Search found 1347 matches

by arango
Fri Mar 15, 2024 3:21 pm
Forum: ROMS Discussion
Topic: 4dvar run hangs using internal lapack module
Replies: 4
Views: 95

Re: 4dvar run hangs using internal lapack module

You are using a very new version of gfortran. This seems like a compiler bug, which I will not be surprised by. If you check the :arrow: trac ticket, you will notice that we are trying to modernize the routines used from this legacy library since NCEP is complaining about the GOTOs.
by arango
Mon Mar 11, 2024 2:41 pm
Forum: ROMS Discussion
Topic: ROMS Radiation Boundary condition (RadNud)
Replies: 11
Views: 729

Re: ROMS Radiation Boundary condition (RadNud)

Except periodic boundary conditions, all the open boundary conditions in ROMS are ill-conditioned from the purest mathematician point of view. The only thing that we can do is minimize its errors. There are several strategies that are available, as you found out. In my experience, we need to first c...
by arango
Fri Mar 01, 2024 2:50 pm
Forum: ROMS Discussion
Topic: Query about FRCNAME Limitation in .in Files
Replies: 2
Views: 405

Re: Query about FRCNAME Limitation in .in Files

Nope, there is no limitation. The filename is limited to 256 characters, and the number of files in the sequence files(:) is allocated internally to the number of files that it finds. This is the first time we have heard of a user providing files for 30 years. If I want to do such a long simulation,...
by arango
Wed Feb 14, 2024 5:02 pm
Forum: ROMS Discussion
Topic: Adjoint blow-up if misfit forcing is too far after initial time
Replies: 14
Views: 1186

Re: Adjoint blow-up if misfit forcing is too far after initial time

I updated the tutorial information in WikiROMS. Thank you! We are usually swamped and will take time to update the information. We also have minimal information and instructions in the GitHub repositories wiki. Some users are unfamiliar with Git and GitHub, and we are given plenty of time to learn.
by arango
Wed Feb 14, 2024 2:19 pm
Forum: ROMS Discussion
Topic: Adjoint blow-up if misfit forcing is too far after initial time
Replies: 14
Views: 1186

Re: Adjoint blow-up if misfit forcing is too far after initial time

I updated all the versions of ROMS in the svn and git repositories, but I recommend the GitHub version since it has branches of other developments that we are working on and will be merged to the default develop branch in the future. We will stop updating the other repositories on January 1, 2025 , ...
by arango
Tue Feb 13, 2024 5:13 pm
Forum: ROMS Discussion
Topic: Adjoint blow-up if misfit forcing is too far after initial time
Replies: 14
Views: 1186

Re: Adjoint blow-up if misfit forcing is too far after initial time

Yes, use the ROMS version on GitHub. We will no longer update all the SVN versions after January 1, 2025. I fixed all the indices in the code.
by arango
Mon Feb 12, 2024 9:39 pm
Forum: ROMS Discussion
Topic: Adjoint blow-up if misfit forcing is too far after initial time
Replies: 14
Views: 1186

Re: Adjoint blow-up if misfit forcing is too far after initial time

You cannot change NADJ in I4DVAR since the primal formulation is only a strong constraint algorithm (the model is assumed to be perfect). However, RBL4DVAR is both strong- and weak-constraint. But I suggest staying in the strong-constraint regime since modeling the model error, Q , is not trivial. N...
by arango
Mon Feb 12, 2024 4:49 pm
Forum: ROMS Discussion
Topic: Adjoint blow-up if misfit forcing is too far after initial time
Replies: 14
Views: 1186

Re: Adjoint blow-up if misfit forcing is too far after initial time

Why do you use the primal formulation I4DVAR ? That algorithm works, but it is deprecated. Please use the dual formulation RBL4DVAR . It is faster! Check the WC13 test cases for RBL4DVAR . The dual formulation works on the space span by the observations and allows impacts and sensitivities. We also ...
by arango
Fri Jan 05, 2024 1:47 pm
Forum: ROMS Discussion
Topic: can i4dvar be run in 3dvar-FGAT mode?
Replies: 2
Views: 7603

Re: can i4dvar be run in 3dvar-FGAT mode?

We never coded 3D-Var in ROMS native variational data assimilation algorithms. But, if you check the literature, 4D-Var performs better than any 3D-Var algorithm. In 3D-Var, we assume that the linearized model (tangent linear kernel) is the identity matrix! It doesn't use the adjoint model. Anyway, ...
by arango
Thu Dec 14, 2023 4:04 pm
Forum: ROMS Documentation
Topic: Math rendering in wikiRoms
Replies: 5
Views: 20623

Re: Math rendering in wikiRoms

It is working again. We don't know what the issue was, but it started to work again when we restarted the server.
by arango
Fri Dec 01, 2023 3:10 am
Forum: ROMS Releases
Topic: ROMS will be distributed exclusively from GitHub after Jan 1, 2025
Replies: 0
Views: 17581

ROMS will be distributed exclusively from GitHub after Jan 1, 2025

WARNING: Starting January 1, 2025 , ROMS will be exclusively distributed from its GitHub repository at :arrow: https://github.com/myroms . Please get familiar with GitHub repository management. The updating of the svn repositories at :arrow: https://www.myroms.org will be discontinued but kept for ...
by arango
Fri Nov 17, 2023 8:22 pm
Forum: Ocean News
Topic: ROMS development cost according to the SCC program
Replies: 1
Views: 15612

ROMS development cost according to the SCC program

A little bit of fun trivia . If we use the Sloc Cloc and Code ( SCC ) program (https://github.com/boyter/scc), it gives us an estimate of the cost in US dollars of developing ROMS, which we give you for free. The number will be much higher if we put the actual salaries of the people involved. So, n...
by arango
Fri Nov 03, 2023 4:34 pm
Forum: ROMS Usage
Topic: "thin dams" in ROMS
Replies: 4
Views: 18240

Re: "thin dams" in ROMS

In ROMS, we have the GAMMA2 parameter to set the slip and no-slip boundary conditions. In the no-slip, the velocity is zero at the wall.

Code: Select all

! Slipperiness parameter: 1.0 (free slip) or -1.0 (no slip)

      GAMMA2 == 1.0d0
by arango
Thu Oct 19, 2023 1:22 pm
Forum: ROMS Ice
Topic: ROMS coupled to CICE
Replies: 21
Views: 62936

Re: ROMS coupled to CICE

We started interfacing ROMS with the UFS-coastal framework. The basic connectivity is working well. We still have to develop the testing applications. So far, the DATA-ROMS coupled components are working as the first step to couple with ESMF/NUOPC -based CDEPS/CMEPS. We use Hurricane Irene to test t...
by arango
Thu Oct 12, 2023 9:25 pm
Forum: Ocean News
Topic: John S. Allen (1937-2023)
Replies: 5
Views: 13859

Re: John S. Allen (1937-2023)

John will be missed, RIP. Chatting with him was always interesting. I remember visiting his office at OSU when we took the summer IOMS course with Andrew Bennett. I don't know how he was able to work at his desk. He had mountains of papers, journals, and books on it, blocking the view of who was sit...
by arango
Tue Sep 05, 2023 2:01 pm
Forum: ROMS Documentation
Topic: Release notes for 4.0 update?
Replies: 1
Views: 3063

Re: Release notes for 4.0 update?

Yes, those summaries take time, which I don't have. My list of priorities is too long. However, every change made to ROMS is well documented on trac. See

https://www.myroms.org/projects/src/report/4
by arango
Wed Aug 23, 2023 9:24 pm
Forum: ROMS Releases
Topic: ROMS Transition to GitHub
Replies: 0
Views: 10085

ROMS Transition to GitHub

We completed the transition of ROMS to GitHub. We have been working on this for the last couple of months. The GitHub ROMS repositories are at :arrow: https://github.com/myroms . For more information and instructions on ROMS framework source code, please visit :arrow: https://github.com/myroms/roms/...
by arango
Mon Aug 21, 2023 12:56 pm
Forum: ROMS Bugs
Topic: A Bug when running WC13/Normalization case
Replies: 2
Views: 3363

Re: A Bug when running WC13/Normalization case

I updated the code last week. I think that I fixed the issue of the state vector variables' indices order. Please update and try again.
by arango
Thu Aug 10, 2023 4:40 pm
Forum: ROMS Bugs
Topic: Cannot run upwelling test case
Replies: 11
Views: 18440

Re: Cannot run upwelling test case

Great. The versioning of the ifort is weird. I used 2023.0.0 in our Spack-Stack for ROMS-JEDI: pontus % which ifort /opt/sw/apps/intel/oneapi/compiler/2023.0.0/linux/bin/intel64/ifort pontus % ifort --version ifort (IFORT) 2021.8.0 20221119 Copyright (C) 1985-2022 Intel Corporation. All rights reser...
by arango
Wed Aug 09, 2023 3:32 pm
Forum: ROMS Documentation
Topic: Math rendering in wikiRoms
Replies: 5
Views: 20623

Re: Math rendering in wikiRoms

Try again, it is fixed. The problem was due to changes in the DNS server at Rutgers. Thank you for bringing this issue to our attention.
by arango
Wed Aug 09, 2023 1:08 pm
Forum: ROMS Problems
Topic: Problem with dimensions.
Replies: 4
Views: 12891

Re: Problem with dimensions.

Please read the preamble and glossary instructions in ROMS standard input file. If you check ROMS/Utility/read_phypar.F , ROMS will only read and process the parameters that it needs and ignore the rest. Several test cases in the ROMS test repository for beginners users show how ROMS is configured a...
by arango
Tue Aug 08, 2023 2:10 pm
Forum: ROMS Bugs
Topic: Cannot run upwelling test case
Replies: 11
Views: 18440

Re: Cannot run upwelling test case

Did you specified the correct location of varinfo.yaml? We recommend Users download the ROMS test repository. Everything is set up and isolated for you.
by arango
Thu Jul 27, 2023 4:43 am
Forum: ROMS Discussion
Topic: Some Questions about make a forecasting system
Replies: 3
Views: 4139

Re: Some Questions about make a forecasting system

All the modern operational forecasting systems for the atmosphere and ocean do not do spinup. They require initial ocean analysis conditions that combine the model with the observations. They use data assimilation, which is a pretty advanced subject. The limitation of true ocean prediction is the av...
by arango
Thu Jul 20, 2023 1:17 pm
Forum: ROMS Problems
Topic: Conflict for units of shflux
Replies: 5
Views: 8122

Re: Conflict for units of shflux

The comments in the YAML file within the brackets indicate the internal ROMS code values after multiplying by the scale factor. It is the units that ROMS needs in the governing equations. It has been like that for decades.
by arango
Mon Jul 10, 2023 2:18 pm
Forum: ROMS Discussion
Topic: PROBLEM WITH THE INSTALLATIONS ROMS
Replies: 4
Views: 5601

Re: PROBLEM WITH THE INSTALLATIONS ROMS

It is telling you the problem! Please, read and understand the error that ROMS is giving you: YAML_TREE_CREATE - Unable to open input YAML file: ~/roms_project/test/varinfo.yaml ERROR: Cannot open file '~/roms_project/test/varinfo.yaml': No such file or directory Do you have varinfo.yaml in you home...
by arango
Sat Jul 08, 2023 10:08 pm
Forum: ROMS Problems
Topic: Error when I try to run roms_upwelling
Replies: 4
Views: 4998

Re: Error when I try to run roms_upwelling

Weird. How was it able to find the location of varinfo.yaml when you got the error in the first posting above? The error is telling you that it cannot find varinfo.yaml . Mostly all the time, you need to specify the full path for that file in roms.in: ! Input variable information file name. This fil...
by arango
Sat Jul 08, 2023 6:04 pm
Forum: ROMS Problems
Topic: Error when I try to run roms_upwelling
Replies: 4
Views: 4998

Re: Error when I try to run roms_upwelling

Yes, there is some garbage in varinfo.yaml. Search for mnbvc43 and remove that line. I will update that file code latter.
by arango
Fri Jul 07, 2023 1:14 pm
Forum: ROMS Discussion
Topic: PROBLEM WITH THE INSTALLATIONS ROMS
Replies: 4
Views: 5601

Re: PROBLEM WITH THE INSTALLATIONS ROMS

In our version of ROMS, we no longer distribute the metadata file varinfo.dat but its equivalent YAML file varinfo.yaml.
by arango
Tue Jun 20, 2023 5:43 pm
Forum: Job Opportunities
Topic: Open position for high-resolution ocean data assimilation
Replies: 0
Views: 4363

Open position for high-resolution ocean data assimilation

The candidate will study the ocean, ice, and coupled data assimilation strategies within the NASA GEOS coupled forecast system. This researcher will help to design novel techniques to assimilate new NASA observations such as laser altimetry from ICESAT-2, high-resolution altimetry from the Surface W...
by arango
Tue May 30, 2023 3:32 pm
Forum: ROMS Problems
Topic: WC13 compilation error of Normalization
Replies: 1
Views: 3261

Re: WC13 compilation error of Normalization

We haven't released the Nested 4D-Var algorithms yet for you to activate the NESTING flag in any of the adjoint-based data assimilation algorithms. Nesting has nothing to do with the computation of the error covariance normalization coefficients. They are computed from the coarser nested grid instea...
by arango
Thu May 04, 2023 2:46 am
Forum: ROMS Discussion
Topic: Interpolation of bed stress for step_floats
Replies: 8
Views: 11105

Re: Interpolation of bed stress for step_floats

I don't have time to look at this now. However, as a guideline, the indexing in the I-direction for the U - and PSI -points are identical. Similarly, the indexing in the J-direction for the V - and PSI -points are identical. Thus, if you look at interpolating at PSI -points are a combination of both...
by arango
Sun Apr 16, 2023 9:46 pm
Forum: ROMS Ice
Topic: Leak/Artifact at CPU Tiles
Replies: 7
Views: 11087

Re: Leak/Artifact at CPU Tiles

That's a classic parallel collision bug of state variables computing horizontal operators. They are tough to find and usually take much TotalView debugging time. It implies that the ice state variable illegally accesses global data belonging to another parallel tile somewhere in the DO-loops. We use...
by arango
Tue Apr 11, 2023 6:55 pm
Forum: ROMS Discussion
Topic: UV_PSOURCE obsolete
Replies: 2
Views: 3350

Re: UV_PSOURCE obsolete

There is no replacement CPP option. Use the switches LuvSrc, LwSrc or LtracerSrc from standard input file roms.in. It was done years ago to facilitate nesting.
by arango
Thu Apr 06, 2023 10:15 pm
Forum: ROMS Installation
Topic: Compilation issue: yaml_parser.f90
Replies: 3
Views: 4992

Re: Compilation issue: yaml_parser.f90

Yes, that's a possibility. But it is a bug in the gfortan compiler! It works for me. I'm using gfortran versions Red Hat 11.3.1-2 and MacPorts gcc11 11.3.0_5. It is telling us how crappy is the gfortran compiler, and the folks at GNU have not read or misinterpreted correctly Fortran 2003 standard an...
by arango
Mon Apr 03, 2023 9:24 pm
Forum: ROMS Problems
Topic: Test-case canyon2d
Replies: 6
Views: 7405

Re: Test-case canyon2d

Nope, if SOLVE3D is undefined, you are solving the vertically integrated shallow-water equations. There are no vertical levels in such an application. Neither vertical mixing parameterization like GLS_MIXING or others. The state variables are only zeta , ubar , and vbar . I updated the repositories....
by arango
Mon Apr 03, 2023 12:52 pm
Forum: ROMS Problems
Topic: Test-case canyon2d
Replies: 6
Views: 7405

Re: Test-case canyon2d

Okay, I will check it out later. I think that in mod_ncparam.F , we need to have instead: ! ! Set generic lateral boundary indices for LBC structure. Use the same ! values of the state variables at the same C-grid location. Generic ! indices are used for testing periodicity. The PSI-variables and ! ...
by arango
Mon Apr 03, 2023 12:36 pm
Forum: ROMS Installation
Topic: Compilation issue: yaml_parser.f90
Replies: 3
Views: 4992

Re: Compilation issue: yaml_parser.f90

Your compiler is too old and does not support 2003 and 2008 updates to the Fortran standard. Need to use a newer version of the ifort compiler or a recent version of gfortran.
by arango
Sun Apr 02, 2023 3:57 pm
Forum: ROMS Problems
Topic: Test-case canyon2d
Replies: 6
Views: 7405

Re: Test-case canyon2d

For the 2D test case, you need to undefine SOLV3D. Check ROMS test repository :arrow: https://www.myroms.org/svn/src/test.
by arango
Wed Mar 22, 2023 5:52 pm
Forum: Ocean News
Topic: Dale B. Haidvogel (1949-2023)
Replies: 18
Views: 35513

Re: Dale B. Haidvogel (1949-2023)

On behave of Bernard Jean Barnier: I first met dale during the first summer school on space oceanography organized by CNES in Grasse in 1985. I was still a Ph.D. student at FSU, and Dale was teaching numerical modeling techniques applied to oceanography. Great class, and no surprise that I decided t...
by arango
Tue Mar 21, 2023 1:06 pm
Forum: ROMS Bugs
Topic: Possible Coding Error in gls_corstep.F: application of gls_Kmin and gls_Pmin to control advection
Replies: 4
Views: 12046

Re: Possible Coding Error in gls_corstep.F: application of gls_Kmin and gls_Pmin to control advection

I haven't had the time to check this issue. We need to analyze the caping of the values. It is probably in the wrong place and needs to be postponed after all the terms are computed. ROMS equations and conservation statements are written in flux form, so things change between horizontal and vertical...
by arango
Sat Mar 18, 2023 1:08 pm
Forum: Ocean News
Topic: Dale B. Haidvogel (1949-2023)
Replies: 18
Views: 35513

Re: Dale B. Haidvogel (1949-2023)

I met Dale when I was a PostDoc at Harvard University. He came to our group and gave an excellent presentation about ocean modeling. We also met in my office to discuss SPEM, which I had been learning. When I was ready to leave Harvard, I emailed him about my chances for me to get a modeling positio...
by arango
Mon Mar 13, 2023 7:35 pm
Forum: ROMS Bugs
Topic: History file archiving intervals: bug in output.F?
Replies: 12
Views: 34200

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

Okay, you don't understand how the multifile option works in ROMS. You CANNOT whatsoever change the values of NTIMES or DSTART to run correctly on your supercomputer with a queue time limits that don't finish your simulation. Then, you have to restart. I suspected this was your problem, so I wrote i...
by arango
Sat Mar 11, 2023 7:56 pm
Forum: ROMS Bugs
Topic: History file archiving intervals: bug in output.F?
Replies: 12
Views: 34200

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

I added information in :arrow: wikiROMS to be used as a guideline when designing the multi-file strategy for a ROMS application. Unfortunately, this is all I can do now in my free time.
by arango
Sat Mar 11, 2023 4:07 am
Forum: ROMS Bugs
Topic: History file archiving intervals: bug in output.F?
Replies: 12
Views: 34200

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

What will happen if you do a single run without restarting? If ROMS creates the multifile correctly, the issue will be the restart mechanism, which is even more complicated in this case. The issue is no longer in output.F but in g et_state.F , def_his.F , and check_multifile.F . I think that the va...
by arango
Thu Mar 09, 2023 7:09 pm
Forum: ROMS Discussion
Topic: Model time issue with SINGLE_PRECISION option
Replies: 1
Views: 3130

Re: Model time issue with SINGLE_PRECISION option

Well, that is weird because when single precision is activated in ROMS, there are still several important variables that are declared in double precision, and time management is one of them. That is, ROMS is compiled in hybrid precision. You can check that easily by typing the following command at t...
by arango
Wed Mar 08, 2023 1:49 pm
Forum: ROMS Installation
Topic: compile with ifort problems
Replies: 2
Views: 5076

Re: compile with ifort problems

You can compile with gfortran ; I do it all the time. However, you need to use a newer version of the compiler. Notice that in the :arrow: message that you referred to, the user solved the memory leak and bug in the compiler by using a newer version. To use ifort, you need to customize the proper *-...
by arango
Mon Mar 06, 2023 7:04 pm
Forum: ROMS Bugs
Topic: History file archiving intervals: bug in output.F?
Replies: 12
Views: 34200

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

It is difficult to diagnose your problem because you are using a version of ROMS that we don't support, and we are blind to how your version departs from the code we release. In addition, there is not enough information here to diagnose the problem, nor do I have the time for it. It is not only the ...
by arango
Sun Mar 05, 2023 8:28 pm
Forum: ROMS Discussion
Topic: ROMS crashing when using LwSrc
Replies: 18
Views: 31137

Re: ROMS crashing when using LwSrc

I will look at it when I get the chance. The ROMS parallel tile indices are shown below and include the interior ( red points) and nesting contact points ( blue ) in the purple area. Things get complicated when dealing with nested grids. The diagram shows the southwestern and northeastern parallel t...
by arango
Wed Mar 01, 2023 9:17 pm
Forum: ROMS Bugs
Topic: History file archiving intervals: bug in output.F?
Replies: 12
Views: 34200

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

Thank you for the detailed information. Yes, this logic is tricky. First, what version of ROMSare you using, We have corrected issues for this logic in the past. It is very subtle and requires lots of time in the TotalView debugger. We need to be sure that you are using the latest version of ROMS fi...
by arango
Wed Mar 01, 2023 1:26 pm
Forum: ROMS Discussion
Topic: Problem about input files for nudging
Replies: 2
Views: 2918

Re: Problem about input files for nudging

If you are a new user of ROMS, get the latest version of the code as you are supposed to. The code that you are using is eight years old! A lot of updates and corrections have been done since then. Nobody here is going or has the time to answer questions about an old version of ROMS. It is the respo...
by arango
Thu Feb 23, 2023 4:10 pm
Forum: ROMS Discussion
Topic: Horizontal surface pressure gradient forcing in 2D and 3D
Replies: 18
Views: 23784

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

I don't have a shallow water (2D kernel) application to test this term. But, yes, a cyclone rotates counterclockwise around a center of low atmospheric pressure in the northern hemisphere. Consequently, the inverted barometer effect causes the water level to rise to form a dome around the low-pressu...
by arango
Mon Jan 30, 2023 8:51 pm
Forum: ROMS Discussion
Topic: ROMS crashing when using LwSrc
Replies: 18
Views: 31137

Re: ROMS crashing when using LwSrc

Hi Parker, we have a new 2D kernel for ROMS that is more accurate and efficient. It is based on Shchepetkin and McWilliams (2005, 2009) formulation for the Generalized Forward-Backward 3rd-order Adams-Bashword 4th-order Adams-Moulton (FB AB3-AM4) time-stepping algorithm. It does a barotropic pressur...
by arango
Fri Jan 13, 2023 3:09 pm
Forum: ROMS Discussion
Topic: ROMS crashing when using LwSrc
Replies: 18
Views: 31137

Re: ROMS crashing when using LwSrc

It seems to me that your surface flux transport is too strong and violates the CFL condition. You can compute the CFL, given your horizontal resolution and timestep size. Then, you need to lower your timestep or reduce your point source transport. It is a basic numerical modeling strategy. The LwSRC...
by arango
Fri Jan 06, 2023 1:32 pm
Forum: ROMS Discussion
Topic: Time problem of ROMS result output
Replies: 1
Views: 2920

Re: Time problem of ROMS result output

Ensure the time in the initial conditions NetCDF file is 2017-08-09. ROMS sets the initial time when reading the initial conditions NetCDF file. You can check that time easily if your NetCDF file has the correct units attribute for time:

Code: Select all

ncdump -t -v ocean_time my_roms_ini.nc
by arango
Sat Dec 24, 2022 8:25 pm
Forum: ROMS Discussion
Topic: Water Level for One-Way Nesting is Wrong but Two-Way Nesting Works
Replies: 7
Views: 8919

Re: Water Level for One-Way Nesting is Wrong but Two-Way Nesting Works

Indeed, how you design your nested grid application and locate the telescoping domains is essential. That's where experience comes to play a role in successful nested applications. We want a smooth transition of bathymetry and dynamics. For example, a canyon or a significant ocean current a the boun...
by arango
Fri Dec 23, 2022 6:17 pm
Forum: ROMS Discussion
Topic: Water Level for One-Way Nesting is Wrong but Two-Way Nesting Works
Replies: 7
Views: 8919

Re: Water Level for One-Way Nesting is Wrong but Two-Way Nesting Works

Yes, this makes a lot of sense to me. In such an active region, the nesting should always be two-way! The issue is that the finer, high-resolution nested grid resolves the smaller-scale processes, and there is no feedback from fine-to-coarse, so the two coarser and finer grid solutions are diverging...
by arango
Fri Dec 09, 2022 3:24 pm
Forum: ROMS Source
Topic: Abnormal shflux when QCORRECTION is defined in ROMS 1147
Replies: 7
Views: 9001

Re: Abnormal shflux when QCORRECTION is defined in ROMS 1147

I always recommend Users to keep the ROMS code up to date. Every time that the code is changed to correct bugs or improvements, detailed information is provided in the trac tickets. Users should never ignore that information, even if they are not updating the code. For example, the surface fluxes we...
by arango
Wed Nov 30, 2022 5:33 pm
Forum: ROMS Discussion
Topic: Question about Flather 2d boundary condition for ubar
Replies: 10
Views: 13902

Re: Question about Flather 2d boundary condition for ubar

Yes, there is an inconsistency in my explanation above. I am trying to show you that 0.5 is associated with x-spacing and not a time-step factor. If the zeta_west is averaged at the u-point, its usage in the zetabc routine for the boundary conditions for zeta is halfway in, but it won't be much trou...
by arango
Wed Nov 30, 2022 4:50 pm
Forum: ROMS Discussion
Topic: Question about Flather 2d boundary condition for ubar
Replies: 10
Views: 13902

Re: Question about Flather 2d boundary condition for ubar

The 0.5 factor is associated with the dx when we evaluate d(zeta)/dx and noting to do with time stepping. The C-grid stencil is: .--------- .-------- vbar(Istr,j+1)-------. + | | + | | zeta(west,j) ubar(Istr,j) zeta(Istr,j) ubar(Istr+1,j) + | | + | | .--------- .-------- vbar(Istr,j)---------. The d...
by arango
Mon Nov 28, 2022 6:26 pm
Forum: ROMS Discussion
Topic: Question about Flather 2d boundary condition for ubar
Replies: 10
Views: 13902

Re: Question about Flather 2d boundary condition for ubar

It can go both ways, but we need to test. The section of the code in question is rarely used since we specify both tidal elevation and tidal currents. For the case that only tidal elevation is activated, we need to approximate the tidal currents with reduced-physics terms evaluated at the open bound...
by arango
Mon Nov 21, 2022 8:46 pm
Forum: ROMS Discussion
Topic: Canyon test case: unable to open restart NetCDF file
Replies: 6
Views: 7021

Re: Canyon test case: unable to open restart NetCDF file

Yes, I fixed main2d.F some time ago in my research repositories, but I forgot to do it in the distributed svn and git repositories. Please update for code. Here is that :arrow: trac ticket.
by arango
Sat Nov 19, 2022 4:36 pm
Forum: ROMS Tools and Techniques
Topic: How does ROMS stratification translate into water depth?
Replies: 1
Views: 3426

Re: How does ROMS stratification translate into water depth?

It would help if you interpolated spatially. In Matlab, there are various native functions to perform the interpolation. Notice that ROMS can also output any of the time-varying depths in the history file: Hout(idpthR) == F ! z_rho time-varying depths of RHO-points Hout(idpthU) == F ! z_u time-varyi...
by arango
Thu Nov 17, 2022 4:18 pm
Forum: ROMS Discussion
Topic: Computing advection using 'utemp' vs 'temp_xadv'
Replies: 6
Views: 5336

Re: Computing advection using 'utemp' vs 'temp_xadv'

We have all the terms for balance studies in the average and diagnostic output files. You need to make sure the time-averaging window is the same ( NAVG=NDIA ). Also, it would help if you considered that ROMS is a finite volume model, and the governing equations are written in flux form (transport)....
by arango
Wed Nov 16, 2022 3:52 am
Forum: ROMS Problems
Topic: tides_date.f90 variable definition
Replies: 14
Views: 21393

Re: tides_date.f90 variable definition

ROMS will run much faster if the code is optimized (executable romsM) than with debugging flags (executable romsG).
by arango
Wed Nov 09, 2022 4:43 pm
Forum: ROMS Problems
Topic: ROMS Blows up on after first time step
Replies: 5
Views: 6705

Re: ROMS Blows up on after first time step

Your model is blowing up right away. I think that it is blowing up in the barotropic kernel ( step2d) because I suspect that your currents are becoming very high. That may be a CFL violation due to surface forcing or, more likely, to lateral boundary conditions data. You should compare that forcing ...
by arango
Sun Nov 06, 2022 10:00 pm
Forum: ROMS Problems
Topic: tides_date.f90 variable definition
Replies: 14
Views: 21393

Re: tides_date.f90 variable definition

I think that the issue here is that something is missing in the configuration. Did you update varinfo.yaml ? Mostly all users ignore trac updates to ROMS. We provide precise information in trac tickets with instructions on using new features. We usually see postings here that we need to reconstruct ...
by arango
Thu Nov 03, 2022 7:04 pm
Forum: ROMS Tools and Techniques
Topic: some possible errors using matlab tool
Replies: 6
Views: 10200

Re: some possible errors using matlab tool

Yes, thank you. We need to put the NetCDF file in define mode. I missed that call. I updated the repository.
by arango
Tue Nov 01, 2022 3:07 pm
Forum: ROMS Tools and Techniques
Topic: some possible errors using matlab tool
Replies: 6
Views: 10200

Re: Unrecognized field name "f" using coarse2fine

Yes, please update.
by arango
Sun Oct 16, 2022 3:02 pm
Forum: ROMS Problems
Topic: How to turn off horizontal advection term just for phytoplankton
Replies: 4
Views: 6876

Re: How to turn off horizontal advection term just for phytoplankton

You need proper treatment for all the tracers and momentum values if you have open boundary conditions. Any suspicious values along the boundaries are an artifact of the ill-posed open boundary conditions. In addition, it is possible to create artificial upwelling/downwelling along the domain edges ...
by arango
Sat Oct 15, 2022 5:04 pm
Forum: ROMS Problems
Topic: How to turn off horizontal advection term just for phytoplankton
Replies: 4
Views: 6876

Re: How to turn off horizontal advection term just for phytoplankton

Why do you want to do a radical thing like that if you are a beginner? The Fennel model is tightly coupled with highly nonlinear terms that depend on phytoplankton and a balance between prey and predactor The 3D time-stepping kernel for tracers is quite complex to start hacking and removing pieces. ...
by arango
Thu Oct 13, 2022 1:30 pm
Forum: ROMS Ecosystem
Topic: adding a new variable to hypoxia_srm
Replies: 4
Views: 7948

Re: adding a new variable to hypoxia_srm

Perhaps, you didn't add the appropriate metadata and logic for the new variables. Nowadays, our version of ROMS uses varinfo.yaml instead of varinfo.dat. I don't know if that change was incorporated into COAWST or the version you are using. But it may explain the issues that you are having.
by arango
Wed Oct 12, 2022 2:57 pm
Forum: ROMS Problems
Topic: 4 Sides Boundary makes ROMs running errors
Replies: 2
Views: 5475

Re: 4 Sides Boundary makes ROMs running errors

This application does not make sense to me. You specified a land mask around all four edges of the grid. However, you are setting East-West periodic with the LBC parameter in roms.in . You will get an unphysical solution closing all four boundaries. It would help if you had a strategy for open bound...
by arango
Thu Sep 29, 2022 2:56 pm
Forum: ROMS Problems
Topic: ERROR: Abnormal termination: NetCDF OUTPUT
Replies: 6
Views: 8248

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: 3024

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: 16253

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: 16253

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: 3
Views: 6034

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: 3216

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: 20688

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: 20688

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: 3270

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: 6850

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: 12762

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: 4898

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: 3413

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: 4898

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: 5236

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: 5236

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: 5485

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: 3551

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: 3152

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: 4049

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: 17
Views: 24211

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: 3993

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: 4032

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: 3294

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: 4347

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: 9722

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: 4160

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: 3421

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: 27996

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: 27996

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: 27996

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: 9636

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: 9636

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: 27996

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: 16273

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: 16273

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: 5
Views: 5474

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: 3552

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: 8940

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: 8940

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: 8940

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: 4753

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: 10125

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: 3436

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: 14247

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: 2907

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: 8226

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: 14247

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: 14247

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: 3826

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: 3974

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: 4845

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: 3375

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: 3133

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: 2608

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: 11375

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: 11375

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: 7759

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: 3139

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: 2935

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: 5534

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: 9147

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: 9147

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: 3350

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: 6323

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: 5799

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: 8231

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: 3305

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: 3700

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: 17378

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: 17378

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: 17378

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: 17378

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: 16846

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: 16846

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: 5049

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: 5049

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: 4
Views: 4334

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: 5705

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: 11526

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: 5705

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: 11526

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: 11526

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: 7128

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: 5099

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: 5099

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: 7128

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: 18
Views: 23784

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: 18
Views: 23784

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: 18
Views: 23784

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: 3448

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: 7325

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: 50448

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: 50448

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: 50448

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: 50448

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: 50448

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: 6818

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: 6818

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: 9443

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: 14148

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: 14148

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: 3541

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: 3262

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: 3506

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: 28843

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: 28843

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: 28843

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: 28843

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: 28843

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: 28843

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: 3547

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: 5619

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: 7889

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: 5115

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: 3844

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: 21810

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: 21810

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: 21810

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: 8751

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: 4178

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: 4102

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: 205610

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: 3915

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: 4
Views: 4212

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: 3874

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: 7486

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: 205610

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: 205610

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: 205610

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: 205610

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: 6567

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: 5617

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: 7880

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: 26063

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: 10510

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: 20741

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: 4102

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: 5991

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: 4050

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: 7812

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: 7812

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: 5384

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: 4114

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: 3326

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: 9443

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: 3395

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: 19367

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: 19367

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: 19367

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: 4426

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: 7468

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: 7468

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: 11910

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: 4030

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: 12195

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: 8708

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: 8708

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: 5367

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: 15558

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: 3685

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: 4019

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: 4709

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: 18574

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: 5870

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: 4237

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: 5870

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: 3962

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: 4878

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: 7035

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: 3540

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: 10771

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: 4212

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: 10771

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: 18574

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: 18574

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...