Search found 4079 matches

by kate
Mon Mar 11, 2024 4:26 pm
Forum: ROMS Discussion
Topic: ROMS Radiation Boundary condition (RadNud)
Replies: 11
Views: 729

Re: ROMS Radiation Boundary condition (RadNud)

If you feel that using the local velocity would be better in your situation than the phase speed, you should try coding it up and seeing how it behaves. I expect that was tried at some point and found wanting, but we only had a limited number of domains when trying this stuff.
by kate
Sat Mar 09, 2024 2:34 pm
Forum: ROMS Discussion
Topic: ROMS Radiation Boundary condition (RadNud)
Replies: 11
Views: 729

Re: ROMS Radiation Boundary condition (RadNud)

For each field using RadNud, the phase speed is computed locally, at each point on the boundary. If you look, that phase speed can be quite noisy, in time and space. You could try using ambient velocity instead, but the point is that you are trying to radiate away waves, which don't necessarily move...
by kate
Sat Mar 02, 2024 2:32 pm
Forum: ROMS Bugs
Topic: Not able to use the make_remap_weights_file.py file
Replies: 5
Views: 819

Re: Not able to use the make_remap_weights_file.py file

It's clear enough, right? You need to look at what line number, what variables it is talking about. I often
add print statements to find out the shapes of things. You might also learn to use breakpoint() to get
into the debugger to query your variables.
by kate
Fri Feb 16, 2024 4:48 pm
Forum: ROMS Bugs
Topic: Not able to use the make_remap_weights_file.py file
Replies: 5
Views: 819

Re: Not able to use the make_remap_weights_file.py file

I don't know what to make of the log file. Yes, your domain size could cause it to run out of memory and get killed.
by kate
Mon Feb 12, 2024 6:16 pm
Forum: ROMS Bugs
Topic: Not able to use the make_remap_weights_file.py file
Replies: 5
Views: 819

Re: Not able to use the make_remap_weights_file.py file

With xesmf, you don’t run make_remap_weights_file.py. I should delete that.
by kate
Thu Feb 08, 2024 4:18 pm
Forum: ROMS Discussion
Topic: writing out time varying atmospheric pCO2 in fennel.h
Replies: 1
Views: 810

Re: writing out time varying atmospheric pCO2 in fennel.h

You wrote to me privately asking this, but I'm quite rusty on all this. I would make sure that there is a pCO2 id in varinfo.dat (is that still how it is done?) and I would hack at all the routines that write all these files. There are plenty of examples with the other fields being written.
by kate
Wed Dec 13, 2023 5:58 pm
Forum: ROMS Discussion
Topic: Blow up before starting
Replies: 5
Views: 14309

Re: Blow up before starting

MOM6 can handle this case, with an open boundary inside the domain. ROMS is not set up to do that.
by kate
Thu Nov 09, 2023 6:22 pm
Forum: ROMS Discussion
Topic: River Input
Replies: 13
Views: 22452

Re: River Input

by kate
Wed Nov 08, 2023 6:05 pm
Forum: ROMS Discussion
Topic: River Input
Replies: 13
Views: 22452

Re: River Input

Rivers can be tricky! Each uv-source is either a u-source or a v-source. Each u-source is either going to the east or to the west. You want one of each, so one is positive, one is negative. When following a realistic coastline, I have some Python code to figure this all out for each source (used to ...
by kate
Mon Oct 23, 2023 5:06 pm
Forum: ROMS Discussion
Topic: How to ensure the CPP option I added works?
Replies: 2
Views: 10587

Re: How to ensure the CPP option I added works?

The place to check is in the build directory. Look at step3d_t.f90 there to see if your conditional code is there.

For the output you were looking at, there is another file that needs to be modified to get that statement added: checkdefs.F
by kate
Thu Oct 19, 2023 4:50 pm
Forum: ROMS Ice
Topic: ROMS coupled to CICE
Replies: 21
Views: 62841

Re: ROMS coupled to CICE

I am not running METROMS and I'm not able to help out either. Out of the box, CICE5 has no open boundary conditions. The Norwegians have added some to their code and they wrote a paper about it, but the last I heard, Elizabeth Hunke was hoping for a pull request from them for the code. For the forci...
by kate
Wed Oct 18, 2023 6:36 pm
Forum: ROMS Tools and Techniques
Topic: Unable to run make_remap_weights_file.py
Replies: 4
Views: 7900

Re: Unable to run make_remap_weights_file.py

Arctic_HYCOM_GLBy
by kate
Tue Oct 17, 2023 3:00 pm
Forum: ROMS Tools and Techniques
Topic: Unable to run make_remap_weights_file.py
Replies: 4
Views: 7900

Re: Unable to run make_remap_weights_file.py

This is using scrip, right? I don't use scrip any more. Use the newer ESMF examples.
by kate
Mon Oct 16, 2023 5:34 pm
Forum: ROMS Ice
Topic: ROMS coupled to CICE
Replies: 21
Views: 62841

Re: ROMS coupled to CICE

This is the forum for the Rutgers ROMS code. I don't know if the person running a 20 km Arctic is reading this forum. Do you have a way to contact them directly?

These big files are a real pain to host and transfer.
by kate
Wed Sep 20, 2023 7:16 pm
Forum: ROMS Installation
Topic: How to Learn ROMS
Replies: 2
Views: 3986

Re: How to Learn ROMS

I wrote a manual https://github.com/kshedstrom/roms_manu ... manual.pdf, but I haven't updated it in five years.

There is also a wiki: https://www.myroms.org/wiki/Documentation_Portal and I don't know how out of date that is. ROMS keeps changing!
by kate
Thu Aug 10, 2023 7:00 pm
Forum: ROMS Discussion
Topic: Problem using kate's pyroms
Replies: 3
Views: 6344

Re: Problem using kate's pyroms

I'm getting an error too: Traceback (most recent call last): File "zlook.py", line 18, in <module> proj=proj, \ File "/import/home/kshedstrom/pyroms/pyroms_toolbox/pyroms_toolbox/zview.py", line 152, in zview resolution='h', area_thresh=5.) File "/import/c1/AKWATERS/kate/.co...
by kate
Wed Aug 09, 2023 6:44 pm
Forum: ROMS Discussion
Topic: Problem using kate's pyroms
Replies: 3
Views: 6344

Re: Problem using kate's pyroms

It is has been said by he who wrote the thing that this should be enough documentation: def zview(var, tindex, depth, grid, filename=None, \ cmin=None, cmax=None, clev=None, clb_format='%.2f', \ fill=False, contour=False, d=4, range=None, fts=None, \ title=None, clb=True, pal=None, proj='merc', \ fi...
by kate
Fri Aug 04, 2023 5:19 pm
Forum: ROMS Tools and Techniques
Topic: Guide for install PYROMS in Python3
Replies: 3
Views: 6049

Re: Guide for install PYROMS in Python3

Yes, exactly.
by kate
Thu Aug 03, 2023 5:21 pm
Forum: ROMS FAQ
Topic: Segmentation Faults
Replies: 12
Views: 30828

Re: Segmentation Faults

It has been years since I ran that. Did you recompile CICE in debug mode too?
by kate
Wed Aug 02, 2023 5:39 pm
Forum: ROMS Tools and Techniques
Topic: Guide for install PYROMS in Python3
Replies: 3
Views: 6049

Re: Guide for install PYROMS in Python3

All there is is in the README. The current default branch is named "python3" and does work with Python 3.
by kate
Thu Jun 29, 2023 5:55 pm
Forum: ROMS Discussion
Topic: ERROR: Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Replies: 10
Views: 12982

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

According to your input file: Lm == 70 ! Number of I-direction INTERIOR RHO-points Mm == 70 ! Number of J-direction INTERIOR RHO-points N == 30 ! Number of vertical levels This is not the same size grid as your boundary file: netcdf lisound_bry { dimensions: xi_rho = 57 ; xi_u = 56 ; xi_v = 57 ; eta...
by kate
Thu Jun 29, 2023 5:30 pm
Forum: ROMS Discussion
Topic: ERROR: Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Replies: 10
Views: 12982

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

No, the rain file is fine. What file does get_data want to read after that for *your* case?
by kate
Thu Jun 29, 2023 4:46 pm
Forum: ROMS Discussion
Topic: BLOWUP. REASON: MaxSpeed = 2.1E+01
Replies: 9
Views: 12705

Re: BLOWUP. REASON: MaxSpeed = 2.1E+01

I'm afraid I'm not the expert on bathy_smoother, but my understanding is that there's more than one way to smooth bathymetry in there. I use an external program that filters bathymetry in a way to target only the roughest patches first, then I finish up with one pass of a Shapiro filter. There's no ...
by kate
Thu Jun 29, 2023 4:40 pm
Forum: ROMS Discussion
Topic: ERROR: Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Replies: 10
Views: 12982

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

The questions is - what does get_data.f90 want to read after the rain field? Is there something wrong with that file? Have you looked at that file with say ncview?
by kate
Wed Jun 28, 2023 4:50 pm
Forum: ROMS Discussion
Topic: BLOWUP. REASON: MaxSpeed = 2.1E+01
Replies: 9
Views: 12705

Re: BLOWUP. REASON: MaxSpeed = 2.1E+01

Maybe you need an even shorter timestep during a typhoon? The model does want a shorter timestep than you might think, especially with lots of vertical levels.
by kate
Fri Jun 16, 2023 4:35 pm
Forum: ROMS Discussion
Topic: module 'pyroms.remapping' has no attribute 'scrip'
Replies: 4
Views: 7024

Re: module 'pyroms.remapping' has no attribute 'scrip'

My latest code is not even trying to load scrip because I commented out these two lines:
```
try:
from pyroms import scrip
```
from pyroms/pyroms/remapping/__init__.py

I got tired of all those scrip warnings! If you really, really want to try loading scrip, uncomment them out again.
by kate
Thu Jun 15, 2023 5:36 pm
Forum: ROMS Discussion
Topic: Nonhydrostatic version of ROMS
Replies: 6
Views: 9260

Re: Nonhydrostatic version of ROMS

You should contact Jim McWilliams and ask him.
by kate
Fri Jun 09, 2023 10:12 pm
Forum: ROMS Discussion
Topic: Difficulties with LMD mixing
Replies: 4
Views: 5484

Re: Difficulties with LMD mixing

I typically have LMD_SKPP and LMD_NON_LOCAL, not the LMD_BKPP.
by kate
Fri Jun 09, 2023 6:57 pm
Forum: ROMS Discussion
Topic: Difficulties with LMD mixing
Replies: 4
Views: 5484

Re: Difficulties with LMD mixing

What happens without LMD_BKPP?
by kate
Thu May 25, 2023 3:44 pm
Forum: ROMS Results
Topic: Why temperature at t=2 and so on looks strange?
Replies: 1
Views: 4123

Re: Why temperature at t=2 and so on looks strange?

I would guess that it's more of a vertical mixing problem than an open boundary problem. Have you looked at vertical cross sections?
by kate
Thu May 25, 2023 3:39 pm
Forum: ROMS Discussion
Topic: Boundary settings are not working for ROMS
Replies: 4
Views: 6673

Re: Boundary settings are not working for ROMS

and OBCFAC == 0.0d0 Tnudge=0. I think this means that I didn't use the nudging. What exactly is OBCFAC == 0.0 doing in the code? Perhaps you should check. You are expecting the boundary to be clamped, so why not clamp the salinity boundary? The reason I don't clamp it is that clamping tends to lead...
by kate
Wed May 24, 2023 3:13 pm
Forum: ROMS Discussion
Topic: River Input
Replies: 13
Views: 22452

Re: River Input

You have two choices: add a second field much like precipitation, or add a bunch of individual sources.
by kate
Mon Apr 24, 2023 1:53 pm
Forum: ROMS Ice
Topic: ROMS coupled to CICE
Replies: 21
Views: 62841

Re: ROMS coupled to CICE

I’m sorry, I don’t remember what I had done there. I’m not at home this week to look into it either.
by kate
Sat Apr 22, 2023 4:08 pm
Forum: ROMS Ice
Topic: ROMS coupled to CICE
Replies: 21
Views: 62841

Re: ROMS coupled to CICE

My https://github.com/kshedstrom/roms repo has a metroms branch which I believe solves the forcing file problem.

Note that this code is completely unsupported!
by kate
Tue Apr 18, 2023 4:45 pm
Forum: ROMS Ecosystem
Topic: Biological Tracer from River
Replies: 6
Views: 9521

Re: Biological Tracer from River

For river tracers, you have to provide values for all of them. Otherwise your run will be unstable, maybe not today or tomorrow, but someday. It's tricky to find good values to use, but you have to use *something*.
by kate
Mon Apr 17, 2023 3:47 pm
Forum: ROMS Ice
Topic: Leak/Artifact at CPU Tiles
Replies: 7
Views: 11057

Re: Leak/Artifact at CPU Tiles

If you want to check out another dead branch, I've got a metroms branch on my ROMS github repo. I did fuss with the forcing.
by kate
Mon Apr 17, 2023 4:40 am
Forum: ROMS Ice
Topic: Leak/Artifact at CPU Tiles
Replies: 7
Views: 11057

Re: Leak/Artifact at CPU Tiles

There were some serious problems with the ice code of roughly seven years ago, since fixed in my branch. Maybe you should start over with METROMS, coupling a modern ROMS with CICE. Or better yet, join me on the MOM6-SIS2 adventure. The frazil ice code is the canary in the coal mine - the most sensit...
by kate
Sun Apr 16, 2023 5:13 pm
Forum: ROMS Ice
Topic: Leak/Artifact at CPU Tiles
Replies: 7
Views: 11057

Re: Leak/Artifact at CPU Tiles

That's a seven year old fork! I suggest you try my moldy two year old repo instead.
by kate
Mon Apr 03, 2023 9:46 pm
Forum: ROMS Ice
Topic: ROMS from github error
Replies: 21
Views: 28686

Re: ROMS from github error

Inside ROMS, each variable can have its own time, no problem. The preferred method (last I was aware) is that each variable in the netcdf file should point to the appropriate time variable through the time attribute. This will override the varinfo.dat file. In terms of units, I wouldn't count on ROM...
by kate
Fri Mar 31, 2023 4:49 pm
Forum: ROMS Ice
Topic: ROMS from github error
Replies: 21
Views: 28686

Re: ROMS from github error

This one is not the fault of the Makefile, but rather a bug. Looking at mod_forces, I have: # ifdef SHORTWAVE real(r8), pointer :: srflx(:,:) # ifndef ANA_SRFLUX real(r8), pointer :: srflxG(:,:,:) # endif # ifdef ALBEDO real(r8), pointer :: albedo(:,:) # ifdef ICE_MODEL real(r8), pointer :: albedo_i...
by kate
Fri Mar 31, 2023 5:36 am
Forum: ROMS Ice
Topic: ROMS from github error
Replies: 21
Views: 28686

Re: ROMS from github error

So the dependency list is wrong and doesn't include the needs of the ice model. I never used Hernan's build system, so there must be something missing in his Makefile. I looked in his makefile and he's pointing to sea ice modules under ROMS/Nonlinear/SeaIce. Maybe if you move the ice routines to tha...
by kate
Fri Mar 31, 2023 4:20 am
Forum: ROMS Ice
Topic: ROMS from github error
Replies: 21
Views: 28686

Re: ROMS from github error

You need to rebuild the dependency list. Some things need to be compiled before other things. The easiest way to do this is "make clean" or removing the build directory or whatever works for how you build the model.
by kate
Tue Mar 28, 2023 2:46 pm
Forum: ROMS Ice
Topic: ROMS from github error
Replies: 21
Views: 28686

Re: ROMS from github error

Is this what you are asking about? read_icepar.f90: remark #5133: The input stream is empty Are you sure you turned on the ice model? I checked and my boundary file only has ocean_time. That's how I set up my varinfo.dat: 'zeta_west' ! Input 'free-surface western boundary condition' 'meter' ! [m] 'z...
by kate
Fri Mar 24, 2023 10:15 pm
Forum: ROMS Ice
Topic: ROMS from github error
Replies: 21
Views: 28686

Re: ROMS from github error

get_data_ 218 get_data.f90 What is it reading here? Are you sure it's the boundary file? It just read salinity climatology - should it read temperature climatology next? I would run it in the debugger or add a print statement to that line you highlighted. I don't know what's going on. Note: all the...
by kate
Wed Mar 22, 2023 3:22 pm
Forum: Ocean News
Topic: Dale B. Haidvogel (1949-2023)
Replies: 18
Views: 35458

Re: Dale B. Haidvogel (1949-2023)

Mohamed Iskandarani asked me to post this: I started working with Dale in the early 90’s, he was just setting up shop at Rutgers with Kate Hedstrom when I joined his research group to develop an ocean model based on spectral elements. I had known of Dale from his articles on spectral methods when I ...
by kate
Mon Mar 20, 2023 6:07 am
Forum: ROMS Usage
Topic: option for wind forcing
Replies: 19
Views: 27601

Re: option for wind forcing

How many times do I have to say "unsupported"?

https://github.com/kshedstrom/roms
by kate
Mon Mar 20, 2023 12:35 am
Forum: Ocean News
Topic: Dale B. Haidvogel (1949-2023)
Replies: 18
Views: 35458

Re: Dale B. Haidvogel (1949-2023)

Looking back, I want to say a few words about the state of ocean modeling when I met Dale in 1988. There was a well-known global model from GFDL which became MOM. There were a few other models, but they weren't open source. Dale wanted to create a new model with unique numerics, suitable for regiona...
by kate
Mon Mar 20, 2023 12:08 am
Forum: ROMS Ice
Topic: ROMS from github error
Replies: 21
Views: 28686

Re: ROMS from github error

The way ROMS is compiled, you view the .F file, then an intermediate .f90 file is created off in some build directory. It is those line numbers you need to look at: read_phypar_ 1839 read_phypar.f90 You need to make sure you have an ocean.in that's compatible with the github ROMS, also varinfo.dat.
by kate
Mon Mar 20, 2023 12:03 am
Forum: ROMS Usage
Topic: option for wind forcing
Replies: 19
Views: 27601

Re: option for wind forcing

Those options you mention are from my (unsupported) rogue version of ROMS, not the trunk code. Which code are you using?
by kate
Sat Mar 18, 2023 3:29 pm
Forum: Ocean News
Topic: Dale B. Haidvogel (1949-2023)
Replies: 18
Views: 35458

Re: Dale B. Haidvogel (1949-2023)

Dale Haidvogel played a big part in getting my career started. My PhD project involved a rotating tank with actual salt water. My first job afterwards was to do ocean modeling, but I didn't know anything about it - there were no classes in it then at Scripps. My new boss at the (now long gone) Insti...
by kate
Fri Mar 17, 2023 4:45 pm
Forum: ROMS Ice
Topic: ROMS from github error
Replies: 21
Views: 28686

Re: ROMS from github error

1. I'm not really supporting that code any more. 2. Yes, turning on the ice cpp flag is all that's needed. 3. You'll get a more useful model output on seg fault if you recompile in debug mode. 4. Your problem is probably in the ocean.in, with the ice code needing different options. 5. I suspect you ...
by kate
Thu Mar 16, 2023 9:00 pm
Forum: ROMS Ice
Topic: How add ice
Replies: 8
Views: 14551

Re: How add ice

My ROMS with ice is no longer being maintained. Hernan was working on a ROMS with ice, haven't heard about it recently.

Your best bet is probably METROMS from the Norwegians.
by kate
Wed Mar 15, 2023 6:05 am
Forum: ROMS Tools and Techniques
Topic: PYROMS installation
Replies: 45
Views: 70188

Re: PYROMS installation

None of those things need lpsolve. It is used for a very specific type of bathymetry smoothing. Bathymetry smoothing is part of grid generation, where you interpolate bathymetry to your grid, then smooth it enough so that ROMS can run. Calling compiled code from Python has been problematic and it's ...
by kate
Tue Mar 14, 2023 11:44 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS installation
Replies: 45
Views: 70188

Re: PYROMS installation

Do you have the latest pyroms? The current README instructions say to use pip install instead.

Depending on what you plan to do with pyroms, you may not need lpsolve at all. I don't use it. What do you need pyroms for?
by kate
Thu Mar 02, 2023 12:31 am
Forum: ROMS Bugs
Topic: History file archiving intervals: bug in output.F?
Replies: 12
Views: 34124

Re: History file archiving intervals: bug in output.F?

Note that my repo hasn't changed in well over a year. I'm not keeping up!
by kate
Fri Jan 20, 2023 1:10 am
Forum: ROMS Ecosystem
Topic: Runoff/river-derived biogeochemical tracer fluxes
Replies: 5
Views: 8010

Re: Runoff/river-derived biogeochemical tracer fluxes

I used point sources which are not through cppdefs, but turned on with LuvSrc and LtracerSrc. I just pushed an update to pyroms for dealing with Dave Hill's runoff.
by kate
Fri Jan 13, 2023 6:50 pm
Forum: ROMS Ecosystem
Topic: Runoff/river-derived biogeochemical tracer fluxes
Replies: 5
Views: 8010

Re: Runoff/river-derived biogeochemical tracer fluxes

I assume the wind-wave parameterization you refer to is the one activated by the LI_FOX_KEMPER flag?
Yes
by kate
Wed Jan 11, 2023 7:29 pm
Forum: ROMS Ecosystem
Topic: Runoff/river-derived biogeochemical tracer fluxes
Replies: 5
Views: 8010

Re: Runoff/river-derived biogeochemical tracer fluxes

My recent runs have used the lateral flux river sources, not the runoff. I stole a wind-wave mixing parameterization (Li and Fox-Kemper) to add more surface mixing. We also changed the vertical profile of the input so that flow comes in below the surface too, instead of just at the surface. There ha...
by kate
Fri Nov 18, 2022 7:25 pm
Forum: ROMS Usage
Topic: Can ROMS handle weir crest overflow and dam discharge (both freshwater into saltwater)?
Replies: 1
Views: 3481

Re: Can ROMS handle weir crest overflow and dam discharge (both freshwater into saltwater)?

This ROMS is fundamentally a hydrostatic model. There are other models which include the non-hydrostatic effects of "not small" vertical accelerations. MITgcm is the one I hear most about.
by kate
Tue Nov 08, 2022 4:19 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 35
Views: 260935

Re: Create boundary and initial file from seagrid and GLBa0.08

There are two options at least: (a) change pyroms to accept the lat, lon variables as they are in the file or (b) change the file to include the fields that pyroms is looking for.
by kate
Thu Oct 27, 2022 3:59 pm
Forum: ROMS Discussion
Topic: Problems in antarctic regional circulation and sea ice simulation
Replies: 2
Views: 3202

Re: Problems in antarctic regional circulation and sea ice simulation

You will have best results using nesting, the large domain being large enough to enclose all the southern ice. Yes, I am no longer maintaining that ROMS ice model. Yes, the Norwegians are using MetROMS and they have put ice open boundaries into their CICE, similar to the ROMS open boundaries. You sh...
by kate
Tue Oct 04, 2022 9:42 pm
Forum: ROMS Discussion
Topic: Lagrangian Floats
Replies: 3
Views: 6012

Re: Lagrangian Floats

It won't do what you want as easily as all that. You have to have 40 different lines with 200 floats each (or vice versa).
by kate
Tue Sep 06, 2022 6:34 pm
Forum: ROMS Discussion
Topic: pan-Arctic grid
Replies: 4
Views: 6714

Re: pan-Arctic grid

I've been using gridpak for my Arctic grids. It's some crazy mess of ancient software that no one else wants to use. It has gotten worse with time - I can't compile xcoast on our current supercomputer. That's one reason the goal is to develop Python tools for all this.
by kate
Sat Sep 03, 2022 7:37 am
Forum: ROMS Discussion
Topic: pan-Arctic grid
Replies: 4
Views: 6714

Re: pan-Arctic grid

Rob suggests creating a GitHub issue. It’s something he hasn’t tried yet.
by kate
Mon Jul 25, 2022 4:55 pm
Forum: ROMS Tools and Techniques
Topic: Pyroms installation error
Replies: 6
Views: 8053

Re: Pyroms installation error

I don't know what to say. Perhaps we should disable the building of scrip? It's not like
I use it anymore, as I've said here in these forums before. For me it builds, but doesn't load.
by kate
Sat Jul 23, 2022 3:00 pm
Forum: ROMS Tools and Techniques
Topic: Pyroms installation error
Replies: 6
Views: 8053

Re: Pyroms installation error

netcdf.inc comes with the NetCDF-Fortran prerequisite. The first question is do you have it? Where is it? The second question is how do you get scrip to find it? There's a makefile in pyroms/pyroms/external/scrip/source using the NETCDF_INCDIR environment variable. Mine is currently pointing to: /us...
by kate
Fri Jul 22, 2022 5:21 pm
Forum: ROMS Tools and Techniques
Topic: Pyroms installation error
Replies: 6
Views: 8053

Re: Pyroms installation error

It says it can't find pyroms/src/iso.f. Do you have pyroms/pyroms/pyroms/src/iso.f? I have seven Fortran files in that directory, including iso.f.
by kate
Tue Jul 19, 2022 3:18 pm
Forum: ROMS Discussion
Topic: Creating initial field, boundary field files from grid files
Replies: 3
Views: 4067

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

You haven't told us which tools you are using to generate initial and boundary files. Impossible to say from here what's wrong.
by kate
Fri Jul 01, 2022 4:09 pm
Forum: ROMS Discussion
Topic: I want to use HYCOM GLB v0.08 as the initial / boundary data of ROMS.
Replies: 17
Views: 24181

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

I should explain the pyroms status: * It's a package written by people who are long gone from Rutgers, no longer using ROMS. * It is only my github repo because I got into git early, I am not a major contributor. * It is no longer representing best modern Python practices. I suggest you dig into som...
by kate
Tue Jun 28, 2022 4:52 pm
Forum: ROMS Discussion
Topic: I want to use HYCOM GLB v0.08 as the initial / boundary data of ROMS.
Replies: 17
Views: 24181

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

If you are missing one day of SSH, can you go to their server and download it directly?
by kate
Sun Jun 05, 2022 9:45 pm
Forum: ROMS Discussion
Topic: problem to use trondkr python codes(era5)-Kate
Replies: 2
Views: 3890

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

Have you considered asking on github? Or asking Trond? For ERA5, I am using the tools in https://github.com/jsimkins2/nwa25. The README in setup/forcing has a link to how to download files. Once they are downloaded, we do several operations on them before using them to force the model. All the codes...
by kate
Mon May 09, 2022 5:06 pm
Forum: ROMS Bugs
Topic: Pyroms scrip Fortran runtime error: Bad FORM parameter in OPEN statement
Replies: 2
Views: 4438

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

You are getting further with scrip than I have in years! My advice is to switch to xesmf. I know, it has its own issues, best to make it its own conda environment.
by kate
Wed Apr 20, 2022 5:24 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 36668

Re: PYROMS error

No, sorry, packing for a trip, not able to help right now.
by kate
Wed Apr 20, 2022 4:58 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 36668

Re: PYROMS error

remap_bdry.py should not be run stand-alone, but rather is called by make_bdry_file.py.
by kate
Wed Apr 20, 2022 12:45 am
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 36668

Re: PYROMS error

It's not working correctly and my husband has no idea why either. mask_t should have three dimensions, just like var. He says the "~" should be returning valid entries. We want to know which points are masked out. For me, ncview looking at the temp variable shows some white patches where i...
by kate
Tue Apr 19, 2022 9:36 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 36668

Re: PYROMS error

So the shape of mask_t is wrong for some reason. What does that "~" do?
by kate
Tue Apr 19, 2022 9:22 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 36668

Re: PYROMS error

I meant inside Python, print out the shapes of the objects in Python.
by kate
Tue Apr 19, 2022 8:28 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 36668

Re: PYROMS error

I don't know. What are the shapes of all the things?
by kate
Tue Apr 19, 2022 4:39 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 11398

Re: error:different horizontal mixing scheme

It is easy to code up and it makes sense over a flat bottom.
by kate
Thu Apr 14, 2022 5:31 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 11398

Re: error:different horizontal mixing scheme

No, no, no MIX_S_TS! It's a terrible thing to do with a sigma coordinate. Why wouldn't MIX_GEO work? My biggest problems with it involve wetting and drying and realistic bathymetry. I don't know what you are trying. I'm just suggesting trying a shorter timestep so that you can rule out CFL troubles....
by kate
Wed Apr 13, 2022 4:05 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 11398

Re: error:different horizontal mixing scheme

Yes, there's a CFL condition. There's also the timescale of damping on the scales you want to damp (2 dx) and the timescale of damping on scales you don't want to damp. A CFL of 1.0 will be unstable. What are you shooting for?
by kate
Tue Apr 12, 2022 4:58 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS: SCRIP installation error
Replies: 9
Views: 9983

Re: PYROMS: SCRIP installation error

It has been a while since I could get scrip to work. The solution is to give up on it, switch to remapping with ESMPy. There's an example using xesmf in examples/Arctic_HYCOM_GLBy.
by kate
Tue Apr 12, 2022 4:39 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 11398

Re: error:different horizontal mixing scheme

They have different timestep constraints, depending on dx. You could try a shorter timestep to see if it runs.
by kate
Mon Apr 11, 2022 4:51 pm
Forum: ROMS Discussion
Topic: error:different horizontal mixing scheme
Replies: 10
Views: 11398

Re: error:different horizontal mixing scheme

Does it run with TNU2? Is this a new domain? Are you sure you have a small enough timestep?
by kate
Tue Apr 05, 2022 3:35 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 28
Views: 36668

Re: PYROMS error

What exactly are you running? It has been a few years since I got scrip to work for me, so I'm switching over to ESMPy. There's one HYCOM example of it.
by kate
Thu Mar 10, 2022 6:25 pm
Forum: ROMS Discussion
Topic: Different boundary scenarios
Replies: 15
Views: 16663

Re: Different boundary scenarios

For what it's worth, this is what I'm using: LBC(isFsur) == Che Che Che Che ! free-surface LBC(isUbar) == Shc Shc Shc Shc ! 2D U-momentum LBC(isVbar) == Shc Shc Shc Shc ! 2D V-momentum LBC(isUvel) == RadNud RadNud RadNud RadNud ! 3D U-momentum LBC(isVvel) == RadNud RadNud RadNud RadNud ! 3D V-moment...
by kate
Tue Mar 08, 2022 5:16 pm
Forum: ROMS Ice
Topic: Sea-Ice Output
Replies: 1
Views: 3589

Re: Sea-Ice Output

You are using an unsupported code! I never ran with the ICESHELF, though there are those who did. Yes, the outputs will go from sea bottom to under the ice. There are diagnostics which should be zero where there's no ice that aren't zero. I wouldn't swear by diagnostics ever being right. I abandoned...
by kate
Thu Jan 20, 2022 8:21 pm
Forum: ROMS Discussion
Topic: Number of history files greater than 9999
Replies: 7
Views: 11347

Re: Number of history files greater than 9999

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

MOM6 files all have names starting with the date, such as 20100101.ice_daily.nc
by kate
Thu Jan 20, 2022 7:45 pm
Forum: ROMS Discussion
Topic: Number of history files greater than 9999
Replies: 7
Views: 11347

Re: Number of history files greater than 9999

He is at least the second person to run into this issue. I ran into it with daily output over 40 years, each day in its own file. Maybe it wouldn't happen with today's code, I don't know.
by kate
Wed Jan 19, 2022 6:54 pm
Forum: ROMS Discussion
Topic: Number of history files greater than 9999
Replies: 7
Views: 11347

Re: Number of history files greater than 9999

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

Code: Select all

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

Code: Select all

  10          FORMAT (a,'_',i4.4,'.nc')
and similar for all the other format statements.
by kate
Wed Jan 19, 2022 5:18 pm
Forum: ROMS Ice
Topic: Sea ice in COAWST
Replies: 1
Views: 3676

Re: Sea ice in COAWST

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

You can use the metroms coupling to use CICE with ROMS, but CICE isn't on an Arakawa C-grid.
by kate
Fri Dec 24, 2021 6:57 pm
Forum: ROMS Installation
Topic: cmpiling error for roms-kate_svn
Replies: 1
Views: 3742

Re: cmpiling error for roms-kate_svn

make: *** No rule to make target `/public/home/hufang/project/ecs922/Build_roms/round.f90', needed by `/public/home/hufang/project/ecs922/Build_roms/round.o'. Stop. I am not aware of any round.F or .f90 file. I haven't updated my code in quite some time, so I'm missing things from the main trunk. W...
by kate
Fri Nov 19, 2021 6:08 pm
Forum: ROMS Discussion
Topic: ROMS blowing up problem
Replies: 19
Views: 23359

Re: ROMS blowing up problem

Those NE boundary conditions look ghastly. Something is going on there, I don't know what.
by kate
Thu Nov 18, 2021 7:01 pm
Forum: ROMS Discussion
Topic: The model blows up in the first step
Replies: 4
Views: 5009

Re: The model blows up in the first step

It is bad before taking the first timestep. I would look carefully at your initial conditions.
by kate
Thu Nov 18, 2021 6:58 pm
Forum: ROMS Discussion
Topic: ROMS blowing up problem
Replies: 19
Views: 23359

Re: ROMS blowing up problem

How long before the final blow-up is this snapshot? You are running COAWST? I have no experience with modes of blowing up for anything but the ocean component. For the ocean, it can go from fine to bad in the blink of an eye. A history snapshot some hours before the trouble can look great. I tend to...
by kate
Sun Oct 31, 2021 5:31 pm
Forum: ROMS Discussion
Topic: Problems with restarting the model
Replies: 11
Views: 16822

Re: Problems with restarting the model

The first thing to do is to track down the restart issue. You can run the model for two steps, restart it for two more, then compare that solution to a run that's four steps long. You have to restart after an even number of steps because the model doesn't save nstp, which alternates between 1 and 2....
by kate
Fri Oct 15, 2021 4:33 pm
Forum: ROMS Installation
Topic: Linking to shared library
Replies: 2
Views: 4205

Re: Linking to shared library

You have already compiled your library externally? There is a mod_eco.mod file in that directory? If so, you need to tell the compiler how to find that file. Or you could copy it into the ROMS build directory, which is what is done with the netcdf.mod and friends files.
by kate
Sat Sep 18, 2021 5:58 pm
Forum: ROMS Usage
Topic: Clarification about ROMS/Utility/get_nudgcoef.F
Replies: 1
Views: 4166

Re: Clarification about ROMS/Utility/get_nudgcoef.F

ROMS does read the varinfo.dat and scale things accordingly.
by kate
Fri Sep 10, 2021 5:43 pm
Forum: ROMS Discussion
Topic: Blow up when restart from history file
Replies: 5
Views: 5453

Re: Blow up when restart from history file

I'm glad you got it to run. As for the restarts matching exactly, you do not have enough information stored in the history files to accomplish that. The nature of the ROMS timestepping requires information from more than one timelevel of some fields, plus some right-hand-side information to do perfe...
by kate
Thu Sep 09, 2021 6:50 pm
Forum: ROMS Discussion
Topic: Blow up when restart from history file
Replies: 5
Views: 5453

Re: Blow up when restart from history file

I have run from an averages file, no problem. Do you have all the fields you need? Did you tell ROMS it was a new run with NRREC=0? If there's biology, did you really save everything you need in the history file? I've had runs die with COBALT when the averages file didn't have say the htotal field w...
by kate
Sat Sep 04, 2021 1:18 pm
Forum: ROMS Discussion
Topic: Change Output Frequency?
Replies: 3
Views: 5527

Re: Change Output Frequency?

You can run for a bit with one output frequency, then restart with a different output frequency. Anything more fancy is going to take hacking the code.
by kate
Sat Sep 04, 2021 1:17 pm
Forum: ROMS Discussion
Topic: Open boundary condition set up
Replies: 3
Views: 5412

Re: Open boundary condition set up

m2 is the barotropic velocity while m3 is the full barotropic plus baroclinic velocity.
by kate
Wed Sep 01, 2021 5:51 am
Forum: ROMS Discussion
Topic: ROMS/TOMS - Output error ............ exit_flag: 3
Replies: 3
Views: 5484

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

Your error might not be in the input files at all. It says:
DEF_VAR - unable to define variable: Tobc_in
in NetCDF file: /scratch/gh9/mx3818/waom/output_1996_2015/
Do you have permission to write to this /scratch/gh9/mx3818/waom/ directory? Does it exist?
by kate
Mon Aug 30, 2021 3:35 pm
Forum: ROMS Discussion
Topic: Open boundary condition set up
Replies: 3
Views: 5412

Re: Open boundary condition set up

You can do the OBC via the ana_ files too. Check out the ana_m2obc.h for example.
by kate
Fri Aug 13, 2021 10:12 pm
Forum: ROMS Discussion
Topic: Multiple Wind Field
Replies: 3
Views: 5136

Re: Multiple Wind Field

Yes, it doesn't care if you have one file or five. The variable names and dimensions all have to be appropriate to their fields.
by kate
Thu Aug 12, 2021 6:54 pm
Forum: ROMS Discussion
Topic: Multiple Wind Field
Replies: 3
Views: 5136

Re: Multiple Wind Field

You can merge them before having ROMS read them and regrid/rotate them if they are both on lat/lon grids of the same resolution. You can copy the ROMS code for reading then regrid/rotating winds to also read/rotate/regrid say Unwind2 and Vwind2. Then you can come up with some means of merging them i...
by kate
Wed Aug 11, 2021 5:49 pm
Forum: ROMS Discussion
Topic: MPI - tiling on POWER8
Replies: 6
Views: 9425

Re: MPI - tiling on POWER8

I would say that any time the answer changes for different tilings, you have a bug. To debug these things, run both tilings for just a timestep and plot the differences between solutions. Which field changes first? If you run 1x4 and 4x1, do you get a grid pattern in the diffs of three vertical stri...
by kate
Sun Aug 01, 2021 7:09 pm
Forum: ROMS Discussion
Topic: Introducing Eulerian tracer during a simulation - flushing time
Replies: 18
Views: 28930

Re: Introducing Eulerian tracer during a simulation - flushing time

I gave up on offline bio because it fought with wetting and drying and all my domains have wetting and drying. Sorry, I probably left it in some half-baked stage.
by kate
Sat Jul 31, 2021 1:27 pm
Forum: ROMS Discussion
Topic: How to save monthly data in average file?
Replies: 3
Views: 5972

Re: How to save monthly data in average file?

There are models which know about the different months, but ROMS isn't one of them. You could add that feature with some effort. You could run for 31 days to average for January, then restart and run for x days for February.
by kate
Fri Jul 30, 2021 5:08 pm
Forum: ROMS Discussion
Topic: ERROR: Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Replies: 10
Views: 12982

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

/home/markus/roms_project2/NORSJO2/Build_romsG/omega.f90:215
Can you show us what is on this line? Each person's omega.f90 can differ from the others due to differing cpp options.
by kate
Fri Jul 30, 2021 5:05 pm
Forum: ROMS Discussion
Topic: How to save monthly data in average file?
Replies: 3
Views: 5972

Re: How to save monthly data in average file?

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

I typically save daily, one record per file, rename the files to have the date in the filename, then average to get monthlies.
by kate
Thu Jul 29, 2021 6:22 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 22078

Re: ROMS grid for conservative remapping

You'd have to try a polar projection instead of Lambert conic. Is that supported by your software?
by kate
Thu Jul 29, 2021 5:31 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 22078

Re: ROMS grid for conservative remapping

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

Your domain is similar but different from my Arctic domains. Mine cover all the Bering, but less of the Atlantic.
by kate
Wed Jul 28, 2021 11:01 pm
Forum: ROMS Discussion
Topic: Introducing Eulerian tracer during a simulation - flushing time
Replies: 18
Views: 28930

Re: Introducing Eulerian tracer during a simulation - flushing time

Yes, I think that should work. There are a few ana_trc_psource.h files in https://github.com/kshedstrom/Apps, mostly (all?) for steady tracer sources. They are meant to go with my ROMS fork so I have no idea how incompatible the trunk code is these days.
by kate
Wed Jul 28, 2021 5:10 pm
Forum: ROMS Adjoint
Topic: INP_PAR, PHYPAR: Problems finding input file.
Replies: 7
Views: 14127

Re: INP_PAR, PHYPAR: Problems finding input file.

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

Code: Select all

// global attributes:
		:type = "ROMS grid file" ;
by kate
Tue Jul 27, 2021 10:48 pm
Forum: ROMS Discussion
Topic: Incorrect water velocity with open boundaries
Replies: 3
Views: 5337

Re: Incorrect water velocity with open boundaries

Is this a time when there should be full pack ice preventing the gyre? I had to have really strong nudging on the ice fields to make things sort of behave.
by kate
Tue Jul 27, 2021 3:57 pm
Forum: ROMS Adjoint
Topic: INP_PAR, PHYPAR: Problems finding input file.
Replies: 7
Views: 14127

Re: INP_PAR, PHYPAR: Problems finding input file.

INP_PAR:FIND_FILE - empty file name string for standard input script KeyWord: SSFNAME
Do you have a line for SSFNAME? That is a newish requirement.
by kate
Tue Jul 27, 2021 3:55 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 22078

Re: ROMS grid for conservative remapping

Yes, gridpak on github. What do you want in an Arctic grid? I've got two you could try as well.
by kate
Tue Jul 27, 2021 3:52 pm
Forum: ROMS Discussion
Topic: Introducing Eulerian tracer during a simulation - flushing time
Replies: 18
Views: 28930

Re: Introducing Eulerian tracer during a simulation - flushing time

I'd think it would be easier to use a restart file. Would this be a problem for some reason?
by kate
Mon Jul 26, 2021 6:57 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 22078

Re: ROMS grid for conservative remapping

Rob Cermak has been working on https://github.com/ESMG/gridtools for making MOM6 grids, including handling polar grids. There's a ROMS-to-MOM6 grid tool and one could easily make the reverse. I make my Arctic grids using old, old grid tools which still work and still produce the psi fields along wit...
by kate
Mon Jul 26, 2021 5:41 pm
Forum: ROMS Discussion
Topic: Incorrect water velocity with open boundaries
Replies: 3
Views: 5337

Re: Incorrect water velocity with open boundaries

I assume you know what I used for a regional Beaufort domain. I would go back to the RadNud option and also use nudging to climatology. If it's blowing up due to high speeds, where is that happening? Is that the usual vertical instability needing a short, short timestep or something else? As for you...
by kate
Fri Jul 23, 2021 6:14 pm
Forum: ROMS Discussion
Topic: ROMS grid for conservative remapping
Replies: 12
Views: 22078

Re: ROMS grid for conservative remapping

How did you make your grid? Some grid generators add more points to the outside of the model domain than others. You can just extrapolate what you need from the interior. Or if all the lat_rho, lon_rho values are zero, then there's a problem in the generation phase.
by kate
Tue Jul 20, 2021 7:05 pm
Forum: ROMS Ice
Topic: blow-up in first time step, using glorys and ERA5
Replies: 8
Views: 11135

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

I'm sure I've said this a number of times before, but it's time to develop some debugging skills. Plot the results after one timestep, try a shorter timestep just in case. Look to see what is going bad and where. If you want ice, I'd keep it on since turning it off isn't helping. The ice-free troubl...
by kate
Tue Jul 20, 2021 6:43 pm
Forum: ROMS Discussion
Topic: tide-calibration
Replies: 7
Views: 6271

Re: tide-calibration

Another option for fussing is the bottom drag. You can make a spatially variable bottom drag and modify it to get a better match.
by kate
Tue Jul 20, 2021 6:42 pm
Forum: ROMS Discussion
Topic: DIURNAL_SRFLUX and cloud fraction
Replies: 3
Views: 5845

Re: DIURNAL_SRFLUX and cloud fraction

The best place to search is the code itself. The file to look at is ROMS/Functionals/ana_srflux.h, which has options both including ALBEDO_CLOUD and not including it.
by kate
Fri Jul 16, 2021 7:01 pm
Forum: ROMS Problems
Topic: Boundary forcing error (t3dbc_im)
Replies: 8
Views: 14232

Re: Boundary forcing error (t3dbc_im)

If you can get xxgdb to work, wonderful! I would expect it to be fine as long as your job fits onto one core/process.
by kate
Wed Jul 14, 2021 6:28 pm
Forum: ROMS Problems
Topic: Boundary forcing error (t3dbc_im)
Replies: 8
Views: 14232

Re: Boundary forcing error (t3dbc_im)

I would look at this in a debugger, but lacking that, try print statements. You know it's something to do with dTdt or dTdx, so print them and the things that go into them. It's happening early enough in the run that this shouldn't be too insane. Print the i,j,k values so you know which point(s) are...
by kate
Mon Jul 12, 2021 9:49 pm
Forum: ROMS Ice
Topic: blow-up in first time step, using glorys and ERA5
Replies: 8
Views: 11135

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

GET_2DFLD - snow fall rate, 1998-01-15 03:00:00.00 (Grid=01, Rec=0000114, Index=1, File: final_snow_1998.nc) (Tmin= 18263.0000 Tmax= 18627.8750) t = 18277.1250 (Min = 1.00000000E+35 Max = -1.00000000E+35) regrid = T You've got some crazy snow fall rates here. The ice frazil thing can be triggered b...
by kate
Mon Jun 28, 2021 4:53 pm
Forum: ROMS Problems
Topic: cannot make bry file larger than 2g
Replies: 3
Views: 3920

Re: cannot make bry file larger than 2g

Yes, old netcdf files had a 2 GB limit. You can make a bunch of under 2 GB files and ask ROMS to read from one, then the next, then the next. Or you can convert them to a newer netcdf format (possibly even with compression) and concatenate them into one file.
by kate
Mon Jun 21, 2021 4:28 pm
Forum: ROMS Discussion
Topic: Issue of exceptionally low velocity
Replies: 8
Views: 15421

Re: Issue of exceptionally low velocity

How large are your wind stresses?
by kate
Fri Jun 18, 2021 5:28 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

Why don't you look through the trunk code examples to see what they use?
#undef MIX_GEO_TS
#define MIX_S_TS
I would swap these.
# define LI_FOX_KEMPER
This is not in the trunk.
by kate
Fri Jun 18, 2021 4:47 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

The trunk code does not have CCSM_FLUX, nor does it have all those albedo options. You should use the .h file consistent with your code.
by kate
Thu Jun 10, 2021 3:58 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

TIME_REF = 2000101.0d0
I think it thinks you have year 200 instead of year 2000. Try adding another 0.
by kate
Wed Jun 09, 2021 8:40 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

Woah! Where did you get that DSTART? It should be the number of days between your time origin (2000) and your starting time (2013?). That would make 13*365 plus the number of leap days in there, so 4749 days.
by kate
Wed Jun 09, 2021 6:16 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

So, do you know what to do next? You need to change your TIME_REF to match that of your forcing files. I have: ! DSTART = 29226.5d0 ! days (1980) DSTART = 42003.5d0 ! days (2015) TIDE_START = -1.0d0 ! days TIME_REF = 19000101.0d0 ! yyyymmdd.dd
by kate
Wed Jun 09, 2021 5:36 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

What about trying "ncdump -h" on one of these things? I get: netcdf JRA55DO_1.5_rain_2020 { dimensions: lon = 640 ; lat = 320 ; time = UNLIMITED ; // (2928 currently) variables: double lon(lon) ; lon:units = "degrees_east" ; lon:valid_min = 0. ; lon:valid_max = 359.4375 ; lon:lon...
by kate
Wed Jun 09, 2021 5:06 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

What is the time variable like in one of these things? You need one common time origin for *everything*.
by kate
Wed Jun 09, 2021 4:33 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

You have only one month of forcing per file? You can string them together in the roms.in file. I have my forcing files with one year each and string them together from one year to the next: NFFILES == 14 ! number of forcing files FRCNAME == /center1/AKWATERS/kate/JRA55-do/JRA55DO_1.4_Pair_2015.nc | ...
by kate
Tue Jun 08, 2021 10:17 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

#define MIX_S_TS
This is OK if your bottom is flat, otherwise it leads to mixing along s-surfaces which can be unrealistic. I don't see anything else wrong, but I could be missing something, who knows.
by kate
Tue Jun 08, 2021 5:57 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

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

Note that I have been using BULK_FLUXES (with CCSM_FLUXES) and atmospheric reanalysis fields for over a decade now.
by kate
Tue Jun 08, 2021 4:52 pm
Forum: ROMS Bugs
Topic: ROMS4 built with PIO, freeze on creating history file
Replies: 17
Views: 28803

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

get_idata.f90(73): error #6404: This name does not have a type, and must have an explicit type. [ING] & TIDE(ing)%pioFile, & -------------------------------^ compilation aborted for get_idata.f90 (code 1) make: *** [/nesi/project/mocean03294/NZB_3/build/get_idata.o] Error 1 Looks to me like...
by kate
Tue Jun 08, 2021 4:50 pm
Forum: ROMS Discussion
Topic: Wrong Temperature and salinity outputs
Replies: 23
Views: 40955

Re: Wrong Temperature and salinity outputs

Your model is salty at the surface when it should be fresh. What are you using for fresh water forcing?
by kate
Sat May 29, 2021 2:36 pm
Forum: ROMS Discussion
Topic: Atmospheric forcing for child grid
Replies: 3
Views: 4122

Re: Atmospheric forcing for child grid

It could be that ROMS only checks once when deciding whether to remap or not. The check happens at line 226 of nf_fread2d.F.
by kate
Thu May 27, 2021 5:17 pm
Forum: ROMS Discussion
Topic: Boundary Condition Choice
Replies: 4
Views: 6500

Re: Boundary Condition Choice

Adding a strip of land-masked cells is fair amount of work.
This is why it is good to know your tools. We have landmask editing in both Matlab and Python. Also, it is worthwhile to learn to edit netcdf files in SOME programming language.
by kate
Thu May 27, 2021 1:05 am
Forum: ROMS Discussion
Topic: WET_DRY compilation problem
Replies: 10
Views: 21774

Re: WET_DRY compilation problem

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

Code: Select all

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

Code: Select all

INI(ng)%Vid(idVwet)=Vindex
instead.
by kate
Thu May 27, 2021 12:00 am
Forum: ROMS Discussion
Topic: WET_DRY compilation problem
Replies: 10
Views: 21774

Re: WET_DRY compilation problem

I would look for idRwet and friends in your varinfo.dat. They need to be there.
by kate
Wed May 26, 2021 5:56 pm
Forum: ROMS Discussion
Topic: Which tool is the stablest tools to create ROMS grid?
Replies: 56
Views: 187353

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

An Arakawa C-grid is supposed to be staggered, with different sizes of the different variables. I haven't used panoply, but you need to teach your plotting tools about the staggered C-grid.
by kate
Fri May 14, 2021 4:30 pm
Forum: ROMS Discussion
Topic: grid-tide blowup
Replies: 3
Views: 4515

Re: grid-tide blowup

So the same configuration runs with 16 vertical levels and blows up with 30? This is not surprising. When you add more vertical levels, the vertical advection requires a shorter timestep. Your run ran long enough that it seems fine except for the timestep limitation. Try a smaller DT. Your vertical ...
by kate
Fri May 07, 2021 5:11 pm
Forum: ROMS Ice
Topic: Landfast ice
Replies: 2
Views: 6308

Re: Landfast ice

You may well be right, but as I said elsewhere, I'm no longer maintaining that code.
by kate
Fri May 07, 2021 5:08 pm
Forum: ROMS Ice
Topic: How to use SEAICE
Replies: 3
Views: 6905

Re: How to use SEAICE

It is true that Paul Budgell put the ICE_SHOREFAST in there for the Caspian, but that was a long, long time ago. The ICE_LANDFAST is what I would use now, it's the Lemieux landfast ice parameterization which is also in CICE6. If you need it in CICE5, I can help with that. Why would you read the manu...
by kate
Fri May 07, 2021 4:36 pm
Forum: ROMS Ice
Topic: How to use SEAICE
Replies: 3
Views: 6905

Re: How to use SEAICE

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

For ice with ROMS, the Norwegians are supporting their metroms package (but don't try to learn git from their example).
by kate
Wed May 05, 2021 6:03 pm
Forum: ROMS Discussion
Topic: How to split the advection and diffusion term
Replies: 4
Views: 7914

Re: How to split the advection and diffusion term

The vertical diffusivity is in Akt, which is dimensioned by three spatial dimensions and the NT (number of tracers) dimension. You can set some to zero. There will still be implicit changes which I don't think you can do anything about other than try different advection schemes.
by kate
Tue May 04, 2021 6:28 pm
Forum: ROMS Discussion
Topic: How to split the advection and diffusion term
Replies: 4
Views: 7914

Re: How to split the advection and diffusion term

In modeling, there is always implicit diffusion from your advection operator. You can reduce this by going to a fourth-order advection scheme. I use the third-order one with its implicit diffusion, then turn off explicit diffusion by turning off the cppdefs for it. Vertical diffusion is trickier. Pe...
by kate
Mon May 03, 2021 12:23 am
Forum: ROMS Discussion
Topic: Blow up ( River run off)
Replies: 7
Views: 11247

Re: Blow up ( River run off)

Did you provide river tracer values?
by kate
Mon Apr 26, 2021 5:27 pm
Forum: ROMS Discussion
Topic: What's the difference between online and offline running?
Replies: 2
Views: 4105

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

As I posted elsewhere, I've given up on offline biology. The point of it was that you run the physics once, saving daily outputs. Then you read those fields in as "climalotogy" for running the biology. The dream is that you can maybe take a longer timestep when you only have the biology go...
by kate
Mon Apr 26, 2021 5:21 pm
Forum: ROMS Bugs
Topic: main3d_offline.F and step3d_t.F in ROMS 3.9
Replies: 2
Views: 4715

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

If this is my code, I've given up on OFFLINE_BIOLOGY. I sort of had it working in the "main" branch, not the default "kate_svn" branch. But for me, I have wetting and drying and it wasn't doing the right thing in the dry parts, nor did it even know if it was wet or dry that day.
by kate
Sun Apr 25, 2021 7:03 pm
Forum: ROMS Discussion
Topic: Blow up
Replies: 2
Views: 4407

Re: Blow up

This is when you need to become a detective. Which field is blowing up. You say it is in the land? Is that the only place going bad?
by kate
Sun Apr 25, 2021 7:01 pm
Forum: ROMS Discussion
Topic: A strange error while open the biological options
Replies: 5
Views: 8735

Re: A strange error while open the biological options

I haven't used BIO_UMAINE since Hernan changed the advection scheme choices. Good catch, John. As for my github code, I have stopped updating it because updates can be disruptive and I don't want to spend the time sorting them out. Mark Hadfield is keeping his github code up to date. If you find any...
by kate
Sat Apr 24, 2021 7:58 pm
Forum: ROMS Discussion
Topic: A strange error while open the biological options
Replies: 5
Views: 8735

Re: A strange error while open the biological options

The check you are running into is in diag.F: IF (maxbio(ibt,ng).gt.max_bio(ibt)) THEN It looks like you have max_bio set to 10000. Does that make sense for the units you are using? You can change it if 10000 is a valid number for your BGC model. I probably added the check for COSINE, but then kept i...
by kate
Fri Apr 23, 2021 10:19 pm
Forum: ROMS Discussion
Topic: problem in open boundary
Replies: 5
Views: 8881

Re: problem in open boundary

That's great that the model is running without any problems. You're all set, then, right? You need to look at your solution to see if you are happy with it. Are you happy with it? If not, there are steps you can take to possibly improve your boundary solution, but nothing is guaranteed when it comes...
by kate
Fri Apr 23, 2021 5:41 pm
Forum: ROMS Discussion
Topic: problem in open boundary
Replies: 5
Views: 8881

Re: problem in open boundary

How are you getting your ROMS information? There is both a manual and a wiki. The wiki page might help you. The manual has much the same information and also examples containing open boundaries.
by kate
Fri Apr 23, 2021 5:39 pm
Forum: ROMS Discussion
Topic: add passive tracer
Replies: 9
Views: 14305

Re: add passive tracer

I see the wiki page on FLOATS is still empty. There is probably something about floats in the manual, though.
by kate
Fri Apr 23, 2021 1:29 am
Forum: ROMS Discussion
Topic: add passive tracer
Replies: 9
Views: 14305

Re: add passive tracer

The FLOATS option is a whole different can of worms. Is that what you want? Online or offline?
by kate
Thu Apr 22, 2021 11:33 pm
Forum: ROMS Discussion
Topic: problem in open boundary
Replies: 5
Views: 8881

Re: problem in open boundary

What sort of open boundary do you want? In the UPWELLING case, the southern edge is in shallow water and typically has a wall. Are you changing the bathymetry? Are you providing fields on the open boundary? I never use a sponge in the ROMS sense of the word. I do use nudging to a climatology, which ...
by kate
Thu Apr 22, 2021 3:29 am
Forum: ROMS Discussion
Topic: add passive tracer
Replies: 9
Views: 14305

Re: add passive tracer

You need these as well:

Code: Select all

# define ANA_BPFLUX        /* analytical bottom passive tracers fluxes */
# define ANA_SPFLUX
unless you want the top and bottom tracer fluxes to be non-zero.
by kate
Wed Apr 21, 2021 5:27 pm
Forum: ROMS Discussion
Topic: add passive tracer
Replies: 9
Views: 14305

Re: add passive tracer

First, you turn on T_PASSIVE and set NPT in roms.in. For the initial conditions, ANA_PASSIVE can be used, otherwise you'll have to put the initial conditions into a netcdf file. I've usually initialized with zero via ANA_PASSIVE, then used sources to introduce the passive dye locally. What is your s...
by kate
Mon Apr 19, 2021 6:07 pm
Forum: Job Opportunities
Topic: Position in Colorado
Replies: 0
Views: 4347

Position in Colorado

The University of Colorado Cooperative Institute for Environmental Sciences (CIRES) jointly with the NOAA/Physical Sciences Lab is hiring an associate scientist in the area of ocean data analysis/visualization. Here is a brief position description: The chosen candidate will assist in the development...
by kate
Mon Apr 19, 2021 5:50 pm
Forum: Job Opportunities
Topic: Postdoc at Princeton/GFDL
Replies: 1
Views: 4854

Re: Postdoc at Princeton/GFDL

This position is closing soon. If you intend to apply, get your application submitted now.
by kate
Fri Apr 16, 2021 4:53 pm
Forum: ROMS Discussion
Topic: Timestamp of ROMS diagnostic files
Replies: 1
Views: 3821

Re: Timestamp of ROMS diagnostic files

Yes, the diagnostics are time-averaged.
by kate
Mon Apr 12, 2021 5:28 pm
Forum: ROMS Problems
Topic: segmentation fault when running the COAWST model
Replies: 16
Views: 19158

Re: segmentation fault when running the COAWST model

Make sure NBCFILES is defined. Some roms.in files have it, some do not. If using COAWST, you need to have it.
by kate
Sat Apr 10, 2021 7:39 pm
Forum: ROMS Discussion
Topic: Direction of Uwind and Vwind
Replies: 2
Views: 3722

Re: Direction of Uwind and Vwind

For the incoming 2-D forcing, it depends. ROMS will check the dimensions of each field you provide. If they match that of your ROMS grid, it assumes Uwind and Vwind are aligned in the directions of the grid. If not, it assumes it needs to do the interpolation and the rotation to the ROMS grid.
by kate
Mon Apr 05, 2021 4:14 pm
Forum: ROMS Problems
Topic: How to solve the speed trouble on the open boundaries?
Replies: 3
Views: 6435

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

I use SODA as my initial condition, no spin-up period. You can try a spin-up and see how much drift you get.
by kate
Sun Apr 04, 2021 5:18 pm
Forum: ROMS Problems
Topic: How to solve the speed trouble on the open boundaries?
Replies: 3
Views: 6435

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

I typically add a nudging to a monthly climatology in a band around the edge of the domain, ramping to zero in the middle. Note that this will overwrite TNUDG and friends in the default ROMS code.
by kate
Tue Mar 30, 2021 5:07 pm
Forum: ROMS Discussion
Topic: Era5 data is not read by the ROMS
Replies: 7
Views: 8352

Re: Era5 data is not read by the ROMS

GET_2DFLD - surface u-wind component, 2013-01-01 00:00:00.00 (Grid=01, Rec=1, Index=1, File: era5_u10_year_2013_roms.nc) (Tmin= 0.0000 Tmax= 30.9583) t = 0.0000 (Min = 1.00000000E+35 Max = -1.00000000E+35) regrid = T GET_2DFLD - surface v-wind component, 2013-01-01 00:00:00.00 (Grid=01, Rec=1, Inde...
by kate
Mon Mar 29, 2021 8:11 pm
Forum: ROMS Discussion
Topic: Era5 data is not read by the ROMS
Replies: 7
Views: 8352

Re: Era5 data is not read by the ROMS

NETCDF_GET_TIME_1D - error while inquiring ID for variable: srf_time in input file: era5_msdwswrf_year_2013_roms.nc What does "ncdump -h era5_msdwswrf_year_2013_roms.nc" look like? Is there a time variable? What is it called? ROMS is looking for srf_time and it could have gotten this from...
by kate
Sat Mar 27, 2021 2:45 am
Forum: ROMS Discussion
Topic: ROMS blowing up problem
Replies: 19
Views: 23359

Re: ROMS blowing up problem

Same answer as above - use a shorter timestep and look more closely at your model output files.
by kate
Tue Mar 23, 2021 5:00 pm
Forum: ROMS Problems
Topic: Speeding up ROMS Model simulation
Replies: 6
Views: 10872

Re: Speeding up ROMS Model simulation

You know your DT and you should be able to figure out how many timesteps per day from that. Say DT=120 leads to 720 steps/day. Three days of steps is therefore 2160 steps.
by kate
Sun Mar 21, 2021 6:25 pm
Forum: ROMS Problems
Topic: Speeding up ROMS Model simulation
Replies: 6
Views: 10872

Re: Speeding up ROMS Model simulation

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

Why not use MPI?
by kate
Sun Mar 21, 2021 6:22 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

The debugger I use is called totalview. There is also ddt. Both are quite expensive, but the supercomputer center I use pays for the license. For free, there is gdb, which works if you run on just one processor. There may be a gui (ddd?) that can make it easier to use, but using these things is stil...
by kate
Sat Mar 20, 2021 5:27 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

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

Personally, I would run this in the debugger to watch it go bad.
by kate
Thu Mar 18, 2021 4:49 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

You know it got to ANA_INITIAL because it printed stuff from there. I think the next calls it would make from initial.F are these: CALL set_depth0 (ng, tile, iNLM) CALL set_depth (ng, tile, iNLM) CALL set_massflux (ng, tile, iNLM) I would add print statements before these, then after these, then aft...
by kate
Tue Mar 16, 2021 4:25 pm
Forum: ROMS Problems
Topic: Fatal erorr after update to ubuntu 20.04
Replies: 2
Views: 5104

Re: Fatal erorr after update to ubuntu 20.04

What I would do is recompile netcdf-fortran. Did you compile it yourself before or use the one from "apt install"?
by kate
Tue Mar 16, 2021 6:41 am
Forum: ROMS Discussion
Topic: ROMS blowing up problem
Replies: 19
Views: 23359

Re: ROMS blowing up problem

I'll say what I always say: try a shorter timestep and look more closely at your solution to see where it is blowing up.
by kate
Sun Mar 14, 2021 3:04 pm
Forum: ROMS Installation
Topic: upwelling - linux-ifort.mk compilation error
Replies: 5
Views: 8313

Re: upwelling - linux-ifort.mk compilation error

Do you have USE_NETCDF4? Do you have netcdf installed properly?
by kate
Sun Mar 14, 2021 7:37 am
Forum: ROMS Installation
Topic: upwelling - linux-ifort.mk compilation error
Replies: 5
Views: 8313

Re: upwelling - linux-ifort.mk compilation error

I think you want to have USE_MPIF90 turned on.
by kate
Mon Mar 08, 2021 7:24 pm
Forum: ROMS Discussion
Topic: The defination of Hz
Replies: 2
Views: 3666

Re: The defination of Hz

Hz is the height of the vertical grid box, which you could call Hz=∂z/∂σ.
For consistency between the baroclinic and barotropic solutions, you also need D=ΣHz.
by kate
Mon Mar 08, 2021 7:19 pm
Forum: Job Opportunities
Topic: Postdoc at Princeton/GFDL
Replies: 1
Views: 4854

Postdoc at Princeton/GFDL

I wanted to let everyone know that Princeton is now accepting applications for a Princeton/GFDL postdoc to further develop the regional capabilities of the MOM6 ocean model: https://puwebp.princeton.edu/AcadHire/apply/application.xhtml?listingId=19521 The position would include algorithmic developm...
by kate
Sun Mar 07, 2021 5:25 pm
Forum: ROMS Discussion
Topic: Modify UPWELLING case to a flat bottom, etc.
Replies: 3
Views: 6545

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

I would not edit UPWELLING, but rather create a new name for your case. Then search the whole code for UPWELLING so you know what files to look in. For the flat bathymetry, the "else" case on ana_grid.h should take care of that for you. For the wind stress, you should be able to find that ...
by kate
Fri Mar 05, 2021 5:44 pm
Forum: ROMS Discussion
Topic: various time indices in ROMS
Replies: 2
Views: 5607

Re: various time indices in ROMS

There is some discussion of the timestepping in the roms manual . Most of them point to the old/new time which alternates between 1 and 2, while 3 is always a working time level for tracers. Note: on restart, the model doesn't save these things and always assumes whatever is true for the first step....
by kate
Tue Mar 02, 2021 7:19 pm
Forum: ROMS Discussion
Topic: MPI_ERR_TRUNCATE
Replies: 4
Views: 7872

Re: MPI_ERR_TRUNCATE

initial_ 219 initial.f90
What is on line 219 of your initial.f90? This would be in your scratch directory.
by kate
Tue Mar 02, 2021 6:03 pm
Forum: ROMS Discussion
Topic: nested grid with pyroms: tutorial and python routines
Replies: 15
Views: 24506

Re: nested grid with pyroms: tutorial and python routines

Yes, you got it.

I don't use Matlab if I can help it. You should get the script from the ROMS Matlab repository.
by kate
Tue Mar 02, 2021 8:20 am
Forum: ROMS Discussion
Topic: nested grid with pyroms: tutorial and python routines
Replies: 15
Views: 24506

Re: nested grid with pyroms: tutorial and python routines

Online nesting requires a special 1:3 or 1:5 relationship between the grids, as in Lake Jersey. Both models are run at the same time and the computer spends a lot of time communicating between the domains for you. That's what the contact stuff is for. I did this only once and it was pretty painfully...
by kate
Tue Mar 02, 2021 8:01 am
Forum: ROMS Discussion
Topic: nested grid with pyroms: tutorial and python routines
Replies: 15
Views: 24506

Re: nested grid with pyroms: tutorial and python routines

You are talking about doing online nesting in that case. I have a lot less experience with that than with offline nesting.
by kate
Tue Mar 02, 2021 7:19 am
Forum: ROMS Discussion
Topic: nested grid with pyroms: tutorial and python routines
Replies: 15
Views: 24506

Re: nested grid with pyroms: tutorial and python routines

When doing offline nesting, each domain is a fully independent domain. You run the larger, coarser one first, then use fields from that domain to create the initial/boundary files for the smaller domain. This creation of boundary files for the child grid happens offline, for instance with pyroms, bu...
by kate
Sun Feb 28, 2021 6:34 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

I always have USE_MPIF90 on so that it knows where to find mpif.h.
Are you using COAWST? It is recommended to use that code when coupling to SWAN. Not that I've done it with any of the versions.
by kate
Wed Feb 17, 2021 5:53 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

All those Dout flags control the output, not the tides. I have this section in my .h file: /* tides */ #define LTIDES #ifdef LTIDES # if defined AVERAGES && !defined USE_DEBUG # define FILTERED # endif # define SSH_TIDES # define UV_TIDES # define ADD_FSOBC # define ADD_M2OBC # undef RAMP_TI...
by kate
Wed Feb 17, 2021 5:48 pm
Forum: ROMS Discussion
Topic: Discharge a chemical substance
Replies: 3
Views: 4403

Re: Discharge a chemical substance

There are people who study oil spills, maybe not on this forum though. What I know of it is that they simulate a spill for all those cases and see where it goes. For some hypothetical spill, you want to be prepared for all the cases, all the sea levels, all the wind directions. Is it from a leaky ba...
by kate
Sat Feb 13, 2021 2:29 pm
Forum: ROMS Tools and Techniques
Topic: Error to plot by the ROMS plotting package
Replies: 17
Views: 26033

Re: Error to plot by the ROMS plotting package

You need to clean out the old build and start fresh. Getting that error in debug mode should give you more useful information than that.
by kate
Fri Feb 12, 2021 7:39 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

Simply add statements such as these marked with the plus signs: diff --git a/ROMS/Nonlinear/initial.F b/ROMS/Nonlinear/initial.F index 6e20ae7d9..25fd9c4e6 100644 --- a/ROMS/Nonlinear/initial.F +++ b/ROMS/Nonlinear/initial.F @@ -677,6 +677,7 @@ END DO END IF #endif + print, *, "after get_state&...
by kate
Thu Feb 11, 2021 6:36 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

Once the model gets the initial conditions, it should start reading in your surface forcing fields. I see you have BULK_FLUXES, so it should read in shortwave, longwave, winds, etc. There's no mention of that in your output so I have no idea what went wrong. There is a listing of your input forcing ...
by kate
Wed Feb 10, 2021 7:13 pm
Forum: ROMS Discussion
Topic: How to setup the river discharges with only salinity but no temperature?
Replies: 6
Views: 6675

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

For numerical stability you must give it something other than the water temperature at that grid point. Using the water temperature there is an unconditionally unstable numerical scheme - downwind advection. In MOM6, the default is to use air temperature instead, something you'd have anyway if you w...
by kate
Wed Feb 10, 2021 6:35 pm
Forum: ROMS Discussion
Topic: How to setup the river discharges with only salinity but no temperature?
Replies: 6
Views: 6675

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

It doesn't make sense numerically to do what you want. As you see, the thing will become unstable. Lacking river temperatures, some have used air temperature instead.
by kate
Mon Feb 08, 2021 7:14 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

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

Code: Select all

ncatted -a time,,m,c,'time'
Note that the missing value between two commas means apply to all variables.
by kate
Mon Feb 08, 2021 5:20 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

You just need to change some attributes in your frc file. You now have: double time(time) ; time:long_name = "time since intialization" ; time:units = "days since 2011-01-01 00:00:00" ; time:calendar = "gregorian" ; float Uwind(time, lat, lon) ; Uwind:long_name = "...
by kate
Sun Feb 07, 2021 10:48 pm
Forum: ROMS Installation
Topic: Compilation error for plotting package
Replies: 10
Views: 13559

Re: Compilation error for plotting package

make: /opt/gfortransoft/serial/netcdf4/bin/nc-config: Command not found
If you have a modern netcdf-c and netcdf-fortran correctly installed, nc-config should be on your search path. Did you install them? What operating system is this? Your laptop or a major computing platform?
by kate
Thu Feb 04, 2021 6:01 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

From your frc file:

Code: Select all

	double time(time) ;
		time:long_name = "time since intialization" ;
		time:units = "days since 2011-01-01 00:00:00" ;
		time:calendar = "gregorian" ;
Can you use 20110101 as your time origin for everything else?
by kate
Tue Feb 02, 2021 6:09 am
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

I always have a TIME_REF of 19000101, which is year 1900, day 1. What year is your time origin? My DSTART is the offset in days from that time, 29225 for 1980, something larger for more recent times. Again, how does the time look in the forcing and what are its attributes?
by kate
Tue Feb 02, 2021 4:00 am
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

The forcing times need to be along the same time axis as everything else. What are the times in your files? It might be easier to make ROMS consistent with them rather than vice versa.
by kate
Sat Jan 30, 2021 3:48 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 110853

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

NFFILES == 1 ! number of unique forcing files FRCNAME == frc_TPXO9_alderneyrace_09Dec2068.nc | ! forcing file 1, grid 1 (tidal forcing) frc_watl_ERA5_bulkflux_new_201805.nc !(wind forcing) This should instead be: NFFILES == 2 ! number of unique forcing files FRCNAME == frc_TPXO9_alderneyrace_09Dec2...
by kate
Thu Jan 28, 2021 5:11 pm
Forum: ROMS Discussion
Topic: How to run COAWST model with real-time data
Replies: 6
Views: 8211

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

I went through this exercise in pyroms, now in the pyroms/examples/Arctic_HYCOM_GLBy directory.
by kate
Wed Jan 27, 2021 4:59 pm
Forum: ROMS Discussion
Topic: Use Bulk Formula or Net Flux Form
Replies: 4
Views: 5796

Re: Use Bulk Formula or Net Flux Form

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

If you don't use bulk_fluxes, it is advised to also use the dQdSST term to account for your SST differing from that used to compute the fluxes.
by kate
Tue Jan 26, 2021 5:54 pm
Forum: ROMS Discussion
Topic: Use Bulk Formula or Net Flux Form
Replies: 4
Views: 5796

Re: Use Bulk Formula or Net Flux Form

Think about say the Gulf Stream or the Kuroshio. If your fluxes were computed when it was wobbling south, colder water would be present and the fluxes would reflect that. If your Gulf Stream was instead wobbling north, the fluxes would therefore be off. Instead, using BULK_FLUXES, you get the fluxes...
by kate
Mon Jan 25, 2021 6:29 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 21882

Re: problem in svn and nf_config

Code: Select all

NETCDF_CREATE - unable to create output NetCDF file:
roms_his.nc
call from: ROMS/Utility/def_his.F
NetCDF: Malformed URL
Found Error: 03 Line: 105 Source: ROMS/Utility/def_his.F
I don't think your problem is in varinfo.dat.
by kate
Mon Jan 25, 2021 5:29 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 21882

Re: problem in svn and nf_config

Wow, I've never seen that one before. I would check for hidden characters in the ocean.in file where you provide the file names. Or is that file somehow in DOS mode?
by kate
Sun Jan 24, 2021 8:25 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 21882

Re: problem in svn and nf_config

Code: Select all

chinook02.rcs.alaska.edu 203% grep id3dPVI var*
varinfo.dat:  'id3dPVI'
varinfo.dat.cobalt:  'id3dPVI'
varinfo_jra.dat:  'id3dPVI'
I ran this in the Apps directory.
by kate
Sun Jan 24, 2021 7:32 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 21882

Re: problem in svn and nf_config

This is due to a change in the varinfo.dat file. Search through mine for that string idStr and you'll find it.
by kate
Sun Jan 24, 2021 7:42 am
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 21882

Re: problem in svn and nf_config

Just change that path to my nf-config to your path to your nf-config.
by kate
Sat Jan 23, 2021 7:21 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 21882

Re: problem in svn and nf_config

The version of netcdf-fortran doesn't matter, but it has to be compiled with the same version of gfortran as you are using. Just search for "netcdf-fortran download" and you find it. Then you need to follow the instructions for compiling it. Or if you have control of the computer, somethin...
by kate
Sat Jan 23, 2021 7:03 pm
Forum: ROMS Discussion
Topic: problem in svn and nf_config
Replies: 13
Views: 21882

Re: problem in svn and nf_config

I don't know that the svn error matters.
/import/home/kshedstrom/bin/nf-config
This is a hard-coded path on a computer here to my home-built netcdf-fortran. You'll have to change it.
by kate
Wed Jan 20, 2021 6:13 pm
Forum: ROMS Discussion
Topic: cmpiling error when using roms-kate_svn
Replies: 3
Views: 4852

Re: cmpiling error when using roms-kate_svn

It is failing to find the netcdf library, part of the build system. Since I don't use Hernan's build script, you'll have to figure out what's different between the two and do the appropriate thing.
by kate
Tue Jan 19, 2021 4:53 pm
Forum: ROMS Ecosystem
Topic: Problems with river input forcing when using NEMURO
Replies: 11
Views: 13492

Re: Problems with river input forcing when using NEMURO

Do you have coastal river sources? Are you providing values of the BGC tracers on them? They can easy go unstable if you don't provide values for all incoming tracers. Look at the global NEWS product for nutrient values. Don't worry about varinfo.dat. Best practice is to have the name of the time va...
by kate
Mon Jan 18, 2021 6:03 pm
Forum: ROMS Ice
Topic: How add ice
Replies: 8
Views: 14551

Re: How add ice

You should read the manual. It has sections on the ice and also on how to use git.
by kate
Sun Jan 17, 2021 10:30 pm
Forum: ROMS Ice
Topic: How add ice
Replies: 8
Views: 14551

Re: How add ice

My code is at: https://github.com/kshedstrom/roms. I'm not now finding an svn option, but you can download a tarball of it from that site. It has been over ten years since I've used svn...
by kate
Sun Jan 17, 2021 7:50 pm
Forum: ROMS Ice
Topic: How add ice
Replies: 8
Views: 14551

Re: How add ice

There is no ice in the ROMS trunk code. There is ice in my code on github, also in COAWST from John Warner. There is also ice in the metroms code on github, where they couple to a more complete ice model (CICE). As for forcing, if you are reading winds, air temp, etc. and using BULK_FLUXES, you are ...
by kate
Thu Jan 14, 2021 5:55 pm
Forum: ROMS Discussion
Topic: Curvilinear grid for ROMS
Replies: 4
Views: 5069

Re: Curvilinear grid for ROMS

Yes, I can make a grid like that. However, you want your corners to be right angles. Also, a boundary across the pack ice will be hard to make well-behaved. We had a grid with a boundary at Bering Strait and we didn't like how that behaved either. I guess it depends on what your goals are. How to do...
by kate
Wed Jan 13, 2021 6:06 pm
Forum: ROMS Ecosystem
Topic: Problems with river input forcing when using NEMURO
Replies: 11
Views: 13492

Re: Problems with river input forcing when using NEMURO

This is when you need to build up some debugging skills. You need to find out if the bio fields are sensible in the model, getting corrupted on output, or if they're just nuts everywhere. Feel free to add print statements at will.
by kate
Tue Jan 12, 2021 5:18 pm
Forum: ROMS Ecosystem
Topic: Problems with river input forcing when using NEMURO
Replies: 11
Views: 13492

Re: Problems with river input forcing when using NEMURO

It has to be something in the varinfo.dat. I seem to have both: 'river_fed' 'fed river source' 'mol.m-2.s-1' 'river_fed, scalar, series' 'runoff_time' 'idriver_fed' 'r2dvar' 1.0d0 and 'river_fed' 'river runoff Dissolved Iron' 'mol/kg' 'fed, scalar, series' 'ocean_time' 'idRtrc(ifed)' 'r3dvar' 1.0d0 ...
by kate
Sat Jan 09, 2021 2:27 pm
Forum: ROMS Tools and Techniques
Topic: NCL
Replies: 16
Views: 30997

Re: NCL

This is not the time to start learning NCL. Support for NCL development has been dropped and the focus is now on developing Python tools instead. While we have some plotting capability in pyroms, it too is now out of date, what with the rapid development in new Python tools. I am hardly the expert o...
by kate
Sat Jan 09, 2021 2:17 pm
Forum: ROMS Tools and Techniques
Topic: plot package problem
Replies: 21
Views: 31136

Re: plot package problem

by kate
Fri Jan 08, 2021 5:09 pm
Forum: ROMS Tools and Techniques
Topic: plot package problem
Replies: 21
Views: 31136

Re: plot package problem

unknown option: --flib Usage: nc-config
Try --flibs instead of --flib
by kate
Fri Jan 08, 2021 5:36 am
Forum: ROMS Tools and Techniques
Topic: plot package problem
Replies: 21
Views: 31136

Re: plot package problem

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

The warnings are a little concerning too, like maybe there's a version inconsistency.
by kate
Thu Jan 07, 2021 5:51 pm
Forum: ROMS Tools and Techniques
Topic: plot package problem
Replies: 21
Views: 31136

Re: plot package problem

cairo is a library which you'll need to link to as well. Try adding -lcairo to your link command.
by kate
Wed Jan 06, 2021 6:46 pm
Forum: ROMS Discussion
Topic: Erorr when applying rivers
Replies: 8
Views: 11094

Re: Erorr when applying rivers

Here's what one of my rivers files looks like: netcdf JRA-1.4_Arctic_rivers_1980 { dimensions: river_time = UNLIMITED ; // (366 currently) river = 18430 ; s_rho = 50 ; variables: double river_time(river_time) ; river_time:units = "days since 1900-01-01 00:00:00" ; river_time:long_name = &q...
by kate
Tue Jan 05, 2021 9:23 pm
Forum: ROMS Discussion
Topic: Erorr when applying rivers
Replies: 8
Views: 11094

Re: Erorr when applying rivers

Yes, exactly. How much do you want shallow and how much deep? For the coastal Gulf of Alaska, I use a linear profile, max at the surface, zero at the very bottom.
by kate
Tue Jan 05, 2021 8:03 pm
Forum: ROMS Discussion
Topic: Erorr when applying rivers
Replies: 8
Views: 11094

Re: Erorr when applying rivers

You could well be dividing by zero because it doesn't have the Vshape. Yes, you need it to be non-zero.
by kate
Thu Dec 31, 2020 3:01 am
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 19286

Re: Issues when running ROMS coupled with bio_UMAINE15 model

If you don't have a working debugger, I would add print statements in there to make sure everything is as you expect it to be. You can add a print of min(pm), max(pm), min(pn), max(pn). Whatever it takes.
by kate
Wed Dec 30, 2020 7:17 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 19286

Re: Issues when running ROMS coupled with bio_UMAINE15 model

758 CALL mp_exchange2d (ng, tile, model, 2, & 759 & LBi, UBi, LBj, UBj, & 760 & NghostPoints, & 761 & EWperiodic(ng), NSperiodic(ng), & 762 & pm, pn) It is unhappy with your pm, pn values.
by kate
Tue Dec 29, 2020 5:45 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 19286

Re: Issues when running ROMS coupled with bio_UMAINE15 model

It means it's trying to pass a bad value in an MPI call. You need to look up a level to:
758 analytical.f90
by kate
Mon Dec 28, 2020 5:32 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 19286

Re: Issues when running ROMS coupled with bio_UMAINE15 model

Now you need to make sure idpthR is in your varinfo.dat.
by kate
Sun Dec 27, 2020 6:09 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 19286

Re: Issues when running ROMS coupled with bio_UMAINE15 model

So now what's on this line?
read_phypar_ 2611 read_phypar.f90
If you're getting your code from Professor Peng, shouldn't you be asking him how to get it to run?
by kate
Fri Dec 25, 2020 5:43 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 19286

Re: Issues when running ROMS coupled with bio_UMAINE15 model

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

As for your line 2002, you still need to make sure your varinfo.dat has everything you need in it. Did professor Peng give you a working one?
by kate
Thu Dec 24, 2020 7:44 pm
Forum: ROMS Problems
Topic: Issues when running ROMS coupled with bio_UMAINE15 model
Replies: 14
Views: 19286

Re: Issues when running ROMS coupled with bio_UMAINE15 model

2002 mod_ncparam.f90 What is on line 2002 of your mod_ncparam.f90? Mine has: CASE ('idRtrc(icadet_calc)') You then need to see if your equivalent to idRtrc(icadet_calc) is in your varinfo.dat. The only varinfo.dat I have that might contain the CoSine stuff is this one: https://github.com/kshedstrom...
by kate
Wed Dec 23, 2020 6:58 pm
Forum: ROMS Discussion
Topic: blowing up error
Replies: 15
Views: 21862

Re: blowing up error

Do you want to have ice in the model? There are numerous options to do so, including my branch, COAWST, Metroms, and Scott Durski's branch. Metroms (on github) has a version coupled to the community CICE model, the most complete/mature of the ice models. On the other hand, before I had ice in the mo...
by kate
Wed Dec 23, 2020 5:45 pm
Forum: ROMS Discussion
Topic: Velocity is too large near open boundary
Replies: 8
Views: 8004

Re: Velocity is too large near open boundary

There are reanalyses out there at better than monthly, starting before 1979. You might have to contact the authors and mail them some harddrives to load it onto to get it, though. A colleague of mine has done that to get both SODA and Mercator.
by kate
Tue Dec 22, 2020 5:55 pm
Forum: ROMS Discussion
Topic: Velocity is too large near open boundary
Replies: 8
Views: 8004

Re: Velocity is too large near open boundary

You haven't told us anything about your boundary conditions except which options you have. What is the frequency of providing new information and what is the source of it? I remember seeing a vast improvement when going from monthly climatology of just T and S to 5-daily SODA fields. The climatology...
by kate
Tue Dec 22, 2020 5:34 pm
Forum: ROMS Discussion
Topic: blowing up error
Replies: 15
Views: 21862

Re: blowing up error

Yes, exactly. However, you know how you have the #ifdef GLS_MIXING... section? Here's what I have for LMD: # define LMD_MIXING # ifdef LMD_MIXING # define LMD_RIMIX # define LMD_CONVEC # define LMD_SKPP # define LI_FOX_KEMPER # undef LMD_BKPP # define LMD_NONLOCAL # define LMD_SHAPIRO # define LMD_D...
by kate
Tue Dec 22, 2020 7:48 am
Forum: ROMS Discussion
Topic: Zeta data in boundary files can't be read
Replies: 2
Views: 3788

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

What is the exact error you are getting?
by kate
Tue Dec 22, 2020 7:44 am
Forum: ROMS Discussion
Topic: blowing up error
Replies: 15
Views: 21862

Re: blowing up error

I bet you have some vertically unstable T and S profiles. If they are what you want, you should turn on a vertical mixing scheme like GLS or LMD.
by kate
Sun Dec 20, 2020 9:55 pm
Forum: ROMS Discussion
Topic: blowing up error
Replies: 15
Views: 21862

Re: blowing up error

You don't have an open boundary. Where is the velocity always 1.4 m/s? Do you expect it to be less? Is that where the blow-up is happening or not? Actually, it reports: REASON: MaxSpeed = 6.2E+03 Rather a larger velocity. So where is that and why? I usually use U3H advection and some fourth-order ve...