Search found 3693 matches

by kate
Tue Nov 19, 2019 9:12 pm
Forum: ROMS Benchmarks
Topic: Speed-up advice?
Replies: 1
Views: 95

Speed-up advice?

We are hoping to have a long simulation of a Pan-Arctic grid with a BGC model. My colleagues have therefore obtained a computing grant at NCAR. I have done a few timings of a day-long simulation on Cheyenne. I'm finding it no faster than a not-so-new Penguin Supercomputing cluster at home: On 216 co...
by kate
Tue Nov 19, 2019 6:50 pm
Forum: ROMS Installation
Topic: Compiling error - undefined reference to ice routines
Replies: 7
Views: 454

Re: Compiling error - undefined reference to ice routines

Actually, there is an AInudgcof for nudging to ice concentration climatology. See the Apps_master/Chukchi or the Apps/Beaufort versions of ana_nudgcoef.h.
by kate
Sun Nov 17, 2019 4:13 pm
Forum: ROMS Discussion
Topic: unmatch surface lateral boundary condition data
Replies: 1
Views: 88

Re: unmatch surface lateral boundary condition data

I would start by upping the temporal frequency of your atmospheric fields. Monthly is going wash out all the storms. I use three-hourly to resolve diurnal cycles as well. I haven't tried monthly boundary information since we stopped using monthly Levitus many, many moons ago, but going to more frequ...
by kate
Sun Nov 17, 2019 4:57 am
Forum: ROMS Installation
Topic: Compiling error - undefined reference to ice routines
Replies: 7
Views: 454

Re: Compiling error - undefined reference to ice routines

COAWST has my sea ice in it now, a one-layer dynamic, thermodynamic sea ice model as part of ROMS. This is a rather simpler model than CICE, the community sea ice model. There are several efforts to couple ROMS with CICE, but that may not be what you want now. There's an effort doing sea ice in a mo...
by kate
Fri Nov 15, 2019 8:00 pm
Forum: ROMS Installation
Topic: Compiling error - undefined reference to ice routines
Replies: 7
Views: 454

Re: Compiling error - undefined reference to ice routines

There are long-standing disagreements between me and Hernan on a number of things, including where the ice code should live and how to compile. I maintain my own Makefiles which point to the ice code where I put it. Since he's not actually distributing the ice code I feel no pressure to comply. Call...
by kate
Thu Nov 14, 2019 10:37 pm
Forum: ROMS Tools and Techniques
Topic: pyroms grid missing libgridgen, unable to solve
Replies: 5
Views: 209

Re: pyroms grid missing libgridgen, unable to solve

Most people separate the vertical grid from the horizontal grid. The ROMS grid file really only has the horizontal grid information while the vertical grid comes from the stretching parameters, THETA_S and so forth. You should be able to create a horizontal grid file with those other tools, then rea...
by kate
Thu Nov 14, 2019 8:57 pm
Forum: ROMS Tools and Techniques
Topic: pyroms grid missing libgridgen, unable to solve
Replies: 5
Views: 209

Re: pyroms grid missing libgridgen, unable to solve

If it is grid generation you are after, I suggest you check out pygridgen and pygridtools . I'm sorry this happened, but pyroms installation has always been troublesome and Mark Hadfield has offered to work on cleaning things up. There has been progress, but there are bumps in the road, as you can s...
by kate
Mon Nov 11, 2019 5:34 pm
Forum: ROMS Discussion
Topic: Is it a must to use VolCons if RadNud activated?
Replies: 8
Views: 403

Re: Is it a must to use VolCons if RadNud activated?

It's blowing up at point 2, 13, 8. Your Courant numbers are getting rather large, so you might start by trying a shorter timestep. You could also look at the fields it has saved for you in the restart file. 122 2018-01-01 20:20:00.00 3.461952E-03 7.113528E+02 7.113563E+02 5.699591E+12 (002,013,10) 1...
by kate
Thu Nov 07, 2019 6:14 pm
Forum: ROMS Discussion
Topic: How to set up outgoing nudging in nud netCDF
Replies: 2
Views: 90

Re: How to set up outgoing nudging in nud netCDF

The answer to this question is in the source code, say in t3dbc_im.F. It looks like it is getting the outgoing value from the nudging field you have specified and the incoming value is obcfac times that. Remember that it has been scaled to be an inverse timescale before being used, so an obcfac of 1...
by kate
Thu Nov 07, 2019 4:36 am
Forum: ROMS Bugs
Topic: DIAG speed trouble
Replies: 4
Views: 303

Re: DIAG speed trouble

GET_NGFLD - river runoff mass transport, 2000-01-08 00:00:00.00 (Grid= 01, Rec=0000008, Index=1, File: create-river_daily2017_cycle_add9rivers_30layers-15-change-huanghe-1996coastl_dye.nc) (Tmin= 0.0000 Tmax= 364.0000) t = 7.0000 (Min = -1.27772940E+23 Max = 2.81650723E-37) GET_NGFLD - river runoff...
by kate
Sun Nov 03, 2019 5:08 pm
Forum: ROMS Discussion
Topic: error in comile a file
Replies: 2
Views: 145

Re: error in comile a file

Actually the error is that it can't find the makefile. Do you have the correct path to your ROMS sources? The makefile should be in the top directory there.
by kate
Thu Oct 31, 2019 5:09 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 23
Views: 405

Re: Problem with setting up inlet_test

And yet:
INP_PAR - Unable to open ROMS/TOMS input script file.
coupling_inlet_test.in is in your current run directory? Plus any files it refers to?
by kate
Wed Oct 30, 2019 5:14 pm
Forum: ROMS Problems
Topic: problems with the addition of tide forcing
Replies: 9
Views: 2255

Re: problems with the addition of tide forcing

There are errors and warnings coming from SWAN. Is this from COAWST or not?
by kate
Tue Oct 29, 2019 5:48 pm
Forum: ROMS Problems
Topic: problems with the addition of tide forcing
Replies: 9
Views: 2255

Re: problems with the addition of tide forcing

You're missing parts of that file - where did you get it from? How did that even compile, since it is missing an ending #endif or two? For the problem you are seeing, before the #ifdef SSW_BBL bit, there should be: /* define only one of the following 5 */ #undef UV_LOGDRAG #undef UV_QDRAG #undef MB_...
by kate
Mon Oct 28, 2019 6:16 pm
Forum: ROMS Problems
Topic: problems with the addition of tide forcing
Replies: 9
Views: 2255

Re: problems with the addition of tide forcing

inlet_test.h has SSW_BBL defined, which should satisfy that bottom drag condition.
by kate
Mon Oct 28, 2019 5:21 pm
Forum: ROMS Problems
Topic: problems with the addition of tide forcing
Replies: 9
Views: 2255

Re: problems with the addition of tide forcing

Which case are you trying to run? I suggest starting with a proven case like UPWELLING. There is an upwelling.h file containing the cppdefs for that case.
by kate
Sun Oct 27, 2019 6:12 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 23
Views: 405

Re: Problem with setting up inlet_test

Error: Invalid character in name at (1) make: *** [/Users/venuscheung/ocean_model/inlet_test/Build_roms/ocpmix.o] Error 1 I would look at these files in an editor which shows hidden characters, including the MakeDepend file. The vi(m) mode to see hidden characters is ":set list" - others can say ho...
by kate
Thu Oct 24, 2019 7:14 pm
Forum: ROMS Bugs
Topic: Error while compiling ROMS
Replies: 4
Views: 175

Re: Error while compiling ROMS

Since my Perl is dated 2015 and yours is rather older, it might help if you could try a newer Perl.
by kate
Thu Oct 24, 2019 6:49 pm
Forum: ROMS Bugs
Topic: Error while compiling ROMS
Replies: 4
Views: 175

Re: Error while compiling ROMS

This is a problem with your Perl. What version of Perl is this? My Perl works:
chinook03.rcs.alaska.edu 435% perl -v

This is perl 5, version 22, subversion 1 (v5.22.1) built for x86_64-linux-thread-multi
by kate
Wed Oct 23, 2019 3:45 pm
Forum: ROMS Source
Topic: Huon_eastward and Hvom_northward
Replies: 9
Views: 330

Re: Huon_eastward and Hvom_northward

If you want transport across some section not aligned with the grid, the proper thing to do is described here.
by kate
Tue Oct 22, 2019 2:02 pm
Forum: ROMS Discussion
Topic: Tracers don't radiate out at boundary
Replies: 4
Views: 253

Re: Tracers don't radiate out at boundary

No, that's not the problem. I use those numbers too. I haven't tried monthly HYCOM, but back in the day we would try monthly Levitus and have a terrible time with the boundaries. I use daily HYCOM and I also nudge to monthly HYCOM in a band around the edge of the domain.
by kate
Mon Oct 21, 2019 6:03 pm
Forum: ROMS Source
Topic: Huon_eastward and Hvom_northward
Replies: 9
Views: 330

Re: Huon_eastward and Hvom_northward

Rotating a velocity is easy while rotating flux through a cell face is less so. You'd have to think carefully about exactly what it is that you want to output, especially if dx and dy are not the same. As for the averages, adding new things to the averages output typically depends on adding new vari...
by kate
Mon Oct 21, 2019 5:54 pm
Forum: ROMS Discussion
Topic: Shchepetkin (Shc) boundary condition reference?
Replies: 1
Views: 144

Re: Shchepetkin (Shc) boundary condition reference?

I believe it to be:
@article(Mason2010,
author = "E. Mason and J. Molemaker and A.~F. Shcheptkin and F. Colas
and J.~C. McWilliams and P. Sangr{\`{a}}",
title = "Procedures for offline grid nesting in regional ocean models",
year = "2010",
journal = om,
volume = "35",
pages = "1--15"
by kate
Mon Oct 21, 2019 5:51 pm
Forum: ROMS Discussion
Topic: Tracers don't radiate out at boundary
Replies: 4
Views: 253

Re: Tracers don't radiate out at boundary

Turning off the temperature of the river source is numerically unstable.

Do you mean that you use monthly means from HYCOM for the boundary files? I have always had better luck with more frequent boundary information and even then it's not perfect.
by kate
Sat Oct 12, 2019 3:35 am
Forum: ROMS Installation
Topic: Finished compiling COAWST Installation - Ubuntu 14.04
Replies: 26
Views: 13441

Re: Finished compiling COAWST Installation - Ubuntu 14.04

The modern way to install netcdf-fortran on Ubuntu is:
sudo apt install netcdf-bin libnetcdf-dev libnetcdff-dev
Then you will have to check to see if nf-config is working because some versions gave a weird error about cmake.
by kate
Wed Oct 09, 2019 5:23 am
Forum: ROMS Discussion
Topic: how to improve vertical profile velocity
Replies: 10
Views: 689

Re: how to improve vertical profile velocity

1. Probably easiest in Matlab or something with similar capabilities, something that knows the vertical coordinate system. 2. If you only want to nudge to surface T/S, there is separate code for that as part of the surface boundary condition. Check out for instance SCORRECTION and SRELAXATION, using...
by kate
Wed Oct 02, 2019 4:00 pm
Forum: ROMS Installation
Topic: Compile error
Replies: 1
Views: 98

Re: Compile error

cp: /opt/gfortransoft/serial/netcdf3/include/netcdf.mod: No such file or directory
make: *** No rule to make target
You need to have netcdf and netcdff installed and you need to know where they are. Best to get netcdf4 and set USE_NETCDF4 which has an nc-config to tell you where things are.
by kate
Mon Sep 23, 2019 10:45 pm
Forum: ROMS Discussion
Topic: how to improve vertical profile velocity
Replies: 10
Views: 689

Re: how to improve vertical profile velocity

If you turn on climatology nudging, it will change the OBC time scales. If you don't want that, change the open boundary code to do what you want it to do - that's what I did in my branch.
by kate
Mon Sep 23, 2019 10:42 pm
Forum: ROMS Discussion
Topic: Asking for cpp and control files
Replies: 1
Views: 95

Re: Asking for cpp and control files

At line 960 of file inp_par.f90
You need to look at your inp_par.f90 and see what is in there at line 960.
by kate
Sun Sep 22, 2019 6:20 pm
Forum: ROMS Discussion
Topic: Amplification in zeta after adding river forcing
Replies: 2
Views: 144

Re: Amplification in zeta after adding river forcing

What about the surface salinity and velocity? Are you getting a run-away estuary where the surface is too fresh and fails to vertically mix down? I would expect there to be enough fresh water input there to change the results, but are they now more sensible or not? I can't tell from zeta.
by kate
Sun Sep 22, 2019 6:08 pm
Forum: ROMS Discussion
Topic: PYROMS error
Replies: 2
Views: 148

Re: PYROMS error

For #1, I get the same error, I'm not using lpsolve, I don't care enough to figure it out. For #2, I don't get that error. It is finding _remapping.cpython-37m-x86_64-linux-gnu.so in my $HOME/python/lib/python3.7/site-packages/pyroms which is where I told it to put stuff. Do you have such a _remappi...
by kate
Fri Sep 20, 2019 6:00 pm
Forum: ROMS Discussion
Topic: Some confusion about boundary condition
Replies: 4
Views: 192

Re: Some confusion about boundary condition

If any part of a boundary is open, you have to set the whole boundary to open. The land masking will take care of the rest. Your north can be closed. If you set it to open, no harm done, but you'll be asking ROMS to do extra work of reading fields (or computing analytic fields).
by kate
Thu Sep 19, 2019 5:15 pm
Forum: ROMS Discussion
Topic: Some confusion about boundary condition
Replies: 4
Views: 192

Re: Some confusion about boundary condition

Yes, ROMS is expecting ubar, vbar in the initial and boundary files. It will ensure consistency between baroclinic and barotropic flows during initialization and after every timestep, but the boundary files ought to be generated in such a way that the u and ubar fields are consistent. If you are doi...
by kate
Thu Sep 19, 2019 5:07 pm
Forum: ROMS Bugs
Topic: Some questions about river input
Replies: 4
Views: 187

Re: Some questions about river input

You want river inputs to be from land to water as in your left arrow. The right arrow appears to be all within the land and will therefore do nothing at all. How much transport are you asking for? What is the corresponding flow rate to go with it? Are you violating the ROMS speed limit? I have done ...
by kate
Thu Sep 19, 2019 3:19 am
Forum: ROMS Bugs
Topic: Some questions about river input
Replies: 4
Views: 187

Re: Some questions about river input

Are we looking at depth there? Where is the land mask? Are you sure you are putting the rivers where you think you are? Blows up how? Are you providing the river tracers (T and S)?
by kate
Wed Sep 18, 2019 5:07 pm
Forum: ROMS Discussion
Topic: WET_DRY option results in too much land_mask?
Replies: 2
Views: 86

Re: WET_DRY option results in too much land_mask?

You are telling the model that it can never have less than 10 m water depth in the "wet" parts. You might try something rather smaller for DCRIT, like 0.5 m. Then you'd have to have 9.5 m of water leaving due to the storm surge before a spot became "dry".
by kate
Tue Sep 17, 2019 4:22 pm
Forum: ROMS Discussion
Topic: erro about MPDATA
Replies: 2
Views: 172

Re: erro about MPDADA

Any of the other advection schemes should work. Is there any reason you can't use MPI on that shared-memory cluster?
by kate
Sat Sep 14, 2019 3:25 am
Forum: ROMS Discussion
Topic: open boundary for future projection of CMIP6 downscaling
Replies: 11
Views: 510

Re: open boundary for future projection of CMIP6 downscaling

Salt looks like you have boundary weirdness, low values right at the edge. Zeta seems to be in balance with a strong boundary current which I'm not seeing in the u, v plots. Have you looked at the boundary files to see if the fields there look reasonable?

What values did you pick for LBC all around?
by kate
Sat Sep 14, 2019 1:22 am
Forum: ROMS Discussion
Topic: open boundary for future projection of CMIP6 downscaling
Replies: 11
Views: 510

Re: open boundary for future projection of CMIP6 downscaling

The blow-up messages are not helpful. You need to look at the fields in the restart record that it saves.
by kate
Fri Sep 13, 2019 5:44 pm
Forum: ROMS Discussion
Topic: open boundary for future projection of CMIP6 downscaling
Replies: 11
Views: 510

Re: open boundary for future projection of CMIP6 downscaling

Well, I also hope to use CMIP for open boundaries in the future. Which of the models did you try and what software did you use to create the OBC files? Did the blow-up happen at the boundary and what did it look like?
by kate
Thu Sep 12, 2019 5:53 am
Forum: ROMS Discussion
Topic: Is it a must to use VolCons if RadNud activated?
Replies: 8
Views: 403

Re: Is it a must to use VolCons if RadNud activated?

I never, ever use VolCons. If you have the Flather boundary condition, the model should not fill or drain excessively - unless of course the zeta boundary conditions you give it suggest that it should fill or drain excessively.
by kate
Wed Sep 11, 2019 4:56 pm
Forum: ROMS Discussion
Topic: if I can set hc=Tcline>hmin?
Replies: 7
Views: 240

Re: if I can set hc=Tcline>hmin?

hmin is no longer used in computing z. If you keep reading in the Warning, it says the restriction was removed.
by kate
Wed Sep 11, 2019 4:52 pm
Forum: ROMS Bugs
Topic: DIAG speed trouble / gridbuilder
Replies: 3
Views: 195

Re: DIAG speed trouble / gridbuilder

You might still need to reduce the timestep. You ran long enough that you should be getting close.
by kate
Wed Sep 11, 2019 4:21 pm
Forum: ROMS Installation
Topic: Error during compilation of build file
Replies: 1
Views: 88

Re: Error during compilation of build file

I think you should have: NETCEDF_INCDIR=/opt/gfortransoft/serial/netcdf3/include if that's where the netcdf.mod and friends live. The FIRST_2D_STEP is a cpp macro defined in globaldefs.h, not a regular Fortran variable. If the compile goes correctly, the compiler should never see it. Step one is a "...
by kate
Wed Sep 11, 2019 3:08 am
Forum: ROMS Discussion
Topic: ROMS processing water sluice in upstream
Replies: 1
Views: 80

Re: ROMS processing water sluice in upstream

I think that should work. What would be problematic is a source turning into a sink sometimes, because the tracers need to come from upstream to be stable.
by kate
Tue Sep 10, 2019 11:23 pm
Forum: ROMS Discussion
Topic: if I can set hc=Tcline>hmin?
Replies: 7
Views: 240

Re: if I can set hc=Tcline>hmin?

Actually, no, you want hc = Tcline = 10 m. It was only with the bad old stretching that the code enforced hc = Tcline = hmin. The stretching is meant to be "z-like" above Tcline (hc). Having the old way meant that the z-like part of your domain could only be above hmin. Meanwhile, I was getting away...
by kate
Mon Sep 09, 2019 4:44 pm
Forum: ROMS Discussion
Topic: if I can set hc=Tcline>hmin?
Replies: 7
Views: 240

Re: if I can set hc=Tcline>hmin?

It depends on which vertical "transform" function you use. The old one needed Tcline <= hmin, but the new one does not. I'm sure there's plenty of code still around from the bad old days. I use: Vtransform == 2 ! transformation equation Vstretching == 4 ! stretching function THETA_S == 7.0d0 ! surfa...
by kate
Fri Sep 06, 2019 8:58 pm
Forum: ROMS Discussion
Topic: The xi_position and eta_position of rivers.nc input
Replies: 4
Views: 210

Re: The xi_position and eta_position of rivers.nc input

It refers to i, j. The western-most u-point is at i=1.
by kate
Mon Sep 02, 2019 4:06 pm
Forum: ROMS Discussion
Topic: surface boundary layer depth
Replies: 2
Views: 157

Re: surface boundary layer depth

You can have positive Hsbl where zeta is positive. The boundary layer thickness is (zeta-Hsbl).
by kate
Sun Sep 01, 2019 3:13 pm
Forum: ROMS Problems
Topic: Interannual simulation
Replies: 8
Views: 701

Re: Interannual simulation

It depends on your ROMS version. Older versions required you to change NTIMES to get a second year while newer ones don't.
by kate
Fri Aug 30, 2019 3:05 pm
Forum: ROMS Problems
Topic: Interannual simulation
Replies: 8
Views: 701

Re: Interannual simulation

I don't see an error in the output you show. That's just the normal ROMS report at the end of a run. How many timesteps did you ask it to do?
by kate
Thu Aug 29, 2019 11:03 pm
Forum: ROMS Tools and Techniques
Topic: problem with pyroms.grid.Gridgen
Replies: 8
Views: 2939

Re: problem with pyroms.grid.Gridgen

For generating grids, you might look into pygridtools. They seem more advanced in their Python support.
by kate
Thu Aug 29, 2019 5:12 am
Forum: ROMS Discussion
Topic: i have a question
Replies: 11
Views: 2395

Re: i have a question

I don't see what the problem is. Yes, it is reading the forcing files for time 0 and for time 6 hours, then it linearly time-interpolates between them to the current model time. It always has two time records in memory for this interpolation. Once six hours pass, it will read hour 12, and so on.
by kate
Wed Aug 28, 2019 3:29 pm
Forum: ROMS Problems
Topic: Interannual simulation
Replies: 8
Views: 701

Re: Interannual simulation

#define TCLM_NUDGING #define TCLIMATOLOGY This is from an older ROMS version. #define BULF_FLUXES /*bulk formulation for surface heat fluxes*/ You have misspelled BULK_FLUXES. If you spell it correctly, it will ask for winds instead of surface stress. ROMS will ignore random strings that it doesn't...
by kate
Tue Aug 27, 2019 4:43 pm
Forum: ROMS Problems
Topic: Interannual simulation
Replies: 8
Views: 701

Re: Interannual simulation

It blew up in the first step - this could be any number of things. The first thing I would try is a shorter barotropic timestep - i.e., a larger NDTFAST. Your surface inputs appear to be well behaved. What other inputs do you have?
by kate
Mon Aug 26, 2019 6:00 pm
Forum: ROMS Problems
Topic: nudging/relaxation time scale field
Replies: 1
Views: 159

Re: nudging/relaxation time scale field

Answers 1, 2 and 3: In t3dbc_im.F, the nudging code has a different nudging constant depending on whether or not LnudgeTCLM is true. You can search for LnudgeTCLM there to see. That is not the behavior I want, so I have modified my code accordingly.
by kate
Fri Aug 23, 2019 4:18 pm
Forum: ROMS Discussion
Topic: Barotropic model Blowing-up with high courant and dt = 1.
Replies: 6
Views: 218

Re: Barotropic model Blowing-up with high courant and dt = 1

The OP said it was a barotropic model which requires NDTFAST = 1.
by kate
Fri Aug 23, 2019 1:58 pm
Forum: ROMS Discussion
Topic: Barotropic model Blowing-up with high courant and dt = 1.
Replies: 6
Views: 218

Re: Barotropic model Blowing-up with high courant and dt = 1

Why not try dt=0.5 or shorter? Your horizontal grid spacing is quite a bit smaller than anything I've tried outside of test problems, so it makes sense that you'd need a short timestep.
by kate
Fri Aug 23, 2019 5:02 am
Forum: ROMS Discussion
Topic: blow up the model
Replies: 3
Views: 170

Re: blow up the model

So save a record right before it blows up and look at it. I can't do it from here.
by kate
Thu Aug 22, 2019 4:06 pm
Forum: ROMS Discussion
Topic: Shortwave and Longwave radiation.
Replies: 3
Views: 263

Re: Shortwave and Longwave radiation.

I always let ROMS compute its own upward longwave flux. There's an option for that.

For the shortwave, it might be worth trying what you say. I use an albedo option because the ice model wants to have its own albedo.
by kate
Thu Aug 22, 2019 4:01 pm
Forum: ROMS Discussion
Topic: blow up the model
Replies: 3
Views: 170

Re: blow up the model

You need to investigate some more. Have you tried a shorter timestep? Have you looked at where the thing died? Is it surface? Boundary? Middle or what?
by kate
Fri Aug 16, 2019 3:53 pm
Forum: ROMS Discussion
Topic: Abnormal Cooling at Shallow Water Area
Replies: 7
Views: 404

Re: Abnormal Cooling at Shallow Water Area

That's better, but still, what are your BODYFORCE parameters? I haven't used that option since DAMEE, which was a long time ago. It applies the surface stress not just at the surface, but over some number of points in the vertical. It was for a time when we couldn't resolve the surface boundary laye...
by kate
Fri Aug 16, 2019 5:04 am
Forum: ROMS Discussion
Topic: Abnormal Cooling at Shallow Water Area
Replies: 7
Views: 404

Re: Abnormal Cooling at Shallow Water Area

Code: Select all

#undef  TS_C4VADVECTION
#define BODYFORCE
These and others of your choices put you into a realm where I have no experience at all. Have you done any bathymetry smoothing?
by kate
Mon Aug 12, 2019 6:42 pm
Forum: ROMS Sediment
Topic: Calculating sediment flux across transect
Replies: 4
Views: 556

Re: Calculating sediment flux across transect

Are you aware of how the whole grid looks? See for example the figure here. To get something in the centers, try something like: Huon_sand_01 = 0.5 * (Huon_sand_01[:,:,1:-1,1:] + Huon_sand_01[:,:,1:-1,:-1]) # u ==> rho Hvom_sand_01 = 0.5 * (Hvom_sand_01[:,:,1:,1:-1] + Hvom_sand_01[:,:,:-1,1:-1]) # v...
by kate
Sun Aug 04, 2019 4:23 pm
Forum: ROMS Problems
Topic: Error climatology file: not include initialization time
Replies: 6
Views: 900

Re: Error climatology file: not include initialization time

Are you starting from a restart file? What is the time in that file? I have a Python script for changing the time(s) in a file because sometimes you just need to.
by kate
Sat Aug 03, 2019 3:15 pm
Forum: ROMS Installation
Topic: upwelling: - Configuration error ..... exit_flag: 5
Replies: 3
Views: 228

Re: upwelling: - Configuration error ..... exit_flag: 5

Here is the real error message:
CHECKDEFS - no bottom stress formulation is selected.
The upwelling case should have one selected in the roms_upwelling.in file.
by kate
Fri Aug 02, 2019 3:09 pm
Forum: ROMS Sediment
Topic: ana_sediment.h:27:0: fatal error: tile.h: No such file
Replies: 8
Views: 253

Re: ana_sediment.h:27:0: fatal error: tile.h: No such file

I don't know if you need a wave model, but if you do, you should contact John Warner to get his version of the wave-coupling code. You might well need a wave model in that region to get the fresh water influx to mix down in a physical way. You will need to think about how to get the river inputs int...
by kate
Fri Aug 02, 2019 5:50 am
Forum: ROMS Sediment
Topic: ana_sediment.h:27:0: fatal error: tile.h: No such file
Replies: 8
Views: 253

Re: ana_sediment.h:27:0: fatal error: tile.h: No such file

Have you tried running a really simple case? Turning on sediments does not explain why you are failing to compile ROMS. What exactly are you doing? Operating system? ROMS version? Build script choices?
by kate
Thu Aug 01, 2019 6:33 pm
Forum: ROMS Sediment
Topic: ana_sediment.h:27:0: fatal error: tile.h: No such file
Replies: 8
Views: 253

Re: ana_sediment.h:27:0: fatal error: tile.h: No such file

You say it's running - was it running before you turned on the sediments? What you show is a failure to compile. I have a ROMS/Include/tile.h and so should you. During the build, it will look for include files in ROMS/Include, thanks to: includes := ROMS/Include vpath %.h $(includes) in the makefile...
by kate
Mon Jul 08, 2019 4:56 pm
Forum: ROMS Installation
Topic: Problem with the file makefile
Replies: 11
Views: 815

Re: Problem with the file makefile

There was a recent update from Hernan in which the makefile was changed. It used to make "oceanM" and so forth, now it makes "romsM" and family. The final letter is "S" for serial, "M" for parallel, and "G" for debug mode (serial or parallel).
by kate
Sun Jul 07, 2019 6:57 am
Forum: ROMS Source
Topic: passive tracers - segmentation error ......help? :(
Replies: 6
Views: 354

Re: passive tracers - segmentation error ......help? :(

It is possible for problems to show up in debug mode that are not fatal when optimized. I still like to get to the bottom of all such issues, if I can.
by kate
Fri Jul 05, 2019 9:02 pm
Forum: ROMS Source
Topic: passive tracers - segmentation error ......help? :(
Replies: 6
Views: 354

Re: passive tracers - segmentation error ......help? :(

Did you change anything in your build except USE_DEBUG? I assume you cleaned out the old build first. Anyway, it's a link error, not a compile error. The netCDF library wants to link to the curl library. Sometimes, "nc-config --flibs" will want to bring in the curl library. You can add it explicitly...
by kate
Fri Jul 05, 2019 7:45 pm
Forum: ROMS Source
Topic: passive tracers - segmentation error ......help? :(
Replies: 6
Views: 354

Re: passive tracers - segmentation error ......help? :(

If you recompile with USE_DEBUG=on, you should get filenames and linenumbers instead of those annoying UNKNOWNS: oceanS 000000000059C85A Unknown Unknown Unknown oceanS 000000000059BF55 Unknown Unknown Unknown Without line numbers, we're pretty blind!
by kate
Wed Jul 03, 2019 4:31 am
Forum: ROMS Discussion
Topic: Marchesiello's RSUP3 in ROMS?
Replies: 9
Views: 1833

Re: Marchesiello's RSUP3 in ROMS?

You might try it first in the UPWELLING problem to see if it works when there is no land mask. If so, then try one of the simpler, smaller domains with a land mask. Build your own small tests, with and without land. If it is some trouble with the land mask, go through the equations in the paper and ...
by kate
Tue Jul 02, 2019 7:09 pm
Forum: ROMS Discussion
Topic: Marchesiello's RSUP3 in ROMS?
Replies: 9
Views: 1833

Re: Marchesiello's RSUP3 in ROMS?

Have you tried the split advection scheme on TS only? For your ellipse a, you may have boundary water too close to the land mask. Terms in the OBC schemes can include the first and second points in from the boundary and if the latter is land, it is not well-behaved. Your ellipses b and d have one-gr...
by kate
Tue Jul 02, 2019 6:38 pm
Forum: ROMS Discussion
Topic: SST less than -10 ℃
Replies: 1
Views: 156

Re: SST less than -10 ℃

Have you looked at the boundary file? Is that where you have inflow going on? It does look like a boundary problem to me.
by kate
Tue Jul 02, 2019 2:19 am
Forum: ROMS Discussion
Topic: Marchesiello's RSUP3 in ROMS?
Replies: 9
Views: 1833

Re: Marchesiello's RSUP3 in ROMS?

Have you looked to see where and how it is blowing up? Is it going for three steps no matter what the timestep?
by kate
Mon Jul 01, 2019 5:43 pm
Forum: ROMS Discussion
Topic: Marchesiello's RSUP3 in ROMS?
Replies: 9
Views: 1833

Re: Marchesiello's RSUP3 in ROMS?

The easiest thing to try is a shorter timestep. Have you tried that?
by kate
Sun Jun 30, 2019 1:12 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

I like to use ncview to get a quick and dirty view of what's in a netCDF file. Looking at 'ncdump -h' on a file can also be useful. If you didn't get temp and salt, then something didn't go right in the boundary extraction. If you like the idea of using these Python scripts, perhaps it's time to lea...
by kate
Sun Jun 30, 2019 12:25 am
Forum: ROMS Installation
Topic: Problem with the file makefile
Replies: 11
Views: 815

Re: Problem with the file makefile

Did you create the out directory for it?
by kate
Fri Jun 28, 2019 5:52 pm
Forum: ROMS Discussion
Topic: Alongshore currents with periodic alongshore boundaries
Replies: 9
Views: 735

Re: Alongshore currents with periodic alongshore boundaries

To answer here or there? You don't need to ask things twice on the ROMS forum. With a rigid-lid model, you can impose the longshore transport via the streamfunction boundary conditions. We no longer have a rigid-lid model, though. If you have too much flow over your shallow areas, perhaps you can ma...
by kate
Fri Jun 28, 2019 2:50 pm
Forum: ROMS Installation
Topic: Problem with the file makefile
Replies: 11
Views: 815

Re: Problem with the file makefile

If you have a romsS, it is a serial executable. Run it with:

Code: Select all

romsS < roms_upwelling.in
The way you had it, it was waiting for you to type in the whole of roms_upwelling to standard-in (stdin).
by kate
Fri Jun 28, 2019 2:47 pm
Forum: ROMS Bugs
Topic: I/O syntax error
Replies: 2
Views: 274

Re: I/O syntax error

If you recompile with USE_DEBUG, then rerun this, it should give you file names and line numbers rather than all those "Unknown"s. Note that you don't want to do a long run with USE_DEBUG but it can be so helpful for solving these problems.
by kate
Thu Jun 27, 2019 11:26 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

What you want is to call do_file for each file in the list. Did it print the list of files to operate on? Is it what you expected? Then you can comment out the chunk with processes = 4 to the end. Add a loop going through the list of files, calling do_file(file, src_grd, dst_grd), something like: fo...
by kate
Thu Jun 27, 2019 5:46 pm
Forum: ROMS Problems
Topic: ROMS different src version leading to unalike results
Replies: 7
Views: 660

Re: ROMS different src version leading to unalike results

You can hunt this down by using the equivalent of "git bisection", where you check out the version in the middle and see which camp it falls into. Pick a simulation of only a day or so to compare to. You can iteratively try intermediate versions until you find out which commit changed your results, ...
by kate
Thu Jun 27, 2019 5:41 pm
Forum: ROMS Discussion
Topic: Nudging time scales working on bry or clim
Replies: 7
Views: 847

Re: Nudging time scales working on bry or clim

First, what is the land mask doing right there? You might want to change:

______
.........|_____

to

________________

filling in the leftmost water points with dirt. That's what I would try first. Next, look to see what the velocities are doing in that corner.
by kate
Wed Jun 26, 2019 9:11 pm
Forum: ROMS Installation
Topic: Problem with the file makefile
Replies: 11
Views: 815

Re: Problem with the file makefile

Now you have to tell it where to find the netCDF libraries at link time, both via the makefile and also via LD_LIBRARY_PATH or whatever the equivalent is on your OS (I live in a Linux world now).
by kate
Wed Jun 26, 2019 4:39 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

Maybe this is biting you:

Code: Select all

memorylocked    16384 kbytes
by kate
Wed Jun 26, 2019 12:36 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

You can read up on multiprocessing online. Something wasn't right about your last attempt. I would check your system limits. With a bash shell: (snowdrifts) [kshedstrom@chinook02 Tidal_bay]$ ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file ...
by kate
Tue Jun 25, 2019 11:38 pm
Forum: ROMS Installation
Topic: Problem with the file makefile
Replies: 11
Views: 815

Re: Problem with the file makefile

cp -f /usr/include/netcdf.mod /home/al/Projects/upwelling/Build_romsG cp -f /usr/include/typesizes.mod /home/al/Projects/upwelling/Build_romsG It is looking for the netcdf.mod file which got copied into the Build directory. You know those files got copied, but what compiler was used to make them? I...
by kate
Tue Jun 25, 2019 4:41 pm
Forum: ROMS Discussion
Topic: ROMS 1D for Mac needed
Replies: 2
Views: 247

Re: ROMS 1D for Mac needed

The way to run in 1D is to set up a very small horizontal grid of say 3x3 or 4x4 with doubly periodic boundary conditions. The grid can be analytic and the boundary conditions don't need any inputs. Apply the same surface forcing to all points and you should be good to go. It should run on a Mac, no...
by kate
Mon Jun 24, 2019 6:07 pm
Forum: ROMS Problems
Topic: one question about boundary condition in an idealized test
Replies: 2
Views: 216

Re: one question about boundary condition in an idealized te

Dynamically, the zeta outside is not playing a direct role, though it can be used in Flather type open boundary condition. You don't say what open boundary options you have chosen. In the model zeta is a second-order field in that it is computed from lateral convergences and divergences - the barotr...
by kate
Mon Jun 24, 2019 4:17 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

Can you try on a system with more memory?
by kate
Mon Jun 24, 2019 6:34 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

Does it object to processes = 1 the same way as processes = 4, or was there a different error? What if you don't let it kill the job?
by kate
Mon Jun 24, 2019 5:18 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

Maybe you should try a pool size of 1, not running in parallel. I'm not familiar with that exact display, but the swap seems high, like it doesn't all fit in memory and none of them are making any progress.
by kate
Sun Jun 23, 2019 7:18 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

Each system is different. I run on one with front-end nodes containing 8 cores, while the compute nodes contain 24-28 cores. I run these scripts on the front-end nodes because they have access to the filesystems containing these files, but I only ask for 4 cores in my "pool" so other people can get ...
by kate
Sun Jun 23, 2019 4:53 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

year = int(sys.argv[1]) Did you give it a year as a command-line argument? It is expecting one. There's also a commented out line: #lst_year = sys.argv[1:] that can be enabled, allowing you to give it a list of years. Or you can edit the script to provide the year(s) internally. For the other, I th...
by kate
Sat Jun 22, 2019 3:40 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

I can give you the PALAU1 chunk of gridid.txt, but then it points to a grid file which you don't have either. Why don't you put in a chunk for your grid, since that is what you want anyway? id = PALAU1 name = PALAU1 grdfile = /import/AKWATERS/kshedstrom/gridpak/Palau/grid_Palau_1.nc N = 50 grdtype =...
by kate
Sat Jun 22, 2019 4:03 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

Sometimes Python evolves so that something that used to run no longer runs. Sometimes when that happens I can figure out how to change it and get it pushed to github. You need to update your code through either "git pull" or just editing it in place.
by kate
Sat Jun 22, 2019 3:35 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

My latest version of that troublesome line is: h[j,i] = depth_bnds[int(bottom[j,i])+1] Sometimes it pays to "git pull". Step 5 happens with this script: #!/bin/ksh print -n "Enter year to process: "; read year; print "" leap=`echo $(($year % 4))` if [ $leap == 0 ] ; then nday=366 else nday=365 fi #n...
by kate
Wed Jun 19, 2019 5:10 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

Are you sure you are downloading on the GLBa0.08 HYCOM grid? They have moved that to the "inactive" status. It was on a tripole grid and needed lat,lon to be functions if both i and j. The newer HYCOM products are on a simpler grid, where lat is a function of j only and lon is a function of i only. ...
by kate
Tue Jun 18, 2019 7:13 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

No, I don't think you have a version problem, unless it's a HYCOM version problem.

Code: Select all

lon_t = lon[1:-1,1:-1]
Longitude is often a 1-D array, not a 2-D array. What do you have?
by kate
Tue Jun 18, 2019 5:20 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

Looks like it should be 'depth', not 'z'.
by kate
Mon Jun 17, 2019 6:25 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 31
Views: 1369

Re: Create boundary and initial file from seagrid and GLBa0.

I have successfully made ROMS IC and BC files from HYCOM using the scripts in pyroms/examples/Arctic_HYCOM/. First you run make_remap_weights_file, then make_ic_file/make_bdry_file. A more equatorial example is in Palau_HYCOM. For the vertical, set the number of vertical points in the gridid.txt fil...
by kate
Sat Jun 15, 2019 9:59 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 951

Re: PYROMS error

The only use I know of for lpsolve is to smooth the bathymetry. I usually use pyroms for other tasks, not grid generation. What do you need pyroms to do for you?
by kate
Sat Jun 15, 2019 4:22 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 951

Re: PYROMS error

Spectral has a capital "S". See for example this Stackoverflow thread. I don't know how you ended up with a lower case spectral.

As for the other, my solution is that I don't use lpsolve. I think I once copied the thing to my current directory and that worked.
by kate
Fri Jun 14, 2019 5:44 pm
Forum: ROMS Discussion
Topic: Floats in nested configuration
Replies: 3
Views: 306

Re: Floats in nested configuration

I assume that would work. Why don't you try it and let us know?
by kate
Fri Jun 14, 2019 5:29 pm
Forum: ROMS Installation
Topic: Tutorial: Installing ROMS in Windows XP / Vista (via Cygwin)
Replies: 20
Views: 11764

Re: Tutorial: Installing ROMS in Windows XP / Vista (via Cyg

I have tried to provide all you need to know (and more!) for Unix in the manual.
by kate
Fri Jun 14, 2019 5:26 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 951

Re: PYROMS error

This troublesome bit: -Inf-config not yet implemented for cmake builds/include is coming from: INCDIR = $(shell $(NC_CONFIG) --prefix)/include which as you point out is from nf-config. It is executing "nf-config --prefix" which on my machine gives: chinook04.rcs.alaska.edu 543% nf-config --prefix /h...
by kate
Thu Jun 13, 2019 4:49 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 951

Re: PYROMS error

No, don't go backwards! We always had problems with python finding those libraries, so going backwards is not the answer. Stick with Python 3 and read the README where I tell you what I have to do for python to find the libraries - I just have copies in three different places, with hopes that at lea...
by kate
Thu Jun 13, 2019 4:46 pm
Forum: ROMS Discussion
Topic: Floats in nested configuration
Replies: 3
Views: 306

Re: Floats in nested configuration

No, it has not. I think you'd be better off doing floats offline with dedicated float-tracking software instead. Adding multi-grid features would still be tricky there too.
by kate
Thu Jun 13, 2019 4:35 am
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 951

Re: PYROMS error

Type "git branch" to see which branch you have. The "python3" branch is the current default, so that is probably what you have already.

As for those libraries, you need to make sure your LD_LIBRARY_PATH environment variable includes the directory they live in.
by kate
Wed Jun 12, 2019 6:45 am
Forum: ROMS Discussion
Topic: pan-Arctic simulations
Replies: 7
Views: 1700

Re: pan-Arctic simulations

You want to be working in a polar stereographic projection so that there is no pole problem. The domain is roughly a rectangle over the pole. The curvilinear orthogonal grids are made in a flat geometry, so you need software that can do map projections and inverse map projections to get back to the ...
by kate
Wed Jun 12, 2019 6:19 am
Forum: ROMS Discussion
Topic: pan-Arctic simulations
Replies: 7
Views: 1700

Re: pan-Arctic simulations

What do you want to know? I'm running a pan-Arctic domain now, which is described in the ROMS manual.
by kate
Tue Jun 11, 2019 6:38 pm
Forum: ROMS Discussion
Topic: Time type in nc file
Replies: 5
Views: 363

Re: Time type in nc file

It doesn't matter. Just be consistent across all your inputs.
by kate
Tue Jun 11, 2019 6:35 pm
Forum: ROMS Discussion
Topic: unrealistic discontinuity of surface salinity
Replies: 2
Views: 246

Re: unrealistic discontinuity of surface salinity

I would try LMD_SHAPIRO as a first step.
by kate
Mon Jun 10, 2019 3:34 pm
Forum: ROMS Discussion
Topic: Slow running of nesting simulation
Replies: 5
Views: 348

Re: Slow running of nesting simulation

Hernan once said that he thought the way to do it is fine-to-coarse, with a fine grid the size of your larger domain. However, as you find, one must use coarse-to-fine because that's the matlab script you have. I made all the grids and did the bathymetry the way I wanted to. What I can help you with...
by kate
Sat Jun 08, 2019 5:48 am
Forum: ROMS Bugs
Topic: WC13/R4DVAR Compiling Problem: rp_set_vbc.f90
Replies: 1
Views: 172

Re: WC13/R4DVAR Compiling Problem: rp_set_vbc.f90

You need to fix rp_set_vbc.F, not the .f90 file.
by kate
Fri Jun 07, 2019 9:35 pm
Forum: ROMS Discussion
Topic: Slow running of nesting simulation
Replies: 5
Views: 348

Re: Slow running of nesting simulation

Yes, the online nesting is extremely slow. I have not seen any ROMS development in the myroms code to lead me to expect that this has changed since those old posts. I am instead doing offline nesting because it gives more flexibility in the child grids.
by kate
Fri Jun 07, 2019 9:29 pm
Forum: ROMS Discussion
Topic: bulk flux advice from clivar community
Replies: 3
Views: 851

Re: bulk flux advice from clivar community

The latest ROMS has the WIND_MINUS_CURRENT, which is what I was talking about. Actually, the CLIVAR people now say that one should not use WIND_MINUS_CURRENT with the new JRA55-do forcings because of how they used the satellite-derived winds in the data assimilation. To get realistic variance, I wou...
by kate
Thu Jun 06, 2019 10:36 pm
Forum: ROMS Bugs
Topic: Error when i try to run the upwelling.in
Replies: 2
Views: 201

Re: Error when i try to run the upwelling.in

We need more information. Are you asking ROMS for USE_NETCDF4? When you say you downloaded netcdf, what exactly do you mean by that? You can download the source code and compile it or you can find a way to get it prebuilt for some systems. So what operating system is this anyway? This is a problem w...
by kate
Wed Jun 05, 2019 5:34 pm
Forum: ROMS Problems
Topic: Segmentation fault after 10 model years of running
Replies: 4
Views: 391

Re: Segmentation fault after 10 model years of running

I don't know how to fix this. I have always used restarts because I operate on a supercomputer with queue length restrictions. You might want to be using PERFECT_RESTART.
by kate
Tue Jun 04, 2019 10:00 pm
Forum: ROMS Problems
Topic: Segmentation fault after 10 model years of running
Replies: 4
Views: 391

Re: Segmentation fault after 10 model years of running

It's possible that there's a memory leak, so that the program grows over time until it hits some limit. I just ran something in debug mode and got a *ton* of these messages: ==6434==ERROR: LeakSanitizer: detected memory leaks Direct leak of 34816 byte(s) in 8 object(s) allocated from: #0 0x7f1d00486...
by kate
Tue Jun 04, 2019 6:01 pm
Forum: ROMS Tools and Techniques
Topic: History/Averages file output for a single sigma layer
Replies: 2
Views: 194

Re: History/Averages file output for a single sigma layer

You should check the Qout values in roms.in and turn on the Quick output feature. It already has the Usur, Vsur, and surT for surface fields.
by kate
Tue Jun 04, 2019 5:41 am
Forum: ROMS Problems
Topic: NESTING RUNTIME ERROR code 59
Replies: 5
Views: 355

Re: NESTING RUNTIME ERROR code 59

The oceanG with USE_DEBUG can certainly be the one using MPI. You can't tell from the name of the executable, just from how you built it. It should be possible to run it in an MPI environment.
by kate
Mon Jun 03, 2019 10:45 pm
Forum: ROMS Problems
Topic: NESTING RUNTIME ERROR code 59
Replies: 5
Views: 355

Re: NESTING RUNTIME ERROR code 59

The generic advice to figure out what's going on is: "recompile with USE_DEBUG, rerun to get the line numbers, look at the lines referred to in the output". This is the preferred method. The other thing people do is post their roms.in file to this list and hope that someone will look at it and tell ...
by kate
Mon Jun 03, 2019 10:41 pm
Forum: ROMS Problems
Topic: How to adjust roms temperature with observation (Bias)
Replies: 2
Views: 252

Re: How to adjust roms temperature with observation (Bias)

You've told us about your vertical and horizontal diffusion, but what is the vertical boundary condition? In other words, the surface heat flux? Can you output it and look at it? Is it computed internally (bulk fluxes) or provided externally?
by kate
Wed May 29, 2019 3:27 pm
Forum: ROMS Problems
Topic: Noisy SST
Replies: 8
Views: 440

Re: Noisy SST

As for MIX_S_TS, it's a really bad idea over a sloping bottom and can lead to unphysical cross-isopycnal mixing. I hear you! But there was no way to solve the issue of punctual alternating high/low temperatures at the slope when mixing along z-planes which would even cause the model to blow up. The...
by kate
Tue May 28, 2019 4:10 pm
Forum: ROMS Discussion
Topic: Extracting temperature
Replies: 9
Views: 476

Re: Extracting temperature

The ROMS default is to write out the grid file into every output netcdf file. I make many, many output netcdf files and have told ROMS not to put the grid into any of them. I know the grid because it is one of the ROMS input files. If you are using someone else's model output, you have to ask them f...
by kate
Tue May 28, 2019 4:07 pm
Forum: ROMS Problems
Topic: Noisy SST
Replies: 8
Views: 440

Re: Noisy SST

The equivalent horizontal smoothing for LMD is LMD_SHAPIRO, to horizontally filter the mixed layer depth. I've heard from some other colleagues that they too need to smooth the mixed layer depth to avoid that sort of noise. As for MIX_S_TS, it's a really bad idea over a sloping bottom and can lead t...
by kate
Tue May 28, 2019 4:03 pm
Forum: ROMS Problems
Topic: How to enhance vertical mixing in roms MY2.5
Replies: 3
Views: 316

Re: How to enhance vertical mixing in roms MY2.5

I've heard it's a difficult problem. We also have too little vertical mixing from all the fresh water input into the Gulf of Alaska. One idea is that we need to couple to a wave model and enable the wind-wave surface mixing in COAWST. Easier said than done; we haven't tried it yet.
by kate
Tue May 28, 2019 4:00 pm
Forum: ROMS Problems
Topic: ROMS restart time steps
Replies: 4
Views: 416

Re: ROMS restart time steps

That's weird, that's not what I get. Is there something about your forcing that ends before the end of the year? Do you see the NaNs in the ROMS output for the last few steps?
by kate
Tue May 28, 2019 3:56 pm
Forum: ROMS Discussion
Topic: Extracting temperature
Replies: 9
Views: 476

Re: Extracting temperature

I think you are saying that the index is xi=91, eta=28. Yes, you can extract the temperature at that location to get a vertical column of numbers for each time.
by kate
Mon May 27, 2019 4:13 am
Forum: ROMS Information
Topic: Error compiling COAWST
Replies: 4
Views: 320

Re: Error compiling COAWST

You need to change yours to look like mine for it to compile.
by kate
Sun May 26, 2019 4:52 am
Forum: ROMS Discussion
Topic: ad passive tracer
Replies: 10
Views: 689

Re: ad passive tracer

Are you by chance asking for Aout(idTTav)? I have never done so and can't guarantee that it would work.
by kate
Sat May 25, 2019 7:09 am
Forum: ROMS Discussion
Topic: Extracting temperature
Replies: 9
Views: 476

Re: Extracting temperature

There should be a grid file somewhere with lat and lon as a function of xi and eta. The algorithm for finding the xi, eta (or i,j) of a given lat, lon is implemented inside ROMS in the routine hindices inside interpolate.F.
by kate
Sat May 25, 2019 7:03 am
Forum: ROMS Discussion
Topic: ad passive tracer
Replies: 10
Views: 689

Re: ad passive tracer

Which mod_ncparam.f90 error are you getting and what is on the line number in question? We want you to look at the file. Maybe you should also explain exactly what it is you want to do with your passive tracer.
by kate
Fri May 24, 2019 4:17 pm
Forum: ROMS Discussion
Topic: Extracting temperature
Replies: 9
Views: 476

Re: Extracting temperature

If you only have a few such location from which you want to extract fields, the easiest thing is to ask ROMS for a STATIONS file. You provide the lat,lon in the stations input file. If you don't have a chance to rerun the model, you will have to build tools for extracting from the ROMS output, using...
by kate
Fri May 24, 2019 4:13 pm
Forum: ROMS Information
Topic: Error compiling COAWST
Replies: 4
Views: 320

Re: Error compiling COAWST

Could you look at your diag.F to see how Nreduce is set and used? My code has: #ifdef DISTRIBUTE # ifdef SOLVE3D # ifdef BIOLOGY integer :: Nreduce # else integer, parameter :: Nreduce = 6 # endif integer, parameter :: Ncourant = 7 # else integer, parameter :: Nreduce = 4 integer, parameter :: Ncour...
by kate
Thu May 23, 2019 6:40 pm
Forum: ROMS Problems
Topic: Blowing up problem
Replies: 2
Views: 279

Re: Blowing up problem

Minimum Z-grid spacing, DZmin = -2.17046894E-01 m This would worry me. It means you need to be using WET_DRY or make the minimum depth deeper. 1)shorten my DT from 10 seconds to 1 second. The standard output is shown below. The maximum barotropic Courant Number is smaller than 1. Minimum barotropic...
by kate
Thu May 23, 2019 4:52 pm
Forum: ROMS Discussion
Topic: ad passive tracer
Replies: 10
Views: 689

Re: ad passive tracer

You've got one clue here:

Code: Select all

At line 2008 of file mod_ncparam.f90
Can you tell us what is at line 2008 of your mod_ncparam.f90 file?

What is NRREC in your roms.in file? The restart file is not necessarily the same as a file needed for initialization, especially when you go changing settings.
by kate
Thu May 23, 2019 4:03 am
Forum: ROMS Discussion
Topic: low velocity in deep water
Replies: 1
Views: 209

Re: low velocity in deep water

We need a good deal more information about what you are doing! By the way, you should be looking at the T and S water mass properties as well. There's a known problem on the basin scale with at least most advection schemes being too dissipative, especially over multi-decadal timescales.
by kate
Wed May 22, 2019 9:09 pm
Forum: ROMS Discussion
Topic: Nudging time scales working on bry or clim
Replies: 7
Views: 847

Re: Nudging time scales working on bry or clim

Your values look like you should use 'second-1' as the units. 'day-1' is also a valid option. See get_nudgcoef.F to check that. You say you want 1 day at the edge and one year in the middle. I think if it rather as strong (1 dayish) at the edge to infinite time (zero coefficient) over some width, sa...
by kate
Mon May 20, 2019 3:55 pm
Forum: ROMS Discussion
Topic: Lateral nudging and nudging to climatology
Replies: 2
Views: 341

Re: Lateral nudging and nudging to climatology

This was discussed just days ago right here.
by kate
Fri May 17, 2019 4:53 pm
Forum: ROMS Discussion
Topic: Nudging time scales working on bry or clim
Replies: 7
Views: 847

Re: Nudging time scales working on bry or clim

Have you tried it without the climatology nudging? I would do that, then evaluate whether or not you need help along the boundaries. You can make your own monthly climatology from the daily HYCOM fields - it would at least be consistent with your OBC values then. Look at your code to see what nudgin...
by kate
Fri May 17, 2019 4:25 pm
Forum: ROMS Problems
Topic: Blowing-up model - tide current+initial state(ocean current)
Replies: 8
Views: 568

Re: Blowing-up model - tide current+initial state(ocean curr

You don't describe the problem you are having. What happens in your run? We don't provide a service of downloading all your files and rerunning your case (at least I don't).
by kate
Fri May 17, 2019 4:28 am
Forum: ROMS Problems
Topic: Performance issues using floats
Replies: 4
Views: 284

Re: Performance issues using floats

The floats implementation works for a modest number of floats, but doesn't scale well. Yes, the floats incur a lot of communications and processing as they figure out which tile each float is on every timestep.
by kate
Thu May 16, 2019 3:24 pm
Forum: ROMS Discussion
Topic: Lagrangian floats
Replies: 1
Views: 242

Re: Lagrangian floats

rho is in situ density which is what we need for horizontal pressure gradients.

From a floats.in file:
T Float trajectory type (1: Lagrangian, 2: isobaric, 3: Geopotential)
The Lagrangian ones move with the local velocity. The others behave differently.
by kate
Tue May 14, 2019 11:23 pm
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 6
Views: 976

Re: compile ROMS error

From the command line, see what "which gfortran" or "which mpif90" give you. That's what the ROMS build system will execute to find the correct path. If it doesn't come up already, you need to change your user path to point there, perhaps in your ~/.bashrc file or similar. On a supercomputer, it mig...
by kate
Mon May 13, 2019 2:52 pm
Forum: ROMS Problems
Topic: Segmentation fault with floats
Replies: 6
Views: 489

Re: Segmentation fault with floats

I suspect that the problem is not the number of floats but something else. The way to debug these things is to save a restart record at the time of the first float release, or just before. Then do your tests in a restart run so that it blows up right away and you're not running forever in debug mode.
by kate
Wed May 08, 2019 3:53 pm
Forum: ROMS Problems
Topic: Segmentation fault with floats
Replies: 6
Views: 489

Re: Segmentation fault with floats

The first step is to recompile in USE_DEBUG mode. The resulting output should look similar but include line numbers for the .f90 files. You then need to look at the appropriate .f90 file and see what is at that line. Next would be to perhaps add print statements around there to see what is in the re...
by kate
Wed May 08, 2019 3:48 pm
Forum: ROMS Discussion
Topic: Climatology as open boundary
Replies: 6
Views: 1556

Re: Climatology as open boundary

You can look through the ROMS output to stdout to watch it reading files. Yes, it reads files once per record, be that daily or monthly. It stores two records in memory and linearly interpolates between them every timestep. The reading happens in get_data.F and the interpolation calls are made from ...
by kate
Mon May 06, 2019 5:57 pm
Forum: ROMS Discussion
Topic: Attempt to fetch from allocatable variable TNUDG_SSS
Replies: 1
Views: 277

Re: Attempt to fetch from allocatable variable TNUDG_SSS

Since this is CoSINE, I assume it is my branch. It sounds like you've hit a bug in the implementation of TNUDG_SSS. It looks like something that fell through the cracks in one of Hernan's big updates. In mod_scalars.F after these lines: IF (.not.allocated(Tnudg)) THEN allocate ( Tnudg(MT,Ngrids) ) E...
by kate
Thu May 02, 2019 3:42 pm
Forum: ROMS Discussion
Topic: cppdefs for BULK_FLUX
Replies: 11
Views: 1038

Re: cppdefs for BULK_FLUX

First, simulating the climatology condition for my study area until model is stable. Forcing fields in this step are come from climatology datasets. Second, simulating the history period forced by CMIP5 history output data. This step use the above last stable output as initial input. Third, simulat...
by kate
Thu May 02, 2019 5:20 am
Forum: ROMS Discussion
Topic: cppdefs for BULK_FLUX
Replies: 11
Views: 1038

Re: cppdefs for BULK_FLUX

I was recently asked to look into the future projection business. One can download CMIP5 results from any number of different models. For CMIP6, some of the early pre-industrial runs are out there now, but only the French have results for a future run so far (searching for three-hourly). The web por...
by kate
Wed May 01, 2019 3:31 pm
Forum: ROMS Discussion
Topic: cppdefs for BULK_FLUX
Replies: 11
Views: 1038

Re: cppdefs for BULK_FLUX

Turning on BULK_FLUX is one step. What are you using to provide the atmospheric fields? How frequently? You have:

Code: Select all

DIURNAL_SRFLUX Modulate shortwave radiation by the local diurnal cycle.
which I would not use if the atmospheric fields are say three-hourly.
by kate
Mon Apr 29, 2019 3:52 pm
Forum: ROMS Usage
Topic: Input files of Downwelling/Upwelling test case
Replies: 5
Views: 2096

Re: Input files of Downwelling/Upwelling test case

If you look through the roms.in file (and any roms documentation you might find) you will see that you provide the paths to the input files.
by kate
Mon Apr 29, 2019 3:49 pm
Forum: ROMS Bugs
Topic: ROMS hangs up reading input file
Replies: 2
Views: 411

Re: ROMS hangs up reading input file

Code: Select all

gdb ./romsG ecna124k.in
If the model was not compiled for MPI, you should do this instead:

Code: Select all

gdb ./romsG < ecna124k.in
and the model will read from the standard input.
by kate
Sun Apr 28, 2019 4:30 pm
Forum: ROMS Installation
Topic: first time running upwelling test case
Replies: 3
Views: 475

Re: first time running upwelling test case

It failed in the call to DEF_HIS. Are you trying to write to somewhere where you don't have permissions? Do you have a local computer support staff to ask for help? #2 0x18f9860 in def_his_ /home/ghasedak/Projects/upwelling/Build_romsG/def_his.f90:69 Does this line have "CALL netcdf_create"? Has you...
by kate
Sun Apr 28, 2019 1:38 am
Forum: ROMS Installation
Topic: first time running upwelling test case
Replies: 3
Views: 475

Re: first time running upwelling test case

ROMS told you the problem: In distributed-memory applications, the input script file is processed in parallel. The Unix routine GETARG is used to get script file name. For example, in MPI applications make sure that command line is something like: mpirun -np 4 romsM roms.in and not mpirun -np 4 roms...
by kate
Fri Apr 19, 2019 9:41 pm
Forum: ROMS Installation
Topic: problem in test case of upwelling(mod_netcdf.f90)
Replies: 14
Views: 4467

Re: problem in test case of upwelling(mod_netcdf.f90)

-lm is a math library, not matlab.

Maybe try putting your junk directory at the front of LD_LIBRARY_PATH instead.
by kate
Fri Apr 19, 2019 8:29 pm
Forum: ROMS Installation
Topic: problem in test case of upwelling(mod_netcdf.f90)
Replies: 14
Views: 4467

Re: problem in test case of upwelling(mod_netcdf.f90)

My hdf libraries are a few years old but are version 10.0.x, but that probably has nothing to do with this at all. Do you get a linking error from NetCDF rather than HDF?
by kate
Fri Apr 12, 2019 5:55 pm
Forum: ROMS Installation
Topic: compiling upwelling
Replies: 10
Views: 826

Re: compiling upwelling

Oh that old Windows problem. Exactly.
by kate
Fri Apr 12, 2019 5:52 pm
Forum: ROMS Tools and Techniques
Topic: sponge layer and diffusive advection schemes
Replies: 1
Views: 324

Re: sponge layer and diffusive advection schemes

I don't use the ROMS sponge feature. When the MOM6 people talk about sponges, they instead mean a nudging to a climatology around the edges of the domain. I do this kind of sponging instead.
by kate
Fri Apr 12, 2019 5:50 pm
Forum: ROMS Tools and Techniques
Topic: How to edit a mask with pyroms
Replies: 2
Views: 458

Re: How to edit a mask with pyroms

Yes, there's an example in examples/stuff/editmask.py The idea is to cut and paste from that file into an instance of "ipython --pylab". Either of the routines edit_mask_mesh or edit_mask_mesh_ij should work, but the latter is faster. Sometimes the latter doesn't show all of the coastline - your mil...
by kate
Thu Apr 11, 2019 9:04 pm
Forum: ROMS Discussion
Topic: How does ROMS treat daily river_transport in the model?
Replies: 2
Views: 419

Re: How does ROMS treat daily river_transport in the model?

The river discharge does not have to be daily. If you want to provide hourly, go for it. ROMS will linearly interpolate between available records to set the discharge of the moment. LtracerSrc == F T Setting the temperature to False here could easily lead to an instability. Better to take a wild gue...
by kate
Wed Apr 10, 2019 8:12 pm
Forum: ROMS Installation
Topic: compiling upwelling
Replies: 10
Views: 826

Re: compiling upwelling

It looks like the Perl script sfmakedepend is failing. First you need to check that ./ROMS/Bin/sfmakedepend exists, then look in it to see what the first line is. I expect that you have the sfmakedepend file, but my first line is: #!/usr/bin/env perl so the problem could be either /usr/bin/env or pe...
by kate
Tue Apr 09, 2019 6:24 pm
Forum: ROMS Ice
Topic: Issue connected to Tnudg_SSS
Replies: 3
Views: 723

Re: Issue connected to Tnudg_SSS

If you are using my code, you really, really need to start from one of my ocean.in files. In particular, you need not only NFFILES for the number of forcing files, but also NBCFILES and NCLMFILES for the number of boundary and climatology files as well. Maybe even NSSFFILES for the rivers if the cod...
by kate
Fri Mar 29, 2019 5:42 pm
Forum: Job Opportunities
Topic: Basin test case
Replies: 1
Views: 487

Re: Basin test case

When I run MPI jobs, I don't typically invoke ./roms, but rather mpirun:

Code: Select all

mpirun -np $SLURM_NTASKS -machinefile ./nodes --mca mpi_paffinity_alone 1 ./oceanM ocean_arctic4.in
Does your supercomputer center have any experts who can tell you what's right on your system?
by kate
Thu Mar 28, 2019 6:48 pm
Forum: ROMS Ice
Topic: coupled ice options
Replies: 9
Views: 6893

Re: coupled ice options

Hernan is working on the coupling to CICE and other models via NUOPC caps. You'd have to ask him where that stands.

The Norwegians are running a ROMS-CICE coupled system (via MCT) which they have put out on github, called metroms.
by kate
Wed Mar 27, 2019 1:17 am
Forum: ROMS Discussion
Topic: Start model in a specific month
Replies: 1
Views: 311

Re: Start model in a specific month

It's all about having a consistent time. How are you setting the time now? The time variables are TIME_REF and DSTART. You can have a TIME_REF in October or you can have it in January, but with DSTART however many days later to be October. Then ending in April is a question of how many timesteps to ...
by kate
Mon Mar 18, 2019 7:29 pm
Forum: ROMS Problems
Topic: How to tell ROMS to exit due to problematic numbers?
Replies: 3
Views: 832

Re: How to tell ROMS to exit due to problematic numbers?

Oh, boy. I fixed my codes, but while it was after Al's fork, it was long enough ago that I don't remember exactly what it took to get that working. Not only do you have to change the error code, you have to check for it (master process) and share it with the other processes. Then *everyone* has to d...
by kate
Fri Mar 15, 2019 4:36 am
Forum: ROMS Discussion
Topic: A confusion in the run
Replies: 6
Views: 796

Re: A confusion in the run

This is why people invest in learning debuggers such as totalview, ddt, gdb. It's a tough road, but sometimes it's the only way to figure out what's really going on.
by kate
Fri Mar 15, 2019 4:33 am
Forum: ROMS Installation
Topic: compilation error
Replies: 1
Views: 300

Re: compilation error

Which test case is this? Obviously something is being set inconsistently. Have you run one of the standard cases?
by kate
Mon Mar 11, 2019 4:31 am
Forum: ROMS Problems
Topic: Shortwave radiation and net surface heat flux inconsistency
Replies: 6
Views: 1010

Re: Shortwave radiation and net surface heat flux inconsiste

Hernan rewrote the caldate routine at some point. All instances of calling it with r_date come from my moldy code (grep -r r_date ROMS). The new style should look like: ROMS/Functionals/ana_specir.h: USE dateclock_mod, ONLY : caldate ROMS/Functionals/ana_specir.h: CALL caldate (tdays(ng), yd_r8=yday...
by kate
Fri Mar 08, 2019 11:25 pm
Forum: ROMS Discussion
Topic: srflx in bulk_flux.F
Replies: 3
Views: 687

Re: srflx in bulk_flux.F

I checked ccsm_flux.F in your latest code and it seems that issues (2) and (3) still apply. (2) is the primary concern: srflx is apparently not corrected for ice/snow albedo (variable albedo_ice). The radiative heating of the ice (qswi) is corrected for albedo_ice, and therefore so are qi_o_n and S...
by kate
Fri Mar 08, 2019 11:11 pm
Forum: ROMS Problems
Topic: Shortwave radiation and net surface heat flux inconsistency
Replies: 6
Views: 1010

Re: Shortwave radiation and net surface heat flux inconsiste

The code I was first given had the test on units for humidity cited above. A colleague of mine didn't like how that test is done and wanted to use only kg/kg as the specific humidity units. The forcing files we've been using for the past decade + have all been specific humidity in kg/kg, so nothing ...
by kate
Mon Mar 04, 2019 9:58 pm
Forum: ROMS Discussion
Topic: A confusion in the run
Replies: 6
Views: 796

Re: A confusion in the run

What we need to see is the ncdump on your Tair file. Are these monthly means you are cycling through? Do you have the cycle_length attribute set?
by kate
Thu Jan 31, 2019 4:25 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 3434

Re: forrtl: severe (151): allocatable array is already alloc

the model runs approx 2 minutes until I get this error: *** glibc detected *** /mnt/lustre01/scratch/b/b380636/Arctic20km/obcatmforceriversinisedbulk/./romsG: corrupted double-linked list: 0x0000000003e5a610 *** ... and further down: /mnt/lustre01/scratch/b/b380636/Arctic20km/obcatmforceriversinise...
by kate
Mon Jan 28, 2019 5:49 am
Forum: ROMS Installation
Topic: Test Cases Error
Replies: 1
Views: 415

Re: Test Cases Error

This is covered in the ROMS FAQ.
by kate
Sat Jan 26, 2019 5:43 pm
Forum: ROMS Problems
Topic: oceanG not created
Replies: 2
Views: 386

Re: oceanG not created

You've gotten a warning, but you didn't show us any error that could explain it. Is there more output that would help us?
by kate
Mon Jan 21, 2019 3:05 am
Forum: ROMS Discussion
Topic: Weights in VSHAPE and layers thickness?
Replies: 6
Views: 1873

Re: Weights in VSHAPE and layers thickness?

It has been many a year since I've heard a recommendation of VSTRETCHING=VTRANSFORM=1.

Parker, if you want to talk in person, I'm just down the street at U.W.M.C.
by kate
Sat Jan 05, 2019 5:56 pm
Forum: ROMS Problems
Topic: INQUIRE - unable to find requested variable: tide_period
Replies: 2
Views: 495

Re: INQUIRE - unable to find requested variable: tide_pe

I would be very careful about the formatting of the list of forcing files. No tabs, no trailing comments. ROMS will skip a line starting with "!", but not skip the stuff following a mid-line "!". Just put the comments on their own lines before the rest.
by kate
Sat Dec 22, 2018 6:23 pm
Forum: ROMS Discussion
Topic: srflx in bulk_flux.F
Replies: 3
Views: 687

Re: srflx in bulk_flux.F

A few years ago I did a big clean-up of the thermal ice code. Since I don't use bulk_flux.F (using ccsm_flux.F instead), it is possible that I missed a few things. I see that SRad is in bulk_flux.F and not the other. ICE_BIO is a part of a biology package for which I have nowhere near the latest cod...
by kate
Tue Dec 18, 2018 5:02 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS : lpsolve55.so not found. & libgu.so not found
Replies: 1
Views: 504

Re: PYROMS : lpsolve55.so not found. & libgu.so not found

I don't know how to fix lpsolve, but the README has this advice for libgu: You might also need libgu.so to be in your LD_LIBRARY_PATH. I'm getting inconsistent results with where the .so files need to be. Best results for me are if I go to the site-packages directory where pyroms got installed and c...
by kate
Tue Dec 11, 2018 6:41 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 951

Re: PYROMS error

The "master" branch of pyroms should work with Python 2.7. The code diffs for that line are: - print " Flinders Peak = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec ), + print(" Flinders Peak = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec ), end=' ') I have the new branch working in Python version 3.6.2.
by kate
Tue Nov 06, 2018 7:38 pm
Forum: ROMS Problems
Topic: How to tell ROMS to exit due to problematic numbers?
Replies: 3
Views: 832

Re: How to tell ROMS to exit due to problematic numbers?

What code are you starting with, exactly? Over the years I have added some of these checks to diag.F, etc. Still need more...
by kate
Thu Oct 11, 2018 2:42 pm
Forum: ROMS Discussion
Topic: Regarding Sea surface height in ROMS
Replies: 1
Views: 552

Re: Regarding Sea surface height in ROMS

The equations of motion are in the manual. Changes in zeta are due to barotropic divergences and convergences.
by kate
Wed Oct 10, 2018 8:01 pm
Forum: ROMS Ice
Topic: Sea Ice - Air drag coefficient
Replies: 10
Views: 1560

Re: Sea Ice - Air drag coefficient

1. One thing you need to learn in this business is to simply try things yourself and see what happens. 2. The sea ice experts in the field are over in the CICE community where you can follow them on github and ask questions on their issue tracker. 3. I used to think I'd be running ROMS-CICE by now, ...
by kate
Wed Oct 10, 2018 1:28 pm
Forum: ROMS Ice
Topic: Sea Ice - Air drag coefficient
Replies: 10
Views: 1560

Re: Sea Ice - Air drag coefficient

Yes, you may make any change you like to your own copy of the code. You can check the ROMS License file to be sure. Github allows for "pull requests" in which you ask me to accept your changes into my code. You'd have to explain yourself and convince me that it doesn't break anything for me to accep...
by kate
Wed Oct 10, 2018 2:45 am
Forum: ROMS Ice
Topic: Sea Ice - Air drag coefficient
Replies: 10
Views: 1560

Re: Sea Ice - Air drag coefficient

The surface stress on the water does not directly depend on ice thickness. The water feels the wind stress where there's no ice and ice stress where there is ice. Note that Bill Hibler swears that we should be "embedding" the ice into the water instead of "levitating" the ice over the water. I'm afr...
by kate
Mon Oct 08, 2018 4:37 pm
Forum: ROMS Installation
Topic: ROMS/TOMS Plotting
Replies: 1
Views: 517

Re: ROMS/TOMS Plotting

/opt/g95soft/serial/netcdf4/bin/nc-config: Command not found
You should have nc-config and/or nf-config in your path. Do you have them and what is the path to them?
cd Build_plt; -c -fno-second_underscore -g -fbounds-check curlz.f90
I wrote it up here.
by kate
Mon Oct 08, 2018 4:11 pm
Forum: ROMS Discussion
Topic: blow-up when lateral gradient increases
Replies: 2
Views: 490

Re: blow-up when lateral gradient increases

Maybe you need a shorter timestep when the winds ramp up. What is the nature of your blow-up?
by kate
Mon Oct 08, 2018 3:34 pm
Forum: ROMS Problems
Topic: Error reading wetdry mask at psi points
Replies: 8
Views: 971

Re: Error reading wetdry mask at psi points

So what is on line 207 of def_his.f90?
by kate
Mon Oct 08, 2018 3:27 pm
Forum: ROMS Ice
Topic: Sea Ice - Air drag coefficient
Replies: 10
Views: 1560

Re: Sea Ice - Air drag coefficient

OK, you're right, there's a big if/then test. If you want the "else" code with ice_mk, why not just copy it up to the "if" part?

I honestly don't remember where any of that came from - it long predates my use of git and the "git blame" feature.
by kate
Sat Oct 06, 2018 6:45 pm
Forum: ROMS Problems
Topic: Error reading wetdry mask at psi points
Replies: 8
Views: 971

Re: Error reading wetdry mask at psi points

Oh, it's probably when the model reads an old history file before adding to it. Probably best to tell ROMS that NRREC = 0 as a fresh start on a run. You might have to extract the one record from the restart file and point to that as your initial file. I'm afraid I was trying something with the wetti...
by kate
Sat Oct 06, 2018 2:29 pm
Forum: ROMS Ice
Topic: Sea Ice - Air drag coefficient
Replies: 10
Views: 1560

Re: Sea Ice - Air drag coefficient

Why do you say that formula is not being used? It looks an awful lot like this code from ice_vbc.F: tauaiu(i,j) = aix*rho_air(ng)* & & (0.5_r8*cdai(ng)*(1.0_r8-COS(2.0_r8*pi*MIN( & & (hix/(aix+0.02_r8)+0.1_r8),0.5_r8)))) & & *spd*windu(i,j)/rhoice(ng) If you don't like the ice_mk code, your best bet...
by kate
Sat Oct 06, 2018 2:11 pm
Forum: ROMS Problems
Topic: Error reading wetdry mask at psi points
Replies: 8
Views: 971

Re: Error reading wetdry mask at psi points

My code is the same as Hernan's for get_wetdry.F.

Code: Select all

chinook03.rcs.alaska.edu 209% git diff trunk/roms-trunk */*/get_wetdry.F
chinook03.rcs.alaska.edu 210% 
My history of that file starts in 2014 and all versions read the psi mask (Pwet).
by kate
Thu Oct 04, 2018 8:47 pm
Forum: ROMS Usage
Topic: What would happen if LMD_BKPP is undefined in LMD scheme?
Replies: 5
Views: 865

Re: What would happen if LMD_BKPP is undefined in LMD scheme

The original KPP has only a surface boundary layer. Scott Durski took the surface BBL and flipped it to add a bottom BBL. Without the bottom one, it is more like pure Large et al.
by kate
Mon Oct 01, 2018 5:27 pm
Forum: ROMS Installation
Topic: ROMS/TOMS Plotting
Replies: 2
Views: 639

Re: ROMS/TOMS Plotting

No, no, better to edit the makefile to match that of ROMS. Specifically, these lines:

Code: Select all

ifneq (3.80,$(firstword $(sort $(MAKE_VERSION) 3.80)))
 $(error This makefile requires GNU make version 3.80 or higher. \
                Your current version is: $(MAKE_VERSION))
endif
by kate
Fri Sep 21, 2018 4:11 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 1608

Re: severe (174): SIGSEGV, segmentation fault occurred. libp

I have a similar problem and am running with gfortran for one domain and with an old code for the other domain. Sorry I don’t have a third fix.
by kate
Thu Sep 06, 2018 6:50 pm
Forum: ROMS Problems
Topic: ECMWF REGRID-input gridded data does not contain model grid
Replies: 3
Views: 1497

Re: ECMWF REGRID-input gridded data does not contain model g

It looks like your model goes to 10.3 degrees south while you only gave it forcing down to 10 degrees south. Try giving it down to 11 south.
by kate
Wed Sep 05, 2018 4:23 pm
Forum: ROMS Bugs
Topic: MPI Tiling - Dumb Question
Replies: 5
Views: 937

Re: MPI Tiling - Dumb Question

Do your nodes indeed have 16 cores or 32 cores? Your admins might be trying to spawn 32 tasks on 16 nodes which can sometimes give good performance (I've heard), but when ROMS checks the numbers, it can't figure out what to do.
by kate
Tue Sep 04, 2018 10:28 pm
Forum: ROMS Discussion
Topic: Cannot find "coordinates" attribute for variable: Uwind
Replies: 15
Views: 1776

Re: Cannot find "coordinates" attribute for variable: Uwind

The files in this case are climatology, boundary and initial files from SODA, converted to ROMS input by Python scripts. That number is time in days, rounded to half a day from the original SODA time. Change it to what makes sense in your case.
by kate
Tue Sep 04, 2018 7:48 pm
Forum: ROMS Discussion
Topic: ROMS blows up "DIAG speed trouble"
Replies: 4
Views: 920

Re: ROMS blows up "DIAG speed trouble"

If you have a closed boundary, it should be closed to all variables. If you have an open boundary and a source of boundary values, I would use them for all variables. But really, look at your boundaries - do you think you have a problem there?
by kate
Tue Sep 04, 2018 7:41 pm
Forum: ROMS Discussion
Topic: Cannot find "coordinates" attribute for variable: Uwind
Replies: 15
Views: 1776

Re: Cannot find "coordinates" attribute for variable: Uwind

I have been known to lie and change the first time in an input file to match my initialization time. Here is the script: import numpy as np import netCDF4 import sys ncfile = sys.argv[1] nc = netCDF4.Dataset(ncfile, 'a', format='NETCDF3_64BIT') time = nc.variables['ocean_time'][0] time = 29226.5 nc....
by kate
Sat Sep 01, 2018 8:18 pm
Forum: ROMS Usage
Topic: New to ROMS
Replies: 3
Views: 836

Re: New to ROMS

Do you know about the roms manual?
by kate
Fri Aug 31, 2018 5:56 pm
Forum: ROMS Discussion
Topic: Cannot find "coordinates" attribute for variable: Uwind
Replies: 15
Views: 1776

Re: Cannot find "coordinates" attribute for variable: Uwind

The problem is that ROMS doesn't know the units "hours" at this time. It knows days and seconds. There is code in get_cycle.F to read the time units, with a default of days. You can add a new case for hours, setting Tscale to 1/24.
by kate
Fri Aug 31, 2018 1:13 am
Forum: ROMS Discussion
Topic: Cannot find "coordinates" attribute for variable: Uwind
Replies: 15
Views: 1776

Re: Cannot find "coordinates" attribute for variable: Uwind

Did you check the times in all your files? Are you sure you have all twelve months there? What are the time units in those files?
by kate
Thu Aug 30, 2018 3:28 pm
Forum: ROMS Information
Topic: Error while running biotoy test case
Replies: 2
Views: 563

Re: Error while running biotoy test case

It told you you have a calendar inconsistency between the initial time and the Tair files. You can use DSTART to change the ROMS time to match the Tair time, but all other files with times have to be consistent too.
by kate
Wed Aug 29, 2018 8:08 pm
Forum: ROMS Discussion
Topic: ROMS blows up "DIAG speed trouble"
Replies: 4
Views: 920

Re: ROMS blows up "DIAG speed trouble"

Blowing up on the first step with this:
Maximum barotropic Courant Number = 1.13952908E+00
points to needing a shorter barotropic timestep.
by kate
Sun Aug 26, 2018 4:08 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 3434

Re: forrtl: severe (151): allocatable array is already alloc

The user has an Arctic domain. I added a GLOBAL_PERIODIC flag to ROMS to handle just this case, interpolating across the dateline. I've attached the patch file.
by kate
Mon Aug 20, 2018 3:30 pm
Forum: ROMS Discussion
Topic: How to setup for rotating frame
Replies: 10
Views: 1465

Re: How to setup for rotating frame

Did you write your own plotting code for these? A positive u will be counterclockwise all the way around, but pointing "down" on the left, "up" on the right. Does your plotting code draw vectors that way?
by kate
Mon Aug 20, 2018 5:21 am
Forum: ROMS Problems
Topic: Problem in latest version of ROMS while compiling
Replies: 4
Views: 715

Re: Problem in latest version of ROMS while compiling

I just checked the trunk code for set_vbc.F and it was last changed six months ago. There is no Tnudg_SSS in the SCORRECTION section. You need to find out where yours is coming from.
by kate
Sun Aug 19, 2018 6:04 pm
Forum: ROMS Problems
Topic: Problem in latest version of ROMS while compiling
Replies: 4
Views: 715

Re: Problem in latest version of ROMS while compiling

Are you sure you aren't mixing up ROMS versions? The trunk code does not have Tnudg_SSS while mine does. Whatever you do, you need to stick with some consistent version.
by kate
Fri Aug 17, 2018 4:29 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 3434

Re: forrtl: severe (151): allocatable array is already alloc

initialize_param is called after NtileJ is read in the input file. You don't happen to have more than one line with NtileJ set do you?
by kate
Thu Aug 16, 2018 6:06 pm
Forum: ROMS Problems
Topic: Error in running the job
Replies: 2
Views: 553

Re: Error in running the job

What is on this line?
At line 951 of file inp_par.f90
The file is in your $SCRATCH_DIR.
by kate
Wed Aug 15, 2018 4:20 am
Forum: ROMS Discussion
Topic: Cannot find "coordinates" attribute for variable: Uwind
Replies: 15
Views: 1776

Re: Cannot find "coordinates" attribute for variable: Uwind

ROMS doesn't care if they are yearly or monthly. You just need to list them all in the correct format. Or you can use ncrcat to mash together twelve months into a year. Up to you.
by kate
Mon Aug 13, 2018 3:22 pm
Forum: ROMS Discussion
Topic: How to setup for rotating frame
Replies: 10
Views: 1465

Re: How to setup for rotating frame

Before that first history record is written, main3d calls ini_fields which does this: ! This routine initializes other time levels for 2D fields. It also ! ! couples 3D and 2D momentum equations: it initializes 2D momentum ! ! (ubar,vbar) to the vertical integral of initial 3D momentum (u,v). ! You ...
by kate
Mon Aug 13, 2018 3:00 pm
Forum: ROMS Tools and Techniques
Topic: Some confusion about the boundary file
Replies: 5
Views: 1227

Re: Some confusion about the boundary file

This is where you have to do more detective work. I wrote up what I know here.
by kate
Mon Aug 13, 2018 5:02 am
Forum: ROMS Discussion
Topic: PyROMS bug
Replies: 5
Views: 1139

Re: PyROMS bug

Thank you, fixed.

Say, do you know about pull requests?
by kate
Fri Aug 10, 2018 2:49 am
Forum: ROMS Discussion
Topic: Cannot find "coordinates" attribute for variable: Uwind
Replies: 15
Views: 1776

Re: Cannot find "coordinates" attribute for variable: Uwind

The structure of the file you show is one that has already been regridded onto the ROMS grid. The structure of a winds file for ROMS to remap is more like: dimensions: lon = 640 ; lat = 320 ; time = UNLIMITED ; // (2920 currently) variables: double lon(lon) ; lon:units = "degrees_east" ; lon:valid_m...
by kate
Fri Aug 10, 2018 2:27 am
Forum: ROMS Information
Topic: Running a test case in ROMS Rutgers
Replies: 1
Views: 566

Re: Running a test case in ROMS Rutgers

I am making those files in Python with pyroms. There's an examples directory with some examples from a few sources.
by kate
Wed Aug 08, 2018 2:57 pm
Forum: ROMS Discussion
Topic: puzzle: write long time averages over many restarts
Replies: 1
Views: 481

Re: puzzle: write long time averages over many restarts

It’s true that ROMS won’t do what you want unless you restart at some fraction of your month and average the files. I save daily and make monthly averages from them with 28 to 31 days.
by kate
Tue Aug 07, 2018 7:02 pm
Forum: ROMS Discussion
Topic: Creating grid with high resolution near the coast
Replies: 1
Views: 534

Re: Creating grid with high resolution near the coast

I think you want high resolution along the whole coast? Easiest is to have uniformly high resolution everywhere. Otherwise I think you are asking for an unstructured grid model, not ROMS.
by kate
Tue Aug 07, 2018 1:35 am
Forum: ROMS Discussion
Topic: VISC2 valuse
Replies: 3
Views: 713

Re: VISC2 valuse

Yes, feel free to try different values.
by kate
Mon Aug 06, 2018 3:26 pm
Forum: ROMS Tools and Techniques
Topic: Some confusion about the boundary file
Replies: 5
Views: 1227

Re: Some confusion about the boundary file

The Flather condition uses zeta in the ubar term. Either fix your zeta or set it to zero.
by kate
Mon Aug 06, 2018 3:23 pm
Forum: ROMS Ecosystem
Topic: NPZD negative concentration for no3 and all bio variables
Replies: 2
Views: 817

Re: NPZD negative concentration for no3 and all bio variable

Many advection schemes can give you the negative values. I limit NPZ tracers to be non-negative. Salt too.
by kate
Mon Aug 06, 2018 3:19 pm
Forum: ROMS Discussion
Topic: VISC2 valuse
Replies: 3
Views: 713

Re: VISC2 valuse

The time scale is damping time, not the time step. You want to damp at about the growth rate of 2 dx noise.
by kate
Mon Aug 06, 2018 3:15 pm
Forum: ROMS Discussion
Topic: How to setup for rotating frame
Replies: 10
Views: 1465

Re: How to setup for rotating frame

Yes, it gets that from you ocean.in.
by kate
Fri Aug 03, 2018 4:31 am
Forum: ROMS Discussion
Topic: River bottom salinity too high
Replies: 9
Views: 1265

Re: River bottom salinity too high

Yes, ROMS will let you do that. The numerics will not be stable.
by kate
Thu Aug 02, 2018 5:06 pm
Forum: ROMS Discussion
Topic: River bottom salinity too high
Replies: 9
Views: 1265

Re: River bottom salinity too high

I don't know about the salt, but you need to set the temperature tracer on inflow as well. The only time you can skip setting the river tracers is when your rivers all flow outward. If you don't on inflow, the model will go unstable.
by kate
Thu Aug 02, 2018 5:05 pm
Forum: ROMS Information
Topic: Domain decomposition for grid with large masked regions
Replies: 2
Views: 624

Re: Domain decomposition for grid with large masked regions

I know that CICE won't compute on tiles which are completely land-covered. Also, HYCOM has done this for many years. I once asked Hernan about this and didn't get a satisfactory answer. It came up because in coupling to CICE, you have to make sure all the CICE tiles have some ocean in them or the co...
by kate
Tue Jul 31, 2018 4:29 pm
Forum: ROMS Discussion
Topic: How to setup for rotating frame
Replies: 10
Views: 1465

Re: How to setup for rotating frame

Check the LAB_CANYON test case which is exactly this geometry (with canyon bathymetry).
by kate
Tue Jul 31, 2018 4:27 pm
Forum: ROMS Tools and Techniques
Topic: ECMWF Forcing metre wind component
Replies: 5
Views: 1369

Re: ECMWF Forcing metre wind component

I don't know about a negative time. You can just set the time value to zero for that record and it should work.
by kate
Mon Jul 30, 2018 3:30 pm
Forum: ROMS Discussion
Topic: I wanna change harmonic to biharmonic
Replies: 3
Views: 714

Re: I wanna change harmonic to biharmonic

The ROMS manual gives advice about checking damping timescales for various spatial scales with lateral viscosity. You want to keep the damping timescale for 2dx noise about the same, but the two will give different timescales on the 10dx features.
by kate
Fri Jul 27, 2018 10:05 pm
Forum: ROMS Discussion
Topic: Analytical Surface Winds...no Bulk Flux
Replies: 5
Views: 918

Re: Analytical Surface Winds...no Bulk Flux

I actually have a simplified bulk_flux lying around: ! ! Compute kinematic, surface wind stress (m2/s2). ! cff = log(blk_ZW(ng)/10._r8)/vonKar DO j=Jstr-1,JendR DO i=Istr-1,IendR Wspeed(i)=SQRT(Uwind(i,j)*Uwind(i,j)+Vwind(i,j)*Vwind(i,j)) U10(i) = Wspeed(i)/(1 + cff*sqrt(1.15e-3_r8)) U10o(i)=0.0_r8 ...
by kate
Fri Jul 27, 2018 10:02 pm
Forum: ROMS Discussion
Topic: Analytical Surface Winds...no Bulk Flux
Replies: 5
Views: 918

Re: Analytical Surface Winds...no Bulk Flux

Just look at bulk_flux.F - it sets sustr to Taux/rho0.
by kate
Fri Jul 27, 2018 9:23 pm
Forum: ROMS Discussion
Topic: Analytical Surface Winds...no Bulk Flux
Replies: 5
Views: 918

Re: Analytical Surface Winds...no Bulk Flux

I think you need tau over ocean density, not air density.
by kate
Fri Jul 27, 2018 4:21 pm
Forum: ROMS Discussion
Topic: I wanna change harmonic to biharmonic
Replies: 3
Views: 714

Re: I wanna change harmonic to biharmonic

I think that's all you need to do. In this business, we encourage you to try something first, then ask if it doesn't work out.
by kate
Fri Jul 27, 2018 4:18 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 1935

Re: huge memory per node when up scaling application

To be honest, I refused to convert all my input files, so I split PARALLEL_IO into PARALLEL_IN and PARALLEL_OUT in my ROMS code. It's been years since I tried any of these things. As for the rest, I'm working towards switching from ROMS to MOM6 in part because it is designed to run on thousands of c...
by kate
Fri Jul 27, 2018 5:47 am
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 1935

Re: huge memory per node when up scaling application

Also, you can use nccopy instead of ncdump | ncgen.
by kate
Fri Jul 27, 2018 5:35 am
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 1935

Re: huge memory per node when up scaling application

Yes, you need to use ncgen with a format_code or format_name that gives you a netCDF4 (HDF5) file, i.e., the "-k nc4" option or maybe "-k nc7".
by kate
Wed Jul 25, 2018 3:41 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 1935

Re: huge memory per node when up scaling application

The French ROMS (croco) comes with XIOS, but it was only really XOS (output) last I checked. I tried and failed to get the NCAR package to work with ROMS several years ago. I might still have that branch if you want to play with it. I got it to run with all the cores in the I/O pool, but not with on...
by kate
Wed Jul 25, 2018 6:49 am
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 1935

Re: huge memory per node when up scaling application

My jobs look a lot more like your 10 km run in size. This code was not designed for such large processor counts as you are trying. Specifically, how are you managing I/O? Are you trying some sort of parallel I/O? What I've heard recommended is something like NCAR's parallel-IO library or the Europea...
by kate
Wed Jul 25, 2018 6:36 am
Forum: ROMS Discussion
Topic: Blowing up problem using GLS mixing
Replies: 8
Views: 1492

Re: Blowing up problem using GLS mixing

I feel they are not working well since I still could mostly not get the recommended rx0 and rx1 whenever I run the model. Or if I do, it would be for a bathymetry smoothed in such a way that some of the real features are no longer recognizable. Indeed, you show neighboring points with rx0 of almost...
by kate
Wed Jul 25, 2018 6:17 am
Forum: ROMS Usage
Topic: Nudging values and OBCFAC clarification
Replies: 6
Views: 1350

Re: Nudging values and OBCFAC clarification

Well, it is a kludge and you might need stronger measures than simply RadNud with the optimal values to get good behavior. One thing that I have found to help is more frequent boundary values to nudge to, such as 5-daily SODA or even daily HYCOM. Monthly never worked well.
by kate
Fri Jul 20, 2018 3:10 pm
Forum: ROMS Usage
Topic: Nudging values and OBCFAC clarification
Replies: 6
Views: 1350

Re: Nudging values and OBCFAC clarification

Yes, exactly.
by kate
Thu Jul 19, 2018 4:55 pm
Forum: ROMS Adjoint
Topic: Inconsistent values of variables in TL initial condition
Replies: 3
Views: 899

Re: Inconsistent values of variables in TL initial condition

I suppose you are focused on the big blobs of extreme values, but my eye is drawn to Y=380 and the weird line there.
by kate
Thu Jul 19, 2018 4:51 pm
Forum: ROMS Usage
Topic: Nudging values and OBCFAC clarification
Replies: 6
Views: 1350

Re: Nudging values and OBCFAC clarification

Yes. But in actual use, there's an inverse, so maybe the code multiplies down in the guts.