Search found 1274 matches

by arango
Thu Sep 29, 2022 2:56 pm
Forum: ROMS Problems
Topic: ERROR: Abnormal termination: NetCDF OUTPUT
Replies: 2
Views: 97

Re: ERROR: Abnormal termination: NetCDF OUTPUT

ROMS is telling what is wrong: GET_GRID - Illegal output type, io_type = 0 I believe that your roms.in is old and missing several parameters. For Example, you need to have logic for I/O: ! Input and Output files processing library to use: ! ! [1] Standard NetCDF-3 or NetCDF-4 library ! [2] Serial or...
by arango
Fri Sep 23, 2022 4:25 pm
Forum: ROMS Bugs
Topic: A Bug for the multifile when using the PIO
Replies: 1
Views: 83

Re: A Bug for the multifile when using the PIO

You didn't post enough information to diagnose the problem. Does ROMS standard output write more specific information? The abort error is internal to the PIO library routine pio_nc.c , so we don't know what ROMS call triggered a such error in the PIO C-routine: Abort with message NetCDF: Attribute n...
by arango
Tue Sep 20, 2022 2:29 pm
Forum: ROMS Tools and Techniques
Topic: no bitcount using roms_write_era5_NCARds633_frcfile.m
Replies: 12
Views: 193

Re: no bitcount using roms_write_era5_NCARds633_frcfile.m

By the way, there are a couple of obscure native Matlab functions in its maputils that can be used to reset the longitude range to [0 360] or [-180 180] : > lon = wrapTo360(lon); > lon = wrapTo180(lon); These functions are helpful when setting ROMS grids and datasets in Matlab. I bet that they are s...
by arango
Sun Sep 18, 2022 4:21 pm
Forum: ROMS Tools and Techniques
Topic: no bitcount using roms_write_era5_NCARds633_frcfile.m
Replies: 12
Views: 193

Re: no bitcount using roms_write_era5_NCARds633_frcfile.m

I added the useful bitcount.m and other helpful Matlab scripts to the Matlab repository. Please update.
by arango
Thu Sep 15, 2022 9:12 pm
Forum: ROMS Discussion
Topic: Lagrangian Floats
Replies: 1
Views: 212

Re: Lagrangian Floats

Your log file doesn't give us useful information about the segmentation fault. In cases like this, it is useful to compile with the debug option ( -g ) in the build script: export USE_DEBUG=on which usually gives better information than the optimized code. Try a different compiler if gfortran doesn'...
by arango
Tue Sep 13, 2022 12:54 pm
Forum: ROMS Discussion
Topic: Configuration of ROMS for Tropical Cyclone Simulation
Replies: 4
Views: 506

Re: Configuration of ROMS for Tropical Cyclone Simulation

It is in our TODO list to update the COARE algorithm to newer version in bulk_flux.F to facilitate stronger wind regimes. However, we don't know when it will be available.
by arango
Tue Aug 30, 2022 12:39 pm
Forum: ROMS Benchmarks
Topic: Consumer-grade desktop for toy-"operational" model running 24/7?
Replies: 19
Views: 1097

Re: Consumer-grade desktop for toy-"operational" model running 24/7?

Throughout the years, there has been excellent discussions and different point of view about benchmarking ROMS on various hardware. Perhaps, it is time to summarize that information in :arrow: wikiROMS for easy and centralized access in the future. Thus, I am adding this task to our TODO list.
by arango
Mon Aug 29, 2022 12:44 pm
Forum: ROMS Benchmarks
Topic: Consumer-grade desktop for toy-"operational" model running 24/7?
Replies: 19
Views: 1097

Re: Consumer-grade desktop for toy-"operational" model running 24/7?

We updated the code last week to use the NAGFOR compiler directly with Apple Silicon. See Darwin-nag.mk. David Robertson is benchmarking ROMS on the new Macs and comparing it with ifort.
by arango
Mon Aug 22, 2022 3:27 pm
Forum: ROMS Bugs
Topic: Typo in ROMS/Nonlinear/lmd_vmix.F
Replies: 1
Views: 326

Re: Typo in ROMS/Nonlinear/lmd_vmix.F

Yes, indeed. Thank you! I will have to check if the boundary values of Akt are used in the numerical kernel. I think that this was done for output purposes.
by arango
Wed Aug 10, 2022 2:29 pm
Forum: ROMS Discussion
Topic: Particle floats in ROMS?
Replies: 4
Views: 330

Re: Particle floats in ROMS?

ROMS will not generate the floats NetCDF file without activating the FLOATS option. You MUST have activated it. Check the ROMS standard output and look at the report of the activated options. There is a test for the 2D and 3D Lagrangian floats in the test repository. We even provide the plt_floats.m...
by arango
Sat Jul 30, 2022 2:44 pm
Forum: ROMS Usage
Topic: An error occurred when running ROMS in COAWST
Replies: 10
Views: 607

Re: An error occurred when running ROMS in COAWST

Gosh, you need to pay attention to what ROMS tells you in the standard output. Where in the ocean can we have velocities of 93 m/s , and what does that mean? Your application is blowing-up because of a violation of the CFL condition. If you don't know what a CFL condition is and how to remediate it,...
by arango
Thu Jul 28, 2022 5:58 pm
Forum: ROMS Problems
Topic: %files memory allocation: Seg fault with NDEFHIS and/or NDEFAVG > 0
Replies: 4
Views: 201

Re: %files memory allocation: Seg fault with NDEFHIS and/or NDEFAVG > 0

Great, that's the way to do it. One needs to get deeper into debugging to solve the problems. Also, users learn the code more intimately and don't get scared of making changes.
by arango
Thu Jul 28, 2022 2:47 pm
Forum: ROMS Adjoint
Topic: Adjoint and tangent input files
Replies: 2
Views: 250

Re: Adjoint and tangent input files

The ITLNAME and IADNAME initialization NetCDF files are needed for specific algorithms like adjoint sensitivities, observation impacts and observation sensitivities. To generate those files you will need to know how to write the adjoint for the specific functional in ADSNAME . They are very advanced...
by arango
Thu Jul 28, 2022 12:23 am
Forum: ROMS Problems
Topic: %files memory allocation: Seg fault with NDEFHIS and/or NDEFAVG > 0
Replies: 4
Views: 201

Re: %files memory allocation: Seg fault with NDEFHIS and/or NDEFAVG > 0

It has a problem reporting to standard output. Put a print statement to check was is the value of ng and ncname. You can modify the def_his.f90 in the Build_romsG directory and recompile it with the -noclean option. You need a little debugging to figure out what is going on.
by arango
Wed Jul 27, 2022 3:52 pm
Forum: ROMS Problems
Topic: ==17629==ERROR: LeakSanitizer: detected memory leaks
Replies: 5
Views: 376

Re: ==17629==ERROR: LeakSanitizer: detected memory leaks

We have many issues with gfortran in the GSW-Fortran (TEOS-10 equation of state) in JEDI. The problem is with various versions of gfortran implementing basic Fortran2003 functionality weirdly or incompletely. For example, the fact that you get memory leaks is a symptom of the problem and bug in the ...
by arango
Wed Jul 27, 2022 12:57 pm
Forum: ROMS Problems
Topic: ==17629==ERROR: LeakSanitizer: detected memory leaks
Replies: 5
Views: 376

Re: ==17629==ERROR: LeakSanitizer: detected memory leaks

I bet that you are using gfortran? What version of the compiler? The YAML parser use features of Fortran2003 that gfortran has issues with them. I update the parser because of it. Have you updated your code to the latest version of ROMS?
by arango
Mon Jul 25, 2022 2:32 pm
Forum: ROMS Problems
Topic: MaxDensity error where the h changes rapidly
Replies: 4
Views: 387

Re: MaxDensity error where the h changes rapidly

The temperature or salinity is getting very high in those places. That is, the model is blowing up. You must check the bathymetry, minimum depth allowed (cannot be zero), and r-factors. Recall that ROMS has terrain-following coordinates and needs to stack N-levels between bathymetry and the free sur...
by arango
Fri Jul 22, 2022 3:27 pm
Forum: ROMS Adjoint
Topic: compiling error#6460 when activate RPCG and RBL4DVAR option
Replies: 2
Views: 228

Re: compiling error#6460 when activate RPCG and RBL4DVAR option

Hmm, you must be doing something wrong. We always need the RPCG solver for the RBL4DVAR data assimilation algorithm. I don't understand the nature of the error because ROMS 4D-Var algorithms need the nonlinear ( NLM ), tangent linear ( TLM ), and adjoint ( ADM ) kernels, and all those variable are i...
by arango
Tue Jul 05, 2022 5:26 pm
Forum: ROMS Bugs
Topic: A bug in the equilibrium_tide.F
Replies: 1
Views: 169

Re: A bug in the equilibrium_tide.F

Yep, good catch! We need an underscore here.

Code: Select all

      &                 COS(S2%omega*t_time_sec+                         &
      &                     deg2rad*(2.0_r8*lonr(i,j)+S2%chi+S2%nu))+    &
by arango
Tue Jul 05, 2022 5:20 pm
Forum: ROMS Bugs
Topic: Possible bug in ROMS/Utility/convolve.F
Replies: 2
Views: 217

Re: Possible bug in ROMS/Utility/convolve.F

It seems that you are using an older version of ROMS. All the I/O routines were modified when the PIO library was added. Such a routine has additional arguments. I think that you need to update.
by arango
Fri Jul 01, 2022 1:18 pm
Forum: ROMS Discussion
Topic: I want to use HYCOM GLB v0.08 as the initial / boundary data of ROMS.
Replies: 16
Views: 1170

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

You seem to be getting ahead of yourself on your modeling priorities. First, you need to learn how to use ROMS and become familiar with its I/O and how applications are set up. We offer plenty of idealized and realistic test cases. Then, you need to get proficient in the preprocessing software. Sinc...
by arango
Tue Jun 28, 2022 12:01 pm
Forum: ROMS Bugs
Topic: Possible (minor?) bug in wrt_ini.F
Replies: 2
Views: 269

Re: Possible (minor?) bug in wrt_ini.F

Never in the history of ROMS ocean_time had units of days, It is always seconds because ROMS state has MKS units. That said, the procedure netcdf_get_time in mod_netcdf.F is smart enough to make a conversion if the units attribute is correctly specified in the NetCDF file. The initial ROMS NetCDF fi...
by arango
Wed Jun 22, 2022 4:21 pm
Forum: ROMS Adjoint
Topic: Are the observation error covariances in wc13 actually instrument errors?
Replies: 2
Views: 278

Re: Are the observation error covariances in wc13 actually instrument errors?

The observation error covariance, R, is assumed to be a diagonal matrix for simplicity. The whole R cannot be computed directly but is modeled. The cross-correlations are ignored. Basically, R has two terms: error of measurement (usually small) plus error of representation (tricky). This error of re...
by arango
Mon Jun 20, 2022 1:05 pm
Forum: ROMS Discussion
Topic: Water type option
Replies: 1
Views: 260

Re: Water type option

Yes, this capability has been available in ROMS for nine years! With a little curiosity, you can find the information that you seek in the ROMS trac system immediately instead of posting here in the Forum. We always recommend to the User to do that basic search first. See the :arrow: following trac ...
by arango
Tue Jun 14, 2022 8:57 pm
Forum: ROMS Bugs
Topic: LwSrc i,j bug
Replies: 1
Views: 233

Re: LwSrc i,j bug

Thanks, John, great catch. Weird, my aggressive compiling/linking flags didn't pick up those out-of-bounce indices in parallel. I will update the code.
by arango
Tue Jun 14, 2022 2:58 am
Forum: ROMS Discussion
Topic: too high bottom temperature result in estuary
Replies: 6
Views: 529

Re: too high bottom temperature result in estuary

WOW, all the tracer advection CPP options were eliminated two years ago! You are using a very old code, please update. Check the following :arrow: track ticket for details. ROMS is a living entity, still evolving and improving.
by arango
Wed Jun 08, 2022 6:15 pm
Forum: ROMS Bugs
Topic: Undefined/uninitialized local variable eps for WET_DRY
Replies: 2
Views: 239

Re: Undefined/uninitialized local variable eps for WET_DRY

Hmm, the option WET_DRY is not supported in any of the adjoint-based algorithms! The reason is that their associated mask variables would become time-dependent, and we need the entire trajectory for stepping backward in time. However, we will need to change the TLM and ADM kernels to add the variati...
by arango
Tue Jun 07, 2022 3:13 pm
Forum: ROMS Bugs
Topic: Typo in matlab/4dvar/d_ssh_obs.m
Replies: 1
Views: 136

Re: Typo in matlab/4dvar/d_ssh_obs.m

Good catch. The provenance is primarily used in the observation sensitivity analysis. It is a minor typo. We need to have instead:

Code: Select all

provenance.Sargo     = 7;    % ARGO floats salinity from Met Office
by arango
Wed Jun 01, 2022 3:18 pm
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1372

Re: Questions about wrf-roms coupling

Nested grids resolve smaller scale physics that may or may not be associated with your wind accuracy in the open ocean. For example, high-resolution winds are required next to mountainous coastal areas to resolve thermal fronts, convention, and other physics. In addition, small-scale phenomena like ...
by arango
Wed Jun 01, 2022 1:03 pm
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1372

Re: Questions about wrf-roms coupling

I mentioned before that your WRF nested grid is ill-conceived. It is inside of ROMS grid. It would be best to think about physics here and what the nesting is doing. You have a solid tropical storm covering the entire area, and there is a horizontal gradient of the wind due to coarse and fine resolu...
by arango
Fri May 27, 2022 2:01 am
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1372

Re: Questions about wrf-roms coupling

We recommended running without nesting, but still, you haven't reported that solution. Unfortunately, there is not much help that we can give you if the suggestions are not followed.
by arango
Fri May 20, 2022 5:09 pm
Forum: ROMS Installation
Topic: Memory leaks - Upwelling
Replies: 8
Views: 472

Re: Memory leaks - Upwelling

Well, that is peculiar. If you are using a relative new version of ROMS, you will notice that in the Build_roms directory, the master.f90 file has: ! !----------------------------------------------------------------------- ! Terminate ocean model execution: flush and close all IO files. !-----------...
by arango
Fri May 20, 2022 1:42 am
Forum: ROMS Installation
Topic: Memory leaks - Upwelling
Replies: 8
Views: 472

Re: Memory leaks - Upwelling

What version of gfortran are you using? I don't have any memory leaks with gfortran and the upwelling test case. Anyway, you get what you pay for the compiler. I have to make some modifications to the YAML parser because gfortran does not support some features of Fortran-2003. It is ridiculous how b...
by arango
Thu May 19, 2022 2:48 pm
Forum: ROMS Discussion
Topic: Questions about wrf-roms coupling
Replies: 20
Views: 1372

Re: Questions about wrf-roms coupling

These grids are badly designed. I suggest that you run without the nested grids first. You always have to start SIMPLE! Then, you add complexity. Tropical storms are large, so the resolution of the coarser grids is sufficient. WFR would need surface temperature everywhere (land/ocean). If the ROMS g...
by arango
Tue Apr 26, 2022 1:09 pm
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 12
Views: 1157

Re: compile ROMS error

The problem that was fixed yesterday was for the makefile in the git repositories. The makefile in the svn repositories was fine. Yes, we always recommend to use build_roms.sh or build_roms.csh to compile ROMS. Alternatively, you can compile ROMS with CMake using cbuild_roms.sh and cbuild_roms.csh ....
by arango
Tue Apr 26, 2022 12:30 am
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 12
Views: 1157

Re: compile ROMS error

Please, update the repository. I forgot to make the required changes to the makefile during the static/share LibROMS update in the git repositories. This should fix the problem that you are having. Good luck.
by arango
Tue Apr 12, 2022 2:52 pm
Forum: ROMS Discussion
Topic: Manning-Strickler for 2d bottom friction
Replies: 2
Views: 245

Re: Manning-Strickler for 2d bottom friction

Yes, set_vbc.F is the correct routine. You can code in the C-preprocessed set_vbc.f90 file if you are experimenting. Make sure the you save that .f90 file because it will be lost when you compile without the -noclean flag. In distributed routine, you just need CPP option and follow the design for ot...
by arango
Mon Apr 11, 2022 2:56 pm
Forum: ROMS Bugs
Topic: adjoint model interpolates two snapshots maybe wrong.
Replies: 2
Views: 326

Re: adjoint model interpolates two snapshots maybe wrong.

Why are you using time-cycling in 4D-Var and adjoint fields? Is this a forcing field? I don't see any reason to do so. There is a misunderstanding of the purposes of 4D-Var! You need to use actual observations and forcing. Get the appropriate forcing for your 4D-Var cycle.
by arango
Thu Mar 31, 2022 3:11 pm
Forum: ROMS Problems
Topic: yaml_parser error with the latest update
Replies: 8
Views: 654

Re: yaml_parser error with the latest update

This an a issue with the gfortran compiler. I already took care of this issue. See the following :arrow: track ticket. It seems that you are ignoring track ROMS updates.
by arango
Mon Mar 28, 2022 10:05 pm
Forum: ROMS Problems
Topic: yaml_parser error with the latest update
Replies: 8
Views: 654

Re: yaml_parser error with the latest update

Well, you have posted two bizarre errors messages due to compilation. It seems to us that you are using a very old gfortran compiler. Also, your NetCDF library is old. We are using NetCDF version 4.7.4. I think that you may need to update your compilers. If you have access to ifort , try to compile ...
by arango
Mon Mar 28, 2022 9:24 pm
Forum: ROMS Problems
Topic: yaml_parser error with the latest update
Replies: 8
Views: 654

Re: yaml_parser error with the latest update

The most important information is missing? What compiler are you using and its version?
by arango
Mon Mar 28, 2022 3:05 pm
Forum: ROMS Documentation
Topic: Missing link to Broquet et al. 2009 journal article
Replies: 2
Views: 533

Re: Missing link to Broquet et al. 2009 journal article

Thank you, check my profile in ResearchGate:

https://www.researchgate.net/profile/He ... o/research

All the papers are there. Then, request access to the ones that you need.
by arango
Sun Mar 27, 2022 5:59 pm
Forum: ROMS Installation
Topic: Fortran runtime error: Assignment of scalar to unallocated array
Replies: 7
Views: 608

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

I know what is the problem. I will load a fix tomorrow. I am taking the day off to take my dogs to the lake.
by arango
Fri Mar 25, 2022 7:41 pm
Forum: ROMS Bugs
Topic: Error in ROMS/Modules/mod_scalars.F
Replies: 2
Views: 356

Re: Error in ROMS/Modules/mod_scalars.F

Thank you for reporting this issue. The problem is that the statement in mod_scalars.F

Code: Select all

      user=0.0_r8
needs to be removed. The other statements that you added are incorrect. The management of the user variable is now done in read_phypar.F.
by arango
Thu Mar 24, 2022 5:43 pm
Forum: ROMS Problems
Topic: Signed Integer Overflow
Replies: 10
Views: 1015

Re: Signed Integer Overflow

It seems that you created a grid and initial conditions NetCDF files for the UPWELLING test case. However, your grid is incorrect. Especially, the bathymetry. You are unavailable to understand the information that ROMS is providing you. You need to master the basics of the ROMS vertical grid to desi...
by arango
Fri Mar 18, 2022 7:47 pm
Forum: ROMS Discussion
Topic: How to make a loop of simulations
Replies: 2
Views: 417

Re: How to make a loop of simulations

Usually, I generate ensemble runs with more sophisticated ROMS algorithms. You can use the roms.in USER parameter to specify the desired wind speeds to be read from standard input: ! Generic User parameters, [1:NUSER]. NUSER = 2 USER = 2.0d0 5.0d0 In your customized ana_winds.h you can have: DO j=Js...
by arango
Tue Mar 08, 2022 1:20 pm
Forum: ROMS Discussion
Topic: SIGSEGV, segmentation fault occurred (with Empty log file)
Replies: 6
Views: 586

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

There are 29 examples cases of idealized and realistic applications in the svn test repository of various complexity. Check :arrow: wikiROMS for how to access that repository. Then, start from one of the cases. It is what we recommend when you register as a user.
by arango
Mon Mar 07, 2022 3:52 pm
Forum: ROMS Problems
Topic: Signed Integer Overflow
Replies: 10
Views: 1015

Re: Signed Integer Overflow

There is no solution other than updating the gfortran compiler or using a different compiler. If you have access to another computer try to see what happens.
by arango
Fri Mar 04, 2022 5:33 pm
Forum: ROMS Problems
Topic: Signed Integer Overflow
Replies: 10
Views: 1015

Re: Signed Integer Overflow

A great percentage of the posts in this forum do not provide adequate information or do not read carefully the error. As a consequence messages are ignored since we are very busy. With a little curiosity, you will notice that routine ran1.F and module ran_state.F exclusively uses 32-bit integers in ...
by arango
Tue Mar 01, 2022 8:37 pm
Forum: ROMS Problems
Topic: netcdf_close with BIOLOGY and multi-file BRY files
Replies: 3
Views: 573

Re: netcdf_close with BIOLOGY and multi-file BRY files

Hi Pierre, great catch! Thank you for reporting this problem. I updated the :arrow: repositories.
by arango
Tue Feb 22, 2022 8:33 pm
Forum: ROMS Bugs
Topic: Typos in roms.in and varinfo.dat
Replies: 2
Views: 519

Re: Typos in roms.in and varinfo.dat

Yes, I did notice those, thank you! As a matter of fact, I replaced varinfo.dat with a YAML file varinfo.yaml. It will released with ROMS 4.1. Stay tuned.
by arango
Thu Feb 17, 2022 2:13 pm
Forum: ROMS Adjoint
Topic: Which ROMS source version to use for the 4DVar tutorial
Replies: 3
Views: 583

Re: Which ROMS source version to use for the 4DVar tutorial

Your best strategy is to start with the latest version of the code. I think that I updated the documentation Readme and PDF files in the test repository. Maybe we need to update some of the files in WikiROMS. Nowadays, we use I4DVAR and RBL4DVAR. Our preferred method is to use the dual formulation R...
by arango
Mon Feb 14, 2022 5:37 pm
Forum: ROMS Bugs
Topic: Typo in build_roms.csh
Replies: 1
Views: 498

Re: Typo in build_roms.csh

Yes, thank you for reporting this typo!
by arango
Mon Feb 14, 2022 5:31 pm
Forum: Job Opportunities
Topic: Marine Data assimilation position at GMAO
Replies: 0
Views: 463

Marine Data assimilation position at GMAO

We have a full-time position open at NASA’s Global Modeling and Assimilation Office (GMAO) to work on marine data assimilation, working with the SOCA system. I wondered if you could forward the info to anyone you think might be interested. It could be a good opportunity for a recent graduate. The po...
by arango
Sat Jan 29, 2022 9:40 pm
Forum: ROMS Discussion
Topic: SCORPIO pio_file_fail_np4_nio2_st2 (Timeout)
Replies: 1
Views: 265

Re: SCORPIO pio_file_fail_np4_nio2_st2 (Timeout)

Well, it seems that you missed the point that we make in that webpage that the SCORPIO library is much slower when compared to PIO. Use the PIO library instead. The SCORPIO library was forked from the PIO library several years ago and evolved separately. The generic interface for parallel I/O in ROM...
by arango
Thu Jan 20, 2022 8:11 pm
Forum: ROMS Discussion
Topic: Number of history files greater than 9999
Replies: 7
Views: 774

Re: Number of history files greater than 9999

Hi Kate, since ROMS now has a full-time management module ( dateclock.F ) that even includes a Fortran version of Matlab's datenum and datestr , it has been in my TODO list to add an option that includes some date format in the filename. Additionally, it also has day-of-the-year, ISO 8601 format, an...
by arango
Thu Jan 20, 2022 7:31 pm
Forum: ROMS Discussion
Topic: Number of history files greater than 9999
Replies: 7
Views: 774

Re: Number of history files greater than 9999

Yes, this is an easy change to make. However, making such a change will affect our nomenclature conventions for ensemble runs, 4D-Var forward solutions, operational set-ups, etc. I am reluctant to make such a change. You are the first user since ROMS was released more than 20 years ago that creates ...
by arango
Wed Jan 19, 2022 2:31 am
Forum: ROMS Discussion
Topic: Error in c_initial matlab script
Replies: 7
Views: 636

Re: Error in c_initial matlab script

Yes, I updated c_initial.m, c_climatology.m, and c_biology.m to use the native Matlab interface to NetCDF. I have been removing slowly the old and obsolete interface to mexnc. Please update your repository. Thank for reporting this issue.
by arango
Wed Jan 05, 2022 3:15 pm
Forum: ROMS Discussion
Topic: zeta calibration
Replies: 2
Views: 401

Re: zeta calibration

Then, you need to check ROMS governing equations in the WikiROMS or the literature to understand it. I give you a clue: It is a quantity related to the vertically-integrated (barotropic) continuity equation and volume conservation. Does that rings any bells? Are you asking us to explain the basic ph...
by arango
Wed Jan 05, 2022 3:06 pm
Forum: ROMS Discussion
Topic: Linear EoS in ROMS
Replies: 1
Views: 316

Re: Linear EoS in ROMS

It is a the bottom of rho_eos.F. As always, you can check the C-preprocessed file rho_eos.f90 in the build directory for the case that NONLIN_EOS is not activated. It is a very simple equation and does not include any of the secant bulk modules terms.
by arango
Wed Dec 22, 2021 6:06 pm
Forum: ROMS Bugs
Topic: Time averaged output during 4dvar
Replies: 3
Views: 631

Re: Time averaged output during 4dvar

Yes, do not mess around with the averages in ROMS 4D-Var because they are used specifically to deal with time-averaged observations operators. If you need NLM time-averaged fields, you need to rerun the nonlinear model with the 4D-Var analysis initial conditions. Did you activate AD_AVERAGES ? It ma...
by arango
Wed Dec 15, 2021 7:14 pm
Forum: ROMS Problems
Topic: Cannot run 2D only mode with ROMS3.9 or higher
Replies: 9
Views: 1086

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

Obviously, this is a compiler bug! We find such bugs in ifort and gfortran from time to time. They disappears when we update the compiler. I added a SOLVE3D conditional to mod_ncpararm.F since such variables are not needed/used in shallow-water configurations.
by arango
Mon Dec 13, 2021 10:11 pm
Forum: ROMS Problems
Topic: Cannot run 2D only mode with ROMS3.9 or higher
Replies: 9
Views: 1086

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

Hmm, that is very weird because the variable isWvel is a scalar and well defined in mod_ncparam.F . It doesn't need an exception because SOLVE3D is not activated. It is used in read_phypar.F is inside a SOLVE3D conditional. I compiled and ran the SOLITON test. It works for me. If you have made chang...
by arango
Mon Dec 06, 2021 10:50 pm
Forum: ROMS Problems
Topic: zero_phase_date
Replies: 1
Views: 430

Re: zero_phase_date

Yes, you need to update varinfo.dat. For more information about that specific update check the following :arrow: trac ticket.
by arango
Wed Dec 01, 2021 9:08 pm
Forum: ROMS Installation
Topic: How to organize custom bio code
Replies: 3
Views: 690

Re: How to organize custom bio code

Very easily, such capability has been available in ROMS since ever. See the test repository directory test/upwelling . Notice that there is a copy of fennel.h that overwrites the one in the distributed master code. Also, notice the following variable in build_roms.sh : export MY_ANALYTICAL_DIR=${MY_...
by arango
Wed Nov 24, 2021 4:29 pm
Forum: ROMS Discussion
Topic: High Temperature in Summer
Replies: 4
Views: 906

Re: High Temperature in Summer

Also, you are using a very old version of ROMS. We no longer have CPP options for tracer advection. The tracer advection is selected in roms.in . There are more options for advection. You have the option to select one scheme for temperature and another scheme for salinity and positive-definite passi...
by arango
Mon Nov 22, 2021 3:56 pm
Forum: ROMS Discussion
Topic: usage of both LuvSrc and LwSrc
Replies: 4
Views: 818

Re: usage of both LuvSrc and LwSrc

John, I think that will be a simple change and a good idea. We can have other values for Dsrc. I assume that your strategy is to have some point sources doing LuvSrc and other doing LwSrc. We cannot have both methods for the same point source.
by arango
Tue Nov 16, 2021 2:11 pm
Forum: ROMS Bugs
Topic: Typo in state_read.F
Replies: 1
Views: 543

Re: Typo in state_read.F

Yes, thank you for reporting this typo!
by arango
Mon Nov 15, 2021 4:17 pm
Forum: ROMS Bugs
Topic: Possible bug in def_tides.F
Replies: 1
Views: 408

Re: Possible bug in def_tides.F

Yes. great catch. Thank you for reporting this problem. I missed those. It seems a little bit confusing to have two different indices. For example, idv3dD in the standard input file and idv3dH for the NetCDF variable metadata. This was introduced when I separated input tidal forcing and output detid...
by arango
Tue Nov 02, 2021 5:23 pm
Forum: ROMS Bugs
Topic: tiling and divide by zero error
Replies: 10
Views: 1138

Re: tiling and divide by zero error

The tile partition in ROMS is computed with Lm and Mm , since everybody has the same number of ghost points. In my possibility values above for NtileI and NtileJ , I assume that the values provided were Lm and Mm . I always prefer less tiles in the I-direction to allow vectorization to accelerate co...
by arango
Tue Nov 02, 2021 4:51 pm
Forum: ROMS Bugs
Topic: tiling and divide by zero error
Replies: 10
Views: 1138

Re: tiling and divide by zero error

That's not good. You need to estimate the tile partition by hand since we are dealing with some prime numbers. Try some of the options that I typed above.
by arango
Tue Nov 02, 2021 4:24 pm
Forum: ROMS Bugs
Topic: tiling and divide by zero error
Replies: 10
Views: 1138

Re: tiling and divide by zero error

That's a very old version of the code. It doesn't have PIO. I released that capability this year. Then, what is your tile partition? It seems to me that it will run more efficiently with fewer processes. Are you activating an ecosystem model or nesting? The memory requirements increase as the tracer...
by arango
Tue Nov 02, 2021 4:01 pm
Forum: ROMS Bugs
Topic: tiling and divide by zero error
Replies: 10
Views: 1138

Re: tiling and divide by zero error

What is the size of your grid? I assume that it is very large since you have been using 400 PETs. What type of I/O library are you using? Using 400 processes can add a substantial bottleneck to the simulation because of I/O. That's the reason I implemented the PIO library for these cases. What versi...
by arango
Mon Nov 01, 2021 1:14 pm
Forum: ROMS Discussion
Topic: Problems with restarting the model
Replies: 11
Views: 1364

Re: Problems with restarting the model

The C-preprocessing option is CHECKSUM . It is there because I code it: ... ASSUMED_SHAPE Using assumed-shape arrays CHECKSUM Report order-invariant checksum (hash) when processing I/O BOUNDARY_ALLREDUCE Using mpi_allreduce in mp_boundary routine ... INITIAL: Configuring and initializing forward non...
by arango
Sun Oct 31, 2021 6:13 pm
Forum: ROMS Discussion
Topic: Problems with restarting the model
Replies: 11
Views: 1364

Re: Problems with restarting the model

Yes, using checksum is a good idea. ROMS also has checksum for I/O processing. You need to activate the CPP option CHECKSUM.
by arango
Sat Oct 23, 2021 5:49 pm
Forum: ROMS Ecosystem
Topic: Understanding tracer identification indices
Replies: 3
Views: 778

Re: Understanding tracer identification indices

The order in the GlOSSARY is subject to the CPP options activated by the user. In the test repository, I show how to use the compact form of the standard input parameters for biology. See upwelling Test Case. It is always advantageous to check standard output since ROMS has lots of CPP options. Lots...
by arango
Sat Oct 23, 2021 3:31 pm
Forum: ROMS Ecosystem
Topic: Understanding tracer identification indices
Replies: 3
Views: 778

Re: Understanding tracer identification indices

Yes, the biology tracer numbering change according to the CPP options. When in doubt, I always recommend to everybody in this forum to check the standard output very carefully, and pipeline it to a log file instead of the screen. The information that you need is always there. For the upwelling test ...
by arango
Thu Oct 14, 2021 3:25 pm
Forum: ROMS Problems
Topic: OUTPUT - multi-file counter AVG(ng)%load = 3, is greater than Nfiles = 2 dimension 247058 in structure when c
Replies: 3
Views: 1026

Re: OUTPUT - multi-file counter AVG(ng)%load = 3, is greater than Nfiles = 2 dimension 247058 in structure when c

Thanks Gordon. I looked in the debugger yesterday and I didn't see anything wrong with it. However, you provided essential information that the problem occurs during restart. That piece of information was not provided before. I didn't check that. Let me see if I can reproduce the problem so I can fi...
by arango
Thu Oct 14, 2021 1:43 am
Forum: ROMS Bugs
Topic: typo in mod_arrays.F and missing in read_phypar.F?
Replies: 4
Views: 958

Re: typo in mod_arrays.F and missing in read_phypar.F?

Yes, I updated the repository but I rejected the changes to read_phypar.F . As I mentioned above, the suggested change is not needed because the time-averaged NetCDF files activated with AVERAGES and DIAGNOSTICS options are special. The user Jianfei Ma didn't provide enough information as to why the...
by arango
Tue Oct 12, 2021 11:39 pm
Forum: ROMS Discussion
Topic: relative/potential vorticity outputs
Replies: 7
Views: 1372

Re: relative/potential vorticity outputs

Notice that we use pden as potential density referenced to the surface. This quantity is not written in ROMS history files, but it can be computed using eos.m , which computes the different quantities from the ROMS equation of state. Notice that: pden = den1 - 1000 where den1 is the density at stand...
by arango
Sun Oct 10, 2021 8:11 pm
Forum: ROMS Bugs
Topic: typo in mod_arrays.F and missing in read_phypar.F?
Replies: 4
Views: 958

Re: typo in mod_arrays.F and missing in read_phypar.F?

Thank you for bringing this to my attention. I agree with the correction to mod_arrays.F . Now, I need to think about the issue with the AVERAGES files and also the DIAGNOSTICS files in read_phypar.F . They are special since the creation of the time-averaged files is delayed due to the time-averagin...
by arango
Sat Oct 09, 2021 1:17 pm
Forum: ROMS Discussion
Topic: relative/potential vorticity outputs
Replies: 7
Views: 1372

Re: relative/potential vorticity outputs

Yes, there is a relative vorticity script rvorticty.m in the Matlab repository.
by arango
Fri Oct 08, 2021 3:05 pm
Forum: ROMS Discussion
Topic: relative/potential vorticity outputs
Replies: 7
Views: 1372

Re: relative/potential vorticity outputs

Nope, the vorticity fields are only available in the AVERAGES output NetCDF file. You control the time-averaging window, NAVG > 1. It is not in the DIAGNOSTICS file because it only contains the various terms of the governing equations, and vorticity is not one of them. You will find vorticity in the...
by arango
Fri Oct 01, 2021 1:05 am
Forum: ROMS Installation
Topic: ROMS Upwelling Idealisation / Test Case Failure
Replies: 7
Views: 1310

Re: ROMS Upwelling Idealisation / Test Case Failure

Yes, your learning process just started. To run over a particular number of processes you need to modify parameters NtileI and NtileJ in roms_upwelling.in. The number of process to use is determined by the product of those two parameters.
by arango
Wed Sep 22, 2021 8:11 pm
Forum: ROMS Bugs
Topic: typo in ad_get_data
Replies: 3
Views: 723

Re: typo in ad_get_data

Yes, I noticed that early today. It also in rp_get_data.F.
by arango
Wed Sep 22, 2021 7:10 pm
Forum: ROMS Bugs
Topic: typo in ad_get_data
Replies: 3
Views: 723

Re: typo in ad_get_data

Yes, thank you. It is weird why I didn't catch that one before.
by arango
Wed Sep 22, 2021 3:06 pm
Forum: ROMS Installation
Topic: ROMS Upwelling Idealisation / Test Case Failure
Replies: 7
Views: 1310

Re: ROMS Upwelling Idealisation / Test Case Failure

Okay, it seems that you are struggling to install the required libraries. The upwelling test case only requires the NetCDF library. You can either use the NetCDF-3 or NetCDF-4 library. The NetCDF-4 library has a lot of options to install. The HDF5 library is only needed for parallel I/O. One of the ...
by arango
Fri Sep 10, 2021 12:49 am
Forum: ROMS Discussion
Topic: Horizontal surface pressure gradient forcing in 2D and 3D
Replies: 16
Views: 6486

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

My understanding is that the nondimensional density scale (see rhoA and rhoS in rhos_eos.F ) enters only in the barotropic pressure gradient in step2d with VAR_RHO_2D . Notice that the paper's equation shows the density evaluated at the free surface, which is only obtained by vertically integrating ...
by arango
Thu Sep 09, 2021 10:09 pm
Forum: ROMS Discussion
Topic: Horizontal surface pressure gradient forcing in 2D and 3D
Replies: 16
Views: 6486

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

Nope, I am taking about the first term: GRho0*z_w(i,j,N(ng)) . It needs to be g*z_w(i,j,N(ng)) , which also gives m2/s2 for kinematic pressure. I am sure that this term needs to be multiplied by gravity only and not scaled by density like it is done the step2d_LF_AM3.h for the barotropic pressure gr...
by arango
Thu Sep 09, 2021 4:48 pm
Forum: ROMS Discussion
Topic: Horizontal surface pressure gradient forcing in 2D and 3D
Replies: 16
Views: 6486

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

Okay, I know that this is an old post, but I have been looking at the 3D and 2D pressure gradient terms and the various algorithms available. I implemented the astronomical tide generation forces ( TGF ) in terms of the equilibrium tide ( ζeq ), defined as the shape that the sea surface (m) would as...
by arango
Mon Sep 06, 2021 4:23 pm
Forum: ROMS Usage
Topic: Can ROMS be used to model flow in a rotating annular flume?
Replies: 1
Views: 538

Re: Can ROMS be used to model flow in a rotating annular flume?

Sure, see LAB_CANYON analytical test case. Everything is already done for you. You just need to modify the analytical expressions.
by arango
Fri Sep 03, 2021 5:02 pm
Forum: ROMS Discussion
Topic: Incorporating phytoplankton floating (Fennel model)
Replies: 6
Views: 1126

Re: Incorporating phytoplankton floating (Fennel model)

I think that it will be simple. You just need to replace the vertical semi-Lagrangian sinking algorithm in fennel.h with the sinking/ascending one in red_tides.h , which you can use for swimming/floating. However, these algorithms are very sophisticated, and you cannot make changes to them. I recall...
by arango
Tue Aug 31, 2021 4:12 pm
Forum: ROMS Tools and Techniques
Topic: Surface geostrophic velocity issue
Replies: 27
Views: 3544

Re: Surface geostrophic velocity issue

Great, I think that we need to design a Matlab function that plots vectors correctly regardless if the grid is curvilinear or not.
by arango
Sat Aug 28, 2021 10:00 pm
Forum: ROMS Tools and Techniques
Topic: Surface geostrophic velocity issue
Replies: 27
Views: 3544

Re: Surface geostrophic velocity issue

Great detective work! I also was starting to suspect about the quiver function or its usage. I am planning to draw the vectors with ROMS native NCAR graphics software next week to see what I get. I am wondering what kind of results we will the m_map ( m_quiver ) tool in Matlab will give. The vectors...
by arango
Fri Aug 27, 2021 11:32 pm
Forum: ROMS Tools and Techniques
Topic: Surface geostrophic velocity issue
Replies: 27
Views: 3544

Re: Surface geostrophic velocity issue

Are you expecting flow to be everywhere along bathymetric contours? We can have bottom boundary layers, turbulence, pressure gradient differences, and friction that may force the flow across isobars and bathymetric contours. I think that what you need to plot are the barotropic currents at every gri...
by arango
Fri Aug 27, 2021 9:32 pm
Forum: ROMS Tools and Techniques
Topic: Surface geostrophic velocity issue
Replies: 27
Views: 3544

Re: Surface geostrophic velocity issue

Hmm, the grid looks very orthogonal to me. It is hard to think that it is due to the averaging of the quiver plot. The angle between the red and green vectors is pretty much constant and around 30 degrees. It is weird. I wonder what do we get with uv_rotate.F when we output the vectors to geographic...
by arango
Fri Aug 27, 2021 7:58 pm
Forum: ROMS Tools and Techniques
Topic: Surface geostrophic velocity issue
Replies: 27
Views: 3544

Re: Surface geostrophic velocity issue

Use Matlab script grid/roms_metrics.m to recompute the angle and other quantities to see what you get. You can download that script from the ROMS Matlab repository. Then, compare your rotation angle arrays. Interpolation is not a good idea!
by arango
Fri Aug 13, 2021 6:12 pm
Forum: ROMS Discussion
Topic: ERROR: Abnormal termination: NetCDF OUTPUT.
Replies: 6
Views: 1144

Re: ERROR: Abnormal termination: NetCDF OUTPUT.

If you are using the latest version of the code, which I recommend using, you need to be sure that your roms.in is up to date. Compile with debugging flags so you get more information about the division by zero. We can get such errors when the arguments to MOD are zero or uninitialized. There are lo...
by arango
Fri Aug 13, 2021 3:12 pm
Forum: ROMS Discussion
Topic: ERROR: Abnormal termination: NetCDF OUTPUT.
Replies: 6
Views: 1144

Re: ERROR: Abnormal termination: NetCDF OUTPUT.

I don't think that is an I/O error: Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO ERROR STOP Something is wrong in your configuration in roms.in that you get a division by zero . I updated the code yesterday to remove those confusing I/O errors when you have a con...
by arango
Thu Aug 12, 2021 4:26 pm
Forum: ROMS Discussion
Topic: MPI - tiling on POWER8
Replies: 6
Views: 1559

Re: MPI - tiling on POWER8

We have not seen parallel bugs in the distributed ROMS code for years. In the past, such parallel bugs are associated with the user implementation of analytical functions. If there is an issue with the BENCHMARK application, we need to look at its analytical functions. I am very busy at the moment. ...
by arango
Wed Jul 28, 2021 5:24 pm
Forum: ROMS Adjoint
Topic: INP_PAR, PHYPAR: Problems finding input file.
Replies: 7
Views: 1390

Re: INP_PAR, PHYPAR: Problems finding input file.

I don't think so. This is because of the PIO library support changes to ROMS. For some reason, inp_type in roms.in is zero. It is weird because it is initialized to zero internally if the user doesn't specified a value.
by arango
Wed Jul 28, 2021 3:36 pm
Forum: ROMS Adjoint
Topic: INP_PAR, PHYPAR: Problems finding input file.
Replies: 7
Views: 1390

Re: INP_PAR, PHYPAR: Problems finding input file.

ROMS is telling you what it is wrong:
GET_GRID - Illegal output type, io_type = 0
Make sure that your roms.in is up to date.
by arango
Sun Jul 18, 2021 4:13 pm
Forum: ROMS Bugs
Topic: Unable to write with PIO in restart runs
Replies: 1
Views: 584

Re: Unable to write with PIO in restart runs

I don't know what is going on here, but NC_INDEPENDENT and NC_COLLECTIVE is for the NetCDF library and NOT for the PIO library. You cannot add things to the PIO interface without knowledge. The nf90_var_par_access function is for the native NetCDF library with parallel I/O (option PARALLEL_IO and HD...
by arango
Tue Jul 13, 2021 3:17 pm
Forum: ROMS Problems
Topic: multi bry files cannot be included
Replies: 2
Views: 718

Re: multi bry files cannot be included

Your question is kind of weird. What do you mean by high-frequency tidal forcing? ROMS has its own tidal forcing file specified in TIDENAME . The tidal forcing file doesn't have a time coordinate but a tide angular period for each constituent. Therefore, a single file is required. This data is deriv...
by arango
Tue Jun 22, 2021 9:52 pm
Forum: ROMS Bugs
Topic: typo in wrt_tides.F and def_tides.F?
Replies: 1
Views: 606

Re: typo in wrt_tides.F and def_tides.F?

Yes, good catch. Thank you for reporting this issue. I will update the code.
by arango
Wed Jun 09, 2021 12:21 am
Forum: ROMS Bugs
Topic: ROMS4 built with PIO, freeze on creating history file
Replies: 17
Views: 2673

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

As mention previously, the information in the Wiki tells you how to inquire the build script about the libraries that your are using to compile ROMS without actually compiling: > build_roms.sh -p LIBS :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::...
by arango
Wed Jun 09, 2021 12:07 am
Forum: ROMS Bugs
Topic: ROMS4 built with PIO, freeze on creating history file
Replies: 17
Views: 2673

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

Check the debugging section of the :arrow: build_roms wiki page to learn how to inquire things about compiling variables and macros. There is lots of useful information in the wiki about the makefile, build scripts, libraries, and how to compile and link ROMS,
by arango
Tue Jun 08, 2021 9:53 pm
Forum: ROMS Bugs
Topic: ROMS4 built with PIO, freeze on creating history file
Replies: 17
Views: 2673

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

I already updated the repositories.
by arango
Tue Jun 08, 2021 4:54 pm
Forum: ROMS Bugs
Topic: ROMS4 built with PIO, freeze on creating history file
Replies: 17
Views: 2673

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

Yes, it is a typo, I will load the update later today.
by arango
Tue Jun 08, 2021 3:23 am
Forum: ROMS Bugs
Topic: ROMS4 built with PIO, freeze on creating history file
Replies: 17
Views: 2673

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

You also need the USE_PIO option in the build script. Both libraries are needed at running time since you may activate both in roms.in.
by arango
Tue Jun 08, 2021 2:38 am
Forum: ROMS Bugs
Topic: ROMS4 built with PIO, freeze on creating history file
Replies: 17
Views: 2673

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

Well, if you are going to use PIO , you need to follow the instructions provided in :arrow: WikiROMS or in the :arrow: trac ticket . Also, there is information available in the wiki for :arrow: roms.in . Please read the documentation carefully. PIO is too complicated to ignore the instructions. The ...
by arango
Mon Jun 07, 2021 1:50 am
Forum: ROMS Bugs
Topic: PIO conflicts with non-zero NDEFHIS
Replies: 1
Views: 589

Re: PIO conflicts with non-zero NDEFHIS

Yes, thank you! Weird, my ifort compiler missed that one.
by arango
Thu Jun 03, 2021 7:22 pm
Forum: ROMS Bugs
Topic: dogbone composite nesting: contact()%Kdg in nesting.f90 not assigned?
Replies: 2
Views: 1107

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

Yes, in set_contat.F we need to have instead: ! ! Set the switch to compute vertical interpolation weights. Currently, ! they are only needed in non-coincident composite grids. ! IF (.not.ANY(Lcoincident).or.ANY(Lcomposite)) THEN get_Vweights=.TRUE. ELSE get_Vweights=.FALSE. END IF we need .or. inst...
by arango
Thu Jun 03, 2021 6:10 pm
Forum: ROMS Ecosystem
Topic: NPZD nesting
Replies: 5
Views: 1204

Re: NPZD nesting

The arguments to load_r are correct. The 1 can be replaced by a colon ( : ) since this routine is called inside a module. The one argument is a valid F77 syntax since load_r will load Ngrids values, which is also an argument, starting from element 1 of the second dimension to BioUni .
by arango
Mon May 31, 2021 9:15 pm
Forum: ROMS Problems
Topic: rectangles delimited by anomalous values
Replies: 4
Views: 996

Re: rectangles delimited by anomalous values

Hmm, I haven't seen this kind of problem in ROMS in a very long time. The squares clearly indicate a parallel partition bug in the code with the exchanges between tiles. Are you using distributed memory (MPI) or shared memory (OpenMP)? What version of the code are you using? And more importantly, di...
by arango
Fri May 28, 2021 6:40 pm
Forum: ROMS Bugs
Topic: typo in wrt_info.F
Replies: 2
Views: 718

Re: typo in wrt_info.F

Those two lines are identical. The code compiles fine for me when STATIONS is activated or not.
by arango
Thu May 27, 2021 9:30 pm
Forum: ROMS Discussion
Topic: WET_DRY compilation problem
Replies: 10
Views: 6610

Re: WET_DRY compilation problem

Okay, thanks. I am getting annoyed with this routine. It needed to be modified because of PIO. I rarely use WET_DRY. Please update again.
by arango
Thu May 27, 2021 2:44 pm
Forum: ROMS Discussion
Topic: WET_DRY compilation problem
Replies: 10
Views: 6610

Re: WET_DRY compilation problem

Okay, I see it now. It is fixed. Please update again. Thank you!
by arango
Thu May 27, 2021 2:07 pm
Forum: ROMS Discussion
Topic: WET_DRY compilation problem
Replies: 10
Views: 6610

Re: WET_DRY compilation problem

Yes, thank you for reporting this bug. It is already fixed. Please check the following :arrow: trac ticket . Please update your code. I will have to check what your other error is. It looks weird. Those routines are private inside the get_grid_mod ( get_grid.F ). Have you made changes to get_grid.F ...
by arango
Thu May 20, 2021 12:39 pm
Forum: ROMS Tools and Techniques
Topic: Missing the ncgm2www script in the ROMS plotting package
Replies: 6
Views: 1535

Re: Missing the ncgm2www script in the ROMS plotting package

Notice that the subdirectory plot/src/Bin have other conversion scripts like ncgm2cgm.sh, ncgm2gif.sh, and ncgm2png.sh. The call to ncgmwww can be replaced with ncgm2git.sh. Anyway, I am attaching the old ncgm2www.sh script.
by arango
Fri May 14, 2021 5:13 pm
Forum: ROMS Bugs
Topic: possible bug in set_tides.F
Replies: 1
Views: 693

Re: possible bug in set_tides.F

Yes, that's definitely a typo. Thank you for bringing that to our attention. Luckily, this logic is only used to detide ROMS fields (AVERAGES_DETIDE) via the :arrow: least-squares fit of time-averaged fields.
by arango
Tue May 11, 2021 2:03 am
Forum: ROMS Installation
Topic: nvfortran
Replies: 2
Views: 934

Re: nvfortran

I didn't know that IBM was using the NVIDIA compiler. It is unfortunate because the PGI compiler is one of the worse compilers that I have come across. We don't longer use it neither pay the license to maintain that compiler. The RSHIFT and SHIFTA intrinsic functions are part of the 2008 Fortran Sta...
by arango
Mon Apr 19, 2021 3:34 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11206

Re: problem with two-way nesting

As you may have noticed, the nesting routines in nesting.F module were designed in a generic way to facilitate expansion and different schemes. The weighted area average is turned off in fine2coarse ( AreaAvg=.FALSE. ). One could try volume-weighted averaging (not coded). Right now, we use bilinear ...
by arango
Fri Apr 16, 2021 7:08 pm
Forum: ROMS Tools and Techniques
Topic: Function roms_metrics
Replies: 1
Views: 681

Re: Function roms_metrics

ROMS uses a horizontal, staggered Arakawa C-grid. You need to study and understand the following grid diagram in :arrow: WikiROMS . You need to look the grid spacing in terms of RHO -, PSI -, U -, and V -points. Then, you will answer your own questions. The code in roms.metrics.m is correct.
by arango
Thu Apr 15, 2021 4:10 pm
Forum: ROMS Discussion
Topic: WC13/RBL4DVAR PROBLEM
Replies: 3
Views: 881

Re: WC13/RBL4DVAR PROBLEM

Yes, this was fixed but that version is not ready for release. You have to wait. This is simply solved by deactivating the BALANCE_OPERATOR C-preprocessing option. We don't activate that option in the tutorials. The balance operator is an advanced feature for experienced users that know their applic...
by arango
Sat Apr 10, 2021 4:50 pm
Forum: ROMS Adjoint
Topic: I4dvar compilation error in new version about get_hash.f90
Replies: 2
Views: 816

Re: I4dvar compilation error in new version about get_hash.f90

Yes, your Fortran compiler is too old and not supporting updates to the standard. The intrinsic function SHIFTR was introduced more than a decade ago in the Fortran 2008 Standard. What compiler are you using? It is highly recommended to keep Fortran compilers up-to-date. Models nowadays use Object O...
by arango
Wed Mar 17, 2021 9:41 pm
Forum: ROMS Problems
Topic: errors when running Lagrangian floats in ROMS 3.9
Replies: 10
Views: 2227

Re: errors when running Lagrangian floats in ROMS 3.9

You need to use any older or the latest versions of our distributed code. I checked the trac history for the mod_floats.F module and I cannot find the offending code in the last five years! Anyway, you need to read and understand the error message: forrtl: severe (194): Run-Time Check Failure. The v...
by arango
Wed Mar 17, 2021 9:13 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11206

Re: problem with two-way nesting

Yes, I recall issues with the global attributes. In such cases, I manipulate the global attributes using my matlab/netcdf functions that are distributed in the ROMS Matlab repository: >> Imin=nc_getatt('my_file.nc', 'parent_Imin'); >> Imax=nc_getatt('my_file.nc', 'parent_Imax'); >> Jmin=nc_getatt('m...
by arango
Tue Mar 16, 2021 11:33 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11206

Re: problem with two-way nesting

Yes, thank you!
by arango
Tue Mar 16, 2021 5:34 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11206

Re: problem with two-way nesting

What software did you use to generate your original GRID NetCDF? Many users really miss the fact that although the application has a spherical grid, it is highly recommended to have the associated Cartesian coordinates to compute the metrics pm and pn since ROMS computational grid is in curvilinear ...
by arango
Fri Mar 12, 2021 8:57 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 58
Views: 11206

Re: problem with two-way nesting

Yes, that's the way to build complicated grids. One thing that you may consider is to avoid sudden bathymetry changes like seamount and ridges across the contact areas between coarse and fine grids. I have done telescoping grids in the Middle Atlantic Bight, which include the Gulf Stream, with tidal...
by arango
Mon Mar 08, 2021 5:16 pm
Forum: ROMS Discussion
Topic: Modify UPWELLING case to a flat bottom, etc.
Replies: 3
Views: 935

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

Alternatively, you can copy Functionals/ana_grid.h to your application directory and make any desired change. Notice that the build_roms.csh or build_roms.sh script have the capability to use your customized analytical headed files ( ana_*.h ) and ignore the ones distributed in ROMS Functionals sub-...
by arango
Fri Mar 05, 2021 7:24 pm
Forum: ROMS Discussion
Topic: various time indices in ROMS
Replies: 2
Views: 710

Re: various time indices in ROMS

All the governing equations in ROMS are time-stepped differently. Recall that we have a three-time level predictor-corrector scheme. The tracer equations are kind of special. The t(:,:,:,3,itrc) are the intermediate tracer values ( n+1/2 ) assigned in the predictor step ( pre_step3d.F) for only hori...
by arango
Wed Mar 03, 2021 4:30 pm
Forum: ROMS Discussion
Topic: MPI_ERR_TRUNCATE
Replies: 4
Views: 1405

Re: MPI_ERR_TRUNCATE

I think that this error has nothing to do with ROMS but communications between your computer processes with the MPI library. Sometimes, when you are using lots of processes one or more do not arrive at the collective MPI synchronization point and the system hangs out or gives this type of error. I g...
by arango
Tue Mar 02, 2021 2:50 am
Forum: ROMS Tools and Techniques
Topic: Error to plot by the ROMS plotting package
Replies: 17
Views: 3614

Re: Error to plot by the ROMS plotting package

Wow, are you really asking how Linux works? No wonder why you are having so many troubles at every step in your application. We have lots of posts in this forum from you. I am expecting users that select ocean modeling as a carrier or hobby to be more curious and familiar with computers. By the way...
by arango
Tue Feb 02, 2021 4:09 pm
Forum: ROMS Installation
Topic: Compiling Error for COAWST
Replies: 6
Views: 2364

Re: Compiling Error for COAWST

Hmm, the call to mp_scatter_state is correct. It is only used for the adjoint-based propagator analysis, which I doubt Users using those algorithms that compact the full ROMS state ( zeta , u , v , T , S ) into a 1D array for matrix operations with the ARPACK library. I think that the issue here is ...
by arango
Thu Jan 28, 2021 3:00 am
Forum: ROMS Installation
Topic: Compilation error for build_roms.sh
Replies: 16
Views: 3301

Re: Compilation error for build_roms.sh

Obviously, you need to work on the libraries available on your computer. There is plenty of information about Compiling and Linking in WikiROMS. If you are using the latest version of ROMS, you may benefit from using CMake . Check cbuild_roms.csh or cbuild_roms.sh . CMake is a different philosophy f...
by arango
Wed Dec 16, 2020 4:25 pm
Forum: ROMS Discussion
Topic: Bottom flux for Fennel model
Replies: 3
Views: 1135

Re: Bottom flux for Fennel model

Yes, good catch. Thank you. The stflx and btflx state variables are used in ROMS governing equations. Contrarily, the stflux and btflux are used exclusively to process data from NetCDF files or analytical functions. The problem here is that the assignment is missing in set_vbc.F : # if defined BIOLO...
by arango
Fri Dec 11, 2020 1:40 am
Forum: ROMS Discussion
Topic: ROMS 3.7 nesting problems
Replies: 8
Views: 1572

Re: ROMS 3.7 nesting problems

I don’t know what you are doing wrong. First, I highly recommend that you use the latest version of ROMS. Right now, we are in version 3.9. We have improved ROMS nesting. It is more efficient. The latest version of ROMS is consistent with all the files in the current test repository. That’s the reas...
by arango
Tue Oct 20, 2020 3:26 pm
Forum: ROMS Discussion
Topic: [Edited] Vertical profiles of EKE budget terms
Replies: 3
Views: 1270

Re: [Edited] Vertical profiles of EKE budget terms

Thank you, Lars. Those are great references. I added them to my reading list. A couple of decades ago, I tried to derive an energy conservation equation for ROMS, so the only way to add energy to the system is from external forcing. I was unable to eliminate the pressure gradient term because of the...
by arango
Tue Oct 13, 2020 5:39 am
Forum: ROMS Adjoint
Topic: station file
Replies: 3
Views: 1224

Re: station file

Nope, that bash script supports both SLURM (BATCH=1) and non SLURM (BATCH=0). You just need to change that flag. See the customizable section. I can run that script in my 14 CPUs Mac or in our SLURM supercomputer. The script is very generic, compact, and complex. It is well documented. You need to s...
by arango
Mon Oct 12, 2020 5:22 pm
Forum: ROMS Adjoint
Topic: station file
Replies: 3
Views: 1224

Re: station file

What is RPG? Did you mean RPCG option for RBL4D-Var minimization algorithm? I have never turned on the STATIONS option with the 4D-Var algorithms. I suppose that we can use the split 4D-Var algorithms that I released yesterday to only run the STATIONS in the background and analysis 4D-Varphases. And...
by arango
Fri Sep 18, 2020 7:50 pm
Forum: ROMS Discussion
Topic: Evaporation + precipitation mass conservation
Replies: 5
Views: 2021

Re: Evaporation + precipitation mass conservation

I think that there is a confusion here with the forcing terminology. The surface and bottom heat ( Q ) and freshwater fluxes ( E-P ) are the boundary conditions to the vertical tracer (temperature and salinity, respectively) diffusion terms in the governing equations. We need to provide boundary con...
by arango
Thu Aug 27, 2020 2:52 am
Forum: ROMS Sediment
Topic: Roms blowup at 1cell bays
Replies: 2
Views: 1085

Re: Roms blowup at 1cell bays in Lake_jersey test case

The lake Jersey test case works for me. What you did is not LAKE_JERSEY :!: You changed the grid, land/sea mask, and added big and small islands. Stop calling it Lake Jersey because it is a different application and will confuse other users with misinformation! If doing nesting, it will require diff...
by arango
Tue Jul 14, 2020 3:24 pm
Forum: ROMS Bugs
Topic: Bug in set_grid.F
Replies: 1
Views: 916

Re: Bug in set_grid.F

Yes, thank you. It just need:

Code: Select all

#ifdef NESTING
      USE mod_nesting
#endif
Please, update.
by arango
Thu Jun 25, 2020 2:12 am
Forum: ROMS Discussion
Topic: MPI - tiling on POWER8
Replies: 6
Views: 1559

Re: MPI - tiling on POWER8

What do you mean by the same results? profiling time or state solution?

Usually, it is much efficient to do less partition in the I-direction (NtileI) and more in the J-direction (NtileJ) because of vectorization. Also, it depends on the computer architecture.
by arango
Wed Jun 24, 2020 7:14 pm
Forum: ROMS Bugs
Topic: Small fortran bug in nl_ocean.h
Replies: 1
Views: 966

Re: Small fortran bug in nl_ocean.h

Yes, thank you!
by arango
Wed Jun 24, 2020 6:13 pm
Forum: ROMS Problems
Topic: mp_collect bug when compiling with define PARALLEL_IO
Replies: 18
Views: 8245

Re: mp_collect bug when compiling with define PARALLEL_IO

Everybody has their own procedure for updating code from repositories. I have several research repositories, and I usually do the following steps: Copy the version that I want to update to a temporary one. So, I have a version of the code that works in case something goes wrong with the updating. I ...
by arango
Tue Jun 23, 2020 4:21 pm
Forum: ROMS Problems
Topic: mp_collect bug when compiling with define PARALLEL_IO
Replies: 18
Views: 8245

Re: mp_collect bug when compiling with define PARALLEL_IO

Well, you cannot pick and choose what routines you need to update. It doesn't work that way. Every change done to ROMS is well documented in the trac system, and the changes sometimes depend on previous changes and may be modified in future changes. The last major update to the Parallel I/O was done...
by arango
Tue Jun 23, 2020 3:07 am
Forum: ROMS Problems
Topic: mp_collect bug when compiling with define PARALLEL_IO
Replies: 18
Views: 8245

Re: mp_collect bug when compiling with define PARALLEL_IO

I can believe that this is done :shock: We are not responsible for corrections to the code by a third party. Your solution is straightforward. Update your code from the official ROMS repositories. The agreement to receive a freely distributed version of the ROMS framework from us is that Users need ...
by arango
Sun Jun 21, 2020 5:17 pm
Forum: ROMS Discussion
Topic: inconsistent explicit time-step splitting in two-way nesting
Replies: 3
Views: 1349

Re: inconsistent explicit time-step splitting in two-way nesting

Well, the error is telling your problem, if you think carefully about it. I assume that you previously defined SOLVE3D . Now, it is undefined , and you are solving the shallow-water equations of ROMS where you must have NDTFAST =1 for all nested grids, and you have NDTFAST = 30 :!: If you don't und...
by arango
Tue Jun 16, 2020 9:27 pm
Forum: ROMS Discussion
Topic: units of omega
Replies: 6
Views: 1890

Re: units of omega

The varinfo.dat is an user-changeable file. In the beginning, we were thinking of writing omega in the restart NetCDF file as m 3 /s, and true vertical velocity in history files. But that's no longer the case. Nowadays, omega is recomputed internally. I rarely activate the switch for writing omega i...
by arango
Tue Jun 16, 2020 8:13 pm
Forum: ROMS Discussion
Topic: units of omega
Replies: 6
Views: 1890

Re: units of omega

Well, the omega vertical velocity in ROMS is special and its orthogonality changes at each grid point because it depends on the bathymetry. It does not have a physical interpretation since it is only related to ROMS descrete, terrain-following coordinates, 3D continuity equation. Internally in ROMS,...
by arango
Tue Jun 09, 2020 8:50 pm
Forum: ROMS Problems
Topic: forcing interpolation not working
Replies: 8
Views: 3082

Re: forcing interpolation not working

I also have been using this capability for years and frequently and I never have any problems. Our group at Rutgers uses the same strategy on a daily basis in our operational system. Something is wrong in your files. When I do nesting, I only specify the forcing files for the first grid, and ROMS wi...
by arango
Tue Jun 09, 2020 3:01 pm
Forum: ROMS Discussion
Topic: two-way nested simulation blowing up with MPI
Replies: 3
Views: 1164

Re: two-way nested simulation blowing up with MPI

The reason why nobody replayed to your post is that you didn't provide any concrete information about the ROMS or Fortran error. We are not magicians or have any potions to see the error written to your standard output. I have mentioned several times over the years in this forum to never never never...
by arango
Mon Jun 08, 2020 3:48 pm
Forum: ROMS Discussion
Topic: the defination of density rho
Replies: 16
Views: 4527

Re: the defination of density rho

Are you trying to change ROMS equation of state? The definition of in situ density anomaly or potential density anomaly is that a 1000 kg m-3 value is subtracted to the density. The in situ density anomaly, as a field, is only used in ROMS in the pressure gradient algorithm where its value is not e...
by arango
Mon Jun 01, 2020 12:45 am
Forum: ROMS Bugs
Topic: compiling 4DVar with WET_DRY + wclock_off problem
Replies: 4
Views: 1720

Re: compiling 4DVar with WET_DRY + wclock_off problem

Yes, that's a small bug, thank you. I am running nowadays with the ROMS_STDOUT option that generates the output file log.roms instead of the standard Fortran output from unit 6. My bad, I forgot to run without the ROMS_STDOUT . Having this option activated is very convenient when running coupled sys...
by arango
Thu May 28, 2020 4:01 pm
Forum: ROMS Bugs
Topic: compiling 4DVar with WET_DRY + wclock_off problem
Replies: 4
Views: 1720

Re: compiling 4DVar with WET_DRY + wclock_off problem

Oh my goodness, no. We cannot use WET_DRY in any of the adjoint-based algorithms including any of the 4D-Var drivers. That's the reason that you will find WET_DRY_NOT_YET in the code. Every time that you see a multiplication of a state variable with a mask array, we will need another term, which is ...
by arango
Wed May 27, 2020 5:16 pm
Forum: ROMS Adjoint
Topic: I4dvar compilation error about i4dvar.f90 and mod_fourdvar
Replies: 3
Views: 1625

Re: I4dvar compilation error about i4dvar.f90 and mod_fourdvar

Yes, gfortran is a stricter compiler. Other compilers relax the Fortran standard rule that we cannot have a module, subroutine, or variable with the same name. I missed this one. Thank you for reporting this issue. Please, update your code.
by arango
Mon May 11, 2020 10:22 pm
Forum: ROMS Adjoint
Topic: Adjoint model blow up
Replies: 13
Views: 4516

Re: Adjoint model blow up

In our experience, it is challenging for either the tangent linear ( TLM ) or adjoint models ( ADM ) to blow-up in the first iteration of the inner loops. Something must be wrong in your step-up. Both models are linearized from the nonlinear model ( NLM ) state trajectory (prior). The TLM and ADM st...
by arango
Fri May 01, 2020 3:07 pm
Forum: ROMS Bugs
Topic: Possible bugs in def_state.F
Replies: 1
Views: 983

Re: Possible bugs in def_state.F

Yes, thank you. Please update your code.
by arango
Tue Apr 28, 2020 3:07 pm
Forum: ROMS Bugs
Topic: Ltracing compiling error
Replies: 2
Views: 1162

Re: Ltracing compiling error

Update your code again!
by arango
Mon Apr 27, 2020 9:11 pm
Forum: ROMS Bugs
Topic: FORTRAN error - Probably related to January changes
Replies: 4
Views: 1404

Re: FORTRAN error - Probably related to January changes

I actually removing that parameter in an update that I am releasing today. Remove the couple of ocurrences of Ltracing in read_phypar.F. I have several reseach repositories and sometimes unwanted features leaks into the trunk. Sorry about that.
by arango
Wed Apr 22, 2020 4:42 pm
Forum: ROMS Bugs
Topic: Possible bug in wetdry.F for nested apps
Replies: 14
Views: 4183

Re: Possible bug in wetdry.F for nested apps

Great work, Stefan. I concur with john about your telescoping approach into meter scales. It will take me some time to digest the changes that you make to the code. If you provide us the modifications that you have to do for the shallow-water nested applications to work, we can incorporate such chan...
by arango
Mon Apr 06, 2020 8:31 pm
Forum: ROMS Discussion
Topic: error in inp_par.F
Replies: 4
Views: 1466

Re: error in inp_par.F

Okay, update your repository. It is now fixed. Here is the :arrow: trac ticket
by arango
Thu Apr 02, 2020 6:59 pm
Forum: ROMS Adjoint
Topic: Where to introduce obs error
Replies: 2
Views: 1195

Re: Where to introduce obs error

Of course, you need the observation error covariance (diagonal matrix) in the ROMS 4D-Var algorithm! The NetCDF variable is obs_error , which is read into ROMS variable ObsErr . You are searching for the wrong variable. Check ROMS/Modules/mod_fourdvar.F for the description of all variables.
by arango
Wed Apr 01, 2020 9:35 pm
Forum: ROMS Discussion
Topic: error in inp_par.F
Replies: 4
Views: 1466

Re: error in inp_par.F

Yes, it will be easy to fix. I will update the repository tonight. Thank you for reporting this issue.
by arango
Sun Mar 22, 2020 3:56 pm
Forum: ROMS Discussion
Topic: Imbalance in Parallel writing in ROMS
Replies: 3
Views: 1373

Re: Imbalance in Parallel writing in ROMS

Hi Koushik, great study, and thank you for the research that you continue doing about ROMS parallel I/O :!: Let me digest the information and come up with a strategy for more efficient parallel I/O. Are you aware that ROMS has the CPP option NO_WRITE_GRID , which suppresses the definition and writin...
by arango
Tue Mar 10, 2020 3:34 pm
Forum: ROMS Source
Topic: Question about HSIMT in step3d_t.F (trunk version)
Replies: 1
Views: 1868

Re: Question about HSIMT in step3d_t.F (trunk version)

Yes, good catch :!: Thank you. I have been looking for a bug in the HSIMT scheme on and off. We fixed the issue that it needs three ghost points a few days ago, but forgot to make changes to the range of oHz . We need have an additional switch, Lhsimt : logical :: LapplySrc, Lhsimt, Lmpdata ... Lhsi...
by arango
Sun Mar 01, 2020 7:47 pm
Forum: ROMS Source
Topic: Typo in roms.in following overhaul of advection schemes
Replies: 4
Views: 1994

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

Yes, thank you for reporting this typo in the documentation. However, why do you want to set a different tracer advection scheme for temperature and salinity across nested grids? I will never do such a thing in any of my nesting applications. It doesn't make sense to me. You need to understand how t...
by arango
Tue Feb 25, 2020 7:07 pm
Forum: ROMS Problems
Topic: Error when compiling 2D test cases
Replies: 2
Views: 1088

Re: Error when compiling 2D test cases

Yes, I already knew about this one and included in a repository update that will be released today.
by arango
Tue Feb 18, 2020 4:06 pm
Forum: ROMS Discussion
Topic: Problem with surface heat flux
Replies: 13
Views: 3692

Re: Problem with surface heat flux

Hmmm, I noticed that you activated both BULK_FLUXES and CCSM_FLUXES . I am not familiar with that version of ROMS. However, my understanding is that you should use a single formulation. You need to choose one and not both. If the sea ice model is activated, we need BOTH freshwater (E-P) and saltwate...
by arango
Tue Feb 18, 2020 1:12 am
Forum: ROMS Bugs
Topic: average file count logic
Replies: 2
Views: 1149

Re: average file count logic

I revised this logic recently. My assumption is that ndefAVG is an exact multiple (integer factor) of ntimes . If it is not the case, the file creation definition is changed. What values are you using that gives you OutFiles=0 ? The time averaged files are special because of its delayed creation. Th...
by arango
Mon Feb 17, 2020 4:36 pm
Forum: ROMS Discussion
Topic: Problem with surface heat flux
Replies: 13
Views: 3692

Re: Problem with surface heat flux

I don't know if this behaviour will be related, but I would turn off SPLINES_VDIFF and SPLINES_VVISC and see what happens. I also noticed that you are using a different version of ROMS that has sea ice modeling. This will complicate your analysis.
by arango
Fri Feb 07, 2020 8:45 pm
Forum: ROMS Bugs
Topic: Possible bug in wetdry.F for nested apps
Replies: 14
Views: 4183

Re: Possible bug in wetdry.F for nested apps

Well, u2dbc_im.F and v2dbc_im.F need to be modified to include code relevant to 2D shallow-water nesting applications. I guess that we never accounted for a User needing nesting in a 2D application. It will need an equation to impose the transport from the donor coarser grid. We will have to figure ...
by arango
Fri Feb 07, 2020 6:35 pm
Forum: ROMS Bugs
Topic: Possible bug in wetdry.F for nested apps
Replies: 14
Views: 4183

Re: Possible bug in wetdry.F for nested apps

Notice that the indices told and tnew are local (dummy) time indices: ! ! Set time snapshot indices for the donor grid data. ! told=3-RollingIndex(cr) tnew=RollingIndex(cr) However, if you are running a 2D shallow-water application ( SOLVE3D is off), why are you dealing with state variables ( DU_avg...
by arango
Fri Feb 07, 2020 4:20 pm
Forum: ROMS Bugs
Topic: Possible bug in wetdry.F for nested apps
Replies: 14
Views: 4183

Re: Possible bug in wetdry.F for nested apps

Hmm. I will have to think about it but maybe it will be needed. It will need to be tested. There are a set of those indices for RHO-, PSI-, U-, and V-points. It will be only relevant it coastlines are present in the contact points.
by arango
Thu Feb 06, 2020 11:44 pm
Forum: ROMS Bugs
Topic: ROMS 3.9 MPDATA bugs
Replies: 2
Views: 1495

Re: ROMS 3.9 MPDATA bugs

Yes, Great catch :!: Thank you for reporting these two bugs. I updated the :arrow: repositories.
by arango
Thu Feb 06, 2020 5:20 pm
Forum: ROMS Adjoint
Topic: 4DVAR assimilation of surface velocities destroy sst
Replies: 5
Views: 2277

Re: 4DVAR assimilation of surface velocities destroy sst

It is all a matter of the assumed background error covariance hypothesis and its parameters. What do you trust more the model or the observations? HF radar velocity observations are very tricky since it is a very noisy data, and depends on the processing: averaging, detiding, super-observations, err...
by arango
Sun Feb 02, 2020 3:36 pm
Forum: ROMS Problems
Topic: A ROMS nesting question
Replies: 10
Views: 3731

Re: A ROMS nesting question

You need to make sure that the variables in your forcing NetCDF files have the _FillValue = 1.e+35 attribute or whatever other value you used. Otherwise, ROMS doesn't know how to process such data without the _FillValue that have land/sea masks. However, the fact the you have Min = 1.0E+35 and Max =...
by arango
Fri Jan 31, 2020 8:57 pm
Forum: ROMS Problems
Topic: A ROMS nesting question
Replies: 10
Views: 3731

Re: A ROMS nesting question

Check your standard input file, roms.in or your standard output log file, which contains lots of information. Notice that in roms.in we have: ! Logical switches (TRUE/FALSE) to nudge the desired climatology field(s). ! If not analytical climatology fields, users need to turn ON the logical ! switche...
by arango
Sun Jan 26, 2020 8:33 pm
Forum: ROMS Problems
Topic: Three nested refined grids - Ngrids vs. Ncontact
Replies: 2
Views: 1323

Re: Three nested refined grids - Ngrids vs. Ncontact

The nesting configuration is tricky since we support various types of grid connectivity. We only provide a Matlab interface to generate the nesting connectivity NetCDF file needed by ROMS. Unfortunately, we don't officially have any other software to create such a connectivity NetCDF file nor have t...
by arango
Thu Jan 16, 2020 10:35 pm
Forum: ROMS Discussion
Topic: ROMS 3.7
Replies: 1
Views: 993

Re: ROMS 3.7

The frozen versions of ROMS are available only on SVN. Usually, one checkout the tags SVN repository: svn checkout https://www.myroms.org/svn/src/tags tags svn checkout https://www.myroms.org/svn/src/tags/roms-3.7 roms-3.7 The GIT repository works in a different way. If you need the version that was...
by arango
Thu Jan 16, 2020 4:04 am
Forum: ROMS Bugs
Topic: Matlab nesting pre-processing program error.
Replies: 2
Views: 1564

Re: Matlab nesting pre-processing program error.

Yes, your first correction is fine. Thank you :!: I updated the repository. We didn't catch that one before because all our grids always have the ( XI , ETA ) coordinates even if the applications grid is spherical. It turns out that in curvilinear grids is better to do the interpolation in ( XI , ET...
by arango
Sat Jan 04, 2020 7:35 pm
Forum: ROMS Bugs
Topic: Segmentation fault
Replies: 9
Views: 2637

Re: Segmentation fault

This is not a bug. It always has to be equal or greater than one by design. If no input forcing files are needed, ROMS will ignore those values on standard input. I don't understand what it is the Fuzz about it. There are a lot of parameters in ROMS standard input that will be only relevant for a sp...
by arango
Mon Dec 23, 2019 2:42 pm
Forum: ROMS Discussion
Topic: calculating ubar and vbar
Replies: 10
Views: 4151

Re: calculating ubar and vbar

Look at Nonlinear/ini_fields.F instead. It is very clear how it is computed there. It is how the inital ubar anf vbar is computed in ROMS.
by arango
Tue Dec 17, 2019 6:16 am
Forum: ROMS Discussion
Topic: Request: Numerical modeling course syllabi
Replies: 11
Views: 4149

Re: Request: Numerical modeling course syllabi

I learned how to program and plot with the NCARG graphical library. I spent so much time reading the manuals and learning how to use that library. It was very satisfying plotting the results with computer-generated contours. I became a pro using that wonderful library. I still used it today. I wrote...
by arango
Tue Dec 17, 2019 2:07 am
Forum: ROMS Discussion
Topic: Request: Numerical modeling course syllabi
Replies: 11
Views: 4149

Re: Request: Numerical modeling course syllabi

Indeed, I took that class from John Klinck when I was a graduate student at Texas A&M. I learned a lot about coding and ocean numerical modeling in that first class. It was a great introduction to a world that it is now my professional life. I recall that we, the students, and John, enjoyed that...
by arango
Mon Dec 09, 2019 3:27 am
Forum: ROMS Bugs
Topic: typo in distribute.F
Replies: 1
Views: 1076

Re: typo in distribute.F

Hi Frank, great catch. Thank you! I updated the repository. See the following :arrow: trac ticket for more information.
by arango
Fri Dec 06, 2019 11:37 pm
Forum: ROMS Discussion
Topic: Parallel IO not scaling over Serial IO for ROMS
Replies: 14
Views: 3602

Re: Parallel IO not scaling over Serial IO for ROMS

An application of size 899x629x40 is TOO small to be run in 1350 PEs :!: No wonder why is not scaling after 240 PEs. You are killing scalability with excessive MPI collective communications and exchanges. Your 20x20 tile size is too small, and it is killing vectorization. The good news is that you f...
by arango
Thu Dec 05, 2019 4:54 pm
Forum: ROMS Discussion
Topic: Parallel IO not scaling over Serial IO for ROMS
Replies: 14
Views: 3602

Re: Parallel IO not scaling over Serial IO for ROMS

Great study. We are missing important information about your simulations. We need the grid size and the parallel domain decomposition. I have mentioned frequently in this forum that ROMS scalability is a function of the application and depends on the domain size and parallel partition. There is alwa...
by arango
Fri Nov 15, 2019 9:55 pm
Forum: ROMS Installation
Topic: Compiling error - undefined reference to ice routines
Replies: 12
Views: 3800

Re: Compiling error - undefined reference to ice routines

The version of the code that we distribute doesn't have a native sea ice model yet. I am sure that it will be included in the future. It has to be located in a subdirectory inside of the Nonlinear directory, like the biology and sediment models. The reason for it is quite logical and straightforward...
by arango
Sun Aug 04, 2019 4:21 pm
Forum: ROMS Installation
Topic: upwelling: - Configuration error ..... exit_flag: 5
Replies: 3
Views: 1657

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

The default upwelling example in ROMS test repository has UV_QDRAG activated in the build script. If you notice, there are various options in build_roms.sh : # can be used to write time-averaged fields. Notice that you can have as # many definitions as you want by appending values. setenv MY_CPP_FLA...
by arango
Thu Jul 25, 2019 4:00 pm
Forum: ROMS Releases
Topic: ROMS 3.7 Released
Replies: 0
Views: 4743

ROMS 3.7 Released

ROMS/TOMS 3.7 Released The latest version of the :arrow: ROMS/TOMS svn repository , revision 974 , was frozen and tagged as ROMS 3.7 . We haven't tagged a frozen version of ROMS in several years. This version is quite stable, and it is the one to be used at the upcoming 2019 ROMS 4D-Var Workshop to...
by arango
Mon Jul 22, 2019 3:03 pm
Forum: ROMS Bugs
Topic: Typo in ad_set_vbc.F line 1165 rev 973
Replies: 1
Views: 1015

Re: Typo in ad_set_vbc.F line 1165 rev 973

Indeed, thank you! I didn't test with LIMIT_STFLX_COOLING activated.
by arango
Tue Jul 09, 2019 8:33 pm
Forum: ROMS Bugs
Topic: Error regarding variable dP in prsgrd44.h or prsgrd42.h
Replies: 1
Views: 1081

Re: Error regarding variable dP in prsgrd44.h or prsgrd42.h

Indeed. Thank you for reporting this issue. Please update.
by arango
Thu Jun 27, 2019 7:48 pm
Forum: ROMS Problems
Topic: ROMS different src version leading to unalike results
Replies: 7
Views: 2771

Re: ROMS different src version leading to unalike results

The ROMS basic numerical kernel has not changed much in a few years. However, configuration, CPP options, and parameters in the standard input have been modified and enhanced. You need to be sure that your header file ( application.h ) and standard input script ( roms.in ) is equivalent between the ...
by arango
Wed Jun 12, 2019 1:06 am
Forum: ROMS Discussion
Topic: Time type in nc file
Replies: 5
Views: 1852

Re: Time type in nc file

ROMS has nothing to do with the time convention and elapsed time. The user selects how the time is managed in an application. There is nothing that we can do about it. It is up to the person(s) that set-up that application to use a consistent time zone in all the input NetCDF files (initial conditio...
by arango
Wed May 15, 2019 6:51 pm
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 7
Views: 11937

Re: compile ROMS error

Your problem is that you haven't configured the build_roms.sh and build_roms.bash correctly. For example, notice that in the build_roms.sh script we have: #-------------------------------------------------------------------------- # If applicable, use my specified library paths. #-------------------...
by arango
Sun May 12, 2019 1:44 pm
Forum: ROMS Problems
Topic: Segmentation fault with floats
Replies: 6
Views: 2390

Re: Segmentation fault with floats

Segmentation violations (SIGSEGV) are usually a sign of memory problems on the computer and available stack for the run. Perhaps, your computer doesn't have too much memory for your application, and you are deploying too many floats for it. I will try to run without floats to see if it works. Then a...
by arango
Wed May 08, 2019 10:35 pm
Forum: ROMS Installation
Topic: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT type
Replies: 4
Views: 2023

Re: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT

You didn't understand at all what I was saying to you, or what WET_DRY does. The wetting and drying option ( WET_DRY ) is modeled in ROMS by changing the associated land/sea masking arrays at every barotropic time-step in step2d , which affect the ocean state variables. The wet/dry mask is a new arr...
by arango
Wed May 08, 2019 6:31 pm
Forum: ROMS Installation
Topic: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT type
Replies: 4
Views: 2023

Re: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT

The WET_DRY option is not adjointed because it not fully differentiable, and because of every time-step of the forward trajectory need to be saved to have a consistent linearization of the tangent linear (TLM) and adjoint (ADM) models. You cannot use such time-depending land/sea masking in any ROMS ...
by arango
Wed May 01, 2019 4:22 pm
Forum: ROMS Discussion
Topic: cppdefs for BULK_FLUX
Replies: 11
Views: 4149

Re: cppdefs for BULK_FLUX

My current strategy is to activate LONGWAVE_OUT and provide downward longwave radiation so bulk_flux will subtract the outgoing IR by using ROMS surface temperature ( K ), infrared emissivity, and Stefan-Boltzmann constant. I also use downward shortwave radiation and I activate COOL_SKIN to correct ...
by arango
Tue Apr 16, 2019 9:50 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 2608

Re: CF compliant units attributes in Varinfo.dat

ROMS has nowadays a very robust calendar. See the routine ROMS/Utility/dateclock.F for more details. It is consistently internally and can handle different reference date ( epoch ) for each forcing field from NetCDF files regardless of what we choose in the ROMS input parameter TIME_REF . I have to ...
by arango
Tue Apr 16, 2019 2:23 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 2608

Re: CF compliant units attributes in Varinfo.dat

I agree with John. This part is not desirable. We and others have been using this standard for years. There are lots of datasets out there that follow this nomenclature. I am sympathetic with the issue of the links but some of the changes suggested are radical.
by arango
Thu Apr 11, 2019 9:33 pm
Forum: ROMS Information
Topic: units of specific humidity
Replies: 10
Views: 8578

Re: units of specific humidity

Indeed, I believe that unsavory piece of code was in the original COARE code. It is quite clever if you ask me. I recall putting enough comments in the code when I did some research about this threshold value many years ago. There is not a standardized unit for specific humidity in the atmospheric d...
by arango
Thu Mar 21, 2019 9:55 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 2608

Re: CF compliant units attributes in Varinfo.dat

Thank you. The ROMS metadata file varinfo.dat is a user file and can be edited in any way that the user feels is necessary. You can even change the language. Some users in France wanted some of the attribute values to be in French. I haven't read the documentation about the UDUNITS-2 package. I look...
by arango
Wed Mar 13, 2019 2:28 am
Forum: ROMS Bugs
Topic: A small bug in ana_srflux.h
Replies: 12
Views: 6866

Re: A small bug in ana_srflux.h

Finally, I have time to browse the literature, Googling, and write a Matlab script to check the issue mentioned above. Indeed, the 15.0 factor used to compute the zenith is incorrect :!: We need to have instead:  zenith=cff1+cff2*COS(Hangle-lonr(i,j)*deg2rad) In my Matlab script, I compared against...
by arango
Sun Mar 10, 2019 10:38 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 3594

Re: Pair and MPI version has problem with regridding

I updated the code to correct the bug in regrid.F. Check the following trac ticket :arrow: src:ticket:808 for more details. The parallel bug was corrected. Good luck.
by arango
Sat Mar 09, 2019 5:53 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 3594

Re: Pair and MPI version has problem with regridding

It doesn't make sense to me. MyXout is a state, tiled variable and it is allocated as the others, and the pointer is passed correctly. It is the only way that this can be done. I bet that the problem is not in regrid . It seems like a memory leakage somewhere else. Yes, you can put the application i...
by arango
Fri Mar 08, 2019 9:04 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 3594

Re: Pair and MPI version has problem with regridding

I took a look in the debugger on our US East Coast application and I cannot find anything wrong. I activated both ATM_PRESS and PRESS_COMPENSATE . I am also using BULK_FLUXES , which also need Pair . I don't see a parallel bug. Pair.png shflux.png The Pair is kind of jagged but it is because of the ...
by arango
Fri Mar 08, 2019 5:16 am
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 3594

Re: Pair and MPI version has problem with regridding

Yes, the Dmem is a diagnostic quantity to estimate the memory requirement for an application. It has nothing to do with the numerical kernel. It is in my TODO list to look at your problem in the debugger. The issues that you are talking about sound like a parallel bug. However, the regrid subroutine...
by arango
Thu Mar 07, 2019 5:27 am
Forum: ROMS Bugs
Topic: A small bug in ana_srflux.h
Replies: 12
Views: 6866

Re: A small bug in ana_srflux.h

Both ana_srflux.h and ana_specir.h were coded longtime ago when we were testing the EcoSim bio-optical model in the late 90's. It was like twenty years ago. So I don't remember the details. At that time, both routines were intended for idealized toy problems for debugging purposes. The EcoSim model ...
by arango
Thu Feb 28, 2019 3:36 am
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 6460

Re: My ROMS

Thank you, Mark. Your logic is correct. We don't need to add processing logic since it needs ATM_PRESS anyway. I loaded your request ticket to the repository.
by arango
Mon Feb 11, 2019 10:34 pm
Forum: ROMS Tools and Techniques
Topic: Soundspeed for ROMS output
Replies: 4
Views: 2170

Re: Soundspeed for ROMS output

Just do it in Matlab.
by arango
Mon Feb 11, 2019 5:12 am
Forum: ROMS Tools and Techniques
Topic: Soundspeed for ROMS output
Replies: 4
Views: 2170

Re: Soundspeed for ROMS output

It has been in ROMS plotting package that uses the NCAR's GKS library since the beginning. Check the file src/Utility/svel.F in the plot repository. It uses the Che and Millero (1976) formula. Chen, C.T. and F.J. Millero, 1976: re-evaluation of Willson sound-speed measurements in pure water. J. Acou...
by arango
Sun Feb 10, 2019 1:14 am
Forum: Ocean News
Topic: Walter Munk (1917-2019)
Replies: 0
Views: 3558

Walter Munk (1917-2019)

The oceanography community and the world lost one of its most renowned scientists. Walter Munk was 101. I met Walter in the mid-'80s when I was a graduate student at Texas A&M University. He visited and gave us an excellent Seminar/Lecture. My thesis advisor Robert O. Reid introduced me to him. ...
by arango
Fri Feb 01, 2019 6:51 pm
Forum: ROMS Results
Topic: ROMS Granular model result in all variables
Replies: 8
Views: 4089

Re: ROMS Granular model result in all variables

:shock: Well, that's your problem. You are using biharmonic diffusivity (m4/s), which scales as 1/12 * ABS(U) * (dx ** 3) . A value for TS_DIF4 of 2 m4/s is too small :!: You need values of the order of 2.0d+8 m4/s . That is, you are using a value that is eight orders of magnitude too small :!: No w...
by arango
Thu Jan 31, 2019 9:09 pm
Forum: ROMS Results
Topic: ROMS Granular model result in all variables
Replies: 8
Views: 4089

Re: ROMS Granular model result in all variables

I guess that the more fundamental question is what type of horizontal advection are you using? Are you specifying explicit diffusion and viscosity? What do you specify for vertical diffusion/viscosity parameterization closure? You should compute your Reynolds Number (U dx/nu), where U is the maximum...
by arango
Tue Jan 22, 2019 10:35 pm
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 6460

Re: My ROMS

Hi Mark, Are you ready to submit the changes due to the PRESS_COMPENSATE?

Thank you.
by arango
Tue Jan 22, 2019 9:22 pm
Forum: ROMS Bugs
Topic: Issue restarting solutions in fraction of a day
Replies: 1
Views: 1487

Re: Issue restarting solutions in fraction of a day

Indeed, good catch :!: Thank you for reporting this bug. I will update the code soon.
by arango
Tue Jan 22, 2019 7:24 pm
Forum: ROMS Bugs
Topic: tiny bugs? in metrics.F and nesting.F
Replies: 1
Views: 1449

Re: tiny bugs? in metrics.F and nesting.F

Thank you for reporting this problem. I forgot to take care of the roundoff issues with the interpolation weights when I implemented the single precision ( SINGLE_PRECISION option) simulations. Your suggested solutions are incorrect :!: We cannot take the ABS value when computing the interpolation w...
by arango
Sat Dec 15, 2018 8:53 pm
Forum: ROMS Bugs
Topic: Equation error in GLS model coded into gls_corstep.F
Replies: 5
Views: 2609

Re: Equation error in GLS model coded into gls_corstep.F

I haven't updated the code yet. I think that Ramsey Harcourt is correct. The shape functions used in mostly all vertical mixing parameterization should be smooth and continuous. We should stay away from sharp discontinuities that lead to eye bullet values in vertical diffusion and vertical viscosity...
by arango
Fri Dec 14, 2018 8:32 pm
Forum: ROMS Bugs
Topic: Equation error in GLS model coded into gls_corstep.F
Replies: 5
Views: 2609

Re: Equation error in GLS model coded into gls_corstep.F

Thank you for looking this carefully and for providing a Matlab script to show the difference between the formulation currently coded in ROMS and the correction to the limiter (green curve). Obviously, the coded formulation has a discontinuity spike just before it remains constant. It is clearly wro...
by arango
Mon Dec 03, 2018 2:14 am
Forum: ROMS Problems
Topic: 'nfast' and 'ndtfast' on Barotropic time step
Replies: 5
Views: 3096

Re: 'nfast' and 'ndtfast' on Barotropic time step

Again, Nope :!: The governing equations are timestep from n (right-hand-side terms) to n+1 (left-hand-side term: time rate of change). The vertically-integrated equations are integrated with smaller timestep to resolve fast dynamics due to gravity wave phenomena. For 3D total momentum coupling, the ...
by arango
Sun Dec 02, 2018 4:19 pm
Forum: ROMS Problems
Topic: 'nfast' and 'ndtfast' on Barotropic time step
Replies: 5
Views: 3096

Re: 'nfast' and 'ndtfast' on Barotropic time step

Nope , there are actually M* barotropic timesteps :!: The reason for it is that the cosine-square shape filter needs to provide time-averaged values of ubar , vbar , and zeta centered at the n+1 baroclinic timestep, which gives us second-order temporal accuracy for time-averaged barotropic motions....
by arango
Wed Nov 14, 2018 5:00 pm
Forum: ROMS Bugs
Topic: tiny little bug in get_state.F for time evolving bathymetry
Replies: 2
Views: 1629

Re: tiny little bug in get_state.F for time evolving bathyme

Done. Thank you for reporting this typo.
by arango
Fri Nov 09, 2018 2:43 pm
Forum: ROMS Bugs
Topic: Error compiling ROMS with new flag SINGLE_PRECISION (svn928)
Replies: 7
Views: 3645

Re: Error compiling ROMS with new flag SINGLE_PRECISION (svn

Nope. What I said above is correct :!: If the last argument to the mp_bcastf routine is single- precision it will use mp_bcast_1d , and if it is double-precision it will use mp_bcastf_1dp . Just look the subroutines in distribute.F :idea: If you don't understard, you need to check a Fortran 1990, 19...
by arango
Wed Nov 07, 2018 9:16 pm
Forum: ROMS Bugs
Topic: Error compiling ROMS with new flag SINGLE_PRECISION (svn928)
Replies: 7
Views: 3645

Re: Error compiling ROMS with new flag SINGLE_PRECISION (svn

You are doing something wrong or something is weird with the compiler. You need to read carefully the following :arrow: trac ticket . Notice that even if SINGLE_PRECISION is activated, there are several variables that are still in double precision ( dp 64-bit kind parameter) and the r8 kind paramete...
by arango
Mon Oct 01, 2018 4:10 pm
Forum: ROMS Discussion
Topic: missing temp_time
Replies: 2
Views: 1550

Re: missing temp_time

You don't need to do that. One of the great things about NetCDF is that it is self-described. I have mentioned in the past that we need to follow CF convections to guarantee the functionality of metadata and avoid missinterpretation issues in ROMS. I highly recommend users to add the units , time , ...
by arango
Fri Sep 28, 2018 7:50 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 6089

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

I am going to try again for the last time. Read carefully :arrow: trac ticket 747 . In the older version of the code, we choose either lower- or higher-level MPI function for exchanges. We no longer do that in the newer versions, you need to experiment and select which options are more efficient in ...
by arango
Thu Sep 27, 2018 1:53 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 6089

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

I think that you need to read the following :arrow: trac ticket and choose the MPI communication options that are more efficient in the computer environment that you are running. You should check the profiling information that ROMS reports to standard output to see in what region of the code are slo...
by arango
Wed Sep 26, 2018 10:08 pm
Forum: ROMS Discussion
Topic: ROMS history file has suddenly included restart record
Replies: 7
Views: 2819

Re: ROMS history file has suddenly included restart record

Hmmm, I haven't had the time to examine the issue that you are having. I haven't modified this part of the code in years. I use the split of history files frequently and I have never observed the behavior that you are reporting. I wonder if it is a matter of configuration. Are you changing DSTART ev...
by arango
Wed Sep 26, 2018 10:00 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 6089

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

Yes, your problem is the stack size per CPU and it seems to be associated with the automatic arrays used in distributed-memory for I/O operations. This is not a direct ROMS problem, but a computer problem because of not enough memory to handle automatic arrays that are either allocated on stack or h...
by arango
Tue Sep 25, 2018 1:48 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 6089

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

It is very simple as I have mentioned several times before. You just need to edit your login script and add one of the lines below:

Code: Select all

.cshrc, .tcshrc, etc.

limit stacksize unlimited

or  .bashrc

ulimit -s unlimited 
I wrote lots of information in previous :arrow: trac ticket.
by arango
Sat Sep 22, 2018 6:18 am
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 6089

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

Nowadays, severe segmentation errors are associated with stack size, which is used for allocating automatic arrays. They are allocated on stack or heap according to you choice of compiler options. I mentioned this in the last trac ticket.
by arango
Thu Sep 13, 2018 9:12 pm
Forum: ROMS Bugs
Topic: Small bugs in CPP BIO_FENNEL with DIAG and DIAGNOSTICS_BIO
Replies: 2
Views: 1786

Re: Small bugs in CPP BIO_FENNEL with DIAG and DIAGNOSTICS_

Nope. That's not what I have in the repository for def_diags.F : # ifdef DIAGNOSTICS_BIO # if defined BIO_FENNEL || defined HYPOXIA_SRM DO ivar=1,NDbio2d ifield=iDbio2(ivar) IF (TRIM(var_name(i)).eq.TRIM(Vname(1,ifield))) THEN got_var(ifield)=.TRUE. DIA(ng)%Vid(ifield)=var_id(i) END IF END DO # endi...
by arango
Tue Sep 11, 2018 9:23 pm
Forum: ROMS Bugs
Topic: bug in mod_tides.F
Replies: 1
Views: 1390

Re: bug in mod_tides.F

Indeed, thank you. I have more stuff to update in the computation of ROMS memory requirements. I am missing arrays to account for. I am trying to come up with the best estimate.
by arango
Mon Sep 10, 2018 7:25 pm
Forum: ROMS Discussion
Topic: ROMS prestep3d , Crack-Nicolson method, lambda
Replies: 1
Views: 1168

Re: ROMS prestep3d , Crack-Nicolson method, lambda

Yes, we need to update the documentation.
by arango
Fri Aug 31, 2018 9:00 pm
Forum: ROMS Discussion
Topic: Cannot find "coordinates" attribute for variable: Uwind
Replies: 15
Views: 4820

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

The ECMWF data has a minimal interval of 3 hours; you can easily create annual files instead monthly. It will be more efficient in ROMS to avoid inquiring and open so many NetCDF files. The time units for forcing file is usually days since the reference date ( epoch ). However, you can have any time...
by arango
Sun Aug 26, 2018 3:44 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 7524

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

Okay, that will do it. I put safeguards to the code when processing standard input file ocean.in . I made a couple of updates recently for it. It looks that your grid is not for a regional application, but it is a global grid. Is that correct? If that's the case, you have a problem with the design o...
by arango
Wed Aug 22, 2018 2:07 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 7524

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

It is a weird error if you didn't repeat the NtileJ parameter in ocean.in , which triggers the allocation of several modules. In yesterday update, I put safeguards for this to never happen. I don't know what to make of your case. I don't think that a corrupted ocean.in should trigger to process the ...
by arango
Mon Aug 20, 2018 4:58 pm
Forum: ROMS Discussion
Topic: How to setup for rotating frame
Replies: 10
Views: 3437

Re: How to setup for rotating frame

It is weird that you are not activating periodic boundary conditions in the south and northern boundaries :!: It is the perfect and appropriate case for it because your grid is an annulus :roll: You can set the desired flow in the initial condition instead of using Flather boundary conditions. If yo...
by arango
Mon Aug 13, 2018 6:08 pm
Forum: ROMS Discussion
Topic: blowing up on nested grid
Replies: 5
Views: 2506

Re: blowing up on nested grid

That can be also a problem. However, the main issue here is that there are one or more grid cells with a value of 1E+40 1/km for both inverse metric factors pm and pn . We cannot multiply those variables with the mask because of division by zero in ROMS. The grid spacing ( DX=1/pm and DY=1/pn ) is a...
by arango
Sun Aug 12, 2018 3:36 pm
Forum: ROMS Discussion
Topic: blowing up on nested grid
Replies: 5
Views: 2506

Re: blowing up on nested grid

The information is in the front of you. If you don't understand that information, you have homework to do before running ROMS. Look the large and a small numbers. Check your grid files. ( DXmin , DYmin ) cannot be zero!!! It is a trillion times smaller than the scales of electrons... I am sure that ...
by arango
Sun Jul 29, 2018 4:38 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 5384

Re: huge memory per node when up scaling application

I usually put lots of information in trac when I update the code. We have noticed that this information is generally ignored and our emails are treated as spam. There is nothing that we can do about it, and we cannot force users to update and or read the detailed information provided. We have thousa...
by arango
Fri Jul 27, 2018 8:00 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 5384

Re: huge memory per node when up scaling application

PARALLEL_IO works for me. You need to use a recent version of the code. Also, make sure that all your input NetCDF files are NetCDF-4 format. You can check which format you have using ncdump : % ncdump -k filename.nc netCDF-4 To convert from NetCDF-3 to Netcdf-4 try: % nccopy -k netCDF-4 nc3name.nc...
by arango
Wed Jul 25, 2018 4:30 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 5384

Re: huge memory per node when up scaling application

First, I don't think that ROMS will run with the PNETCDF library. It will need special function calls in ROMS. I never tried that library, it is a third party library. If you use PARALLEL_IO, you need to compile with the NetCDF-4 library with parallel MPI I/O and HDF5 support and your computer need ...
by arango
Wed Jul 18, 2018 9:43 pm
Forum: ROMS Problems
Topic: Problem generating contact file with three refined grids
Replies: 5
Views: 2843

Re: Problem generating contact file with three refined grids

Hi Marc and John,

I removed the restriction of having the noncoincident grid points in the indirect connectivity between grids for telescoping applications. See the following :arrow: trac ticket for more information.

Please update. Your particular set-up should work now.