Search found 1208 matches

by arango
Wed Nov 24, 2021 4:29 pm
Forum: ROMS Discussion
Topic: High Temperature in Summer
Replies: 4
Views: 434

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: 3
Views: 275

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: 213

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: 119

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: 389

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: 389

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: 389

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: 389

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: 10
Views: 416

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: 10
Views: 416

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: 304

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: 304

Re: Understanding tracer identification indices

Yes, the biology tracer numbering change according to the CPP options. When in doubt, I always recommend to everybody in this forum to check the standard output very carefully, and pipeline it to a log file instead of the screen. The information that you need is always there. For the upwelling test ...
by arango
Thu Oct 14, 2021 3:25 pm
Forum: ROMS Problems
Topic: OUTPUT - multi-file counter AVG(ng)%load = 3, is greater than Nfiles = 2 dimension 247058 in structure when c
Replies: 3
Views: 599

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: 517

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: 798

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: 517

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: 798

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: 798

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: 666

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: 289

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: 289

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: 666

Re: ROMS Upwelling Idealisation / Test Case Failure

Okay, it seems that you are struggling to install the required libraries. The upwelling test case only requires the NetCDF library. You can either use the NetCDF-3 or NetCDF-4 library. The NetCDF-4 library has a lot of options to install. The HDF5 library is only needed for parallel I/O. One of the ...
by arango
Fri Sep 10, 2021 12:49 am
Forum: ROMS Discussion
Topic: Horizontal surface pressure gradient forcing in 2D and 3D
Replies: 16
Views: 5292

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

My understanding is that the nondimensional density scale (see rhoA and rhoS in rhos_eos.F ) enters only in the barotropic pressure gradient in step2d with VAR_RHO_2D . Notice that the paper's equation shows the density evaluated at the free surface, which is only obtained by vertically integrating ...
by arango
Thu Sep 09, 2021 10:09 pm
Forum: ROMS Discussion
Topic: Horizontal surface pressure gradient forcing in 2D and 3D
Replies: 16
Views: 5292

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

Nope, I am taking about the first term: GRho0*z_w(i,j,N(ng)) . It needs to be g*z_w(i,j,N(ng)) , which also gives m2/s2 for kinematic pressure. I am sure that this term needs to be multiplied by gravity only and not scaled by density like it is done the step2d_LF_AM3.h for the barotropic pressure gr...
by arango
Thu Sep 09, 2021 4:48 pm
Forum: ROMS Discussion
Topic: Horizontal surface pressure gradient forcing in 2D and 3D
Replies: 16
Views: 5292

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: 241

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: 628

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: 1867

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: 1867

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: 1867

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: 1867

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: 1867

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: 4
Views: 333

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: 4
Views: 333

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: 1072

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: 638

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: 638

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: 281

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: 361

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: 314

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: 1459

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: 1459

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: 1459

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: 1459

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: 1459

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: 1459

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: 320

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: 708

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: 690

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: 558

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: 390

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: 5883

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: 5883

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: 5883

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: 982

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: 389

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: 543

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: 7955

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: 385

Re: Function roms_metrics

ROMS uses a horizontal, staggered Arakawa C-grid. You need to study and understand the following grid diagram in :arrow: WikiROMS . You need to look the grid spacing in terms of RHO -, PSI -, U -, and V -points. Then, you will answer your own questions. The code in roms.metrics.m is correct.
by arango
Thu Apr 15, 2021 4:10 pm
Forum: ROMS Discussion
Topic: WC13/RBL4DVAR PROBLEM
Replies: 3
Views: 599

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: 458

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: 1340

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: 7955

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: 7955

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: 7955

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: 7955

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: 577

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: 420

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: 645

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: 2409

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: 1487

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: 17
Views: 2188

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: 804

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: 6
Views: 893

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: 948

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: 792

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: 792

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: 1560

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: 726

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: 643

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: 1072

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: 676

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: 7147

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: 7147

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: 7147

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: 1015

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: 1365

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: 1365

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: 2266

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: 870

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: 3445

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: 1271

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: 1271

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: 1205

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: 3608

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: 713

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: 832

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: 1025

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: 3186

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: 1117

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: 858

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: 1117

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: 1070

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: 1215

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: 1510

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: 839

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: 2900

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: 860

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: 2900

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: 3186

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: 3186

Re: Possible bug in wetdry.F for nested apps

Notice that the indices told and tnew are local (dummy) time indices: ! ! Set time snapshot indices for the donor grid data. ! told=3-RollingIndex(cr) tnew=RollingIndex(cr) However, if you are running a 2D shallow-water application ( SOLVE3D is off), why are you dealing with state variables ( DU_avg...
by arango
Fri Feb 07, 2020 4:20 pm
Forum: ROMS Bugs
Topic: Possible bug in wetdry.F for nested apps
Replies: 14
Views: 3186

Re: Possible bug in wetdry.F for nested apps

Hmm. I will have to think about it but maybe it will be needed. It will need to be tested. There are a set of those indices for RHO-, PSI-, U-, and V-points. It will be only relevant it coastlines are present in the contact points.
by arango
Thu Feb 06, 2020 11:44 pm
Forum: ROMS Bugs
Topic: ROMS 3.9 MPDATA bugs
Replies: 2
Views: 1137

Re: ROMS 3.9 MPDATA bugs

Yes, Great catch :!: Thank you for reporting these two bugs. I updated the :arrow: repositories.
by arango
Thu Feb 06, 2020 5:20 pm
Forum: ROMS Adjoint
Topic: 4DVAR assimilation of surface velocities destroy sst
Replies: 5
Views: 1728

Re: 4DVAR assimilation of surface velocities destroy sst

It is all a matter of the assumed background error covariance hypothesis and its parameters. What do you trust more the model or the observations? HF radar velocity observations are very tricky since it is a very noisy data, and depends on the processing: averaging, detiding, super-observations, err...
by arango
Sun Feb 02, 2020 3:36 pm
Forum: ROMS Problems
Topic: A ROMS nesting question
Replies: 10
Views: 2953

Re: A ROMS nesting question

You need to make sure that the variables in your forcing NetCDF files have the _FillValue = 1.e+35 attribute or whatever other value you used. Otherwise, ROMS doesn't know how to process such data without the _FillValue that have land/sea masks. However, the fact the you have Min = 1.0E+35 and Max =...
by arango
Fri Jan 31, 2020 8:57 pm
Forum: ROMS Problems
Topic: A ROMS nesting question
Replies: 10
Views: 2953

Re: A ROMS nesting question

Check your standard input file, roms.in or your standard output log file, which contains lots of information. Notice that in roms.in we have: ! Logical switches (TRUE/FALSE) to nudge the desired climatology field(s). ! If not analytical climatology fields, users need to turn ON the logical ! switche...
by arango
Sun Jan 26, 2020 8:33 pm
Forum: ROMS Problems
Topic: Three nested refined grids - Ngrids vs. Ncontact
Replies: 2
Views: 1022

Re: Three nested refined grids - Ngrids vs. Ncontact

The nesting configuration is tricky since we support various types of grid connectivity. We only provide a Matlab interface to generate the nesting connectivity NetCDF file needed by ROMS. Unfortunately, we don't officially have any other software to create such a connectivity NetCDF file nor have t...
by arango
Thu Jan 16, 2020 10:35 pm
Forum: ROMS Discussion
Topic: ROMS 3.7
Replies: 1
Views: 765

Re: ROMS 3.7

The frozen versions of ROMS are available only on SVN. Usually, one checkout the tags SVN repository: svn checkout https://www.myroms.org/svn/src/tags tags svn checkout https://www.myroms.org/svn/src/tags/roms-3.7 roms-3.7 The GIT repository works in a different way. If you need the version that was...
by arango
Thu Jan 16, 2020 4:04 am
Forum: ROMS Bugs
Topic: Matlab nesting pre-processing program error.
Replies: 2
Views: 1185

Re: Matlab nesting pre-processing program error.

Yes, your first correction is fine. Thank you :!: I updated the repository. We didn't catch that one before because all our grids always have the ( XI , ETA ) coordinates even if the applications grid is spherical. It turns out that in curvilinear grids is better to do the interpolation in ( XI , ET...
by arango
Sat Jan 04, 2020 7:35 pm
Forum: ROMS Bugs
Topic: Segmentation fault
Replies: 9
Views: 2019

Re: Segmentation fault

This is not a bug. It always has to be equal or greater than one by design. If no input forcing files are needed, ROMS will ignore those values on standard input. I don't understand what it is the Fuzz about it. There are a lot of parameters in ROMS standard input that will be only relevant for a sp...
by arango
Mon Dec 23, 2019 2:42 pm
Forum: ROMS Discussion
Topic: calculating ubar and vbar
Replies: 10
Views: 3386

Re: calculating ubar and vbar

Look at Nonlinear/ini_fields.F instead. It is very clear how it is computed there. It is how the inital ubar anf vbar is computed in ROMS.
by arango
Tue Dec 17, 2019 6:16 am
Forum: ROMS Discussion
Topic: Request: Numerical modeling course syllabi
Replies: 11
Views: 3401

Re: Request: Numerical modeling course syllabi

I learned how to program and plot with the NCARG graphical library. I spent so much time reading the manuals and learning how to use that library. It was very satisfying plotting the results with computer-generated contours. I became a pro using that wonderful library. I still used it today. I wrote...
by arango
Tue Dec 17, 2019 2:07 am
Forum: ROMS Discussion
Topic: Request: Numerical modeling course syllabi
Replies: 11
Views: 3401

Re: Request: Numerical modeling course syllabi

Indeed, I took that class from John Klinck when I was a graduate student at Texas A&M. I learned a lot about coding and ocean numerical modeling in that first class. It was a great introduction to a world that it is now my professional life. I recall that we, the students, and John, enjoyed that...
by arango
Mon Dec 09, 2019 3:27 am
Forum: ROMS Bugs
Topic: typo in distribute.F
Replies: 1
Views: 821

Re: typo in distribute.F

Hi Frank, great catch. Thank you! I updated the repository. See the following :arrow: trac ticket for more information.
by arango
Fri Dec 06, 2019 11:37 pm
Forum: ROMS Discussion
Topic: Parallel IO not scaling over Serial IO for ROMS
Replies: 14
Views: 2765

Re: Parallel IO not scaling over Serial IO for ROMS

An application of size 899x629x40 is TOO small to be run in 1350 PEs :!: No wonder why is not scaling after 240 PEs. You are killing scalability with excessive MPI collective communications and exchanges. Your 20x20 tile size is too small, and it is killing vectorization. The good news is that you f...
by arango
Thu Dec 05, 2019 4:54 pm
Forum: ROMS Discussion
Topic: Parallel IO not scaling over Serial IO for ROMS
Replies: 14
Views: 2765

Re: Parallel IO not scaling over Serial IO for ROMS

Great study. We are missing important information about your simulations. We need the grid size and the parallel domain decomposition. I have mentioned frequently in this forum that ROMS scalability is a function of the application and depends on the domain size and parallel partition. There is alwa...
by arango
Fri Nov 15, 2019 9:55 pm
Forum: ROMS Installation
Topic: Compiling error - undefined reference to ice routines
Replies: 12
Views: 2950

Re: Compiling error - undefined reference to ice routines

The version of the code that we distribute doesn't have a native sea ice model yet. I am sure that it will be included in the future. It has to be located in a subdirectory inside of the Nonlinear directory, like the biology and sediment models. The reason for it is quite logical and straightforward...
by arango
Sun Aug 04, 2019 4:21 pm
Forum: ROMS Installation
Topic: upwelling: - Configuration error ..... exit_flag: 5
Replies: 3
Views: 1291

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

The default upwelling example in ROMS test repository has UV_QDRAG activated in the build script. If you notice, there are various options in build_roms.sh : # can be used to write time-averaged fields. Notice that you can have as # many definitions as you want by appending values. setenv MY_CPP_FLA...
by arango
Thu Jul 25, 2019 4:00 pm
Forum: ROMS Releases
Topic: ROMS 3.7 Released
Replies: 0
Views: 3318

ROMS 3.7 Released

ROMS/TOMS 3.7 Released The latest version of the :arrow: ROMS/TOMS svn repository , revision 974 , was frozen and tagged as ROMS 3.7 . We haven't tagged a frozen version of ROMS in several years. This version is quite stable, and it is the one to be used at the upcoming 2019 ROMS 4D-Var Workshop to...
by arango
Mon Jul 22, 2019 3:03 pm
Forum: ROMS Bugs
Topic: Typo in ad_set_vbc.F line 1165 rev 973
Replies: 1
Views: 784

Re: Typo in ad_set_vbc.F line 1165 rev 973

Indeed, thank you! I didn't test with LIMIT_STFLX_COOLING activated.
by arango
Tue Jul 09, 2019 8:33 pm
Forum: ROMS Bugs
Topic: Error regarding variable dP in prsgrd44.h or prsgrd42.h
Replies: 1
Views: 848

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

Indeed. Thank you for reporting this issue. Please update.
by arango
Thu Jun 27, 2019 7:48 pm
Forum: ROMS Problems
Topic: ROMS different src version leading to unalike results
Replies: 7
Views: 2273

Re: ROMS different src version leading to unalike results

The ROMS basic numerical kernel has not changed much in a few years. However, configuration, CPP options, and parameters in the standard input have been modified and enhanced. You need to be sure that your header file ( application.h ) and standard input script ( roms.in ) is equivalent between the ...
by arango
Wed Jun 12, 2019 1:06 am
Forum: ROMS Discussion
Topic: Time type in nc file
Replies: 5
Views: 1509

Re: Time type in nc file

ROMS has nothing to do with the time convention and elapsed time. The user selects how the time is managed in an application. There is nothing that we can do about it. It is up to the person(s) that set-up that application to use a consistent time zone in all the input NetCDF files (initial conditio...
by arango
Wed May 15, 2019 6:51 pm
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 6
Views: 11069

Re: compile ROMS error

Your problem is that you haven't configured the build_roms.sh and build_roms.bash correctly. For example, notice that in the build_roms.sh script we have: #-------------------------------------------------------------------------- # If applicable, use my specified library paths. #-------------------...
by arango
Sun May 12, 2019 1:44 pm
Forum: ROMS Problems
Topic: Segmentation fault with floats
Replies: 6
Views: 1876

Re: Segmentation fault with floats

Segmentation violations (SIGSEGV) are usually a sign of memory problems on the computer and available stack for the run. Perhaps, your computer doesn't have too much memory for your application, and you are deploying too many floats for it. I will try to run without floats to see if it works. Then a...
by arango
Wed May 08, 2019 10:35 pm
Forum: ROMS Installation
Topic: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT type
Replies: 4
Views: 1560

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

You didn't understand at all what I was saying to you, or what WET_DRY does. The wetting and drying option ( WET_DRY ) is modeled in ROMS by changing the associated land/sea masking arrays at every barotropic time-step in step2d , which affect the ocean state variables. The wet/dry mask is a new arr...
by arango
Wed May 08, 2019 6:31 pm
Forum: ROMS Installation
Topic: Compile ROMS Error: Symbol 'eps' at (1) has no IMPLICIT type
Replies: 4
Views: 1560

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

The WET_DRY option is not adjointed because it not fully differentiable, and because of every time-step of the forward trajectory need to be saved to have a consistent linearization of the tangent linear (TLM) and adjoint (ADM) models. You cannot use such time-depending land/sea masking in any ROMS ...
by arango
Wed May 01, 2019 4:22 pm
Forum: ROMS Discussion
Topic: cppdefs for BULK_FLUX
Replies: 11
Views: 3390

Re: cppdefs for BULK_FLUX

My current strategy is to activate LONGWAVE_OUT and provide downward longwave radiation so bulk_flux will subtract the outgoing IR by using ROMS surface temperature ( K ), infrared emissivity, and Stefan-Boltzmann constant. I also use downward shortwave radiation and I activate COOL_SKIN to correct ...
by arango
Tue Apr 16, 2019 9:50 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 2149

Re: CF compliant units attributes in Varinfo.dat

ROMS has nowadays a very robust calendar. See the routine ROMS/Utility/dateclock.F for more details. It is consistently internally and can handle different reference date ( epoch ) for each forcing field from NetCDF files regardless of what we choose in the ROMS input parameter TIME_REF . I have to ...
by arango
Tue Apr 16, 2019 2:23 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 2149

Re: CF compliant units attributes in Varinfo.dat

I agree with John. This part is not desirable. We and others have been using this standard for years. There are lots of datasets out there that follow this nomenclature. I am sympathetic with the issue of the links but some of the changes suggested are radical.
by arango
Thu Apr 11, 2019 9:33 pm
Forum: ROMS Information
Topic: units of specific humidity
Replies: 10
Views: 7530

Re: units of specific humidity

Indeed, I believe that unsavory piece of code was in the original COARE code. It is quite clever if you ask me. I recall putting enough comments in the code when I did some research about this threshold value many years ago. There is not a standardized unit for specific humidity in the atmospheric d...
by arango
Thu Mar 21, 2019 9:55 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 2149

Re: CF compliant units attributes in Varinfo.dat

Thank you. The ROMS metadata file varinfo.dat is a user file and can be edited in any way that the user feels is necessary. You can even change the language. Some users in France wanted some of the attribute values to be in French. I haven't read the documentation about the UDUNITS-2 package. I look...
by arango
Wed Mar 13, 2019 2:28 am
Forum: ROMS Bugs
Topic: A small bug in ana_srflux.h
Replies: 12
Views: 6120

Re: A small bug in ana_srflux.h

Finally, I have time to browse the literature, Googling, and write a Matlab script to check the issue mentioned above. Indeed, the 15.0 factor used to compute the zenith is incorrect :!: We need to have instead:  zenith=cff1+cff2*COS(Hangle-lonr(i,j)*deg2rad) In my Matlab script, I compared against...
by arango
Sun Mar 10, 2019 10:38 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 2855

Re: Pair and MPI version has problem with regridding

I updated the code to correct the bug in regrid.F. Check the following trac ticket :arrow: src:ticket:808 for more details. The parallel bug was corrected. Good luck.
by arango
Sat Mar 09, 2019 5:53 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 2855

Re: Pair and MPI version has problem with regridding

It doesn't make sense to me. MyXout is a state, tiled variable and it is allocated as the others, and the pointer is passed correctly. It is the only way that this can be done. I bet that the problem is not in regrid . It seems like a memory leakage somewhere else. Yes, you can put the application i...
by arango
Fri Mar 08, 2019 9:04 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 2855

Re: Pair and MPI version has problem with regridding

I took a look in the debugger on our US East Coast application and I cannot find anything wrong. I activated both ATM_PRESS and PRESS_COMPENSATE . I am also using BULK_FLUXES , which also need Pair . I don't see a parallel bug. Pair.png shflux.png The Pair is kind of jagged but it is because of the ...
by arango
Fri Mar 08, 2019 5:16 am
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 2855

Re: Pair and MPI version has problem with regridding

Yes, the Dmem is a diagnostic quantity to estimate the memory requirement for an application. It has nothing to do with the numerical kernel. It is in my TODO list to look at your problem in the debugger. The issues that you are talking about sound like a parallel bug. However, the regrid subroutine...
by arango
Thu Mar 07, 2019 5:27 am
Forum: ROMS Bugs
Topic: A small bug in ana_srflux.h
Replies: 12
Views: 6120

Re: A small bug in ana_srflux.h

Both ana_srflux.h and ana_specir.h were coded longtime ago when we were testing the EcoSim bio-optical model in the late 90's. It was like twenty years ago. So I don't remember the details. At that time, both routines were intended for idealized toy problems for debugging purposes. The EcoSim model ...
by arango
Thu Feb 28, 2019 3:36 am
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 5588

Re: My ROMS

Thank you, Mark. Your logic is correct. We don't need to add processing logic since it needs ATM_PRESS anyway. I loaded your request ticket to the repository.
by arango
Mon Feb 11, 2019 10:34 pm
Forum: ROMS Tools and Techniques
Topic: Soundspeed for ROMS output
Replies: 4
Views: 1754

Re: Soundspeed for ROMS output

Just do it in Matlab.
by arango
Mon Feb 11, 2019 5:12 am
Forum: ROMS Tools and Techniques
Topic: Soundspeed for ROMS output
Replies: 4
Views: 1754

Re: Soundspeed for ROMS output

It has been in ROMS plotting package that uses the NCAR's GKS library since the beginning. Check the file src/Utility/svel.F in the plot repository. It uses the Che and Millero (1976) formula. Chen, C.T. and F.J. Millero, 1976: re-evaluation of Willson sound-speed measurements in pure water. J. Acou...
by arango
Sun Feb 10, 2019 1:14 am
Forum: Ocean News
Topic: Walter Munk (1917-2019)
Replies: 0
Views: 2526

Walter Munk (1917-2019)

The oceanography community and the world lost one of its most renowned scientists. Walter Munk was 101. I met Walter in the mid-'80s when I was a graduate student at Texas A&M University. He visited and gave us an excellent Seminar/Lecture. My thesis advisor Robert O. Reid introduced me to him. ...
by arango
Fri Feb 01, 2019 6:51 pm
Forum: ROMS Results
Topic: ROMS Granular model result in all variables
Replies: 8
Views: 3388

Re: ROMS Granular model result in all variables

:shock: Well, that's your problem. You are using biharmonic diffusivity (m4/s), which scales as 1/12 * ABS(U) * (dx ** 3) . A value for TS_DIF4 of 2 m4/s is too small :!: You need values of the order of 2.0d+8 m4/s . That is, you are using a value that is eight orders of magnitude too small :!: No w...
by arango
Thu Jan 31, 2019 9:09 pm
Forum: ROMS Results
Topic: ROMS Granular model result in all variables
Replies: 8
Views: 3388

Re: ROMS Granular model result in all variables

I guess that the more fundamental question is what type of horizontal advection are you using? Are you specifying explicit diffusion and viscosity? What do you specify for vertical diffusion/viscosity parameterization closure? You should compute your Reynolds Number (U dx/nu), where U is the maximum...
by arango
Tue Jan 22, 2019 10:35 pm
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 5588

Re: My ROMS

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

Thank you.
by arango
Tue Jan 22, 2019 9:22 pm
Forum: ROMS Bugs
Topic: Issue restarting solutions in fraction of a day
Replies: 1
Views: 1217

Re: Issue restarting solutions in fraction of a day

Indeed, good catch :!: Thank you for reporting this bug. I will update the code soon.
by arango
Tue Jan 22, 2019 7:24 pm
Forum: ROMS Bugs
Topic: tiny bugs? in metrics.F and nesting.F
Replies: 1
Views: 1209

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

Thank you for reporting this problem. I forgot to take care of the roundoff issues with the interpolation weights when I implemented the single precision ( SINGLE_PRECISION option) simulations. Your suggested solutions are incorrect :!: We cannot take the ABS value when computing the interpolation w...
by arango
Sat Dec 15, 2018 8:53 pm
Forum: ROMS Bugs
Topic: Equation error in GLS model coded into gls_corstep.F
Replies: 5
Views: 2195

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

I haven't updated the code yet. I think that Ramsey Harcourt is correct. The shape functions used in mostly all vertical mixing parameterization should be smooth and continuous. We should stay away from sharp discontinuities that lead to eye bullet values in vertical diffusion and vertical viscosity...
by arango
Fri Dec 14, 2018 8:32 pm
Forum: ROMS Bugs
Topic: Equation error in GLS model coded into gls_corstep.F
Replies: 5
Views: 2195

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

Thank you for looking this carefully and for providing a Matlab script to show the difference between the formulation currently coded in ROMS and the correction to the limiter (green curve). Obviously, the coded formulation has a discontinuity spike just before it remains constant. It is clearly wro...
by arango
Mon Dec 03, 2018 2:14 am
Forum: ROMS Problems
Topic: 'nfast' and 'ndtfast' on Barotropic time step
Replies: 5
Views: 2457

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

Again, Nope :!: The governing equations are timestep from n (right-hand-side terms) to n+1 (left-hand-side term: time rate of change). The vertically-integrated equations are integrated with smaller timestep to resolve fast dynamics due to gravity wave phenomena. For 3D total momentum coupling, the ...
by arango
Sun Dec 02, 2018 4:19 pm
Forum: ROMS Problems
Topic: 'nfast' and 'ndtfast' on Barotropic time step
Replies: 5
Views: 2457

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

Nope , there are actually M* barotropic timesteps :!: The reason for it is that the cosine-square shape filter needs to provide time-averaged values of ubar , vbar , and zeta centered at the n+1 baroclinic timestep, which gives us second-order temporal accuracy for time-averaged barotropic motions....
by arango
Wed Nov 14, 2018 5:00 pm
Forum: ROMS Bugs
Topic: tiny little bug in get_state.F for time evolving bathymetry
Replies: 2
Views: 1371

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

Done. Thank you for reporting this typo.
by arango
Fri Nov 09, 2018 2:43 pm
Forum: ROMS Bugs
Topic: Error compiling ROMS with new flag SINGLE_PRECISION (svn928)
Replies: 7
Views: 3098

Re: Error compiling ROMS with new flag SINGLE_PRECISION (svn

Nope. What I said above is correct :!: If the last argument to the mp_bcastf routine is single- precision it will use mp_bcast_1d , and if it is double-precision it will use mp_bcastf_1dp . Just look the subroutines in distribute.F :idea: If you don't understard, you need to check a Fortran 1990, 19...
by arango
Wed Nov 07, 2018 9:16 pm
Forum: ROMS Bugs
Topic: Error compiling ROMS with new flag SINGLE_PRECISION (svn928)
Replies: 7
Views: 3098

Re: Error compiling ROMS with new flag SINGLE_PRECISION (svn

You are doing something wrong or something is weird with the compiler. You need to read carefully the following :arrow: trac ticket . Notice that even if SINGLE_PRECISION is activated, there are several variables that are still in double precision ( dp 64-bit kind parameter) and the r8 kind paramete...
by arango
Mon Oct 01, 2018 4:10 pm
Forum: ROMS Discussion
Topic: missing temp_time
Replies: 2
Views: 1290

Re: missing temp_time

You don't need to do that. One of the great things about NetCDF is that it is self-described. I have mentioned in the past that we need to follow CF convections to guarantee the functionality of metadata and avoid missinterpretation issues in ROMS. I highly recommend users to add the units , time , ...
by arango
Fri Sep 28, 2018 7:50 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 4822

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

I am going to try again for the last time. Read carefully :arrow: trac ticket 747 . In the older version of the code, we choose either lower- or higher-level MPI function for exchanges. We no longer do that in the newer versions, you need to experiment and select which options are more efficient in ...
by arango
Thu Sep 27, 2018 1:53 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 4822

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

I think that you need to read the following :arrow: trac ticket and choose the MPI communication options that are more efficient in the computer environment that you are running. You should check the profiling information that ROMS reports to standard output to see in what region of the code are slo...
by arango
Wed Sep 26, 2018 10:08 pm
Forum: ROMS Discussion
Topic: ROMS history file has suddenly included restart record
Replies: 7
Views: 2352

Re: ROMS history file has suddenly included restart record

Hmmm, I haven't had the time to examine the issue that you are having. I haven't modified this part of the code in years. I use the split of history files frequently and I have never observed the behavior that you are reporting. I wonder if it is a matter of configuration. Are you changing DSTART ev...
by arango
Wed Sep 26, 2018 10:00 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 4822

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

Yes, your problem is the stack size per CPU and it seems to be associated with the automatic arrays used in distributed-memory for I/O operations. This is not a direct ROMS problem, but a computer problem because of not enough memory to handle automatic arrays that are either allocated on stack or h...
by arango
Tue Sep 25, 2018 1:48 pm
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 4822

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

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

Code: Select all

.cshrc, .tcshrc, etc.

limit stacksize unlimited

or  .bashrc

ulimit -s unlimited 
I wrote lots of information in previous :arrow: trac ticket.
by arango
Sat Sep 22, 2018 6:18 am
Forum: ROMS Problems
Topic: severe (174): SIGSEGV, segmentation fault occurred. libpthre
Replies: 13
Views: 4822

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

Nowadays, severe segmentation errors are associated with stack size, which is used for allocating automatic arrays. They are allocated on stack or heap according to you choice of compiler options. I mentioned this in the last trac ticket.
by arango
Thu Sep 13, 2018 9:12 pm
Forum: ROMS Bugs
Topic: Small bugs in CPP BIO_FENNEL with DIAG and DIAGNOSTICS_BIO
Replies: 2
Views: 1508

Re: Small bugs in CPP BIO_FENNEL with DIAG and DIAGNOSTICS_

Nope. That's not what I have in the repository for def_diags.F : # ifdef DIAGNOSTICS_BIO # if defined BIO_FENNEL || defined HYPOXIA_SRM DO ivar=1,NDbio2d ifield=iDbio2(ivar) IF (TRIM(var_name(i)).eq.TRIM(Vname(1,ifield))) THEN got_var(ifield)=.TRUE. DIA(ng)%Vid(ifield)=var_id(i) END IF END DO # endi...
by arango
Tue Sep 11, 2018 9:23 pm
Forum: ROMS Bugs
Topic: bug in mod_tides.F
Replies: 1
Views: 1195

Re: bug in mod_tides.F

Indeed, thank you. I have more stuff to update in the computation of ROMS memory requirements. I am missing arrays to account for. I am trying to come up with the best estimate.
by arango
Mon Sep 10, 2018 7:25 pm
Forum: ROMS Discussion
Topic: ROMS prestep3d , Crack-Nicolson method, lambda
Replies: 1
Views: 986

Re: ROMS prestep3d , Crack-Nicolson method, lambda

Yes, we need to update the documentation.
by arango
Fri Aug 31, 2018 9:00 pm
Forum: ROMS Discussion
Topic: Cannot find "coordinates" attribute for variable: Uwind
Replies: 15
Views: 4100

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

The ECMWF data has a minimal interval of 3 hours; you can easily create annual files instead monthly. It will be more efficient in ROMS to avoid inquiring and open so many NetCDF files. The time units for forcing file is usually days since the reference date ( epoch ). However, you can have any time...
by arango
Sun Aug 26, 2018 3:44 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 6331

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

Okay, that will do it. I put safeguards to the code when processing standard input file ocean.in . I made a couple of updates recently for it. It looks that your grid is not for a regional application, but it is a global grid. Is that correct? If that's the case, you have a problem with the design o...
by arango
Wed Aug 22, 2018 2:07 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 6331

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

It is a weird error if you didn't repeat the NtileJ parameter in ocean.in , which triggers the allocation of several modules. In yesterday update, I put safeguards for this to never happen. I don't know what to make of your case. I don't think that a corrupted ocean.in should trigger to process the ...
by arango
Mon Aug 20, 2018 4:58 pm
Forum: ROMS Discussion
Topic: How to setup for rotating frame
Replies: 10
Views: 3026

Re: How to setup for rotating frame

It is weird that you are not activating periodic boundary conditions in the south and northern boundaries :!: It is the perfect and appropriate case for it because your grid is an annulus :roll: You can set the desired flow in the initial condition instead of using Flather boundary conditions. If yo...
by arango
Mon Aug 13, 2018 6:08 pm
Forum: ROMS Discussion
Topic: blowing up on nested grid
Replies: 5
Views: 2135

Re: blowing up on nested grid

That can be also a problem. However, the main issue here is that there are one or more grid cells with a value of 1E+40 1/km for both inverse metric factors pm and pn . We cannot multiply those variables with the mask because of division by zero in ROMS. The grid spacing ( DX=1/pm and DY=1/pn ) is a...
by arango
Sun Aug 12, 2018 3:36 pm
Forum: ROMS Discussion
Topic: blowing up on nested grid
Replies: 5
Views: 2135

Re: blowing up on nested grid

The information is in the front of you. If you don't understand that information, you have homework to do before running ROMS. Look the large and a small numbers. Check your grid files. ( DXmin , DYmin ) cannot be zero!!! It is a trillion times smaller than the scales of electrons... I am sure that ...
by arango
Sun Jul 29, 2018 4:38 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 4447

Re: huge memory per node when up scaling application

I usually put lots of information in trac when I update the code. We have noticed that this information is generally ignored and our emails are treated as spam. There is nothing that we can do about it, and we cannot force users to update and or read the detailed information provided. We have thousa...
by arango
Fri Jul 27, 2018 8:00 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 4447

Re: huge memory per node when up scaling application

PARALLEL_IO works for me. You need to use a recent version of the code. Also, make sure that all your input NetCDF files are NetCDF-4 format. You can check which format you have using ncdump : % ncdump -k filename.nc netCDF-4 To convert from NetCDF-3 to Netcdf-4 try: % nccopy -k netCDF-4 nc3name.nc...
by arango
Wed Jul 25, 2018 4:30 pm
Forum: ROMS Problems
Topic: huge memory per node when up scaling application
Replies: 14
Views: 4447

Re: huge memory per node when up scaling application

First, I don't think that ROMS will run with the PNETCDF library. It will need special function calls in ROMS. I never tried that library, it is a third party library. If you use PARALLEL_IO, you need to compile with the NetCDF-4 library with parallel MPI I/O and HDF5 support and your computer need ...
by arango
Wed Jul 18, 2018 9:43 pm
Forum: ROMS Problems
Topic: Problem generating contact file with three refined grids
Replies: 5
Views: 2416

Re: Problem generating contact file with three refined grids

Hi Marc and John,

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

Please update. Your particular set-up should work now.
by arango
Tue May 22, 2018 7:05 am
Forum: ROMS Bugs
Topic: ifort compile (make) error
Replies: 4
Views: 2334

Re: ifort compile (make) error

Yes, it is Darwin configuration that needs it. As Kate said, just comment the line in the Linux-ifort configuration file. Linux will take the unlimited value from the environmental variable. It is the loader LD that it is having the problem. It depends on what you have in your computer.
by arango
Thu Apr 26, 2018 7:04 pm
Forum: ROMS Problems
Topic: unable to open existing NetCDF file GET GRID
Replies: 10
Views: 2676

Re: unable to open existing NetCDF file GET GRID

By the way, you don't need to modify that routine. ROMS prints out the NetCDF error code at the end of the standard output file when it closes all the files. Notice that there are NetCDF-3 and NetCDF-4 input files for this application. You may be using the wrong one for the compiled code.
by arango
Fri Mar 30, 2018 5:54 pm
Forum: ROMS Problems
Topic: Could not read in multiple boundary files correctly
Replies: 2
Views: 1416

Re: Could not read in multiple boundary files correctly

You need to provide more information. The new inquiry.F was modified to provide the correct transition between annual files.
by arango
Wed Feb 28, 2018 5:30 pm
Forum: ROMS Problems
Topic: Contact point problem with salinity in Two Way Nesting run
Replies: 6
Views: 3028

Re: Contact point problem with salinity in Two Way Nesting r

I haven't noticed this in my applications that have run stable for years. Are you using those three refinement grids? If so, one of the refined grids is touching the boundary of the other. That will affect the order of the contact points between them. It is the chicken and egg question, what came fi...
by arango
Tue Feb 20, 2018 3:54 pm
Forum: ROMS Bugs
Topic: List of analytical header files
Replies: 3
Views: 1742

Re: List of analytical header files

It cannot be done during initialization because the CPP include syntax <*****.h> allows to use the header files from user's directories other than ROMS/Functionals . Notice that in analytical.F , we have # ifdef SOLVE3D # if defined ANA_BIOLOGY && defined BIOLOGY # include <ana_biology.h> # ...
by arango
Tue Feb 20, 2018 5:30 am
Forum: ROMS Bugs
Topic: List of analytical header files
Replies: 3
Views: 1742

Re: List of analytical header files

There is a reason for it that I need to remember exactly. It is not a bug, but why does it matter? I think that it has to do with with the global attributes of output NetCDF files and the fact that the user can overwrite the location of the code header files instead of using the ones distributed by ...
by arango
Tue Dec 12, 2017 6:35 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 7897

Re: CPU time and MPI issues with nested grids

Yes, you need to select a better option for MPI communications as I mentioned yesterday. Check the information on the svn trac ticket. If you are using too many processes for this application, the data exchanges due to nesting is a bottleneck. See the number for point data gathering . It explains th...
by arango
Tue Dec 12, 2017 1:24 am
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 7897

Re: CPU time and MPI issues with nested grids

Maybe your application is not big enough to justify 144 nodes, and your application is slowing down because of excessive MPI communications. It is a critical issue that some users ignore always. There is always an optimal parallel partition for each ROMS application. Now if you are using a recent ve...
by arango
Sat Dec 09, 2017 5:27 pm
Forum: ROMS Bugs
Topic: A little bug in get_cycle.F of src 884 and the fixing
Replies: 5
Views: 3264

Re: A little bug in get_cycle.F of src 884 and the fixing

Do you have the cycle_length attribute in the time variable? For the forward time-stepping, we can also have the following logic in get_cycle.F: IF (job.gt.0) THEN ! forward: Tval(i) =< mday =< Tval(i+1) IF (Linside) THEN tstart=Tmin DO i=2,ntime IF ((tstart.le.mday).and.(mday.le.Tval(i))) THEN Tstr...
by arango
Fri Dec 08, 2017 5:07 pm
Forum: ROMS Bugs
Topic: A little bug in get_cycle.F of src 884 and the fixing
Replies: 5
Views: 3264

Re: A little bug in get_cycle.F of src 884 and the fixing

Something is weird here. It doesn't make sense to me. Notice that the logic in get_cycle.F that set the switches is: ! ! Is the model time inside the data time range? If not, check if the ! data just has the LOWER- or the UPPER-snapshot interpolant. ! IF ((Tmin.le.mday).and.(mday.le.Tmax)) THEN Lins...
by arango
Tue Nov 21, 2017 6:32 pm
Forum: ROMS Bugs
Topic: Bug in output time step in DEF_DIAGS after restart
Replies: 5
Views: 3737

Re: Bug in output time step in DEF_DIAGS after restart

Smaller values of NDIA are possible but its value needs to be an exact factor of NRST, say NDIA=NRST/2 should give you an integer. The time window (in seconds) should be exactly divided by DT.
by arango
Fri Nov 17, 2017 6:26 pm
Forum: ROMS Bugs
Topic: Bug in output time step in DEF_DIAGS after restart
Replies: 5
Views: 3737

Re: Bug in output time step in DEF_DIAGS after restart

Well, this logic has worked for us for years. Your problem is that NAVG and NDIA are inconsistent with NRST . If you have AVERAGES and DIAGNOSTICS_TS and/or DIAGNOSTICS_UV activated, you need to set NAVG=NDIA . It doesn't make any sense to have different values because if you are going to compute ba...
by arango
Tue Sep 26, 2017 1:24 am
Forum: ROMS Problems
Topic: mp_collect bug when compiling with define PARALLEL_IO
Replies: 18
Views: 7147

Re: mp_collect bug when compiling with define PARALLEL_IO

The PARALLEL_IO is slower than serial I/O, and it won't help you to improve I/O performance. The last time that I checked that option, it was not working well, and I haven't checked if the NetCDF4 library has made progress on it. I can fix the issue with nf_read2d.F but it will not help you much. Th...
by arango
Tue Aug 29, 2017 4:27 pm
Forum: ROMS Problems
Topic: Error in ROMS execution
Replies: 7
Views: 2519

Re: Error in ROMS execution

You cannot change those values capriciously. They have to be exactly the same values used by the person that generated the initial conditions, boundary conditions, atmospheric forcing, and observations for data assimilation. The time clock has to be the same in all those files for consistency. The t...
by arango
Mon Aug 28, 2017 7:35 pm
Forum: ROMS Problems
Topic: Error in ROMS execution
Replies: 7
Views: 2519

Re: Error in ROMS execution

There is a weird set-up of the ROMS time clock here. You need to ask the person that set-up this application. First, the input parameters: 13295.000 dstart Time-stamp assigned to model initialization (days). 19000101.00 time_ref Reference time for units attribute (yyyymmdd.dd) It implies that the RO...
by arango
Mon Aug 28, 2017 4:36 pm
Forum: ROMS Problems
Topic: Error in ROMS execution
Replies: 7
Views: 2519

Re: Error in ROMS execution

Provide more information from the log file, not just the end. If you are using the latest version of ROMS, there is detailed information in the log file with source code and line number where the error occurred.
by arango
Tue Jul 11, 2017 10:10 pm
Forum: ROMS Benchmarks
Topic: Understanding ROMS output
Replies: 5
Views: 3440

Re: Understanding ROMS output

Yes, the primal formulation I4DVAR is very expensive because the minimization is done in the physical space (i.e. full application grid for the state vector, 10^5 to 10^7 points) so we need to do a lot of I/O manipulations in cgradient to compute and orthogonalize the Lanczos vectors. We need to rea...
by arango
Mon Jul 10, 2017 2:27 pm
Forum: ROMS Benchmarks
Topic: Understanding ROMS output
Replies: 5
Views: 3440

Re: Understanding ROMS output

What do you mean by the Lanczos algorithm? Are you talking about the minimization routine, rpcg_lanzos (RPCG)? The Lanczos vectors are stored in a NetCDF and use the adjoint model iterations over all outer and inner loops. I recently profiled WC13 with W4DPSAS : Nouter=2 and Ninner=50 on 4 CPUs on m...
by arango
Wed Jun 07, 2017 6:14 pm
Forum: Job Opportunities
Topic: Postdoctoral Research Position at UCLA
Replies: 0
Views: 2159

Postdoctoral Research Position at UCLA

Postdoctoral Researcher Position in Continental Shelf Currents and Their Surface Wave Interactions Departments of Atmospheric and Oceanic Sciences University of California, Los Angeles (UCLA) We are seeking a researcher to work on problems of oceanic circulation dynamics using the Regional Oceanic ...
by arango
Fri May 26, 2017 8:17 pm
Forum: ROMS Bugs
Topic: A new Y2K bug!
Replies: 2
Views: 2270

Re: A new Y2K bug!

Fixed the bug. It was not a Y2K bug. I coded datevec incorrectly in module dateclock.F . I was able to reproduce your problem with a simple test. Now, I get: 1 2000-02-28 00:02:30.00 9.193018E-09 1.954312E+04 1.954312E+04 1.659839E+17 (001,32,30) 1.799562E-05 8.159871E-10 0.000000E+00 4.667957E-03 2...
by arango
Thu May 25, 2017 11:04 pm
Forum: ROMS Bugs
Topic: A new Y2K bug!
Replies: 2
Views: 2270

Re: A new Y2K bug!

Weird. What calendar are you using? The behavior of your time reporting indicates to me that you are using the Proleptic Gregorian Calendar ( time_ref=0 or time_ref>0 ). The datenum and datevec routines in ROMS starts in in March 1, 0000 to facilitate the management of leap years: MyMonth=MOD(month+...
by arango
Sat Apr 29, 2017 2:00 pm
Forum: ROMS Installation
Topic: ran_state compilation error in ROMS
Replies: 5
Views: 2937

Re: ran_state compilation error in ROMS

Weird, I compiled with ifort , gfortran , and pgi and didn't get those errors. It turns out that I missed to transfer the updated files gasdev.F , nrutil.F , and ran1.F when I committed the ticket in another computer. We need these files to have i8b instead i4b . This is the reason why you are havin...
by arango
Wed Apr 26, 2017 8:22 pm
Forum: ROMS Ecosystem
Topic: Compiling error: dateclock?
Replies: 5
Views: 3196

Re: Compiling error: dateclock?

Yes, thank you for reporting this one. The weird thing is that I ran and debugged ( TotalView ) this version several times with the ifort compiler and didn't report any errors or warnings. It seems to be happy with the dot syntax. Of course, the correct syntax in Fortran is to use Rclock % . This ha...
by arango
Fri Apr 14, 2017 8:29 pm
Forum: ROMS Adjoint
Topic: nonlinear cost function not calculated in PSAS
Replies: 2
Views: 1962

Re: nonlinear cost function not calculated in PSAS

What are you reporting does not make sense to me. The NL_iDataPenalty and NL_fDataPenalty is computed and any of the 4D-Var drivers; w4dpsas_ocean.h in your case. In none of those drivers the VERIFICATION option is used. You just need to use the grep command to confirn this. The definition of these ...
by arango
Fri Apr 14, 2017 6:46 pm
Forum: ROMS Discussion
Topic: ROMS not bit-reproducible: northern boundary?
Replies: 32
Views: 11148

Re: ROMS not bit-reproducible: northern boundary?

Well, it seems that there is a problem with the latest version of OpenMPI . I wonder what did they change. This kind of problem is difficult to track and frustrating. Compilers and libraries are known to have bugs. One thing to check is if the OpenMPI library was compiled correctly with the same com...
by arango
Wed Jan 25, 2017 11:17 pm
Forum: ROMS Bugs
Topic: History file output fails using WRITE_WATER and river inflow
Replies: 2
Views: 3019

Re: History file output fails using WRITE_WATER and river in

Good catch, thank you :!: I updated the repository. Check the following :arrow: trac ticket for more information.
by arango
Tue Jan 24, 2017 3:18 am
Forum: ROMS Bugs
Topic: Error in Flux Integrals in Correct_Tracer - two-way nesting
Replies: 1
Views: 6007

Re: Error in Flux Integrals in Correct_Tracer - two-way nest

Yes, thank you very much for reporting this problem with great detail and providing a solution :!: I know that this kind of problems are kind of frustrating and takes a lot of patience to find them. It is refreshing when users get deep into the code and try to understand and find solutions to the pr...
by arango
Tue Jan 24, 2017 2:51 am
Forum: ROMS Bugs
Topic: Error with Multifiles
Replies: 9
Views: 8303

Re: Error with Multifiles

Yes, thank you for reporting this. It is difficult to guess the length of that string. I set it to 4096. See the following :arrow: trac ticket for more information.
by arango
Tue Jan 24, 2017 2:44 am
Forum: ROMS Bugs
Topic: Quicksave bug
Replies: 1
Views: 1877

Re: Quicksave bug

Yes, thank you. It is always a good strategy to initialize all the switches and variables. I updated the repository. For more information check the following :arrow: trac ticket.
by arango
Tue Jan 24, 2017 1:50 am
Forum: ROMS Bugs
Topic: A possible bug in get_data.F
Replies: 1
Views: 7491

Re: A possible bug in get_data.F

Yes, I can see why some compilers may have problems with this type of syntax. Thank you for reporting this issue. This is now fixed. See following :arrow: trac ticket.
by arango
Mon Oct 10, 2016 7:48 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, 4D-Var Tutorial Slides
Replies: 0
Views: 7663

2016 ROMS Asia-Pacific Workshop, 4D-Var Tutorial Slides

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 20, 2016 Andrew M. Moore will be giving a half day tutorial on ROMS 4D-Var. We are posting the slides for this presentation :arrow: here ahead of time so attendees can...
by arango
Tue Oct 04, 2016 5:03 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - Final Notice
Replies: 0
Views: 5457

2016 ROMS Asia-Pacific Workshop, Tasmania - Final Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 20, 2016 We have had several cancellations, making it necessary to rework the agenda. If you are presenting , please check :arrow: the agenda again as your presentatio...
by arango
Fri Sep 23, 2016 4:41 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS/TOMS Workshop T-shirt
Replies: 0
Views: 5664

2016 ROMS/TOMS Workshop T-shirt

This is our design for the ROMS T-shirt for the upcoming Asia-Pacific Workshop. The front is the an artistic rendition of the Hobart skyline with Mt. Wellington as a backdrop.
front.png
front.png (197.79 KiB) Viewed 5664 times
back.png
back.png (179.06 KiB) Viewed 5664 times
sleeve.png
sleeve.png (135.73 KiB) Viewed 5664 times
front_detail.png
front_detail.png (17.64 KiB) Viewed 5664 times
back_detail.png
sleeve_detail.png
sleeve_detail.png (2.24 KiB) Viewed 5664 times
by arango
Fri Sep 23, 2016 3:00 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 5th Notice
Replies: 0
Views: 5185

2016 ROMS Asia-Pacific Workshop, Tasmania - 5th Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 20, 2016 :!: NOTE: :!: Due to scheduling conflicts with other meetings the workshop has been compressed into 4 days. We apologize for the late notice on this. Please r...
by arango
Wed Aug 17, 2016 2:11 am
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 4th Notice
Replies: 0
Views: 6350

2016 ROMS Asia-Pacific Workshop, Tasmania - 4th Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 21, 2016 This is a reminder that the abstract deadline has passed. Please check the :arrow: participants list to confirm that your abstract has been submitted. If your...
by arango
Wed Aug 10, 2016 2:11 pm
Forum: ROMS Bugs
Topic: ROMS attempts to close un-named files
Replies: 3
Views: 4474

Re: ROMS attempts to close un-named files

Yes, please update. The error is due to the lack of the QCKNAME keyword in ocean.in . Notice that in :arrow: ticket 706 the field for NetCDF file ID, XXX%ncid=-1 , is initialized to close state in all the I/O structure arrays. This will allow to run newest ROMS version with old input ocean.in scripts.
by arango
Wed Jul 27, 2016 3:56 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 3rd Notice
Replies: 0
Views: 7036

2016 ROMS Asia-Pacific Workshop, Tasmania - 3rd Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 21, 2016 The extended registration deadline for the 2016 ROMS/TOMS Asia-Pacific Workshop is less than a week away. This is a reminder that registration deadline was ex...
by arango
Fri Jul 15, 2016 2:12 pm
Forum: ROMS Tools and Techniques
Topic: standard_name for U,V current components
Replies: 6
Views: 5409

Re: standard_name for U,V current components

Nope. It is not a vertical sum divided by the number of levels. It is a matter of semantics here. Perhaps, depth-averaged will be more appropriate. The shallow water equations are obtained by vertically integrating momentum and continuity equations in flux form. In curvilinear coordinates (xi, eta) ...
by arango
Thu Jul 14, 2016 5:06 pm
Forum: ROMS Tools and Techniques
Topic: standard_name for U,V current components
Replies: 6
Views: 5409

Re: standard_name for U,V current components

Nope, this cannot be done in varinfo.dat . I have thought about this in the past but we have so many variables. However, I can see how this is important for velocity components and third-party potting tools. It is very easy to add the standard_name to the variables in def_avg.F and def_his.F . We ju...
by arango
Thu Jun 09, 2016 5:55 pm
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 2nd Notice
Replies: 0
Views: 8072

2016 ROMS Asia-Pacific Workshop, Tasmania - 2nd Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 21, 2016 The registration deadline for the 2016 ROMS/TOMS Asia-Pacific Workshop is approaching. This is a reminder that registration is open until June 30, 2016 . The ...
by arango
Thu Apr 21, 2016 3:38 pm
Forum: ROMS Bugs
Topic: Bug with grid coordinates for station file
Replies: 2
Views: 2757

Re: Bug with grid coordinates for station file

Thank you. I have to think about this. I need to reproduce your problem so I can look in the debugger.
by arango
Fri Feb 19, 2016 10:15 pm
Forum: ROMS Problems
Topic: Unrealisitic thickness of mixed layer
Replies: 15
Views: 13201

Re: Unrealisitic thickness of mixed layer

The MY2.5 scheme is coded correctly in ROMS and has several corrections that are not available in the original published formulation of the Mellor-Yamada 2.5. There are several papers in the literature about this. Also some people argue that the MY2.5 was not originally formulated correctly and the ...
by arango
Fri Feb 19, 2016 3:38 am
Forum: Meetings/Workshops
Topic: 2016 ROMS Asia-Pacific Workshop, Tasmania - 1st Notice
Replies: 0
Views: 5017

2016 ROMS Asia-Pacific Workshop, Tasmania - 1st Notice

2016 ROMS/TOMS Asia-Pacific Workshop Institute for Marine and Antarctic Studies Hobart Waterfront, Tasmania, Australia October 17 - 21, 2016 We are inviting you to participate at the 2016 ROMS Asia-Pacific Workshop to be held at the Institute for Marine and Antarctic Studies building on the Hobart ...
by arango
Thu Oct 29, 2015 2:54 pm
Forum: ROMS Problems
Topic: MP_EXCHANGE2D - communication buffer too small
Replies: 6
Views: 4648

Re: MP_EXCHANGE2D - communication buffer too small

This is not related to earlier posts in this forum thread. Anyway, this is weird. If you added biology, only mp_exchange4d is used in just two routines: pre_step3d.F: # ifdef DISTRIBUTE CALL mp_exchange4d (ng, tile, iNLM, 1, & & LBi, UBi, LBj, UBj, 1, N(ng), 1, NT(ng), & & NghostPoin...
by arango
Fri Oct 02, 2015 4:19 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 7897

Re: CPU time and MPI issues with nested grids

That's good that you guys use the full stencil at the interface to compute the mass fluxes entering the refined grid. I haven't observed smoothness problems in my testing applications with one-way nesting and 1:5 ratios. Anyway, we should always use two-way nesting since the one-way interaction has ...
by arango
Mon Sep 21, 2015 6:53 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 7897

Re: CPU time and MPI issues with nested grids

We need to take into account that ROMS_AGRIF has a reduced and simpler barotropic stepping engine ( step2d.F ), so it is more efficient. Therefore, we are not comparing apples with apples. Rutgers version of step2d.F includes additional terms so it is slower. In ROMS_AGRIF, all of those terms are in...
by arango
Fri Sep 18, 2015 1:15 pm
Forum: ROMS Problems
Topic: Online Nesting slow
Replies: 5
Views: 3698

Re: Online Nesting slow

What is the size of your grids? Also, what are the partitions that you are using? I want to be sure that you are not using excessive parallel nodes. There is always an optimal partition in ROMS. This is computer engineering and we should abstain to put a lot of processes just because they are availa...
by arango
Wed Sep 16, 2015 2:15 am
Forum: ROMS Installation
Topic: Can ROMS run just in Matlab?
Replies: 2
Views: 2903

Re: Can ROMS run just in Matlab?

Absolutely not. Why do you want to do such a thing? ROMS has over a million lines of code. There are ways to run simple and small Fortran programs in Matlab but the capability is very limited and you need to write an interface.
by arango
Fri Sep 11, 2015 10:47 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 6142

Re: two-way nesting only in the first refined grid

Please update. I fixed the problem that you were having. See the following :arrow: trac ticket for details. Thank you for reporting this problem :!:
by arango
Thu Sep 10, 2015 7:57 pm
Forum: ROMS Problems
Topic: Online Nesting slow
Replies: 5
Views: 3698

Re: Online Nesting slow

Yes, we are aware of this and it is in our TO-DO list. The issue here is that in two-way nesting (default) we are currently making global gathering of data (full 2D and 3D arrays) between all the MPI nodes to compute easily the fine-to-coarse averaging. This causes a bottle neck because of the exces...
by arango
Wed Sep 09, 2015 2:59 pm
Forum: ROMS Problems
Topic: Bug in large spherical nested run?
Replies: 5
Views: 3113

Re: Bug in large spherical nested run?

I have a new version of the Matlab scripts that I haven't released yet. I am still thinking about them. They are experimental and I will send them to your e-mail latter today. It provides alternatives to computing the metrics via interpolation instead of the great circle formula. Please sent me an e...
by arango
Tue Sep 08, 2015 5:09 pm
Forum: ROMS Problems
Topic: Bug in large spherical nested run?
Replies: 5
Views: 3113

Re: Bug in large spherical nested run?

Thanks Jamie for the detailed information. I have to think about this one. Obviously, the spherical grid is doing something to it. It makes me suspicious of the area/volume conservation. I wonder if the grid spacing (area) between coarse and fine grids is conserved in the sherical case. I assume tha...
by arango
Sat Sep 05, 2015 3:17 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 6142

Re: two-way nesting only in the first refined grid

I will have to reproduce this problem with a test case to see what it is going on. Your fix to main3d.F is not correct.
by arango
Fri Sep 04, 2015 10:10 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 6142

Re: two-way nesting only in the first refined grid

Refined grid by a factor of 4 is illegal. I don't know why contact.m allowed you to work by such a factor. You should get an error warning and stop. You only can have refimnement ratios of 3 , 5 , 7 , 9 , etc in ROMS because it is discritized on a C-grid . As a matter of dynamics and because of nume...
by arango
Fri Sep 04, 2015 5:47 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 6142

Re: two-way nesting only in the first refined grid

Perhaps, you should show us a diagram (plot) of all grids and their refinement ratio with respect the donor grid to check if you are setting the grids correctly.
by arango
Fri Sep 04, 2015 4:24 pm
Forum: ROMS Problems
Topic: two-way nesting only in the first refined grid
Replies: 12
Views: 6142

Re: two-way nesting only in the first refined grid

Nope, this is not a good idea! because of the internal manipulations in several routine inside module nesting . It seems to me that you didn't specified the parameters correctly. The order of the grids are crucial. You need to think about the logical order when generating the contact NetCDF file wi...
by arango
Fri Sep 04, 2015 1:31 am
Forum: ROMS Bugs
Topic: bug in check_massflux in nesting.F
Replies: 2
Views: 2754

Re: bug in check_massflux in nesting.F

Yes, I did moved this code after I tested. Thank you for report this. I updated the repository. Nope, the values of BOUNDARY_CONTACT(:,:)%Mflux(:) are only used during debugging and testing to write several diagnostics to Fortran fort.100 , fort.200 , and fort.300 output files. Yes, they are loaded ...
by arango
Wed Aug 19, 2015 5:09 pm
Forum: ROMS Bugs
Topic: Bug in nesting when MASKING not defined
Replies: 1
Views: 2003

Re: Bug in nesting when MASKING not defined

Yep, good catch. Thank yTo be precise we need instead:

Code: Select all

# if defined MASKING || defined WET_DRY
      PRIVATE :: mask_hweights
# endif
I will update the code today.
by arango
Tue Jul 21, 2015 8:41 pm
Forum: ROMS Bugs
Topic: Bug in fine2coarse.m for nesting
Replies: 6
Views: 3433

Re: Bug in fine2coarse.m for nesting

There are two ways to construct refined nested grids: (1) coarse to fine grid refinement or (2) fine to coarse grid extraction. I prefer to do option (2) since all the quantities needed in the contact area are already available in the donor grid. If you don't see this, think about refinement and com...
by arango
Tue Jul 21, 2015 12:12 am
Forum: ROMS Usage
Topic: How to generate and use composite grids?
Replies: 16
Views: 10353

Re: How to generate and use composite grids?

Yes, it needs that information from the global attributes. Otherwise, contact.m will not work. These scripts are complex and there is a lot of internal details. They need to be used as a full package. I won't guarantee that a mixture of third party scripts will work together. There is a lot of subtl...
by arango
Mon Jul 20, 2015 7:06 pm
Forum: ROMS Usage
Topic: How to generate and use composite grids?
Replies: 16
Views: 10353

Re: How to generate and use composite grids?

That's your problem! You need to use Lmask=false when generating the contact points with the Matlab script. Please read the instructions! Notice that the default value is false . :idea: I have said several times in this forum that if we don't have experience in nesting applications for a particular ...
by arango
Thu Jul 16, 2015 7:02 pm
Forum: ROMS Bugs
Topic: Possible IO bug in close_io.F
Replies: 1
Views: 2101

Re: Possible IO bug in close_io.F

This is weird because close_inp is used in the adjoint-based algorithms to facilitate the iterations in the propagators and 4D-Var algorithms. This means that these files were already processed when reading input forcing fields. In the example that you provide above, which is exactly what I wrote in...
by arango
Thu Jul 16, 2015 6:29 pm
Forum: ROMS Bugs
Topic: Small bug in ad_v2dbc_im.F
Replies: 4
Views: 3084

Re: Small bug in ad_v2dbc_im.F

I don't know what are you talking about. I checked the code and it already have that correction! I think that you need to update. As you see below, ad_v2dbc_im.F already have the change as shown on :arrow: trac for Revision 767:
by arango
Thu Jul 16, 2015 5:15 pm
Forum: ROMS Problems
Topic: Create a sponge layer
Replies: 5
Views: 3925

Re: Create a sponge layer

I did a major overhaul of the sponge areas in ROMS sometime ago. We can have now visc_factor and diff_factor in the Grid NetCDF file. This is the way all application (simple or complex) that require areas of enhanced viscosity and diffusion. See the following :arrow: trac ticket for details. Notice ...
by arango
Thu Jul 16, 2015 4:35 pm
Forum: ROMS Wish List
Topic: Wish list
Replies: 2
Views: 2992

Re: Wish list

The nesting in ROMS (one- or two-way) is designed for all tracers active and passive. The nesting interface is generic for all tracers. The only constraint is that the bio-geochemical or sediment model needs to be activated in all grids in order to compute the contact point data between all grids (d...
by arango
Wed Apr 01, 2015 12:36 am
Forum: ROMS Bugs
Topic: Possible Issue with White_noise
Replies: 4
Views: 2741

Re: Possible Issue with White_noise

The routines in the white noise module white_noise.F are specific to the adjoint algorithms and we pass the Imin , Imax , Jmin , Jmax dummy variables as arguments. These are tiled parallel routines and need to be used by passing the appropriate values for these I- and J-range parameters. Using the a...