Search found 1098 matches

by jcwarner
Thu Sep 01, 2022 2:34 pm
Forum: ROMS Installation
Topic: Error compiling ROMS in COAWST
Replies: 5
Views: 246

Re: Error compiling ROMS in COAWST

there is a lot of info in the COAWST_User manual.doc. if you only select the roms model, then coawstM is essentially romsM. if you select additional other models, only 1 executable is created, coawstM. That would run roms + wrf, or whatever. this is a different approach than what Rutgers does, so if...
by jcwarner
Thu Sep 01, 2022 12:01 pm
Forum: ROMS Installation
Topic: Error compiling ROMS in COAWST
Replies: 5
Views: 246

Re: Error compiling ROMS in COAWST

use the coawst.bash file in the main dir. I have modified the build to be able to compile all the different models.
if you have more issues please post here:
https://github.com/jcwarner-usgs/COAWST/issues
thanks, j
by jcwarner
Tue Aug 23, 2022 12:40 pm
Forum: ROMS Discussion
Topic: Issue with the interpolation between time steps in forcing file
Replies: 3
Views: 217

Re: Issue with the interpolation between time steps in forcing file

seems odd.
when you did the test with the extra time step in the middle, what did roms report out when it read the file?
it always reports out the min, max, times, etc. check that.
by jcwarner
Sat Jul 30, 2022 11:34 pm
Forum: ROMS Usage
Topic: An error occurred when running ROMS in COAWST
Replies: 10
Views: 613

Re: An error occurred when running ROMS in COAWST

DIAG speed trouble 93.106400122773167 DIAG speed ijk 131.67231528779021 96 64 1 1 Found Error: 01 Line: 341 Source: ROMS/Nonlinear/main3d.F Found Error: 01 Line: 331 Source: ROMS/Drivers/nl_ocean.h, ROMS_run Blowing-up: Saving latest model state into RESTART file REASON: MaxSpeed = 9.3E+01 WRT_RST -...
by jcwarner
Sat Jul 30, 2022 1:52 pm
Forum: ROMS Usage
Topic: An error occurred when running ROMS in COAWST
Replies: 10
Views: 613

Re: An error occurred when running ROMS in COAWST

I see still: GET_GRID - bathymetry at RHO-points: h (Grid = 01, File: Projects/Katrina/roms_grid_Katrina.nc) (Min = 5.95202990E-03 Max = 3.35037820E+03) that is a min of 0.005 m . I dont think you need a min of 5 mm. try again. in the grid file to set h to have a minimum depth. maybe something like ...
by jcwarner
Fri Jul 29, 2022 8:51 pm
Forum: ROMS Discussion
Topic: Issue with HISTORY file logical switch for Hbbl
Replies: 4
Views: 184

Re: Issue with HISTORY file logical switch for Hbbl

for gls i typically use

# define GLS_MIXING
# ifdef GLS_MIXING
# define RI_SPLINES
# define KANTHA_CLAYSON
# define N2S2_HORAVG
# endif

it can get more options, for surface mixing etc, not sure what type of applications you are using.

for LMD i will let someone else answer.
by jcwarner
Fri Jul 29, 2022 7:49 pm
Forum: ROMS Discussion
Topic: Issue with HISTORY file logical switch for Hbbl
Replies: 4
Views: 184

Re: Issue with HISTORY file logical switch for Hbbl

gls and tke will only be output if you activate GLS_MIXING or maybe also MY25_MIXING.

for the hsbl, those go with the LMD options.

-j
by jcwarner
Fri Jul 29, 2022 2:58 pm
Forum: ROMS Usage
Topic: An error occurred when running ROMS in COAWST
Replies: 10
Views: 613

Re: An error occurred when running ROMS in COAWST

GET_GRID - bathymetry at RHO-points: h (Grid = 01, File: Projects/Katrina/roms_grid_Katrina.nc) (Min = -2.15744419E+02 Max = 3.33282292E+03) you need to activate wet dry if you have negative h values. Suggest you take a look at your grid and decide if you are really resolving wet/dry processes. if n...
by jcwarner
Wed Jul 27, 2022 12:36 am
Forum: ROMS Discussion
Topic: Didn't create average files
Replies: 3
Views: 175

Re: Didn't create average files

how many time steps did you run it for?
by jcwarner
Mon Jul 25, 2022 11:45 am
Forum: ROMS Problems
Topic: MaxDensity error where the h changes rapidly
Replies: 4
Views: 391

Re: MaxDensity error where the h changes rapidly

where are the locations for the : LwSrc == T
by jcwarner
Mon Jul 25, 2022 11:37 am
Forum: ROMS Problems
Topic: ROMS<kshedstrom version> blow at the fist timestep
Replies: 9
Views: 1417

Re: ROMS<kshedstrom version> blow at the fist timestep

we have MAIN: Abnormal termination: BLOWUP. REASON: MaxDensity = 3.4E+02 can you look in the ocean_rst.nc and see where that density is large? is it at the open boundary? at a river location? maybe try to turn off the rivers, and turn off clm nudging. see if it runs without them to help diagnose the...
by jcwarner
Sun Jul 24, 2022 1:10 pm
Forum: ROMS Problems
Topic: ROMS<kshedstrom version> blow at the fist timestep
Replies: 9
Views: 1417

Re: ROMS<kshedstrom version> blow at the fist timestep

ok so this is a different user on the same post. to zhaoyun- all you are telling us is that it blows up on first time step. You need to provide more information. Look at the std out and see if there is any information like h<0 and no wetdry, or nans in input forc fields, etc. the warnings are ok, th...
by jcwarner
Sat Jul 23, 2022 1:42 pm
Forum: ROMS Problems
Topic: ROMS<kshedstrom version> blow at the fist timestep
Replies: 9
Views: 1417

Re: ROMS<kshedstrom version> blow at the fist timestep

did you also update your ocean.in file to include the BC's and advection choices?
-j
by jcwarner
Sat Jul 23, 2022 1:41 pm
Forum: ROMS Bugs
Topic: Model running error: REASON: KEchar = NaN, PEchar = NaN
Replies: 3
Views: 743

Re: Model running error: REASON: KEchar = NaN, PEchar = NaN

there can be many reasons why the model is not starting. i remember seeing this GET_GRID - bathymetry at RHO-points: h (Grid = 02, File: Projects/Mangkhut/Mangkhut_roms_grid_ref3.nc) (Min = 0.00000000E+00 Max = 3.49541846E+03) if your min depth is 0, you need to define wet_dry. -j
by jcwarner
Fri Jul 22, 2022 1:33 pm
Forum: ROMS Discussion
Topic: The roms simulates a 6 hour difference in tide levels.
Replies: 2
Views: 240

Re: The roms simulates a 6 hour difference in tide levels.

looks like the simulation starts with zeta = -0.5 but the obs are at +0.5. so it will take a while for that barotropic mode to slosh out of the model. after 2 days the water levels look like they are starting to get into phase. if that storm at time 40 is your main interest, i suggest you start the ...
by jcwarner
Sun Jul 17, 2022 2:56 pm
Forum: ROMS Discussion
Topic: How to download HYCOM GLBa0.08 expt60.5 data?
Replies: 7
Views: 440

Re: How to download HYCOM GLBa0.08 expt60.5 data?

oops, not enough coffee yet. those ecmwf is for bulk fluxes. there are other posts on getting hycom data, such as: https://www.myroms.org/forum/viewtopic.php?p=23944&hilit=hycom#p23944 https://www.myroms.org/forum/viewtopic.php?p=23938&hilit=hycom#p23938 https://www.myroms.org/forum/viewtopi...
by jcwarner
Sun Jul 17, 2022 2:45 pm
Forum: ROMS Discussion
Topic: How to download HYCOM GLBa0.08 expt60.5 data?
Replies: 7
Views: 440

Re: How to download HYCOM GLBa0.08 expt60.5 data?

doing griddata u for HYCOM level 1 ... doing griddata u for HYCOM level 2 catch u Unable to download HYCOM u data at17-Jul-2022 23:08:30 if it worked for level 1, but not for level 2, that is an internet or Thredds issue. this is common. you can try again, or try some other way. Also, if you want to...
by jcwarner
Sun Jul 17, 2022 1:36 pm
Forum: ROMS Discussion
Topic: How to download HYCOM GLBa0.08 expt60.5 data?
Replies: 7
Views: 440

Re: How to download HYCOM GLBa0.08 expt60.5 data?

the tools we have there are for aggregated data

https://tds.hycom.org/thredds/catalog.html
i dont see the 60.5 on that list.

-j
by jcwarner
Sat Jul 09, 2022 1:30 am
Forum: ROMS Information
Topic: LIMIT_VVISC
Replies: 5
Views: 517

Re: LIMIT_VVISC

i dont think GLS has changed much in several years, so it should be the same.
-j
by jcwarner
Fri Jul 08, 2022 10:01 pm
Forum: ROMS Information
Topic: LIMIT_VVISC
Replies: 5
Views: 517

Re: LIMIT_VVISC

ok. First of all let's tackle the AKV_limit issue. This option is intended to prevent the values of Akt and Akv from getting very large. I do a lot of estuary work with lots of mixing, so I recommend setting these limiter values be at something like AKV_limit=1.0d0 and Akt_limit=1.0d0. IF you are un...
by jcwarner
Wed Jul 06, 2022 12:36 am
Forum: ROMS Tools and Techniques
Topic: obc_roms2roms.m
Replies: 1
Views: 239

obc_roms2roms.m

Is anyone else using obc_roms2roms.m? I am getting a size mismatch at lines 720-723 B.(ufield) = u .* cos(angle.(edge)) - ... v .* sin(angle.(edge)); the ufield = 'u_west' size(u) = 2 327 40 size(cos(angle.(edge))) = 2 327 40 size(v) = 2 326 40 size(sin(angle.(edge))) = 2 327 40 obviously u and v ar...
by jcwarner
Sat Jul 02, 2022 3:17 pm
Forum: ROMS Discussion
Topic: The problem of creating initial boundary conditions
Replies: 1
Views: 247

Re: The problem of creating initial boundary conditions

the variable names change over the years. I have no control in that. I just pushed out an update to the m files. please do an update and try again. thanks. if you have more troubles, please post a message on the coawst git site, as this issue for those tools. https://github.com/jcwarner-usgs/COAWST/...
by jcwarner
Tue Jun 14, 2022 6:55 pm
Forum: ROMS Bugs
Topic: LwSrc i,j bug
Replies: 1
Views: 236

LwSrc i,j bug

For the LwSrc, in step3d_t.F near lines 1146 we need to change cff=dt(ng)*pm(i,j)*pn(i,j) to cff=dt(ng)*pm(Isrc,Jsrc)*pn(Isrc,Jsrc) and the same near lines 1343 from cff=dt(ng)*pm(i,j)*pn(i,j) to cff=dt(ng)*pm(Isrc,Jsrc)*pn(Isrc,Jsrc) -j
by jcwarner
Mon Jun 13, 2022 11:51 pm
Forum: ROMS Discussion
Topic: How to improve modelled salinity and salinity initial condition
Replies: 14
Views: 1124

Re: How to improve modelled salinity and salinity initial condition

what bottom stress are you using? UV_LOGDRAG?
what is your Zob?
by jcwarner
Mon Jun 13, 2022 2:51 pm
Forum: ROMS Discussion
Topic: How to improve modelled salinity and salinity initial condition
Replies: 14
Views: 1124

Re: How to improve modelled salinity and salinity initial condition

i think you need more Volume to be filled on the flood, and then this will allow increased flows on the ebb. I was hoping to see more overtides in that water level time series (ie quicker rise to peak water level and longer tail to lower water level). do you see that further into the estuary? i see ...
by jcwarner
Mon Jun 13, 2022 1:04 pm
Forum: ROMS Discussion
Topic: How to improve modelled salinity and salinity initial condition
Replies: 14
Views: 1124

Re: How to improve modelled salinity and salinity initial condition

some quick looks: -how long did you run this for? looks like the salt is getting better as time goes on. -in the attached ppt, the vel in Charcoal bay does not get as strong (peaky) as the observations. So the salt will not get advected as far at those peaks, and that is exactly what you see in the ...
by jcwarner
Sun Jun 12, 2022 3:19 pm
Forum: ROMS Discussion
Topic: too high bottom temperature result in estuary
Replies: 6
Views: 533

Re: too high bottom temperature result in estuary

you need to look at how the temperature is evolving over time. does it get warmer from the surface net fluxes and then mix downwards? does it get warmer from the offshore boundary and then propagate in? i see: GET_3DFLD - potential temperature climatology, t = 45 15:45:04 (Rec=0000002, Index=2, File...
by jcwarner
Mon Jun 06, 2022 11:48 am
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1382

Re: Questions about wrf-roms coupling

glad it is working for you!
-j
by jcwarner
Fri Jun 03, 2022 12:30 pm
Forum: ROMS Sediment
Topic: unable to find variable: sand in input NetCDF
Replies: 8
Views: 2605

Re: unable to find variable: sand in input NetCDF

not exactly sure what is going on from that information. but it looks like you are doing a restart, and the model is looking for fields in that restart file. did you do a run with sediment and now restarting that? or did the first run not have sediment? if the first run did not have sediment, then y...
by jcwarner
Thu Jun 02, 2022 8:09 pm
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1382

Re: Questions about wrf-roms coupling

ok i spent some time on this. I think the issue is a bathy mismatch between the child and the parent, especially near the boundary. At the location of that vortex, the child grid has a bathymetric rise, but the parent grid did not see it. So i recommend that you use average child bathy to replace th...
by jcwarner
Wed Jun 01, 2022 12:48 pm
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1382

Re: Questions about wrf-roms coupling

I looked at the grids and they seem ok. the bathy matches well. the dmde looks large in the parent grid. are you running with curvgrid on? also the parent has spherical ='T' and the child has spherical = 1. this is probably not an issue. how did you set the init conditions? are the T/S fields consis...
by jcwarner
Tue May 31, 2022 12:01 pm
Forum: ROMS Discussion
Topic: How to calculate turbulent shear rate / energy dissipation
Replies: 3
Views: 331

Re: How to calculate turbulent shear rate / energy dissipation

the turbulence and the sediment should be separate. Both MY25 and GLS will output tke and gls. IF you use MY25, then tke is 0.5q^2 (i think, it has been a while) and gls will be the q^2l. IF you use GLS , then tke is tke and gls will be the set depending on the p m n parameters (gls can be dissipati...
by jcwarner
Mon May 30, 2022 10:54 pm
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1382

Re: Questions about wrf-roms coupling

looks like the only differences for roms is along the southern boundary.
with nesting, does the vortex start and grow, is it formed during the experiment at the boundary and advect in?
does the child bathy match the parent?
i assume this probably gets deep along that child southern boundary.
-j
by jcwarner
Fri May 27, 2022 12:20 am
Forum: Job Opportunities
Topic: USGS Woods Hole Technician V Coastal Modeler Support
Replies: 0
Views: 492

USGS Woods Hole Technician V Coastal Modeler Support

Akima is hiring a Technician V position to support the USGS Woods Hole Coastal and Marine Science Center (WHCMSC), Woods Hole, Massachusetts. The Technician V will assist the WHCMSC in developing, implementing, testing, and applying a coupled ocean-atmosphere-wave-sediment transport modeling system ...
by jcwarner
Mon May 23, 2022 5:36 pm
Forum: ROMS Discussion
Topic: How to run COAWST model with real-time data
Replies: 6
Views: 1479

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

if you are having trouble getting hycom data, suggest that you use ECMWF data. John Wilkin has a nice set of tools to do this:
roms_get_era5_NCARds633_bulkflux.m
and
roms_write_era5_NCARds633_frcfile.m
from here:
https://github.com/johnwilkin/roms_wilkin
by jcwarner
Mon May 23, 2022 12:55 pm
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1382

Re: Questions about wrf-roms coupling

i am not worried about the free surface, if that is all dry anyway. do you have wet dry on? did you set hmin = 5 in both the parent and child? is this vortex created at the boundary and advected in? can you do me a favor, i made a change to my version of nesting.F, Are you using COAWST? if so please...
by jcwarner
Fri May 20, 2022 3:47 pm
Forum: ROMS Installation
Topic: Memory leaks - Upwelling
Replies: 8
Views: 478

Re: Memory leaks - Upwelling

all those 'mem leaks' are for calls to allocate state variables such as allocate ( OCEAN(ng) % rubar(LBi:UBi,LBj:UBj,2) ) allocate ( OCEAN(ng) % rvbar(LBi:UBi,LBj:UBj,2) ) allocate ( OCEAN(ng) % rzeta(LBi:UBi,LBj:UBj,2) ) allocate ( OCEAN(ng) % ubar(LBi:UBi,LBj:UBj,3) ) allocate ( OCEAN(ng) % vbar(L...
by jcwarner
Fri May 20, 2022 1:22 am
Forum: ROMS Installation
Topic: Memory leaks - Upwelling
Replies: 8
Views: 478

Re: Memory leaks - Upwelling

ok i need another one. Build/mod_ocean.f90
-j
by jcwarner
Thu May 19, 2022 7:15 pm
Forum: ROMS Installation
Topic: Memory leaks - Upwelling
Replies: 8
Views: 478

Re: Memory leaks - Upwelling

not sure what these are, but if you got a netcdf output file, then the model ran fine.
can you post
Build/mod_arrays.f90
that seems to come up a lot.
thanks
j
by jcwarner
Thu May 19, 2022 3:04 pm
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1382

Re: Questions about wrf-roms coupling

I think this person is using COAWST. And yes they should add SST to cover non-Roms areas, and they probably are. We have had this option since the beginning of the coupling. What we do is use the SST from the WRFlow file, and replace that with ROMS data wherever the ocean is. We do that for each rom...
by jcwarner
Tue May 17, 2022 11:44 am
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1382

Re: Questions about wrf-roms coupling

is this the nest or the parent grid?
if this is the nest, are the vortices advected into the nest from the parent?
what do the temp and salt fields look like? you are using radnudge on the south, so what are you nudging to?
by jcwarner
Tue May 10, 2022 12:08 pm
Forum: ROMS Discussion
Topic: How to create the hycom_time with the real-time data
Replies: 4
Views: 466

Re: How to create the hycom_time with the real-time data

it is not possible for me to tell what is going on. The issue is with the array sizes. You will need to put in break points, see what the arrays are, the sizes, the values, and follow the arrays as they are passed to each routine. it is not that hard, just put in break points. when matlab stops at t...
by jcwarner
Fri May 06, 2022 12:03 pm
Forum: ROMS Discussion
Topic: How to create the hycom_time with the real-time data
Replies: 4
Views: 466

Re: How to create the hycom_time with the real-time data

for example here https://tds.hycom.org/thredds/dodsC/GLBy0.08/expt_93.0/FMRC/runs/GLBy0.08_930_FMRC_RUN_2022-05-05T12:00:00Z.html the variable list will show for time: units: hours since 2022-04-30 12:00:00.000 UTC so the 120 is hours since that time. You need to look for these attributes on the dat...
by jcwarner
Wed May 04, 2022 11:50 am
Forum: ROMS Discussion
Topic: An ocean_coupler problem when compiled
Replies: 2
Views: 284

Re: An ocean_coupler problem when compiled

sorry. i think you posted a message on the coawst issues and i did not get back to you.
i think you have a misspelled cpp def

define ATM2OCE_FLUXES
should be
define ATM2OCN_FLUXES

then do a ./coawst.bash and see if that compiles better.
-john
by jcwarner
Wed Apr 27, 2022 7:42 pm
Forum: ROMS Discussion
Topic: River runoff problem
Replies: 9
Views: 630

Re: River runoff problem

https://www.myroms.org/wiki/River_Runof ... _Eposition
is a good description of the river locations.
it needs to be coming out of the land masked cell.
by jcwarner
Wed Apr 27, 2022 4:47 pm
Forum: ROMS Discussion
Topic: River runoff problem
Replies: 9
Views: 630

Re: River runoff problem

it could be i, j, or transport.
make sure the Q is positive for flow to the right.
look at the u values and ensure the rivers are coming from the correct locations.
those locations should be masked points. the river flow will overwrite the zero values at the masked locations.

-j
by jcwarner
Wed Apr 27, 2022 12:56 pm
Forum: ROMS Discussion
Topic: converting roms grid to swan grid
Replies: 6
Views: 1585

Re: converting roms grid to swan grid

if you are using coawst, you can post a message here:
https://github.com/jcwarner-usgs/COAWST/issues

also i suggest you look at the Inlet_test case and the User manual for descriptions on how to set these up.
-j
by jcwarner
Wed Apr 27, 2022 12:54 pm
Forum: ROMS Discussion
Topic: How do I solve the simulation speed anomaly?
Replies: 3
Views: 395

Re: How do I solve the simulation speed anomaly?

ok. if you min depth = 5 meters, and then wet/dry helped, i suggest you look at the zeta values to make sure the tides are ok. what is the tide range in this area? for the next problem, that is probably a density issue. closely look at what is being put along that boundary for temp salt u v etc. you...
by jcwarner
Tue Apr 26, 2022 1:26 pm
Forum: ROMS Problems
Topic: Runtime error line 322 of inp_decode.f90
Replies: 1
Views: 241

Re: Runtime error line 322 of inp_decode.f90

you could look at
At line 322 of file inp_decode.f90
and see what is trying to be read. looks like it wants a real but getting an integer or something like that.
by jcwarner
Fri Apr 22, 2022 11:54 am
Forum: ROMS Discussion
Topic: How do I solve the simulation speed anomaly?
Replies: 3
Views: 395

Re: How do I solve the simulation speed anomaly?

what is the bathy in that corner? i see you have 2 Vtransform S-coordinate transformation equation. 4 Vstretching S-coordinate stretching function. 5.0000E+00 theta_s S-coordinate surface control parameter. 4.0000E-01 theta_b S-coordinate bottom control parameter. 50.000 Tcline S-coordinate surface/...
by jcwarner
Thu Apr 21, 2022 2:31 pm
Forum: ROMS Problems
Topic: At line 1895 of file mod_ncparam.f90 Fortran runtime error
Replies: 5
Views: 521

Re: At line 1895 of file mod_ncparam.f90 Fortran runtime error

not sure if this is the correct answer, but you need to be consistent with salinity and NT value settings.

If you use
#define SALINITY
then make sure ocean.in has NAT = 2

If you use
#undef SALINITY or not even mention salinity,
then make sure ocean.in has NAT = 1

-j
by jcwarner
Tue Apr 19, 2022 4:48 pm
Forum: ROMS Discussion
Topic: tracers(temp and salt )distributed noisy
Replies: 2
Views: 354

Re: passive temp and salt distributed unphysically

not sure what you mean by the visc values. Are you using horiz viscosity: #define UV_VIS2 #define MIX_S_UV then you can set VISC2 == 2.0d0 ! m2/s ??? or something like that Perhaps the tracer horiz diffusivity is more what you need: # define TS_DIF2 # define MIX_GEO_TS TNU2 == 0.5d0 ! m2/s ??? or so...
by jcwarner
Wed Apr 13, 2022 12:15 am
Forum: ROMS Discussion
Topic: "gls" in the output file, and calculation of TKE dissipation
Replies: 7
Views: 575

Re: "gls" in the output file, and calculation of TKE dissipation

oh ok. let me look at that glossary, it might not be worded clearly.
can you paste that part of the glossary here?
if you choose k-e coeffs, then gls will be e (dissipation).
by jcwarner
Tue Apr 12, 2022 8:18 pm
Forum: ROMS Discussion
Topic: "gls" in the output file, and calculation of TKE dissipation
Replies: 7
Views: 575

Re: "gls" in the output file, and calculation of TKE dissipation

here is a good paper with lots of info: Warner, J.C., Sherwood, C., Arango, H., and Signell, R. (2005). “Performance of Four Turbulence Closure Models Implemented Using a Generic Length Scale Method.” Ocean Modelling, v. 8/1-2, p. 81-113. the GLS scheme is a method that transports tke and 'gls' = ge...
by jcwarner
Fri Apr 08, 2022 6:53 pm
Forum: ROMS Installation
Topic: Finished COAWST installation ubuntu 18.04
Replies: 2
Views: 1927

Re: Finished COAWST installation ubuntu 18.04

that is only a warning.
For WRF you need to
export NETCDF=/location/of/netcdf
did you set that?
by jcwarner
Wed Apr 06, 2022 12:27 pm
Forum: ROMS Discussion
Topic: Couple WRF and ROMS:Could not find input parameter: NestLayers
Replies: 1
Views: 304

Re: Couple WRF and ROMS:Could not find input parameter: NestLayers

this is more of a coawst configuration issue, and should be posted here:
https://github.com/jcwarner-usgs/COAWST/issues
can you post this and the coupling.in file over there.
-j
by jcwarner
Tue Apr 05, 2022 12:09 pm
Forum: ROMS Discussion
Topic: ROMS not bit-reproducible: northern boundary?
Replies: 35
Views: 12629

Re: ROMS not bit-reproducible: northern boundary?

i had a little trouble following your logic, but it is not really clear what is causing the differences in the tke. Can you look at fields of temp, u, v, AKv, etc to see if there is something noticeably different in the runs? like something happening along the open boundary. Are there rivers (with f...
by jcwarner
Mon Apr 04, 2022 2:22 pm
Forum: ROMS Installation
Topic: COAWST installation through Cygwin on Windows 10
Replies: 4
Views: 636

Re: COAWST installation through Cygwin on Windows 10

this is a common issue with gfortran
you need to edit the Makefile.conf (i think) and add a fflag
-fallow-argument-mismatch

-j
by jcwarner
Sat Apr 02, 2022 2:44 pm
Forum: ROMS Installation
Topic: Error when installing SCRIP_COAWST
Replies: 1
Views: 272

Re: Error when installing SCRIP_COAWST

your executable is created here: -o ./scrip_coawst so it does not have a .exe on the end. do a ls -ltr and do you see ..... -rw-rw-r-- 1 jwarner domain users 103960 Jan 10 2020 remap_write.o -rw-rw-r-- 1 jwarner domain users 19413 Jan 10 2020 scrip.fpp -rw-rw-r-- 1 jwarner domain users 20302 Jan 10 ...
by jcwarner
Fri Apr 01, 2022 12:53 pm
Forum: ROMS Installation
Topic: COAWST installation through Cygwin on Windows 10
Replies: 4
Views: 636

Re: COAWST installation through Cygwin on Windows 10

make sure you have
c:/cygwin64/usr/include/mpif.h
if not then you missed something during the setup, like libopenmpifh40 or something like that
cygwinlib.png
by jcwarner
Mon Mar 28, 2022 2:37 pm
Forum: ROMS Discussion
Topic: EW_periodic,NS_periodic
Replies: 2
Views: 343

Re: EW_periodic,NS_periodic

All the boundary condition options have been moved to the ocean.in file. You dont need the boundary cpp options like EW_PERIODIC or FSCLAMPED etc. it is all in the ocean.in For Example: ! Set lateral boundary conditions keyword. Notice that a value is expected ! for each boundary segment per nested ...
by jcwarner
Sun Mar 27, 2022 6:19 pm
Forum: ROMS Installation
Topic: Fortran runtime error: Assignment of scalar to unallocated array
Replies: 7
Views: 616

Re: Fortran runtime error: Assignment of scalar to unallocated array

Sunny up here but looks like rain coming your way Hernan. Enjoy the day! -j
by jcwarner
Sun Mar 27, 2022 3:16 pm
Forum: ROMS Installation
Topic: Fortran runtime error: Assignment of scalar to unallocated array
Replies: 7
Views: 616

Re: Fortran runtime error: Assignment of scalar to unallocated array

maybe you could help a bit and track that message, what is on

/mnt/c/Users/lyras/OneDrive/install_roms/folder_tes/Build_romsG/mod_scalars.f90:2595
by jcwarner
Thu Mar 24, 2022 4:56 pm
Forum: ROMS Problems
Topic: Signed Integer Overflow
Replies: 10
Views: 1022

Re: Signed Integer Overflow

i am not sure the difference between those 2 output files. the server.log has - bathymetry at RHO-points: h (Grid = 01, File: bowl_grid.nc) (Min = 2.00018817E-02 Max = 1.00000000E+03) Minimum Z-grid spacing, DZmin = 6.53658218E-04 m that is a small dz somewhere. you have thetas =10. maybe adjust the...
by jcwarner
Thu Mar 24, 2022 4:49 pm
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 12
Views: 1165

Re: compile ROMS error

both the Netcdf libs and roms need to be built with the same compiler and version of that compiler.

type this:
nf-config --all

and this
mpif90 -v

find out what compiler was used to build the Netcdf libs, or have someone rebuild the netcdf with the same mpif90 that you are using.
by jcwarner
Wed Mar 23, 2022 12:46 pm
Forum: ROMS Problems
Topic: Signed Integer Overflow
Replies: 10
Views: 1022

Re: Signed Integer Overflow

how about you post the whole output, not just the last part.
there might be something wrong with the init conditions.
by jcwarner
Mon Mar 21, 2022 1:08 pm
Forum: ROMS Discussion
Topic: Different boundary scenarios
Replies: 15
Views: 1922

Re: Different boundary scenarios

I am nots really sure what all to suggest here. A few images back , you had zeta on the west side at -8m. Can you figure out why that happened? Even a super strong wind would have trouble to do that. I thought the winds might not be rotated to the grid correctly. Suggest you set roms to write out th...
by jcwarner
Wed Mar 16, 2022 6:43 pm
Forum: ROMS Discussion
Topic: Different boundary scenarios
Replies: 15
Views: 1922

Re: Different boundary scenarios

do you have
#define CURVGRID
that might help with some of the advection.
take a look at the winds in that ncviewer. how strong are they on the west side?

-j
by jcwarner
Mon Mar 14, 2022 2:00 am
Forum: ROMS Ice
Topic: blow-up in first time step, using glorys and ERA5
Replies: 8
Views: 2189

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

does it run without the clm nudging?
look at the entire output file, there might have been more info before the nan.
by jcwarner
Mon Mar 14, 2022 1:56 am
Forum: ROMS Bugs
Topic: An error was reported after only a few hours of operation
Replies: 2
Views: 399

Re: An error was reported after only a few hours of operation

1581120 2008-07-02 00:00:00.00 0.000000E+00 1.453619E+04 1.453619E+04 1.282427E+15 (000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 DEF_HIS - creating history file, Grid 01: Ev08_his_coupled_00184.nc WRT_HIS - wrote history fields (Index=1,1) in record = 0000001 DEF_AVG - creating av...
by jcwarner
Mon Mar 14, 2022 12:17 am
Forum: ROMS Discussion
Topic: Different boundary scenarios
Replies: 15
Views: 1922

Re: Different boundary scenarios

think you are changing too many things here. ERA winds should not affect the tides. and dont rely on ncview to give you the max/min. click at a point and get a time series. try this: You have this: Variable Grid West Edge South Edge East Edge North Edge --------- ---- ---------- ---------- ---------...
by jcwarner
Fri Mar 11, 2022 1:26 pm
Forum: ROMS Discussion
Topic: Different boundary scenarios
Replies: 15
Views: 1922

Re: Different boundary scenarios

1.JPG
on this page, top figure, what is 'wrong' with the zeta?
by jcwarner
Wed Mar 09, 2022 1:44 pm
Forum: ROMS Results
Topic: ROMS output. Best technique to interpolate in the vertical
Replies: 8
Views: 1025

Re: ROMS output. Best technique to interpolate in the vertical

looking better.
there are 'extrapolation' options, which need to be used with caution.
but give that a try.
maybe someone else has a better idea.
by jcwarner
Wed Mar 09, 2022 12:14 am
Forum: ROMS Results
Topic: ROMS output. Best technique to interpolate in the vertical
Replies: 8
Views: 1025

Re: ROMS output. Best technique to interpolate in the vertical

it just wants you to enter the data as a column. lets say this is a 2D field in x and z. lets also say that you have 10 vertical layers and we are looking at the y index of 35 (just picking any number here). N=10; yidx=35; X=repmat(lon_rho(:,yidx),N); Z=z_rho(:,yidx,:); S=squeeze(salt(:,yidx,:,tidx)...
by jcwarner
Tue Mar 08, 2022 8:03 pm
Forum: ROMS Results
Topic: ROMS output. Best technique to interpolate in the vertical
Replies: 8
Views: 1025

Re: ROMS output. Best technique to interpolate in the vertical

" linear interpolation over one column at the time" - that is probably not a good idea.
try a 2D interpolation scheme. Are you using matlab?
help scatteredInterpolant
F = scatteredInterpolant(x_rho,z_rho,salt);
saltnew= F(xnew,znew);
by jcwarner
Mon Mar 07, 2022 1:43 pm
Forum: ROMS Discussion
Topic: SIGSEGV, segmentation fault occurred (with Empty log file)
Replies: 6
Views: 595

Re: SIGSEGV, segmentation fault occurred (with Empty log file)

take a look at the file Build/mod_ncparam.f90 at line 1039 and see what it is looking for.

romsS 00000000005696B9 mod_ncparam_mp_in 1039 mod_ncparam.f90
by jcwarner
Sat Mar 05, 2022 6:48 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 8
Views: 777

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

"forrtl: severe (408): fort: (2): Subscript #2 of the array FRC has value 1 which is greater than the upper bound of -1" i looked in your ocean.in and you have: !NFFILES = 1 ! number of unique forcing files !FRCNAME == /disk3/chenzhixing/ROMS/cases/laizhou/laizhou-frc.nc ! forcing file 1, ...
by jcwarner
Thu Mar 03, 2022 1:14 pm
Forum: ROMS Discussion
Topic: DIAG speed trouble 20.125553145124616. Blowing-up: Saving latest model state into RESTART file
Replies: 6
Views: 675

Re: DIAG speed trouble 20.125553145124616. Blowing-up: Saving latest model state into RESTART file

this configuration is for ROMS by itself. the model runs for a while, as you say, and then 13510 2010-01-04 03:03:20.00 5.896200E-02 1.757339E+04 1.757345E+04 1.160390E+16 (127,016,32) 1.571469E-02 1.362909E-02 7.575998E+00 2.012555E+01 DIAG speed trouble 20.125553145124616 ... Blowing-up: Saving la...
by jcwarner
Thu Mar 03, 2022 1:08 pm
Forum: ROMS Discussion
Topic: boundary condition
Replies: 2
Views: 378

Re: boundary condition

" Cha for free-surface and Rad for momentum in 2D and 3D mode, the boundary file is not read" Yes, those BC's do not need any external data. so a file does not need to be read. " RadNud for free-surface or Fla mode for momentum in 2D mode, the input boundary file is usually read"...
by jcwarner
Sat Feb 26, 2022 3:35 pm
Forum: ROMS Discussion
Topic: shallow water blow up due to large wind speed or too much cooling?
Replies: 3
Views: 466

Re: shallow water blow up due to large wind speed or too much cooling?

difficult to assess why the model would blow up with that limited information. if you want to run the simulation and have the blow up occur, look at the rst file, his file time steps right before the blow up, etc. that can help to diagnose what may have been going on. look at water levels, currents,...
by jcwarner
Fri Feb 04, 2022 2:52 am
Forum: ROMS Discussion
Topic: Curvilinear grid and velocity at rho-points problem
Replies: 2
Views: 445

Re: Curvilinear grid and velocity at rho-points problem

what does the grid angle look like?
also, when you make those pcolor plots, are they
pcolorjw(lon_rho,lat_rho,angle)
and use
pcolorjw(lon_u,lat_u,ubar)
etc

You said the u and v are ok, but the u_east and v_north are not? so that might be an angle issue.
by jcwarner
Wed Jan 05, 2022 12:18 am
Forum: ROMS Bugs
Topic: SINGLE_PRECISION bug
Replies: 0
Views: 381

SINGLE_PRECISION bug

small but tricky bug when #define SINGLE_PRECISION 1) in get_idata we have real(r8) :: time_save = 0.0_r8 but it needs to be real(dp) :: time_save = 0.0_dp 2) And then there are multiple uses of: time_save=time(ng) time(ng)=8640000.0_r8 .... call get2d.. time(ng)=time_save I think this should be : t...
by jcwarner
Tue Jan 04, 2022 2:30 pm
Forum: ROMS Problems
Topic: Question about tracer routine
Replies: 4
Views: 762

Re: Question about tracer routine

you need to be careful in here, as some routines (like MPDATA) are a little different than others.
but at the bottom of step3d_t is where the units become Tracer only. it can happen in the diffusion step, and here again you need to be careful if splines are on or not.
by jcwarner
Thu Dec 30, 2021 10:49 pm
Forum: ROMS Discussion
Topic: Adding a river runoff in simulation
Replies: 2
Views: 556

Re: Adding a river runoff in simulation

i just downloaded the code the other day, and the RIVERPLUME1 test case worked fine for me. give that a try. i dont understand if you are using RIVERPLUME1 or trying to use that as a guide. if it is a guide, then you need to define your own application in ana_psource and copy those lines of code to ...
by jcwarner
Wed Dec 29, 2021 3:23 pm
Forum: ROMS Discussion
Topic: qeustion about ROMS+SWAN(COAWST)
Replies: 1
Views: 784

Re: qeustion about ROMS+SWAN(COAWST)

sorry for the very long delay on this response. i had lost this thread. when coupled to swan, the wec breaking is the wave dissipation from swan. it comes from swan as a variable DISSURF and put into roms variable Dissip_break. That Dissip_break is used: - #define WEC_VF then it is used to drive cur...
by jcwarner
Tue Dec 28, 2021 3:31 pm
Forum: ROMS Discussion
Topic: usage of both LuvSrc and LwSrc
Replies: 4
Views: 822

Re: usage of both LuvSrc and LwSrc

starting with the most recent version of Rutgers code, I used the RIVER_PLUME1 test case because it has 1 UV_Psource location for a river entering a N-S Periodic domain with East and West walls. Therefore, the entire volume change within the domain is due to the river inflow. I ran the test case 'as...
by jcwarner
Tue Dec 28, 2021 2:13 pm
Forum: ROMS Installation
Topic: why my roms src has no WAVE?
Replies: 1
Views: 353

Re: why my roms src has no WAVE?

if you want to use a coupled roms+swan, then you need to use COAWST
https://github.com/jcwarner-usgs/COAWST
-j
by jcwarner
Mon Dec 27, 2021 2:29 pm
Forum: ROMS Discussion
Topic: bottom boundary layer height calculation (Hbbl)
Replies: 2
Views: 475

Re: bottom boundary layer height calculation (Hbbl)

i did a grep -nir hbbl ROMS/* and got a lot of results, but i think the most relevant is in ROMS/Nonlinear/lmd_bkpp.F and it says "This routine determines the depth of bottom oceanic boundary ! ! layer, hbbl, as the deepest depth where the bulk Richardson ! ! number is equal to the critical val...
by jcwarner
Mon Dec 27, 2021 2:27 pm
Forum: ROMS Discussion
Topic: Inlet_test:the Swan output has no result
Replies: 1
Views: 287

Re: Inlet_test:the Swan output has no result

if you are going to use ROMS + SWAN coupling, then please use the COAWST code here:
https://github.com/jcwarner-usgs/COAWST

that should run 'as is' and give the outputs, this is an example test case.
thanks,
john
by jcwarner
Wed Dec 22, 2021 2:19 pm
Forum: ROMS Discussion
Topic: READ_PHYPAR - Invalid dimension parameter
Replies: 11
Views: 1226

Re: READ_PHYPAR - Invalid dimension parameter

there are probably a few things not correct here, you will need to try and figure them out. for swan Err file01 -001 : this is for grid 1, tile 1 (so probably left side) it has Error : invalid boundary point Error : ( -99 -99) is outside computational grid so most likely one of the Boundspec locatio...
by jcwarner
Tue Dec 21, 2021 1:44 pm
Forum: ROMS Discussion
Topic: READ_PHYPAR - Invalid dimension parameter
Replies: 11
Views: 1226

Re: READ_PHYPAR - Invalid dimension parameter

half right, half not. for ini and clm: you can use the parent ini and clm to make the first child ini and clm. Then use those first child ini and clm to make the files for the 3rd grid. for the contact: roms only wants 1 contact file, so to create a contact file for 3 grids you need to make all 3 gr...
by jcwarner
Mon Dec 20, 2021 1:36 pm
Forum: ROMS Discussion
Topic: READ_PHYPAR - Invalid dimension parameter
Replies: 11
Views: 1226

Re: READ_PHYPAR - Invalid dimension parameter

this is now a SWAN error. I see in Errfile02-001 (this is for swan grid 2, tile partition 1) Error : invalid boundary point Error : ( -99 -99) is outside computational grid Error : invalid boundary point Error : ( -99 -99) is outside computational grid Error : File is already opened: Projects/Tembin...
by jcwarner
Sat Dec 18, 2021 3:43 pm
Forum: ROMS Discussion
Topic: READ_PHYPAR - Invalid dimension parameter
Replies: 11
Views: 1226

Re: READ_PHYPAR - Invalid dimension parameter

this is for ROMS.
It looks like your ocean.in has

Ngrids = 2
NestLayers = 2

but it must have been compiled without nesting. the error is saying that you can only have NestLayers = 1 for non-nesting.
think you need to add
#define NESTING
to *.h file and recompile.
-j
by jcwarner
Wed Dec 15, 2021 5:46 pm
Forum: ROMS Problems
Topic: Cannot run 2D only mode with ROMS3.9 or higher
Replies: 9
Views: 1092

Re: Cannot run 2D only mode with ROMS3.9 or higher

wow! thanks for diggin in. But i see in mod_ncparam.F

ic=5
DO i=1,MT
ic=ic+1
isTvar(i)=ic
END DO
....
isWvel=ic+1

are you saying ifort can not do "DO i=1,0" ?

there still should be a value for ic =5.
by jcwarner
Mon Dec 13, 2021 8:39 pm
Forum: ROMS Problems
Topic: Cannot run 2D only mode with ROMS3.9 or higher
Replies: 9
Views: 1092

Re: Cannot run 2D only mode with ROMS3.9 or higher

what is on line 904 of mod_ncparam.f90
(the f90, not the F)
mod_ncparam_mp_in 904 mod_ncparam.f90
by jcwarner
Tue Nov 30, 2021 1:25 pm
Forum: ROMS Installation
Topic: COAWST compilation error -- wec_vf.f90
Replies: 4
Views: 1095

Re: COAWST compilation error -- wec_vf.f90

can you post the issue here:
https://github.com/jcwarner-usgs/COAWST/issues
and include the output during the run or during the build?
thanks,
j
by jcwarner
Mon Nov 22, 2021 5:37 pm
Forum: ROMS Discussion
Topic: usage of both LuvSrc and LwSrc
Replies: 4
Views: 822

Re: usage of both LuvSrc and LwSrc

thanks Hernan. yes of course. the user would create a single file for all the points (LuvSrc and Lwsrc). Then for each point, the user would define a Dsrc value. If Dsrc is 0, then it is for a u point (LuvSrc). If Dsrc is 1, then it is for a v point (LuvSrc). If Dsrc is -1, then it is for rho point ...
by jcwarner
Mon Nov 22, 2021 3:42 pm
Forum: ROMS Discussion
Topic: usage of both LuvSrc and LwSrc
Replies: 4
Views: 822

usage of both LuvSrc and LwSrc

Dear ROMS- I am trying to use both LuvSrc and LwSrc at the same time. However, the code currently is not allowing that configuration, but i need to make it happen. Can we make some simple modifications, such as defining a new direction of -1 to be used for the LwSrc? This will need some minor code c...
by jcwarner
Mon Nov 08, 2021 1:04 pm
Forum: ROMS Discussion
Topic: Vertical and horizontal mixing
Replies: 1
Views: 560

Re: Vertical and horizontal mixing

the horizontal viscosity is usually a function of grid size and horizontal velocities. the horiz mixing also has several choices, https://www.myroms.org/wiki/Horizontal_Mixing the vertical viscosity is usually a function of the vertical stratification (temp, salt, sediment sometimes) and the vertica...
by jcwarner
Mon Nov 01, 2021 11:41 pm
Forum: ROMS Bugs
Topic: tiling and divide by zero error
Replies: 10
Views: 1140

Re: tiling and divide by zero error

is ​there any more relevant info? i assume you change the NtileI NtileJ values accordingly.
also, looks like the error might be in output. did you change anything in wrt_his or any other place to write things out for your setup?
-j
by jcwarner
Mon Nov 01, 2021 5:21 pm
Forum: ROMS Discussion
Topic: The intensity of tropical cyclone
Replies: 3
Views: 694

Re: The intensity of tropical cyclone

i guess i was not really clear in my suggestion, sorry. The plots you just posted show the initial conditions for the TC centered at 12Z02Nov2017. What do the initial conditions look like west of that region, where the TC will make landfall? The WRF CTL SST looks warmer than the WRF-sstupdate and th...
by jcwarner
Sun Oct 31, 2021 2:00 am
Forum: ROMS Discussion
Topic: The intensity of tropical cyclone
Replies: 3
Views: 694

Re: The intensity of tropical cyclone

What did the SST for ROMS look like before the TC crossed into the domain, and compare that to the SST from the WRF control.
How did you set the initial vertical stratification for ROMS?
-j
by jcwarner
Tue Oct 26, 2021 12:35 pm
Forum: ROMS Installation
Topic: COAWST compilation error when coupling ROMS with other models
Replies: 2
Views: 521

Re: COAWST compilation error when coupling ROMS with other models

can you post the entire output of the build? there might have been something earlier.
and can you create a new post for this issue here:
https://github.com/jcwarner-usgs/COAWST/issues

thanks,
john
by jcwarner
Tue Sep 28, 2021 1:03 pm
Forum: ROMS Installation
Topic: output files of SWAN model
Replies: 7
Views: 4504

Re: output files of SWAN model

i think for some versions of gfortran you need to add

FFLAGS += -fconvert=big-endian

see if that works.
what do you get for
gfortran --version
by jcwarner
Thu Sep 23, 2021 1:44 pm
Forum: ROMS Discussion
Topic: Question about the typhoon-induced sea surface cooling in ROMS-WRF coupled simulation
Replies: 3
Views: 849

Re: Question about the typhoon-induced sea surface cooling in ROMS-WRF coupled simulation

it looks like the ocean SST is higher in roms all around than in the GHRSST. so maybe your initial conditions are not matching the SST data even before the storm. How did you set the initial stratification? perhaps that could be too thin of a surface mixed layer allowing the cooler temp to mix upwar...
by jcwarner
Thu Sep 23, 2021 1:39 pm
Forum: ROMS Problems
Topic: Overmixing in stripes
Replies: 5
Views: 980

Re: Overmixing in stripes

all this limit does is put a maximum value on the AKt and AKv. if you set it to 1e-5 (a very low example) then the mixing will never get above those values (not recommended). If you set it to 10, then the mixing will never go above 10. It doesnt mean that the mixing is 10 everywhere, is just means t...
by jcwarner
Wed Sep 22, 2021 5:26 pm
Forum: ROMS Problems
Topic: Overmixing in stripes
Replies: 5
Views: 980

Re: Overmixing in stripes

you stated that the stripes go away if you undef the AKV limit. i see your ocean.in has AKT_LIMIT == 1.0d-3 1.0d-3 ! m2/s AKV_LIMIT == 1.0d-3 1.0d-3 ! m2/s if you undef the limit, what are the values of AKV? if they are above 1e-3, then your limiters are preventing the mixing. that could be the issu...
by jcwarner
Fri Sep 10, 2021 12:23 am
Forum: ROMS Discussion
Topic: u and u_stokes & zeta and zeta_w clarification
Replies: 2
Views: 497

Re: u and u_stokes & zeta and zeta_w clarification

this was a discussion point, and we decided to always have u- v- ubar- vbar be Eulerian. then we also can write out u_stokes, v_stokes, ubar_stokes, vbar_stokes. the lagrangian would then be eulerian + stokes. "In the history file, does u = u_e + u_stokes, v = v_e + v_stokes, and zeta_c = zeta ...
by jcwarner
Fri Sep 10, 2021 12:17 am
Forum: ROMS Discussion
Topic: Horizontal surface pressure gradient forcing in 2D and 3D
Replies: 16
Views: 6490

Re: Horizontal surface pressure gradient forcing in 2D and 3D

GRho0 * z_w = 1000.0_r8 * GRho * z_w = 1000.0_r8* g/rho0 * z_w so this is g*z_w * 1000/rho0 and you want it to be g*z_w well, the difference is 1000/1025 = 0.97, as you said. But it does not have the wrong units. The units are correct. The 1000/rho0 is density over density and those units cancel. I ...
by jcwarner
Thu Sep 09, 2021 9:42 pm
Forum: ROMS Discussion
Topic: Horizontal surface pressure gradient forcing in 2D and 3D
Replies: 16
Views: 6490

Re: Horizontal surface pressure gradient forcing in 2D and 3D

I think the original code was correct. P is only an internal variable for this routine. Maybe you want to re-define it for the tides, but the way it was originally seemed correct. It was: P(i,j,N(ng))=GRho0*z_w(i,j,N(ng))+ & & GRho*(rho(i,j,N(ng))+cff2)* & & (z_w(i,j,N(ng))-z_r(i,j,N...
by jcwarner
Wed Aug 25, 2021 6:47 pm
Forum: ROMS Discussion
Topic: Thin Wall Between Grid Cells
Replies: 3
Views: 622

Re: Thin Wall Between Grid Cells

just try the adjustment to just mask _u _v for now and see if that works. it may look strange, as there could be dzeta/dx gradients across the rho cells, but no flow. but give it a try.
-j
by jcwarner
Wed Aug 25, 2021 4:59 pm
Forum: ROMS Discussion
Topic: Thin Wall Between Grid Cells
Replies: 3
Views: 622

Re: Thin Wall Between Grid Cells

Typically to provide a permanent wall, then use the mask _u _v _rho variables. ROMS is solved on a staggered grid, so when you set the mask_rho, then edit_mask (or similar) can determine the appropriate settings for mask_u and mask_v and mask_psi. However, it seems you want a special case, where 2 a...
by jcwarner
Mon Aug 09, 2021 11:30 pm
Forum: ROMS Discussion
Topic: grid cell switches from dry to wet while (u,v) are NaN
Replies: 1
Views: 438

Re: grid cell switches from dry to wet while (u,v) are NaN

the cells will become wet when ever the total water depth is > Dcrit. The water will move from all the processes in the model, such as pressure gradients from gravity or density, wind, horiz mixing, etc. At the model init, how did you set the water level (zeta) on the grid? did you use an init file,...
by jcwarner
Wed Aug 04, 2021 1:56 pm
Forum: ROMS Discussion
Topic: How to erase sediment-variables in ROMS?
Replies: 9
Views: 1360

Re: How to erase sediment-variables in ROMS?

if go back to your original setup, and activate #define ANA_SEDIMENT this will create the vars needed. to do this, i suggest you - copy the ROMS/Functionals/ana_sediment.h to your project folder -edit build.bash or whatever to set the path to the ANALYTICAL files -edit ANA_SEDIMENT and copy or chang...
by jcwarner
Mon Aug 02, 2021 6:44 pm
Forum: ROMS Information
Topic: conversion of sigma levels in to depth
Replies: 4
Views: 3373

Re: conversion of sigma levels in to depth

wow, i originally answered this in 2006. there are some different options now. i am not sure if that m file is still around, but you can also use get_roms_grid.m and you can enter the grid name, or this ocean_his name, and the time index from a history file. that m file has example input commands at...
by jcwarner
Fri Jul 16, 2021 12:20 pm
Forum: ROMS Problems
Topic: SWAN encountered 'Unexpected end of file while reading DUMMY', produces constant SWH
Replies: 3
Views: 960

Re: SWAN encountered 'Unexpected end of file while reading DUMMY', produces constant SWH

not sure what you mean '2 more lines for the date." please read the swan manual for the proper format.
you need to have data for each cell
424*24*227*181*2=836202624
or something close to taht. you have about half of that, so maybe that is why it stops short.
by jcwarner
Thu Jul 15, 2021 12:45 pm
Forum: ROMS Problems
Topic: SWAN encountered 'Unexpected end of file while reading DUMMY', produces constant SWH
Replies: 3
Views: 960

Re: SWAN encountered 'Unexpected end of file while reading DUMMY', produces constant SWH

i can give this a try. suggest you look in the swan manual for the syntax on the wind lines. There are more lines for the wind, something like: && KEYWORD TO CREATE WIND GRID && INPGRID WIND REGULAR -105 10 0 220 160 0.25 0.25 & NONSTATIONARY 20121028.000000 6 HR 20121031.000000 ...
by jcwarner
Wed Jul 14, 2021 1:53 pm
Forum: ROMS Discussion
Topic: Plotting vector velocity u and w and bedload_coeff
Replies: 1
Views: 599

Re: Plotting vector velocity u and w and bedload_coeff

sorry for late reply. 1. i think u-east and v-north have been averaged to rho points (?). but normally the u- and v- points are on a staggered grid, see here: https://www.myroms.org/wiki/Fractional_Coordinate_System_(%CE%BE_-_%CE%B7_space) and similar pages. you can interpolate the velocities to the...
by jcwarner
Sat Jul 10, 2021 12:12 pm
Forum: ROMS Bugs
Topic: Error to run roms_clm_roms_master_climatology_coawst_mw
Replies: 6
Views: 1607

Re: Error to run roms_clm_roms_master_climatology_coawst_mw

if it works sometimes and not others, then it is your internet connection or the thredds server on the other end.
suggest you try from a hard wired connection (not wifi), and try to acquire data for a short period of time.

-j
by jcwarner
Thu Jun 24, 2021 12:29 pm
Forum: ROMS Sediment
Topic: Bed armoring
Replies: 4
Views: 1087

Re: Bed armoring

yes the armoring effect would not work well if the top layer is very thick. if you are interested in having multiple layers you may need to run some test simulations to see what would work best for you. there is a flag 'new bed layer thick' set in the sediment.in that tells the model when to combine...
by jcwarner
Wed Jun 23, 2021 1:37 pm
Forum: ROMS Sediment
Topic: Bed armoring
Replies: 4
Views: 1087

Re: Bed armoring

i am not sure what NONCOHESIVE_BED1 is, but for bed armoring- there is not an explicit armoring routine. Instead, as the finer grain material is eroded, the surface will become composed of coarser grain sizes. this coarsening will increase the bottom(i,j,itauc), and thus create a higher critical str...
by jcwarner
Mon Jun 14, 2021 3:28 pm
Forum: ROMS Usage
Topic: Queries regarding possible use of modified test_chan case in ROMS
Replies: 4
Views: 1189

Re: Queries regarding possible use of modified test_chan case in ROMS

maybe it needs a leading /
change
home/sbasak08/roms/Projects/test_chan/External/sediment_test_chan.in
to
/home/sbasak08/roms/Projects/test_chan/External/sediment_test_chan.in

??
by jcwarner
Mon Jun 14, 2021 2:39 pm
Forum: ROMS Usage
Topic: Queries regarding possible use of modified test_chan case in ROMS
Replies: 4
Views: 1189

Re: Queries regarding possible use of modified test_chan case in ROMS

I think you are modifying the ana_sediment in ROMS/Functionals ??? what did you set for the path to the analytical files, in the build.bash or whatever you are using? export MY_HEADER_DIR=${MY_PROJECT_DIR}/?????? export MY_ANALYTICAL_DIR=${MY_PROJECT_DIR}/???? - what did you set here??? I suggest yo...
by jcwarner
Thu Jun 03, 2021 2:25 am
Forum: ROMS Bugs
Topic: dogbone composite nesting: contact()%Kdg in nesting.f90 not assigned?
Replies: 2
Views: 1112

Re: dogbone composite nesting: contact()%Kdg in nesting.f90 not assigned?

i think there is a issue with the updated calls for z_weights. There is a check in set_contact that has IF (.not.ANY(Lcoincident).and.ANY(Lcomposite)) THEN get_Vweights=.TRUE. ELSE get_Vweights=.FALSE. END IF i think we need this to allow get_vweights to be true. then at top of nesting we have IF ((...
by jcwarner
Mon May 31, 2021 11:05 pm
Forum: ROMS Problems
Topic: rectangles delimited by anomalous values
Replies: 4
Views: 1000

Re: rectangles delimited by anomalous values

i have seen this problem if the ocean.in does not have the updated section to select the tracer advection schemes. Check to make sure your input file is current.
by jcwarner
Thu May 20, 2021 12:50 pm
Forum: ROMS Installation
Topic: Error to compile WRF+SWAN
Replies: 1
Views: 684

Re: Error to compile WRF+SWAN

ok. so you have set #undef ROMS_MODEL #undef NESTING #define WRF_MODEL #define SWAN_MODEL #undef WW3_MODEL #define MCT_LIB #define MCT_INTERP_OC2AT #define MCT_INTERP_WV2AT #define MCT_INTERP_OC2WV if you only use swan and wrf, then you do not need INTERP_OC2AT or INTERP_OC2WV so set this as #undef ...
by jcwarner
Mon May 17, 2021 5:26 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Send: Other MPI error, error stack:
Replies: 1
Views: 852

Re: Fatal error in MPI_Send: Other MPI error, error stack:

i see "MCT::m_SparseMatrixPlus::initFromRoot_:: FATAL--length of vector y different from row count of sMat.Length of y = 128250 Number of rows in sMat = 127516 01E.MCT(MPEU)::die.: from MCT::m_SparseMatrixPlus::initFromRoot_()" so this is probably due to the scrip weights not being compute...
by jcwarner
Mon May 10, 2021 12:53 pm
Forum: ROMS Discussion
Topic: Question about SST in WRF-ROMS coupling
Replies: 6
Views: 2145

Re: Question about SST in WRF-ROMS coupling

something is making roms get 2-3 degrees cooler in 6 hour is quite extreme. I do not think it is the waves.
what if you ran roms by itself, with surface forcing from wrf or other source?

-j
by jcwarner
Fri May 07, 2021 1:54 pm
Forum: ROMS Discussion
Topic: Question about SST in WRF-ROMS coupling
Replies: 6
Views: 2145

Re: Question about SST in WRF-ROMS coupling

Looking back at the original post, i see that the SST from NCEP and the SST from ROMS are very different. So the 'coupling' is not the issue. It seems that the issue is "how did you set up the initial conditions for ROMS?" If ROMS is starting out 2-3 degrees cooler, then you cant expect si...
by jcwarner
Wed Apr 28, 2021 12:28 pm
Forum: ROMS Discussion
Topic: How to run COAWST model with real-time data
Replies: 6
Views: 1479

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

you may have to do a little work for yourself, modify existing tools, or create new tools for your own particular application. For example, the HYCOM variable 'u' has now been replaced in some locations with the variable 'water_u', etc. If you look here: http://tds.hycom.org/thredds/catalog.html thi...
by jcwarner
Wed Apr 28, 2021 1:03 am
Forum: ROMS Discussion
Topic: COAWST zeta output in VF mode
Replies: 1
Views: 607

Re: COAWST zeta output in VF mode

from my understanding, the output 'zeta' does not include zetaw, bh, or qsp. Those terms are separate, but i have not looked at Kumar's paper in a long time. Suggest you look here for more reference. I can spend some time to look deeper at some point in the future. https://www.sciencedirect.com/scie...
by jcwarner
Wed Apr 28, 2021 12:55 am
Forum: ROMS Discussion
Topic: Using wind data to model wind induced current when coupling ROMS and SWAN
Replies: 1
Views: 554

Re: Using wind data to model wind induced current when coupling ROMS and SWAN

Leah- i am not completely clear of what you are saying. If you are looking to couple ROMS and SWAN, that has been accomplished. It has taken lots of work and many years. I would recommend you use the COAWST system here: https://github.com/jcwarner-usgs/COAWST and read Kumar's paper: https://www.scie...
by jcwarner
Thu Apr 22, 2021 12:43 pm
Forum: ROMS Problems
Topic: Error aobut COAWST parallel mode
Replies: 2
Views: 855

Re: Error aobut COAWST parallel mode

I think you are barking up the wrong tree. it is most likely not an mpi issue. Now that you changed to mpich you need to make sure that the mpirun call points to mpich, and that all the libraries (hdf5, netcdf ,etc ...) are all with that flavor of mpi. Suggest you go back to openmpi and fix the mess...
by jcwarner
Tue Apr 20, 2021 3:33 pm
Forum: ROMS Discussion
Topic: Error when run restart file in cygwin
Replies: 2
Views: 797

Re: Error when run restart file in cygwin

I have been running roms in cygwin for a long time, mostly for debugging small test cases when we add new physics. You do need to be careful when an ascii character file is convert to windows, the ascii line character endings can be problematic, sometimes tabs appear (tabs are bad), etc. there shoul...
by jcwarner
Mon Apr 19, 2021 2:51 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11214

Re: problem with two-way nesting

it might be on the call to set_depth before the call to fine2coarse of the r3dvars in nesting. just a long shot but if i could get a copy of this setup, i can dig into this.
-j
by jcwarner
Fri Apr 16, 2021 1:23 pm
Forum: ROMS Problems
Topic: segmentation fault when running the COAWST model
Replies: 16
Views: 2990

Re: segmentation fault when running the COAWST model

it is not that big of an effort. Just do a diff of your ocean.in to lets say the Sandy ocean.in. that is all. It will probably not be the issue.

Suggest you compile in debug mode, and run that.
by jcwarner
Thu Apr 15, 2021 12:18 pm
Forum: ROMS Problems
Topic: segmentation fault when running the COAWST model
Replies: 16
Views: 2990

Re: segmentation fault when running the COAWST model

not sure. if you are using COAWST, make sure you start with a COAWST ocean input file. Compare yours to the one in Inlet Test or Sandy or something like that. We have a few differences to Rutgers, such as NBCfiles and NCLmfiles, etc. Another thing to try is to compile in debug=on and that gives a &q...
by jcwarner
Wed Apr 14, 2021 1:20 pm
Forum: ROMS Problems
Topic: segmentation fault when running the COAWST model
Replies: 16
Views: 2990

Re: segmentation fault when running the COAWST model

good that you are making progress. but at this point, there is not much information there to help. look through that entire log file, are there any NaN's? does the data look correct? use ncview or ncdump or matlab or anything to look at the fields in your "mycase-ini.nc" file. maybe start ...
by jcwarner
Tue Apr 13, 2021 4:55 pm
Forum: ROMS Problems
Topic: segmentation fault when running the COAWST model
Replies: 16
Views: 2990

Re: segmentation fault when running the COAWST model

so the ana_sediment and sediment.in are different files. If you need sediment, then you can provide initial information in a netcdf file, or by using ana_sediment. - Suggest you copy ana_sediment from the Sandy or inlet_test case, and move that file to the location of your project.h file. -Edit the ...
by jcwarner
Tue Apr 13, 2021 11:51 am
Forum: ROMS Problems
Topic: segmentation fault when running the COAWST model
Replies: 16
Views: 2990

Re: segmentation fault when running the COAWST model

the sediment is required if you set SSW_BBL or any other BBL.
you can use ana_sediment and set some basic properties in there.
-j
by jcwarner
Mon Apr 12, 2021 5:08 pm
Forum: ROMS Discussion
Topic: Increase Bottom Vertical Grid Resolution
Replies: 4
Views: 1240

Re: Increase Bottom Vertical Grid Resolution

here is a good start:
https://www.myroms.org/wiki/Vertical_S-coordinate

there is also an m file "roms_getnplot_grid_rutgers" that you can use to see what an adjustment to the various parameters will do to the vertical stretching.
-j
by jcwarner
Mon Apr 12, 2021 12:33 pm
Forum: ROMS Problems
Topic: segmentation fault when running the COAWST model
Replies: 16
Views: 2990

Re: segmentation fault when running the COAWST model

it probably has to do with reading the names or numbers of boundary files.
make sure you do not have NBCFILES listed twice or something like that.
by jcwarner
Mon Apr 12, 2021 1:21 am
Forum: ROMS Problems
Topic: segmentation fault when running the COAWST model
Replies: 16
Views: 2990

Re: segmentation fault when running the COAWST model

couple of things.
the error are asking about the Build/*.f90 files, not the .F.

can you look at the correct lines in the .f90 's ?

1629 inp_decode.f90
1557 read_phypar.f90
by jcwarner
Fri Mar 26, 2021 7:50 pm
Forum: ROMS Problems
Topic: Blowing up problem when using sediment
Replies: 12
Views: 3893

Re: Blowing up problem when using sediment

this gets into a world of research. Suggest you spend a good bit of time looking thru literature, and doing some model sensitivity tests. this all depends on fractions of non-cohesive, cohesive, is it mixed, etc. There are other sediment bed options in the code now for mixed beds. Here is an example...
by jcwarner
Tue Mar 23, 2021 1:17 pm
Forum: ROMS Discussion
Topic: Error to create the ww3partition_2TPAR
Replies: 1
Views: 738

Re: Error to create the ww3partition_2TPAR

can you please post this message on the coawst forum:
https://github.com/jcwarner-usgs/COAWST/issues
thanks, -j
by jcwarner
Thu Mar 18, 2021 8:08 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 13
Views: 3042

Re: Fatal error in MPI_Recv

not sure if you figured this out yet, but maybe i misled you . For the scrip file you need to list the full size of the SWAN grid in your scrip file use SWAN_COORD(1)='../../Projects/Mangkhut/swan_coord.grd', SWAN_BATH(1)='../../Projects/Mangkhut/swan_bathy.bot', SWAN_NUMX(1)=525, SWAN_NUMY(1)=351, ...
by jcwarner
Sun Mar 07, 2021 3:42 pm
Forum: ROMS Problems
Topic: Blowing up problem when using sediment
Replies: 12
Views: 3893

Re: Blowing up problem when using sediment

time to put on your investigator hat. keep digging.
what else is weird there? what is forcing this? winds? tides? what did bottom stress look like? ubar? zeta?
the answer is in there.
by jcwarner
Fri Mar 05, 2021 1:54 pm
Forum: ROMS Discussion
Topic: ** Warnin: Quadruplets will be updated per iteration
Replies: 5
Views: 1280

Re: ** Warnin: Quadruplets will be updated per iteration

this is becoming non-roms related, so can you post this message here:
https://github.com/jcwarner-usgs/COAWST/issues
thanks,
j
by jcwarner
Wed Mar 03, 2021 6:17 pm
Forum: ROMS Discussion
Topic: ** Warnin: Quadruplets will be updated per iteration
Replies: 5
Views: 1280

Re: ** Warnin: Quadruplets will be updated per iteration

for the quadruplets, swanmain.F says "! ! Here the various problems with quadruplets are checked ! The combination of quadruplets and sectors is an error ! in the calculation of quadruplets when the SECTOR option is ! used in the CGRID command. This error should be corrected ! in the future ! I...
by jcwarner
Tue Mar 02, 2021 7:05 pm
Forum: ROMS Problems
Topic: Blowing up problem when using sediment
Replies: 12
Views: 3893

Re: Blowing up problem when using sediment

with any blowup, you need to look at the rst file, his file, and stdout to see what information it is telling you. if you look at the rst file, where is the problem? at the boundary? at the wet/dry masking (for example). try to restart it before the solution occurred. you can typically restart from ...
by jcwarner
Sun Feb 28, 2021 10:05 pm
Forum: ROMS Discussion
Topic: Problem in getting started with SWAN+ROMS
Replies: 1
Views: 597

Re: Problem in getting started with SWAN+ROMS

Neel- It seems like you could use our COAWST model, it has the same ROMS version and we have added many updates to SWAN Coupling and other capabilities. If you want to get that code here: https://github.com/jcwarner-usgs/COAWST we have a user manual that describes how to setup some basic cases like ...
by jcwarner
Sun Feb 28, 2021 2:50 pm
Forum: ROMS Problems
Topic: Problem when I try to compile ROMS with "make" command
Replies: 1
Views: 596

Re: Problem when I try to compile ROMS with "make" command

i am not sure about that tutorial, but to build roms you need to use one of the build scripts.

go here
https://www.myroms.org/wiki/Getting_Started
and read that page.

also make sure you see the section about
https://www.myroms.org/wiki/build_Script

that should help a bit.
by jcwarner
Fri Feb 26, 2021 12:03 am
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11214

Re: problem with two-way nesting

either way please let us know. would like to figure this one out.
by jcwarner
Thu Feb 25, 2021 2:49 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11214

Re: problem with two-way nesting

we have a 3 nest of USeast - Carolinas - Outer Banks and i am not seeing this behavior of the currents along the boundaries. can you put the grids and the contact files somewhere accessible?
by jcwarner
Wed Feb 24, 2021 6:22 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11214

Re: problem with two-way nesting

the exterior points of the child grid are replaced with information from the contact file during initialization, in get_grid. At those points, data is interpolated from the parent and the nesting needs characteristics of the parent at those locations. I have found some issues with this for the maski...
by jcwarner
Mon Feb 22, 2021 3:16 am
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 13
Views: 3042

Re: Fatal error in MPI_Recv

in your scrip file use (1) SWAN_COORD='../../Projects/Mangkhut/swan_coord.grd', SWAN_BATH='../../Projects/Mangkhut/swan_bathy.bot', SWAN_NUMX=524, SWAN_NUMY=350, CARTESIAN=0, SWAN_COORD(1)='../../Projects/Mangkhut/swan_coord.grd', SWAN_BATH(1)='../../Projects/Mangkhut/swan_bathy.bot', SWAN_NUMX(1)=5...
by jcwarner
Mon Feb 22, 2021 3:12 am
Forum: ROMS Discussion
Topic: Error to run script_coawst
Replies: 5
Views: 1479

Re: Error to run script_coawst

i downloaded all of your files, compiled SCRIP, and I can duplicate your error. but there is more information: " Error in netWarning! ***HDF5 library version mismatched error*** The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which thi...
by jcwarner
Sat Feb 20, 2021 3:23 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 13
Views: 3042

Re: Fatal error in MPI_Recv

the sparse matrix calls are reading the scrip interpolation weights.
What do you have in the scrip.in to compute the interpolation weights?
-j
by jcwarner
Tue Feb 09, 2021 10:21 pm
Forum: ROMS Discussion
Topic: Error to run script_coawst
Replies: 5
Views: 1479

Re: Error to run script_coawst

sorry for the late reply.
did you figure this out?
can you attach the scrip.in file?
by jcwarner
Tue Feb 09, 2021 9:48 pm
Forum: ROMS Installation
Topic: Compiling Error for COAWST
Replies: 6
Views: 2394

Re: Compiling Error for COAWST

are you still having this problem?
can you send the full output of the std out.
-j
by jcwarner
Tue Feb 09, 2021 1:22 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11214

Re: problem with two-way nesting

I have been working on the nesting for a while now. There are some simple steps that i can take to check on a few things. Is your setup easy to share out?
what ts_advection are you using? time steps?
-j
by jcwarner
Mon Feb 08, 2021 2:51 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 13
Views: 3042

Re: Fatal error in MPI_Recv

if your roms grid size(h) is 525 351

then, for the SWAN INPUT file, you need to have
INPGRID BOTTOM CURVILINEAR 0 0 524 350 EXC 9.999000e+003
by jcwarner
Thu Feb 04, 2021 9:14 pm
Forum: ROMS Installation
Topic: COAWST compilation error -- wec_vf.f90
Replies: 4
Views: 1095

Re: COAWST compilation error -- wec_vf.f90

looks like a couple of issues.
a year ago or so i changed some parts of the makefile and coawst.bash files and the Compilers files.
are you using most recent versions of them?
which Compilers/ ? file are you using.
-j
by jcwarner
Wed Feb 03, 2021 1:36 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 13
Views: 3042

Re: Fatal error in MPI_Recv

if you look in the output, you will see that you basically have the same error with different values MCT::m_SparseMatrixPlus::initFromRoot_:: FATAL--length of vector y different from row count of sMat.Length of y = 185152 Number of rows in sMat = 184275 031.MCT(MPEU)::die.: from MCT::m_SparseMatrixP...
by jcwarner
Tue Feb 02, 2021 7:39 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 13
Views: 3042

Re: Fatal error in MPI_Recv

please read all of the Err* files. This is half way through: "MCT::m_SparseMatrixPlus::initFromRoot_:: FATAL--length of vector y different from row count of sMat.Length of y = 184275 Number of rows in sMat = 183400 010.MCT(MPEU)::die.: from MCT::m_SparseMatrixPlus::initFromRoot_()" so the ...
by jcwarner
Tue Feb 02, 2021 3:16 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 13
Views: 3042

Re: Fatal error in MPI_Recv

there is not enough information here to figure out what the issue is.
can you dig in a bit deeper?
by jcwarner
Tue Feb 02, 2021 3:13 pm
Forum: ROMS Installation
Topic: Compiling Error for COAWST
Replies: 6
Views: 2394

Re: Compiling Error for COAWST

yes, the compiler flags might be set too strict, and reducing that can help. But fundamentally there is a potential issue that an integer is being broadcasted as a real. I did a search in distribute.F for "CALL mpi_bcast (A, Asize" and the only place that shows up is once near the bottom i...
by jcwarner
Sat Jan 23, 2021 3:42 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6674

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

those other errors were initiated by the first one, so get the init file method figured out then try again.
by jcwarner
Fri Jan 22, 2021 5:43 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 37
Views: 6674

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

looks closely at the output text, and you will see INP_PAR:FIND_FILE - empty file name string for standard input script KeyWord: ININAME so the code is looking for a file listed in the ININAME field in the ocean.in If you use #define ANA_INITIAL then it will not look for the ininame and you can use ...
by jcwarner
Thu Jan 21, 2021 3:30 pm
Forum: ROMS Problems
Topic: Blowing up problem when using sediment
Replies: 12
Views: 3893

Re: Blowing up problem when using sediment

I am not really clear what you are trying to do but here are some thoughts. The estuary test case has grid cells on the order of 100m (or so, i dont remember exactly). So therefore it can not generate ripples that are on the order of 10's of cm. Instead, we have coded different methods to 'predict' ...
by jcwarner
Wed Jan 20, 2021 12:54 pm
Forum: ROMS Problems
Topic: netcdf output from SWAN
Replies: 3
Views: 3357

Re: netcdf output from SWAN

that is a known issue for me. Currently you can only have netcdf output for one of the grids when using my swan nesting. it is on my list to correct soon. sorry. also, for future reference, can you and others who read this please post non-roms issues on this other github site: https://github.com/jcw...
by jcwarner
Sat Jan 09, 2021 3:08 am
Forum: ROMS Discussion
Topic: forrtl: severe (194): Run-Time Check Failure
Replies: 3
Views: 1313

Re: forrtl: severe (194): Run-Time Check Failure

this says "Run-Time Check Failure. "
so it could be that the compiler flags are set to check for certain issues. these issues may or may not affect the simulation.
I have not dug into SWAN lately, but maybe you could look at the compiler flags and see what is doing this.
by jcwarner
Fri Jan 08, 2021 9:42 pm
Forum: ROMS Sediment
Topic: Estuary_test: are sediment size units and output critical stress right?
Replies: 1
Views: 1106

Re: Estuary_test: are sediment size units and output critical stress right?

sorry for the late reply. i looked into this and the values written to the his files are ok, but the units may not be. The stresses tau_ce tau_cd are /rho when read, so they are written out as m2/s2. so it should say m2/s2 in the his nc file. The Sd50 is read in and converted to m, so that should al...
by jcwarner
Wed Dec 30, 2020 9:40 pm
Forum: ROMS Discussion
Topic: forrtl: severe (194): Run-Time Check Failure
Replies: 3
Views: 1313

Re: forrtl: severe (194): Run-Time Check Failure

this is really a SWAN question.
are you trying to run a swan grid driven by a nest output from a different run?
by jcwarner
Wed Dec 23, 2020 4:34 pm
Forum: ROMS Discussion
Topic: Error to run script_coawst
Replies: 5
Views: 1479

Re: Error to run script_coawst

looks to me like a netcdf/hdf5 issue. make sure you have the correct paths for
NETCDF_INCDIR and NETCDF_LIBDIR.
if you cant figure it out. please post a ticket here:
https://github.com/jcwarner-usgs/COAWST
thanks,
j
by jcwarner
Wed Dec 23, 2020 3:15 am
Forum: ROMS Discussion
Topic: COMPUTE command in swan
Replies: 2
Views: 757

Re: COMPUTE command in swan

are you trying to do this with swan by itself or in a coupled mode?
it would not work in a coupled mode.
the coupled mode is setup to only work with swan running over a computational period that is the same as the other models.
by jcwarner
Sun Dec 20, 2020 6:03 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 3320

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

getting close, but it still looks like something is wrong with the ocean times. what is the ocean_time in the ocean ini netcdf file? and what are the attributes for that (ncdump and ncks the ocean_time in the ini file). these need to be consistent with the dstart and time_ref. try to figure it out. -j
by jcwarner
Fri Dec 18, 2020 9:08 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 3320

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

so the problem is that the forcing time is at 4983379200 days. that number is probably in seconds (not days), 4983379200/3600/24=57678 and that number is probably julian(2016,10,1)-2400000=57678 So you need to change the values of time in that forcings file from v2d_time[0]=4983379200 days v2d_time[...
by jcwarner
Fri Dec 18, 2020 2:38 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 3320

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

looks to me like something is wrong with "time". the error is: "MULTIFILE_INFO_S2D - Error while processing lateral boundary multi-files: data does not include initialization time = 2174-09-15 00:00:00.00 ****-**-** 00:00:00.00 ****-**-** 00:00:00.00 Projects/Sarika/merged_coawst_bdy....
by jcwarner
Thu Dec 17, 2020 6:24 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 3320

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

ok. so this is looking for the Quick output file writes.
Your ocean.in has
! NQCK == 0
! NDEFQCK == 0
lets try it with this:
NQCK == 0
NDEFQCK == 0
and see if that works.
by jcwarner
Thu Dec 17, 2020 5:14 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 3320

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

in the *.err file we have: mage PC Routine Line Source coawstM 0000000003C4696A Unknown Unknown Unknown libpthread-2.17.s 00002AAF329CD5D0 Unknown Unknown Unknown coawstM 000000000092471A edit_file_struct_ 212 edit_multifile.f90 coawstM 000000000090A307 read_phypar_ 2198 read_phypar.f90 coawstM 0000...
by jcwarner
Thu Dec 17, 2020 4:29 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 3320

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

there is not enough information for me to determine what is going wrong.
You need to dig into the full output being written.
Did SWAN give Err* files? Maybe try to run the system with one model at a time, to see if each model can handle your new application. then slowly add each component.
by jcwarner
Thu Dec 17, 2020 3:25 pm
Forum: ROMS Discussion
Topic: Error to run coupling WRF+ROMS+SWAN
Replies: 5
Views: 1375

Re: Error to run coupling WRF+ROMS+SWAN

SWAN uses the symbol & for a comment line, not ! Does this work: && KEYWORD TO CREATE WIND GRID && INPGRID WIND REGULAR 0 0 299 219 0.25 0.25 & NONSTATIONARY 20161016.000000 6 HR 20161018.000000 &READINP WIND 1 'Projects/Sarika_new/swan_GFS_Oct2012.dat' 4 0 FREE This is g...
by jcwarner
Thu Dec 17, 2020 2:08 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 3320

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

ok. you have this NCLMFILES == 2 ! number of climate files CLMNAME == Projects/Sarika4/coawst_clm_20161016.nc | Projects/Sarika4/coawst_clm_20161017.nc NBCFILES == 2 ! number of boundary files ! BRYNAME == Projects/Sandy/Sarika_bdy.nc BRYNAME == Projects/Sarika4/coawst_bdy_20161016.nc | Projects/Sar...
by jcwarner
Wed Dec 16, 2020 2:04 pm
Forum: ROMS Discussion
Topic: Bottom flux for Fennel model
Replies: 3
Views: 1138

Re: Bottom flux for Fennel model

are you sure it gets in that loop with the btflux variable? i dont see that variable in the code, it should be btflx.
do this:
grep -nir btflux ROMS/*
and
grep -nir btflx ROMS/*

do you see btflux as a variable anywhere else??
-j
by jcwarner
Sun Dec 13, 2020 3:06 am
Forum: ROMS Discussion
Topic: Error to run coupling WRF+ROMS+SWAN
Replies: 5
Views: 1375

Re: Error to run coupling WRF+ROMS+SWAN

try this && KEYWORD TO CREATE WIND GRID && INPGRID WIND REGULAR -105 10 0 220 160 0.25 0.25 & NONSTATIONARY 20121028.000000 6 HR 20121031.000000 &READINP WIND 1 'Projects/Sandy/swan_GFS_Oct2012.dat' 4 0 FREE this sets the INPGRID for WIND, so then SWAN knows that it will get ...
by jcwarner
Sat Dec 12, 2020 8:05 pm
Forum: ROMS Discussion
Topic: Error to run coupling WRF+ROMS+SWAN
Replies: 5
Views: 1375

Re: Error to run coupling WRF+ROMS+SWAN

this is an error from SWAN. it is saying "Error : It is not recommended to use quadruplets Error : in combination with zero wind conditions." Also looks like you turned off the winds: !&& KEYWORD TO CREATE WIND GRID && !INPGRID WIND REGULAR -105 10 0 220 160 0.25 0.25 &...
by jcwarner
Fri Dec 11, 2020 12:44 am
Forum: ROMS Bugs
Topic: a potential bug: SWAN not receives or not processes the sea surface level from ROMS
Replies: 7
Views: 2194

Re: a potential bug: SWAN not receives or not processes the sea surface level from ROMS

glad you figured it out!
SWAN needs those flags in the input file so that internally it create the input grids, etc. they are the same effect as roms cppdefs, but swan uses keywords not cpp options.
I will make this more clear in the documentation.
-j
by jcwarner
Fri Dec 11, 2020 12:40 am
Forum: ROMS Problems
Topic: Subscript error regarding BED array in stratified cohesive sediment application (with COAWST)
Replies: 12
Views: 2737

Re: Subscript error regarding BED array in stratified cohesive sediment application (with COAWST)

ok. glad you are digging in.
What is a deep sea water fall? can you show a pcolor of the bottom stresses? how high do they get?
i am sure we can come up with something, but let me see what the domain looks like.
thanks,
j
by jcwarner
Fri Dec 11, 2020 12:36 am
Forum: ROMS Discussion
Topic: ROMS 3.7 nesting problems
Replies: 8
Views: 1574

Re: ROMS 3.7 nesting problems

i am not familiar with this test case but maybe you should re-create the connectivity file. that error should not occur if the grids and connections are set up correctly. can you show a plot of the 3 grids, and the outline of grid 2 and grid 3? how much space is there between the perimeter of grid 3...
by jcwarner
Mon Dec 07, 2020 2:22 pm
Forum: ROMS Problems
Topic: Subscript error regarding BED array in stratified cohesive sediment application (with COAWST)
Replies: 12
Views: 2737

Re: Subscript error regarding BED array in stratified cohesive sediment application (with COAWST)

i think this path your are on will help, and you have identified several issues that need to be addressed. However we are in hope that your statement: "Why the available sediments are being reduced so fast is another question but it could just be due to some spin up artefacts which would take u...
by jcwarner
Fri Dec 04, 2020 1:49 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 9
Views: 2476

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

you need to look more closely at the whole output. The coupled simulation ran for 0.5 hours: ....... 622479824 2174-09-15 00:29:52.00 5.370047E-03 2.261209E+04 2.261210E+04 4.180266E+16 (191,053,16) 1.041893E-05 2.883283E-04 1.864959E-01 1.586292E+00 622479825 2174-09-15 00:30:00.00 5.370267E-03 2.2...
by jcwarner
Thu Dec 03, 2020 1:41 pm
Forum: ROMS Bugs
Topic: a potential bug: SWAN not receives or not processes the sea surface level from ROMS
Replies: 7
Views: 2194

Re: a potential bug: SWAN not receives or not processes the sea surface level from ROMS

i am not seeing much wrong here. need to keep looking. i went back to the original log file and searched for WLEV 42480 2015-07-18 11:48:00.00 6.631682E-03 1.852537E+03 1.852543E+03 7.089705E+10 (374,563,15) 1.241157E-02 2.806246E-04 3.950358E+00 9.911014E-01 ..... ** ROMS grid 1 sent data to SWAN g...
by jcwarner
Wed Dec 02, 2020 6:06 pm
Forum: ROMS Bugs
Topic: a potential bug: SWAN not receives or not processes the sea surface level from ROMS
Replies: 7
Views: 2194

Re: a potential bug: SWAN not receives or not processes the sea surface level from ROMS

so i just ran the inlet test again and it is fine. so there is something wrong in your setup.
can we look at the PRINT* files? how did you set the swan depths?
what does your INPUT file have?
-j
by jcwarner
Wed Dec 02, 2020 4:18 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 9
Views: 2476

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

ok. SWAN has some issues with the arrays, and depending on the debug flags, it will stop compiling. swan is not the problem, so lets not go down this road. the problem you were having is with roms. it stopped when it tried to close a file. how about you setup the application to only use roms. then c...
by jcwarner
Tue Dec 01, 2020 2:32 pm
Forum: ROMS Bugs
Topic: a potential bug: SWAN not receives or not processes the sea surface level from ROMS
Replies: 7
Views: 2194

Re: a potential bug: SWAN not receives or not processes the sea surface level from ROMS

that looks strange.
What is the 2.25 from? do you have wet/dry on, so that 2.25 is on land and probably masked out in swan.
can you make a pcolor plot of swan water level and roms water level at 07/18/06?
you do not have define ZETA_CONST ?
-j
by jcwarner
Tue Dec 01, 2020 2:07 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 9
Views: 2476

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

1. Yes, Kate is suggesting you edit the coawst.bash (or roms.bash) and set USE_DEBUG=on 2. can you post your cleaned ocean.in 3. the error was coawstM 000000000092471A edit_file_struct_ 212 edit_multifile.f90 coawstM 000000000090A307 read_phypar_ 2198 read_phypar.f90 so if you edit Build/read_phypar...
by jcwarner
Sat Nov 28, 2020 2:48 pm
Forum: ROMS Discussion
Topic: Problem and question about SWAN in COAWST
Replies: 1
Views: 844

Re: Problem and question about SWAN in COAWST

sorry for the late reply on this. Looks like the wind data to drive swan is not constructed correctly, or the swan grid file was not constructed correctly. That is why the lines look like that. Can you try to run swan by itself with just one grid? You could even do WIND 20. 45. (wind speed dir) in t...
by jcwarner
Sat Nov 28, 2020 2:23 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 9
Views: 2476

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

i looked at your ocean.in and there are a lot of TABS in there. if dont know if this is exactly the problem, but i remember other people had trouble when there are tabs in the ocean.in. You need to clean up that file. there are editing tools to do this. then give it another try. for coawst related i...
by jcwarner
Tue Nov 24, 2020 1:51 pm
Forum: ROMS Discussion
Topic: Issues with tides in COAWST Estuary_Test2
Replies: 3
Views: 1193

Re: Issues with tides in COAWST Estuary_Test2

Looks like you are digging in deep to the estuary test 2. I think Hans Burchard and I made up this case (mostly him) to have something different than the straight standard case we had before. To get the system to be the way you want, will require some tests. But here are some suggestions. the easter...
by jcwarner
Mon Nov 09, 2020 12:56 am
Forum: ROMS Discussion
Topic: Adding Sediment to the Latte Example
Replies: 3
Views: 1244

Re: Adding Sediment to the Latte Example

there are many other test cases to choose from. if you want to grab our version of the COAWST system, we distribute a rip current test, inlet test, etc. Most of them have sediment so there are several examples to choose from.
https://github.com/jcwarner-usgs/COAWST
-j
by jcwarner
Mon Nov 02, 2020 11:33 pm
Forum: ROMS Discussion
Topic: Problem with ssh response to uniform winds.
Replies: 4
Views: 1119

Re: Problem with ssh response to uniform winds.

is there a reason you dont use NS periodic? also there is an upwelling test case distributed with the code that you might want to try first, just to get an idea of what that case can do.
-j
by jcwarner
Sun Nov 01, 2020 12:32 am
Forum: ROMS Discussion
Topic: run error when applying forcing file
Replies: 7
Views: 1626

Re: run error when applying forcing file

check your ocean.in file make sure you dont have nffiles twice
NFFILES ==
...
NFFILES ==

the FRC array is allocated in read_phypar
CASE ('NFFILES')
...
allocate ( FRC(max_Ffiles,Ngrids) )

so it seems to be doing that call twice.
-j
by jcwarner
Wed Oct 21, 2020 1:46 pm
Forum: ROMS Discussion
Topic: Bathymetry differences in nested simulations
Replies: 5
Views: 1589

Re: Bathymetry differences in nested simulations

i am not sure why a 3 would have an issue but a 5 factor would work. If it blew up right away, that is the best type of problem. Look at the std out and make sure there are no nans, look at the rst file to see where it had troubles. You have to be a detective some times.
by jcwarner
Tue Oct 20, 2020 5:40 pm
Forum: ROMS Discussion
Topic: Bathymetry differences in nested simulations
Replies: 5
Views: 1589

Re: Bathymetry differences in nested simulations

nice animation! For your bathy question, i am not sure there is an exact answer. It could depend on the grid sizes, bathy itself, wet/dry if that is active, etc. IF what you have is working well, then i would suggest you can modify the bathy in most of the child, but dont adjust the child bathy alon...
by jcwarner
Wed Oct 07, 2020 3:03 pm
Forum: ROMS Sediment
Topic: Diffusion of sediment tracers in the water column
Replies: 1
Views: 971

Re: Diffusion of sediment tracers in the water column

sorry i did not get to this earlier. for now, the horiz diffusion of sediment is treated like any other tracer. so you would need to add a horiz mix (like your ts_dif2 and mix_geo_ts). the coeffs will be the TNU2 set in the ocean .in file. Also, you may want to update your code and use the new featu...
by jcwarner
Thu Sep 17, 2020 12:36 pm
Forum: ROMS Problems
Topic: segmentation fault occurred when read initial condition
Replies: 3
Views: 1487

Re: segmentation fault occurred when read initial condition

suggest you do this.
recompile with DEBUG=on, that will give a coawstG
run it with just 1 proc, this will make the error more easy to see.
by jcwarner
Wed Sep 16, 2020 11:10 pm
Forum: ROMS Discussion
Topic: SWAN+WRF coupling problem using COAWST
Replies: 2
Views: 1075

Re: SWAN+WRF coupling problem using COAWST

can you try an update to the code and make sure you have the most recent version? i think that was an issue we corrected.
If you still have troubles, can you make an issue here:
https://github.com/jcwarner-usgs/COAWST
thanks,
j
by jcwarner
Wed Sep 16, 2020 1:02 pm
Forum: ROMS Problems
Topic: segmentation fault occurred when read initial condition
Replies: 3
Views: 1487

Re: segmentation fault occurred when read initial condition

not sure. but both inlet test and upwelling use ana_initial. So how about you try something that needs an initial netcdf file. You could try our Sandy case, set it up to just use roms only (undef swan and undef wrf). That case uses a netcdf initial file. lets see if that works.
-j
by jcwarner
Tue Sep 15, 2020 12:05 am
Forum: ROMS Problems
Topic: ROMS<kshedstrom version> blow at the fist timestep
Replies: 9
Views: 1417

Re: ROMS<kshedstrom version> blow at the fist timestep

are you using the newest version of the input scrip? you need to have the tracer advection schemes selected, such as ! Set horizontal and vertical advection schemes for active and inert ! tracers. A different advection scheme is allowed for each tracer. ! For example, a positive-definite (monotonic)...
by jcwarner
Mon Sep 14, 2020 12:09 am
Forum: ROMS Bugs
Topic: Error to run roms_clm_roms_master_climatology_coawst_mw
Replies: 6
Views: 1607

Re: Error to run roms_clm_roms_master_climatology_coawst_mw

this is a tough one. the netcdf variable must be interpolated incorrectly, or something like that. try a different time period just to try and get it to work.
by jcwarner
Mon Aug 24, 2020 1:16 pm
Forum: ROMS Sediment
Topic: Lake_jersey test case error at first time steps
Replies: 4
Views: 1706

Re: Lake_jersey test case error at first time steps

can you look through the entire stdout and see if there are any nans above that? maybe there is something wrong with the forcings??
by jcwarner
Mon Aug 24, 2020 1:14 pm
Forum: ROMS Installation
Topic: COAWST V3.6 Compiling error
Replies: 1
Views: 995

Re: COAWST V3.6 Compiling error

can you please re=post this message here:
https://github.com/jcwarner-usgs/COAWST/issues
by jcwarner
Mon Aug 24, 2020 1:13 pm
Forum: ROMS Bugs
Topic: Error to run netcdf_load command on Matlab
Replies: 1
Views: 929

Re: Error to run netcdf_load command on Matlab

this is a matlab issue. You need to include the path(s) to all the mfiles so that matlab knows where those scripts are.
-j
by jcwarner
Tue Aug 04, 2020 12:57 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 2887

Re: Compiling COAWST_v3.6 errror

lets move this conversation over here. put a post here:
https://github.com/jcwarner-usgs/COAWST/issues
by jcwarner
Mon Aug 03, 2020 1:44 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 2887

Re: Compiling COAWST_v3.6 errror

looks like a WRF/ WPS issue. I am not sure this is the correct forum for a question like that. try the WRF forum
https://forum.wrfforum.com/
by jcwarner
Fri Jul 31, 2020 12:27 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 2887

Re: Compiling COAWST_v3.6 errror

your build.log shows a coawstM. So you are good to go.
the ls command display is messy, but i see a coawstM in there.
As i said earlier, it will not create a wrf.exe, I make it create a libwrf.a and then i link with that file.
-j
by jcwarner
Thu Jul 30, 2020 5:27 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 2887

Re: Compiling COAWST_v3.6 errror

Thanks David.
dont worry about the wrf.error. I do not let the system build a wrf.exe, i do not let swan build a swan.exe, nor a ww3.exe etc. I just make libraries, pull them all together as a coawstM.

i agree with your netcdf analysis. thanks,
-j
by jcwarner
Thu Jul 30, 2020 12:20 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 2887

Re: Compiling COAWST_v3.6 errror

i think your problem is a general roms issue, and i think it has to do with the final link at the end. it is having trouble with the netcdf f90 libs. i see: -L/work/apps/gnu_4.8.5/netcdf/4.3.3.1/lib -lnetcdff -L/work/apps/gnu_4.8.5/netcdf/4.3.3.1/lib -lnetcdf -lnetcdf try to clean this up, remove th...
by jcwarner
Tue Jul 21, 2020 7:41 pm
Forum: ROMS Discussion
Topic: Profiling COAWST with 2-way coupled ROMS/SWAN
Replies: 2
Views: 1002

Re: Profiling COAWST with 2-way coupled ROMS/SWAN

not sure what Unused 03 is. But for the coupling, if you see something like this: 97 2020-07-21 04:51:00.00 3.755311E-02 2.266493E+04 2.266496E+04 2.088627E+16 (762,292,16) 3.718707E-02 5.124825E-02 4.006800E-01 3.243301E+00 98 2020-07-21 04:54:00.00 3.755672E-02 2.266491E+04 2.266495E+04 2.088623E+...
by jcwarner
Sun Jul 19, 2020 11:16 pm
Forum: ROMS Discussion
Topic: time-dependent bottom fluxes in roms?
Replies: 3
Views: 1518

Re: time-dependent bottom fluxes in roms?

how about using Wilkin's new LwSrc? This is a vertical point source at a rho point and can have tracers with it. (as opposed to LuvSrc which is a lateral point source at a u- or v- point). You need to set the correct flags (now in the ocean.in) but it could be a viable option. The LwSrc is in get_da...
by jcwarner
Mon Jul 13, 2020 2:25 pm
Forum: ROMS Discussion
Topic: error compiling ana_lrflux
Replies: 2
Views: 875

Re: error compiling ana_lrflux

here is what's happening. You defined solar_source, and in globaldefs there is : #if defined LMD_SKPP || defined SOLAR_SOURCE || \ defined BULK_FLUXES || defined BIOLOGY # define SHORTWAVE #endif so with shortwave now automatically defined, we go to mod_forces we have # ifdef SHORTWAVE real(r8), poi...
by jcwarner
Thu Jul 02, 2020 2:09 pm
Forum: ROMS Discussion
Topic: Running error: unable to open existing NetCDF file
Replies: 8
Views: 2177

Re: Running error: unable to open existing NetCDF file

i am wondering if your ocean.in files are older. because all the ocean.in were renamed to roms_ini.nc a while ago.
by jcwarner
Tue Jun 23, 2020 9:23 pm
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 3096

Re: Roms with ice module in Coawst

rhoAir(i)=PairM*100.0_r8/(blk_Rgas*TairK(i)* & & (1.0_r8+0.61_r8*Q(i))) can you also check Q(i)? #if defined CORE_FORCING || defined SPECIFIC_HUMIDITY ! Incoming humidity is specific humidity in (kg/kg) Q(i)=RH #else IF (RH.lt.2.0_r8) THEN !RH fraction cff=cff*RH !Vapor pres (mb) Q(i)=0.6219...
by jcwarner
Tue Jun 23, 2020 7:07 pm
Forum: ROMS Bugs
Topic: Sandy case in Coawst with WW3 only
Replies: 1
Views: 1044

Re: Sandy case in Coawst with WW3 only

can you post this as an issue here:

https://github.com/jcwarner-usgs/COAWST
by jcwarner
Tue Jun 23, 2020 4:57 pm
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 3096

Re: Roms with ice module in Coawst

well, my guess is the '/' sign, it probably has a zero on the bottom. .../(rhoAir(i)*blk_Cpa) so now we start to go backwards. -blk_Cpa is a constant, so no issue there. -rhoAir(i) is computed in bulk flux as rhoAir(i)=PairM*100.0_r8/(blk_Rgas*TairK(i)* & & (1.0_r8+0.61_r8*Q(i))) PairM = Pai...
by jcwarner
Sat Jun 20, 2020 8:10 pm
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 3096

Re: Roms with ice module in Coawst

can you try and run without ICE_MODEL and see if the T and S are ok?
that may help identify the issue.
-j
by jcwarner
Tue Jun 16, 2020 7:28 pm
Forum: ROMS Discussion
Topic: units of omega
Replies: 6
Views: 1898

Re: units of omega

i think omega is written to the his file as m/s. here is what i see: in omega.F, W (omega) is computed as W(i,j,k)=W(i,j,k-1)- & & (Huon(i+1,j,k)-Huon(i,j,k)+ & & Hvom(i,j+1,k)-Hvom(i,j,k)) so it has units of m3/s in wrt his, we have ! ! Write out S-coordinate omega vertical velocity...
by jcwarner
Thu Jun 11, 2020 10:37 pm
Forum: ROMS Discussion
Topic: Compiling problem of inlet_test
Replies: 7
Views: 1801

Re: Compiling problem of inlet_test

can you create an issue here
https://github.com/jcwarner-usgs/COAWST/issues
and post output of the full build.
it has a problem earlier than what you showed.
by jcwarner
Thu Jun 11, 2020 1:13 pm
Forum: ROMS Discussion
Topic: Compiling problem of inlet_test
Replies: 7
Views: 1801

Re: Compiling problem of inlet_test

i am not sure. it looks like you have -DMPI in the cpp. If you want to use the Inlet_test and run wave -current interaction, i suggest you use our COAWST code. we have this on github now:
https://github.com/jcwarner-usgs/COAWST
the setups are very similar.
-j
by jcwarner
Tue Jun 09, 2020 8:33 pm
Forum: ROMS Discussion
Topic: Compiling problem of inlet_test
Replies: 7
Views: 1801

Re: Compiling problem of inlet_test

the file ROMS/Utility/mp_exchange.F for tile_neighbors has .. USE mod_parallel ... # if defined MPI Null_Value=MPI_PROC_NULL # else Null_Value=-1 # endif and then the MODULE mod_parallel ... #ifdef MPI include 'mpif.h' #endif so the mpif.h should be passed to the mp_exchange routines. mpif.h should ...
by jcwarner
Tue Jun 09, 2020 8:18 pm
Forum: ROMS Problems
Topic: forcing interpolation not working
Replies: 8
Views: 3086

Re: forcing interpolation not working

i just checked my forcing for the Sandy test case and the atm forcing is on a separate grid that is not identical to either of the roms grids. I remember changing this a while ago to make the test case forcing files a lot smaller, it is just a test case. So for the Sandy case, ROMS does read correct...
by jcwarner
Mon Jun 08, 2020 11:47 pm
Forum: ROMS Discussion
Topic: grid generation for idealized geometry
Replies: 4
Views: 1667

Re: grid generation for idealized geometry

For the ROMS distribution we have the classic estuary test grid from our 2005 OM paper, that was rectangular. In COAWST we have an estuary_test 2 "This application tests the ROMS for a prismatic shaped estuary that is 110 km long with the ocean end being 60 kms wide. The width of the estuary de...
by jcwarner
Thu Jun 04, 2020 8:19 pm
Forum: ROMS Problems
Topic: forcing interpolation not working
Replies: 8
Views: 3086

Re: forcing interpolation not working

i just ran the Sandy test case with grid refinement 2 grids roms +swan and it worked fine. it reads in met data for both roms grids. The output you show: Min = 1.00000000E+35 Max = -1.00000000E+35) is a pure report from roms of what it reads from your netcdf forcing file. do an ncview of that forcin...
by jcwarner
Thu Jun 04, 2020 8:14 pm
Forum: ROMS Usage
Topic: How do I input my own netCDF grid file for the ROMS Upwelling test case?
Replies: 10
Views: 3195

Re: How do I input my own netCDF grid file for the ROMS Upwelling test case?

probably something to do with the bathy Minimum Z-grid spacing, DZmin = -5.58178863E+04 m Maximum Z-grid spacing, DZmax = 6.41893191E+04 m at 1 km grid spacing, you probably should not have any negative depths (these would be elevations on land above the sea level). suggest you set a min depth = 1 m...
by jcwarner
Tue May 26, 2020 2:46 pm
Forum: ROMS Discussion
Topic: Unread or missing keyword 'NBCFILES' from input script
Replies: 1
Views: 784

Re: Unread or missing keyword 'NBCFILES' from input script

looks like you need to update your ocean.in to a more recent version.

-j
by jcwarner
Sat May 23, 2020 12:51 am
Forum: ROMS Discussion
Topic: Graphite loop optimizations cannot be used (isl is not available)
Replies: 4
Views: 2193

Re: Graphite loop optimizations cannot be used (isl is not available)

it does not relate to MCT. It has to do with your compiler, maybe the gcc, ?? , maybe the optimizations?
i did a little googling
https://gcc.gnu.org/gcc-4.8/changes.html
that page has some info. i am really not sure, have not seen this one before. looks like a compiler issue, not the code.
by jcwarner
Thu May 21, 2020 3:57 pm
Forum: ROMS Discussion
Topic: Graphite loop optimizations cannot be used (isl is not available)
Replies: 4
Views: 2193

Re: Graphite loop optimizations cannot be used (isl is not available)

you need to edit a file in your Compilers dir. most likely:
Compilers/Linux-gfortran.mk
but i did a search and dont see any graphite flags in there. maybe post more of the build.
where is that flag coming from??
by jcwarner
Thu May 21, 2020 1:18 pm
Forum: ROMS Usage
Topic: How do I input my own netCDF grid file for the ROMS Upwelling test case?
Replies: 10
Views: 3195

Re: How do I input my own netCDF grid file for the ROMS Upwelling test case?

for the upwelling case you would need to edit
ROMS/Include/upwelling.h and change
#define ANA_GRID
to
#undef ANA_GRID

recompile,

and change ROMS/External/roms_upwelling.in from
GRDNAME == roms_grd.nc
to
GRDNAME == YOUR GRID NAME here

-j
by jcwarner
Tue May 19, 2020 5:23 pm
Forum: ROMS Discussion
Topic: Blow up problem in ROMS 3.9
Replies: 2
Views: 1260

Re: Blow up problem in ROMS 3.9

a new feature in the latest ROMS is the ability to choose different advection schemes for each tracer. But you need to be careful to use the new ocean.in format. from your output is see: Tracer Advection Scheme: NLM ======================== Variable Grid Horizontal Vertical --------- ---- ----------...
by jcwarner
Mon May 18, 2020 4:16 pm
Forum: ROMS Discussion
Topic: using MPI for nested simulations
Replies: 1
Views: 776

Re: using MPI for nested simulations

currently you need to use the same number of tiles for each grid. So if you have 12 tiles, then grid 1 could be NtileI=3 and NtileJ = 4; grid 2 could be NtileI=12 NtileJ=1; etc. but the total has to be 12 (or whatever you use) for each grid. I am looking into changing this, but it takes a redistribu...
by jcwarner
Sun May 17, 2020 1:06 am
Forum: ROMS Discussion
Topic: Blow up problem
Replies: 3
Views: 1521

Re: Blow up problem

these values seem odd: GET_GRID - mask on RHO-points: mask_rho (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc) (Min = 0.00000000E+00 Max = 1.15000000E+02) GET_GRID - mask on U-points: mask_u (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc) (Min = ...