Replies: 2
Views: 1323

Re: ROMS<kshedstrom version> blowing-up with ' REASON: KEchar = NaN, PEchar = NaN' report

That's a very intensified surface layer. Did you try a shorter timestep? There are numerical limitations on the vertical operations which can cause blow-ups like that.
by kate
Wed Sep 30, 2020 6:13 pm
Forum: ROMS Information
Topic: How to link an external library (CFIO) to ROMS
Replies: 1
Views: 942

Re: How to link an external library (CFIO) to ROMS

Simply linking to it may not be enough, but adding a library to link to is done in the Compilers file for your system. Just add to the LIBS macro - there are plenty of examples where it gets added to with a "+=". To get ROMS to call your library is another story unless the library has rout...
by kate
Wed Sep 23, 2020 4:25 pm
Forum: ROMS Bugs
Topic: Error with wclock_on subroutine
Replies: 1
Views: 1038

Re: Error with wclock_on subroutine

If you recompile with USE_DEBUG you should get some line numbers in the error report. Those line numbers refer to your files in the SCRATCH_DIR, so it helps if you go looking there to find out say which call to wclock_on is failing.
by kate
Tue Sep 22, 2020 9:29 pm
Forum: ROMS Discussion
Topic: mpirun has exited due to process rank 28 with PID 108752 on
Replies: 2
Views: 825

Re: mpirun has exited due to process rank 28 with PID 108752 on

Because each of us runs with different cpp options, we get differing line numbers. You should look at your lines here: coawstG 00000000009A1EFC load_s2d_ 1722 inp_par.f90 coawstG 0000000000A83CE5 read_phypar_ 1456 read_phypar.f90 However, I suspect that you might be using a roms.in file which is inc...
by kate
Fri Aug 21, 2020 5:08 pm
Forum: ROMS Discussion
Topic: ROMS-CICE test case
Replies: 2
Views: 994

Re: ROMS-CICE test case

Some config files are in my https://github.com/kshedstrom/Apps repository, though most were run with just ROMS ice. In terms of all the big netcdf files you'd need, those are not available online anywhere. Maybe you should ask the Norwegians who are actually running that coupled code.
by kate
Fri Aug 14, 2020 6:01 am
Forum: ROMS Discussion
Topic: Input Initial Conditions from External sources
Replies: 2
Views: 1003

Re: Input Initial Conditions from External sources

There are tools in various languages for creating these files from various input sources. Sometimes we have to get our hands dirty and create the exact tool we need from what's out there. I'm working with the pyroms package which can read the old HYCOM files but not the new HYCOM files. Also, the py...
by kate
Wed Aug 12, 2020 6:30 am
Forum: ROMS Discussion
Topic: NBCFILES' unread or misssing from input script 'roms.in'
Replies: 2
Views: 893

Re: NBCFILES' unread or misssing from input script 'roms.in'

You must use roms.in files which are compatible with whatever version of ROMS you are using. I added the ability to use multiple BRY, etc. files to my branch of ROMS. If you are using my branch, you must use an ocean.in that provides everything my branch wants.
by kate
Wed Aug 05, 2020 10:22 pm
Forum: ROMS Discussion
Topic: River Sinks
Replies: 7
Views: 2082

Re: River Sinks

Do you only have river sinks or are there sources as well? You always want the tracer advection to be "upwind", using the tracer value of the upwind point. For sources, that means specifying the river temperature. For sinks, that means using the ambient temperature.
by kate
Wed Jul 29, 2020 6:16 pm
Forum: ROMS Discussion
Topic: bottom freshwater flux
Replies: 2
Views: 907

Re: bottom freshwater flux

In the model, the variable is called "btflx". Most of us set it to zero and #define ANA_BTFLUX and #define ANA_BSFLUX so that no files are used for the zeros.
by kate
Thu Jul 16, 2020 6:34 am
Forum: ROMS Discussion
Topic: River input file in ROMS.
Replies: 3
Views: 1347

Re: River input file in ROMS.

I never have enough data to make use of the full power of the model to import depth-dependent information. To make smaller river files, I hacked ROMS to read in river tracers either as a function of time only or as a function of time and river, but not depth.
by kate
Wed Jul 15, 2020 4:04 pm
Forum: ROMS Discussion
Topic: River input file in ROMS.
Replies: 3
Views: 1347

Re: River input file in ROMS.

Yes, this is a problem. For salinity, we just use 0.0. For the temperature, some climate modelers use the air temperature. If you were already reading air temperature for the bulk fluxes, you could modify the code to just use it. For Gulf of Alaska waters, Seth Danielson gave me a year of daily temp...
by kate
Mon Jul 13, 2020 6:48 pm
Forum: ROMS Discussion
Topic: error compiling ana_lrflux
Replies: 2
Views: 830

Re: error compiling ana_lrflux

In my code, I added the option to have an analytic longwave flux for the ICE_BOX test case. See if you can copy what I did into COAWST to make it work if that's what you need. The sea ice needs the separate longwave and shortwave fluxes to compute its own bulk fluxes (if you are using sea ice).
by kate
Thu Jul 09, 2020 4:29 pm
Forum: ROMS Discussion
Topic: Budgell vs. CICE sea ice model with ROMS
Replies: 7
Views: 2340

Re: Budgell vs. CICE sea ice model with ROMS

There's a CICE forum at https://bb.cgd.ucar.edu/cesm/forums/cic ... rtium.146/ which would be another place to ask this sort of question.
by kate
Wed Jul 08, 2020 5:29 pm
Forum: ROMS Discussion
Topic: Running error: unable to open existing NetCDF file
Replies: 8
Views: 2087

Re: Running error: unable to open existing NetCDF file

There is a dying art known as "debugging". The lucky few have access to interactive debuggers such as totalview, ddt, ddd. Many have access to gdb, without a gui. If you compile ROMS with USE_DEBUG then you can run it within one of these debuggers and watch what's going on line by line. Th...
by kate
Thu Jul 02, 2020 5:44 pm
Forum: ROMS Discussion
Topic: Running error: unable to open existing NetCDF file
Replies: 8
Views: 2087

Re: Running error: unable to open existing NetCDF file

Weird, you've got ANA_INITIAL so it shouldn't have a reason to read a file instead.
by kate
Wed Jul 01, 2020 8:02 pm
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 2986

Re: Roms with ice module in Coawst

FILTERED is the five-day running mean tidal filter on AVERAGE output, one way of detiding things.
by kate
Wed Jul 01, 2020 6:45 am
Forum: ROMS Discussion
Topic: Add the path of a new Fortran90 file
Replies: 5
Views: 1335

Re: Add the path of a new Fortran90 file

If I were to overhaul this now, I would check to see if the compilers now in use can all invoke the C-preprocessor automatically for .F90 files. If so, take out the cpp step and the cpp_clean step and just have compile-time errors point to the line number of the .F90 file. I did once meet a compiler...
by kate
Wed Jul 01, 2020 5:55 am
Forum: ROMS Discussion
Topic: Add the path of a new Fortran90 file
Replies: 5
Views: 1335

Re: Add the path of a new Fortran90 file

I don't think so. It instead uses:

Code: Select all

define compile-rules
  $(foreach f, $(local_src),       \
    $(call one-compile-rule,$(call source-to-object,$f), \
    $(call f90-source,$f),$f))
endef
and friends. The compile-rules function is called in the Module.mk files.
by kate
Wed Jul 01, 2020 5:01 am
Forum: ROMS Discussion
Topic: Add the path of a new Fortran90 file
Replies: 5
Views: 1335

Re: Add the path of a new Fortran90 file

The makefile has rules for going from .F files to .f90 files to compile them into .o files. You would have to add rules for .F90 files if you refuse to rename your file.
by kate
Wed Jun 24, 2020 5:44 pm
Forum: ROMS Discussion
Topic: Budgell vs. CICE sea ice model with ROMS
Replies: 7
Views: 2340

Re: Budgell vs. CICE sea ice model with ROMS

CICE is a much fancier model, with compile time choices of the number of ice categories, choices for melt ponds, you name it. I don't know your domain well enough to know if you need the extra features. For our needs, we ran the ROMS ice because it's cheaper. Now we're moving away from that for the ...
by kate
Wed Jun 24, 2020 5:32 pm
Forum: ROMS Problems
Topic: mp_collect bug when compiling with define PARALLEL_IO
Replies: 18
Views: 8161

Re: mp_collect bug when compiling with define PARALLEL_IO

I suggest learning about git. You can have a git repo with (a) the old ROMS you started from (b) the old ROMS with your modifications and (c) new ROMS. Or the crude thing to do is diff old ROMS vs. your code and save those diffs to a file. Then apply those changes to the new ROMS by hand. I assume t...
by kate
Tue Jun 23, 2020 5:25 am
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 2986

Re: Roms with ice module in Coawst

What is it trying to read at line 222 of your get_data.f90?
by kate
Sat Jun 20, 2020 11:44 pm
Forum: ROMS Tools and Techniques
Topic: pyroms with mercator dataset
Replies: 4
Views: 1769

Re: pyroms with mercator dataset

Here is the ncdump of the thing: chinook02.rcs.alaska.edu 207% ncdump -h GL2V1_mesh_mask_new.nc netcdf GL2V1_mesh_mask_new { dimensions: y = 1021 ; x = 1442 ; z = 75 ; variables: int y(y) ; y:axis = "Y" ; y:standard_name = "projection_y_coordinate" ; y:units = " " ; int...
by kate
Sat Jun 20, 2020 6:25 am
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 2986

Re: Roms with ice module in Coawst

You can attack this with print statements or by doing the big diff between the two codes. At least you know it's going bad very, very quickly. That sort of problem is easier to debug than those which go bad after days or years of run time.
by kate
Fri Jun 19, 2020 5:28 pm
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 2986

Re: Roms with ice module in Coawst

trouble in ice_frazil 40 31 9 21.255285453705273 -3705.3862141090412
If you check this print statement, you'll see that it is telling you the i,j,k location of where it thinks there is trouble. Next are the T and S values there. That S value is not good.
by kate
Fri Jun 19, 2020 5:23 pm
Forum: ROMS Installation
Topic: Shared libraries error: libnetcdff.so.5
Replies: 2
Views: 1245

Re: Shared libraries error: libnetcdff.so.5

Is it possible for you to recompile the program so that it uses the new library instead of the old library? It is assumed that you will be compiling this code to avoid these problems.
by kate
Fri Jun 19, 2020 5:21 pm
Forum: ROMS Tools and Techniques
Topic: pyroms with mercator dataset
Replies: 4
Views: 1769

Re: pyroms with mercator dataset

The thing is half a GB in size. Can you ask for it from your source of GLORYS files?
by kate
Tue Jun 16, 2020 5:12 pm
Forum: ROMS Discussion
Topic: Boundary condition problems
Replies: 4
Views: 1422

Re: Boundary condition problems

I'm not sure about the boundary conditions, but for the initial conditions, the ubar/vbar fields are set in ini_fields.F.
by kate
Fri Jun 05, 2020 4:20 pm
Forum: ROMS Discussion
Topic: the defination of density rho
Replies: 16
Views: 4379

Re: the defination of density rho

OK, but I'm surprised.
by kate
Fri Jun 05, 2020 4:15 am
Forum: ROMS Discussion
Topic: the defination of density rho
Replies: 16
Views: 4379

Re: the defination of density rho

The variable "rho" in the model is insitu density anomaly. You add rho0 to it to get full density. Note that rho0 may or may not be 1000.
by kate
Sat May 16, 2020 7:35 pm
Forum: ROMS Discussion
Topic: Blow up problem
Replies: 3
Views: 1470

Re: Blow up problem

For once I can't say try a shorter timestep because you are already in trouble before you've taken any timesteps: 0 0001-01-01 00:00:00.00 NaN NaN NaN NaN (000,000,0) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 I'm not sure what has gone wrong.
by kate
Thu Apr 30, 2020 4:47 pm
Forum: ROMS Discussion
Topic: Could I repeat the simulation forced by bulk flux by using its output?
Replies: 3
Views: 1304

Re: Could I repeat the simulation forced by bulk flux by using its output?

Also, it depends on the frequency of the forcing. I'm using three-hourly forcing files and if I were to apply them as daily averages from the ROMS output, that would be different.
by kate
Fri Apr 24, 2020 4:41 pm
Forum: ROMS Tools and Techniques
Topic: pyroms error during initial condition remapping process
Replies: 2
Views: 1329

Re: pyroms error during initial condition remapping process

I think perhaps you need to change this in make_ic_file.py: xrange=(400, 500), yrange=(180, 280) To save time, it doesn't search the whole world, but just the part of the world where your grid is (or in this case where the CCS1 grid is). In my case, num_links is rather large: netcdf remap_weights_SO...
by kate
Sat Apr 18, 2020 3:08 pm
Forum: ROMS Discussion
Topic: grid generation for idealized geometry
Replies: 4
Views: 1608

Re: grid generation for idealized geometry

I just want to point out that your two western corners are not right angles and will lead to weirdness for an orthogonal grid.
by kate
Thu Apr 16, 2020 3:17 am
Forum: ROMS Discussion
Topic: Test of open boundary conditions
Replies: 12
Views: 3285

Re: Test of open boundary conditions

Flather does allow introduction of outside information.
by kate
Wed Apr 15, 2020 5:50 pm
Forum: ROMS Discussion
Topic: Writing out wT (time average)
Replies: 2
Views: 851

Re: Writing out wT (time average)

One usually simply does a simple average between T points to get values at w points. For the top and bottom, just use the nearest value.
by kate
Mon Apr 13, 2020 4:34 pm
Forum: ROMS Discussion
Topic: Test of open boundary conditions
Replies: 12
Views: 3285

Re: Test of open boundary conditions

So should I keep Chapman+Flather or Chapman+Shc for 2D variables and use radiation+nudging for 3D u,v, t, and s?
Yes, exactly.