Ocean Modeling Discussion

stlaur

Good morning, I would like to report a problem compiling ROMS with SSW_BBL, or MB_BBL, or SG_BBL.
Today's (14 May 2025) "develop" branch produces the following compilation errors.
(This is with ifx and the default Linux-ifx.mk file.)

With SOLVE3D, SEDIMENT, and SSW_BBL:

cd /ches/home00/pierre ...

stlaur

If you run ROMS domains that have realistic bathymetry, resolution <=500m, tides, and your timestep is dictated by Cw, you might want to give OMEGA_IMPLICIT a try (Shchepetkin 2015 https://doi.org/10.1016/j.ocemod.2015.03.006). It's available inside the feature/kernel branch. In our case, the ...

stlaur

In "develop" branch, in ROMS/Modules/mod_ncparam.F, lines 1087-1088 are:

Code: Select all

      IF (allocated(idsurT))      deallocate ( idsurT )
      IF (allocated(idsurT))      deallocate ( idzslT )

I suspect the second line should be:

Code: Select all

      IF (allocated(idzslT))      deallocate ( idzslT )

stlaur

Inside ROMS/Nonlinear/Biology/fennel_mod.h, the 15 biological tracers (here I'm assuming that the user has activated RIVER_DON,PO4,CARBON,OXYGEN) are attributed the following identification index:

1-NO3,2-NH4,3-chlorophyll,4-phytoplankton,5-zooplankton,6-LdetritusN,7-SdetritusN,8-RdetritusN,9-PO4 ...

stlaur

Line #1 of ROMS/Nonlinear/Biology/red_tide.h appears to have a typo:
#undef NEWMAN -> #undef NEUMANN

stlaur

Information about the vertical discretization is to be provided in the text file roms_*.in.
I think the idea is that if one uses an analytical initial condition, then they would be able to change `N' (number of vertical levels) or the stretching parameters inside roms_*.in, without having to modify ...

stlaur

A quick update on this---"artificial ponding" is the proper term for what I was referring to.
E.g., https://doi.org/10.1016/j.coastaleng.2022.104246
Since the initial post, I came up with a satisfyingly-fast function to handle the ponds in postprocessing.
Happy to share if someone is interested (psl ...

stlaur

When using realistic coastal topography and inundation (WET_DRY), it is not uncommon for wetdry_mask_rho to feature a few wet `puddles' that are disconnected from the main body of water, at least temporarily.
I'm looking for a fast `puddle drying' algorithm, i.e. one that is provided a logical mask ...

stlaur

The Department of Meteorology and Atmospheric Science at The Pennsylvania State University is seeking a postdoctoral scholar in the area of numerical modeling of coastal waters . The postdoctoral scholar will work with Raymond Najjar, Professor of Oceanography ( https://www.ems.psu.edu/directory ...

stlaur

Since you mention it, there was a short paper circulating around back in ~2011 about running ROMS on a NVIDIA GPU. I don't remember what it said, but I attached it to this post.

stlaur

The line:

Code: Select all

# if defined PC02AIR_DATA

has a typo; it should be a upper case letter o (oxygen) but the line has a zero.

stlaur

A few typos in the trunk version. In file User/External/roms.in:

! Input lateral boundary conditions and climatology file names. The
! USER has the option to split input data time records into several
! NetCDF files (see prologue instructions above). If so, use a single
! line per entry with a ...

stlaur

I'm running ROMS with the trunk version, BIOLOGY activated, and I have "multi-file" BRY files (one BRY file per calendar year).
The code is compiled in serial mode with ifort, USE_DEBUG and USE_NETCDF4.
At the end of the year, when ROMS is ready to switch to the next BRY file, it enters this block ...

stlaur

Code: Select all

#setevn USE_HDF5            on          # compile with HDF5 library

should be setenv

stlaur

I accidentally ran ROMS with the default values of Linux-gfortran.mk, meaning ffast-math and O3.
Since I had this unexpected data point in hand, I thought I should conduct a few more tests and then report on this thread, in support of the original post (by John Warner) recommending the removal of ...

stlaur

Good afternoon,

I have a little question related to ROMS/Utility/get_nudgcoef.F, first introduced in the post:
https://www.myroms.org/projects/src/ticket/627

As described in the post, get_nudgcoef.F is designed to handle values in either day-1 or s-1.
Its logic follows the "units" metadata ...

stlaur

Good afternoon,

I have two suggestions regarding Nonlinear/Biology/fennel.h (Rutgers trunk version):

(1) On line 516, the code splits into two cases according to surface PAR:

IF (PARsur(i).gt.0.0_r8) THEN

followed on line 714 by:

ELSE

I'll refer to those two cases as "day-time" (PAR>0) and ...

stlaur

Good morning,

I apologize in advance if I'm wrong about what follows. I could be misinterpreting the code.

Early on in step3d_t.F (lines 334-350), oHz is computed as:

IF (Lmpdata) THEN
DO k=1,N(ng)
DO j=Jstrm2,Jendp2
DO i=Istrm2,Iendp2
oHz(i,j,k)=1.0_r8/Hz(i,j,k)
END DO
END DO
END DO ...

stlaur

Just to complete the earlier post---here is the relevant part of ROMS/Utility/read_phypar.F (as of rev.1008):

CASE ('Hadvection')
IF (itracer.lt.(NAT+NPT)) THEN
itracer=itracer+1
ELSE
itracer=1 ! next nested grid
END IF
itrc=itracer
Npts=load_tadv(Nval, Cval, line, nline, itrc, igrid ...

stlaur

Good afternoon,

I think there is a typo in the GLOSSARY section of roms.in.
It says:

! or in nested applications
!
! Hadvection == U3 \ ! temperature, Grid 1
! U3 \ ! temperature, Grid 2
! U3 \ ! temperature, Grid 3
! HSIMT \ ! salinity, Grid 1
! HSIMT \ ! salinity, Grid 2
! HSIMT ! salinity ...

stlaur

A Post-Doctoral Scholar position is available at The Pennsylvania State University to study the transport and fate of plastics in the Chesapeake Bay using numerical models and to collaborate with experimentalists. The Post-Doctoral Scholar will work with an interdisciplinary team at two institutions ...

stlaur

Hi,
There is a typo in ad_set_vbc.F on line 1165:

Code: Select all

     &            ad_stfx(i,j,itemp)

should be

Code: Select all

     &            ad_stflx(i,j,itemp)

(needs a "l" between "f" and "x").
Pierre

stlaur

Good afternoon,

I think there's a tiny typo in the recent versions of mod_scalars.F (revision >=919):

#ifdef T_PASSIVE
IF (.not.allocated(inert)) THEN
allocate ( inert(NPT) )
END IF
#endif

Since "inert" is a pointer, I think it should be "IF(.not.associated(inert)" rather than "IF(.not ...

stlaur

Maybe you can figure out what the parameters should be - probably a very small but finite value not zero

WTYPE=9 (dark coastal water) is absent from the original papers (e.g. Paulson & Simpson JPO 1977) but the following publication (attached) from:
https://publications.europa.eu/en/publication ...

stlaur

I would like to report a division by zero that occurs when WTYPE=9 and SOLAR_SOURCE are selected.

WTYPE=9 is defined in mod_scalars.F as:

real(r8), dimension(9) :: lmd_mu1 = &
& (/ 0.35_r8, 0.6_r8, 1.0_r8, 1.5_r8, 1.4_r8, &
& 0.42_r8, 0.37_r8, 0.33_r8, 0.0_r8 /)

Note that lmd_mu1 is 0.0_r8 ...

stlaur

Just a suggestion---sensitivity to the choice of the advection scheme may possibly indicate that your grid stretching is more than it should be.

Could be worth trying:
(1) decreasing the number of vertical levels,
(2) use conservative stretching parameters,
(3) increase the horizontal resolution ...

stlaur

Yes, that would work for my purpose. I see the option in my own version of the code (v.~3.3) and I will give it a try. Thanks for the reply.
Pierre

stlaur

Hi,

I have high-resolution outputs from ROMS and I would like to advect+diffuse an arbitrary 3-D scalar field using an `offline' implementation of ROMS advection-diffusion schemes.
In other words, I'm looking for a Fortran/C/whatever program that takes as input the netcdf files, interpolates them ...

stlaur

I updated my code and it works great!
Thank you very much for providing this fix.

Best regards,

Pierre

stlaur

I would be very grateful if anybody that does not encounter this issue could describe what is happening in his roms code during the reading of boundary input data such as zeta_north(:,:). It can be simply a matter of inserting a couple of write(*,*) in your code to see what roms does. Just (please ...

stlaur

I get the runtime error with:

gfortran (gcc version 4.3.2, from Linux Debian Lenny).

I also get the error on a different machine that uses:

f95: Sun Fortran 95 8.3 SunOS_i386 Patch 127002-04 2008/04/16

and it says

****** FORTRAN RUN-TIME SYSTEM ******
An array expression does not conform ...

stlaur

Thanks for this reply! Unfortunately, I checked with ncdump -h, and by opening the file in Matlab, and zeta_north correctly has two dimensions (zeta_time and xi_rho), with one record in time.
Numerous users of ROMS use boundary files and this is the first time that this is reported.
I agree that ...

stlaur

Perhaps a minimal testcase would make things clearer:
program testcase
implicit none
integer, parameter :: UBi = 403, LBi = -2, UBj = 1 ! Dummy values.
integer :: ng, model, ncid, Trec, Iend, Istr
character(400) :: ncfile, Vname
real, dimension((UBi-LBi+1)*UBj) :: A
! Dummy values for testcase ...

stlaur

Thanks for your help!
ROMS is trying to get zeta_north(:,:) from my ocean_bry.nc file. My zeta_north(:,:) array has only one record in time, and the other dimension is space (size Lm+2). What happens then is that net_cdf_get_fvar is called over line 400 of get_ngfld:
CALL netcdf_get_fvar (ng, mode ...

stlaur

Hello,
I have a small question regarding subroutine netcdf_get_fvar. This routine is called within get_ngfld.F around line 400 (SVN rev.491M, very recent) to obtain a one-dimensional array called 'A(:)', yet the 'start' and 'total' arguments each have two elements (as if A(:) was two-dimensional ...

Ocean Modeling Discussion

Search found 35 matches

Problem compiling SSW_BBL, or MB_BBL, or SG_BBL (develop)

OMEGA_IMPLICIT in estuaries

Typo in ROMS/Modules/mod_ncparam.F

Typos in ROMS/External/bio_Fennel.in

Typo in ROMS/Nonlinear/Biology/red_tide.h

Re: 2 grid questions

Re: Fast `puddle drying' algorithm

Fast `puddle drying' algorithm

Postdoctoral scholar position in numerical modeling of coastal waters

Re: Running ocean models on GPU

Typo in ROMS/Utility/checkdefs.F

Typos in roms.in and varinfo.dat

netcdf_close with BIOLOGY and multi-file BRY files

Typo in build_roms.csh

Re: gfortran -ffast-math experience

Clarification about ROMS/Utility/get_nudgcoef.F

Suggestions for Nonlinear/Biology/fennel.h

Question about HSIMT in step3d_t.F (trunk version)

Re: Typo in roms.in following overhaul of advection schemes

Typo in roms.in following overhaul of advection schemes

Postdoctoral scholar position in Estuarine Plastics Modeling

Typo in ad_set_vbc.F line 1165 rev 973

Typo in mod_scalars.F of rev. >=919

Re: WTYPE=9 causes division by zero in lmd_swfrac.F

WTYPE=9 causes division by zero in lmd_swfrac.F

Re: Spurious supercooling in ROMS-CICE simulation

Re: Offline implementation of ROMS advection-diffusion schem

Offline implementation of ROMS advection-diffusion schemes

Re: Question on subroutine netcdf_get_fvar from mod_netcdf.F

Re: Question on subroutine netcdf_get_fvar from mod_netcdf.F

Re: Question on subroutine netcdf_get_fvar from mod_netcdf.F

Re: Question on subroutine netcdf_get_fvar from mod_netcdf.F

Re: Question on subroutine netcdf_get_fvar from mod_netcdf.F

Re: Question on subroutine netcdf_get_fvar from mod_netcdf.F

Question on subroutine netcdf_get_fvar from mod_netcdf.F