Ocean Modeling Discussion

rsignell

I know WRF runs on ARM architecture (e.g. https://aws.amazon.com/blogs/hpc/numerical-weather-prediction-on-aws-graviton2/).

To run on ARM, changes may be needed if code uses x86-specific instructions, and sometimes there are bugs that have been hidden that ARM uncovers.

So.... has anyone ...

rsignell

I just discovered this paper https://www.geosci-model-dev-discuss.net/gmd-2017-270/gmd-2017-270.pdf in which the authors use the AWS Elastic Network Adaptor (ENA) to deliver up to 20 Gbps with low latency. They were able to obtain similar performance compared to their 128 core HPC Cluster with ...

rsignell

Dear Colleagues,

We are pleased to announce that the 15th International Estuarine and Coastal Modeling Conference (ECM15) will be held in Seattle, WA, USA, June 25-27, 2018.

This conference provides a unique venue for academic, commercial and government scientists and engineers from around the ...

rsignell

We have a much more mature image that we use here at MetOcean nowadays to run ROMS in our internal systems. Ripping out the system-dependent stuff to create an opensource general purpose one wouldn't be too far fetched. I'd be happy to collaborate if there is interest.

@rsoutelino, that would be ...

rsignell

Has anyone developed a Docker container for ROMS?

I'm thinking the Dockerfile would be quite similar to WRF:
https://github.com/NCAR/container-wrf/b ... Dockerfile

rsignell

Charlie Zender's NCO tools (of "ncks" fame) have regridding capabilities, and they look quite capable, but also a bit complex. See: http://nco.sourceforge.net/nco.html#ncr ... F-Remapper. Has anyone tried using these to, say, regrid curvilinear ROMS output onto a uniform grid?

rsignell

I haven't tried GridBuilder, but from the documentation it looks pretty powerful, with SeaGrid's capabilities and then some. And even though available from a consulting company, it's free: http://austides.com/downloads/. If someone tries it, please report back to this thread!

rsignell

Uh, there is no interpolation going on there in the vertical section. If you want to plot color filled contours, just replace pcolormesh with contourf and contour , something like:
fig=figure(figsize=(12,10))
plt.contourf(lon3d[:,jval,irange],z[:,jval,irange],temp[:,jval,irange])
plt.colorbar()
plt ...

rsignell

I have a simple Jupyter notebook example using matplotlib here, does that help?
https://github.com/rsignell-usgs/notebo ... ture.ipynb

rsignell

So you must be using the flags to write out rotated velocity at grid cell centers, right?
For example:
Hout(idu3dE) == T ! u_eastward 3D U-eastward at RHO-points
Hout(idv3dN) == T ! v_northward 3D V-northward at RHO-points

For sure these should be using standard_name values from the official ...

rsignell

The USGS Sediment Transport Group in Woods Hole, MA, USA is looking for an oceanographer with modeling and analytic skills to support their research.
Salary range is: $92,448.00 to $120,187.00 / Per Year
Apply by Wednesday 7/20/2016.
Must be US Citizen.

See details and apply at:
https://www ...

rsignell

14th International Estuarine and Coastal Modeling Conference (ECM14) will be held in Kingston, Rhode Island, June 13-15, 2016.

This conference provides a unique venue for commercial, academic, and government scientists and engineers from around the world to present and discuss the latest results ...

rsignell

The 14th International Estuarine and Coastal Modeling Conference (ECM14) will be held in Kingston, Rhode Island, June 13-15, 2016.

This conference provides a unique venue for commercial, academic, and government scientists and engineers from around the world to present and discuss the latest ...

rsignell

"CSS-Dynamac seeks a full-time computational ecologist with expertise in computer programming, hydrodynamic modeling (especially the Regional Ocean Modeling System, ROMS), ecological modeling, and familiarity with high-performance computing systems. The successful candidate will join an ...

rsignell

Thanks John, that for sure is the fastest way!

Unfortunately we've got a bunch of existing ROMS output from different providers, so I'm still interested if anyone has a fast post-model-run solution, using NCO or otherwise.

rsignell

I was thinking of writing a script using NCO's NCAP2 to average the U,V velocity components to rho points and rotating to true east/north. Then I thought someone might already have done that. True?

And yes, I know how to do this in Matlab or Python. Was just looking for the fastest way.

rsignell

NCTOOLBOX is now on Github at http://nctoolbox.github.io/nctoolbox/. I recommend getting the stable ZIP or TAR release. Or you could just use ERDDAP, which requires installing nothing -- just using a web-form to grab the digital terrain model data you want (topo/bathy) and then save as Mat file. The ...

rsignell

I have updated the SEAGRID wikiroms page to point to the seagrid and RPSstuff toolboxes on Github instead of the no-longer-used SVN repository.

In addition to using read_strm30plus.m for bathymetry, I find that NOAA's ERDDAP is very useful for topography (as well as remote sensing and insitu data ...

rsignell

ROMS folk,

We tried using bzhang's harm_roms.m script to calculate the tidal amplitudes and phases from the AVERAGES_DETIDE output, but our amplitudes are more than a factor or 30 too high. bzhang couldn't see anything wrong. In case someone is willing to take a look, the output file is at:
http ...

rsignell

Excellent. I forgot one of the fundamentals of modeling: when in doubt, look at the code!

So if we are forcing with M2 only, but want to look at nonlinear tidal effects, we need to add M4, M6, M8 to the forcing file so that they get included in the least-squares fit, right?

rsignell

Looking at the output from a simulation run with the AVERAGES_DETIDE option, I see:

$ncdump -h bbleh_base_detide.nc

netcdf bbleh_base_detide {
dimensions:
xi_rho = 160 ;
eta_rho = 800 ;
tide_period = 9 ;
eta_u = 800 ;
eta_v = 799 ;
xi_v = 160 ;
xi_u = 159 ;
s_rho = 7 ;
harmonics = 19 ...

rsignell

I just received from Eric Anderson at GLERL:

The NOAA Great Lakes Environmental Research Lab (GLERL) is advertising for a Supervisory Scientist (Branch Chief) to lead our Modeling and Forecasting group. This is to fill the position previously held by Dave Schwab. The Branch Chief will be ...

rsignell

Seems like potentially a problem also knowing what the most up-to-date "pyroms" distribution is:

I see that on https://github.com/kshedstrom/pyroms, it says:
"Pyroms is a collection of tools to help with input and output files
from the Regional Ocean Modeling System (ROMS). It was originally ...

rsignell

Colleagues,

The 13th International Estuarine and Coastal Modeling Conference
(ECM13) will be held in San Diego, California, Nov 4-6, 2013.

This conference provides a unique venue for commercial, academic, and government scientists and engineers from around the world to present and discuss the ...

rsignell

With the large domain you are showing and with your target being a beach, I think you will need to take a nesting approach -- trying to use a single stretched curvilinear grid will not give you the resolution you want near the beach without creating high resolution in areas outside the area of ...

rsignell

One easy way to get netcdf4-python is to pick up the Enthought Python Distribution:
http://www.enthought.com/products/epd.php
The latest version (7.3) includes netcdf4-python built with OPeNDAP support and 100+ other packages as well. The key thing is it works the same on 32 and 64 bit versions of ...

rsignell

Unfortunately NASA took down the WMS site, but fortunately, it's easy to get
subsetted global and other bathymetry data using NCTOOLBOX:

1. Get NCTOOLBOX for Matlab (easy install at http://code.google.com/p/nctoolbox/)

2. Use the "geosubset" method to subset bathy data. For SRTM30PLUS, it would ...

rsignell

ROMS Folk,
Has anyone tried running ROMS on HPC Cloud (e.g. Amazon)? I was looking at the web page for High Performance Computing (HPC) on Amazon Web Services (AWS) and then watched this video on How to set up a 64 Core HPC system on AWS in 10 minutes . Looks easy and cool! Seems like it would be ...

rsignell

Gustavo,
I'm curious about why you chose VisIT over Mayavi or Paraview. Are there certain features you found there that make life easier for visualizing ROMS results?
Thanks,
Rich

rsignell

Gang,
Has anyone tried doing 3D visualization of ROMS output using Mayavi?

It looks like the underlying VTK data model might be capable of supporting the curvilinear grid, but don't know about the vertical:
http://www.vtk.org/Wiki/index.php?title=ParaView/Users_Guide/VTK_Data_Model#Curvilinear_Grid ...

rsignell

The function "gmean" just calculates the mean over the "good" (not NaN) values. If you google "m_cmg" and "gmean.m" you will find it. Please let me know if that delft2roms.m function you found works for you. I might not have completely finished it.

It would be interesting to compare this with Lyon ...

rsignell

Folks,

The application deadline for the 2011 Gordon Research Conference on Coastal Ocean Modeling (see John Wilkin's post https://www.myroms.org/forum/viewtopic.php?f=11&t=2194) is May 29, just 6 days away! This conference only happens once every four years, and most folks say it's the best ...

rsignell

Flavien,

I'm glad to see that you and others are working on this. This subject came up when discussing improvements to Elizabeth North's LTRANS particle tracking model, which would use the horizontal mixing in the deterministic model (e.g. ROMS) to specify the horizontal random walk parameters for ...

rsignell

Burchard & Rennau (Ocean Modeling 20 (2008) 293-311) have a simple way to calculate physical and numerical mixing of tracers in ocean models. The physical mixing is simply the rate of change in the turbulent mean tracer variance and the numerical mixing is simply the rate of change of the difference ...

rsignell

You need the netcdf_toolbox, which I just found out was removed from the instructions on the mexcdf page, because John Evans, who maintains these pages, doesn't want to support it. But it's still there:

Use SVN to get the latest mexnc, snctools and netcdf_toolbox and you should be good to go with ...

rsignell

After being conspicuously absent in 2009, ocean modelling is back on the agenda for EGU 2010 with its own session!

OS20 Ocean modelling: developments and applications
---------------------------------------------------
Convener: David Ham, Imperial College London
Co-Conveners: Anne Marie Treguier ...

rsignell

Charlie Barronvia, Richard Allardvia, and Patrick Hoganvia?

I had no idea so many Italians worked at NRL!

-Rich

rsignell

You don't really need to modify the SRTM script. Just read your topography NetCDF file using any Matlab/NetCDF tool (snctools, for example), and save off some subsampled set of points as xbathy, ybathy and zbathy in a mat file. Then you can use these points as the "bathymetry data" for seagrid just ...

rsignell

If you have used the "join_cst" Matlab routine to make your coastline segments continuous, you will find them sorted from longest piece to shortest piece separated by a row containing NaN values. Unless you have an unusual coastline, it's normal that you have to add a few points to your first ...

rsignell

Is it really the land masking that is taking a long time, or the bathymetry gridding?

Seagrid uses a rather slow inverse distance algorithm for bathymetry interpolation, so if you have a large number of bathymetry points, it takes a long time.

There is really no need to do bathymetry gridding in ...

rsignell

I do NOT recommend avoiding the mex files with SeaGrid. Chuck Denham, the author of this tool, tried to make non-mex versions of the elliptic solver and the other mex files, but it didn't work out so well. If you don't use the mex files, you will get a grid, but it may be wildly nonorthogonal.

rsignell

Leon,

I just tried it, and it works for me. You are supposed to click-and-drag to move the spacers closer or further apart. I had to keep clicking on <toggle>=>refresh to keep the spacers visible, but other than that, it worked okay, and I used it to focus grids toward the center of a test grid as ...

rsignell

That would be great! I'm sure if you took a look you would find a few other things worth fixing up, and it's only two little routines...

rsignell

Congrats! While it's fresh in your mind, it would be great if you would make a few notes on the problems you encountered and how you solved them. I'd be happy to add them to the WikiROMS section on grid generation.
-Rich

rsignell

Hernan, do you have benchmark tests that illustrate the performance increases with the new NetCDF4 parallel I/O?

rsignell

Yes, the easy way is just increase the array sizes in mexsepeli.inc and recreate the mex file. You might also have to increase the array sizes in mexrect.F (e.g. global replacement of 40000 to 80000 or whatever).

The better way would be to make these allocate memory dynamically, but that would ...

rsignell

Yes, you can recompile it using a larger dimension. Or even better, you could rewrite it to use dynamic memory allocation so people wouldn't have to do this in the future!
-Rich

rsignell

That is pretty amazing, and shows that having some way to represent the shallow region and deep region with a different number of vertical levels (sigma-over-z, z-over-sigma) would pretty much solve your problem. Clearly your workaround is not a viable solution for your 10 m shallo shelf region ...

rsignell

Jacopo,
I think you are right that the vertical stretching in this case will cause numerical mixing of the pycnocline over time. Rob Hetland and I saw the same thing with shallow surface trapped river plumes moving back and forth across the sloping shelf under repetitive upwelling/downwelling cycles ...

rsignell

https://www.myroms.org/wiki/index.php/Tools

rsignell

In releases of ROMS prior to R224 (released Aug 19, 2008), if you specified your sediment as MUD or SAND, it didn't really matter, as they were treated identically.

With versions R224 and higher, MUD and SAND are treated differently. BEDLOAD for example, only works with SAND.

I found this out ...

rsignell

Yes, I agree also that supplying the compression parameters should be controllable by the user. The folks testing NETCDF4 so far have found that while there is a huge savings going from deflate=0 to deflate=1, there is not much savings going to deflate=2 or higher. For more information on deflation ...

rsignell

Folks,

I went ahead and tested my own suggestion about testing NetCDF4 deflation and I'm happy to report that it worked great, reducing the ROMS NetCDF output file size significantly. On the test case I was using, which is 40% masked, the history file ended up 8 times smaller!.

Here's what I did ...

rsignell

Mathieu wrote:
The real problem of the mask is the excessive use of disk space. The READ_WATER, WRITE_WATER options of ROMS allow to write only the sea points and are certainly nice. However, Hernan indicated me that the resulting files are not CF-compliant. What would be a better solution ...

rsignell

Folks,

We would like to add a state variable to ROMS. I thought I remembered something like a 17-step instructional guide, perhaps by Neil Banas? But I can't find anything on the web, wikiROMS or the ROMS forum. Does anyone have instructions or things to watch out for?

Thanks,
Rich

rsignell

John,

Most Matlab/netcdf routines default to handling missing values via
"_fillValue" and scaling via "add_offset"/"scale_factor", but not the
NetCDF Toolbox. You have to turn them on. So in my Matlab
startup.m, I have these lines:

% Netcdf Toolbox global options (turn autoscale & autonan on ...

rsignell

Hernan,

I did an SVN update to grab the latest ROMS (r247), ran RIVERPLUME2, and then fired up NCVIEW on ocean_his.nc.
Yes!!!! The land is masked:
http://coast-enviro.er.usgs.gov/models/share/ocean_his_fill_value.png

I tried it with "nc_varget" in Matlab, and works great there too.
No more ...

rsignell

Hernan,

I totally agree with you that we should use "_FillValue" instead of "missing_value" and that we should specify this explicitly. For floats and doubles, I guess the value of 1.0e35 is fine. But for the rest, I suggest we go with the default Unidata values, but also specify them explicitly as ...

rsignell

I am moving away from the missing_value attribute and using the _FillValue attribute instead. Notice that the missing_value attribute:
is not treated in any special way by the library or conforming generic applications.

What about adding a new attribute, say mask , which points to the array used ...

rsignell

ROMS folk,

Although ROMS 3.0 NetCDF output files are "CF-compliant", there is currently no CF-standard to specify masking. As a result, these tools plot whatever values are in the masked regions, which can be ugly at best, misleading at worst.

Since CF visualization and access clients already ...

rsignell

Folks,

It would be nice to have a list of ROMS models running in operational or quasi-operational mode. I know of two:

Adriatic Sea:
http://www.arpa.emr.it/sim/?mare

Southern California Bight:
http://ourocean.jpl.nasa.gov/SCB/index.jsp

Are there more?

Thanks,
Rich

rsignell

Applied Science Associates, Inc. (ASA) is a science and technology consulting firm serving clients worldwide from offices in the United States, Brazil, Australia and Dubai. We specialize in solving problems related to physical, chemical and biological processes for a varied public and private ...

rsignell

Folks, I'm passing this message along from Michel Rixen. I worked at NURC (formerly called NATO SACLANT) for a few years and it was a great experience. I'd be willing to chat about my experience with folks who are considering it. - Rich Signell

Dear All,

There is a job opening at NURC for a data ...

rsignell

It would be indeed very interesting to hear an update from Hernan on how the work on nesting is going in ROMS 3.x. It would also be interesting to hear how the work on two-way nesting is going in ROMS AGRIF, which as I understand it is supposed to come out in ROMS AGRIF 2.0. And is there also ...

rsignell

ROMS folks,

The recent discussion of ETOPO2 for creating ROMS grids reminded me of something folks building grids will likely find useful. I have put a collection of global and regional bathymetric grids on our THREDDS server, which means that you can access the data via OpenDAP, Web Coverage ...

rsignell

I also avoid downloading NetCDF Toolbox separately from http://mexcdf.sourceforge.net as I found all that toolbox directories are included on matlab directory under ROMS processing package.

I'm not sure if this is the problem, but I recommend going to
http://mexcdf.sourceforge.net/
and getting ...

rsignell

When I use seagrid2roms, I call it with two arguments: the name of the mat file that seagrid produced, and the name of the output grid file for ROMS, like this:

seagrid2roms('seagrid.mat','roms_grid.nc');

-Rich

rsignell

It can be found by clicking Documentation on the ROMS homepage and choosing Diagnostics.

I could not find this link. When I click on "Documentation" on what I guess is "the ROMS homepage" (I'm not sure anymore what the ROMS homepage is), I get transported to WikiROMS Documentation Portal. I don ...

rsignell

seagrid2roms uses the NetCDF Toolbox, which in turn uses mexnc. It works fine on win32 with any version of matlab, but you need to get the right mexnc mex file. Then you just need:
The mex file in a directory that is in your Matlab path
The netcdf.dll in a directory that is in your Windows system ...

rsignell

J.Paul,

Judging from this Ticket,
https://www.myroms.org/projects/src/ticket/115
it looks like the best way to remove the tide would be to rerun your simulation with these new detiding options.

But if you are stuck with your existing 1/2 hour history files, you could certainly analyze your output ...

rsignell

Merrywish,

Indeed, it appears there are some discrepancies between (1) the test cases listed on the USGS test_cases web page, (2) the paper where the test case results were reported (Warner et al, Ocean Modeling 8 (2005) 81-113), and (3) the test case configurations that come supplied with the ROMS ...

rsignell

Nacholibre,

I don't know what you are doing wrong, but I hope this will help. This is the output from a successful compilation of the seagrid mex files I just performed on my RHEL4 Linux system on Intel32 with Matlab 7.2. The compilers are just gcc and g77. I'm including the verbose output only for ...

rsignell

I've added some more information about how to create and format coastline and bathymetry data for SeaGRID to the WikiROMS. Check

https://www.myroms.org/wiki/index.php/seagrid

-Rich

rsignell

Sasha,
I agree that the top sigma layer velocity is not equivalent to the surface velocity, especially when there is strong near-surface shear caused by the wind and coarse vertical resolution.

One could argue, however, that as far as the surface fluxes are concerned, accounting for the surface ...

rsignell

Folks,

Oops -- It turns out I can answer the question about gustiness myself.

If I look a bit further down in the bulk_flux.F routine, the 0.5 m/s is only used as an initial value, and the actual value of Wgus(i) that is used is set within the iteration loop via an empirical formula:

633 ...

rsignell

I'm wondering about a couple of issues with the bulk fluxes:

1. Shouldn't we be subtracting the surface current in the direction of the wind before computing bulk fluxes so that we have wind speed relative to the sea surface?

When I read the COARE3.0 paper at:
ftp://ftp.etl.noaa.gov/user/cfairall ...

rsignell

there are some kind of option of "-ffree-line-length-none" which ought to be "-ffixed-line-length-none'. I think it's a typo?

It's not a typo. It's there to make sure the preceding "-ffree-form" option isn't limited to 132 characters, which was causing a problem at least in CYGWIN when USE_DEBUG ...

rsignell

Ivica,

Whenever you want to see what's changed recently with the ROMS code, go to:

https://www.myroms.org/projects/src/browser

then click on "Last Change" (in the upper right area of your window).

At this revision (Changeset 81) you can see that Ticket 59 was resolved, and see exactly what the ...

rsignell

Could it also be that machine accuracy small perturbations of your initial conditions would also lead to the types of differences you are seeing?

Ten years ago we were evaluating different computers for running POM, and we were surprised to discover that the same executable running on the SGI ...

rsignell

Oops. Okay, I missed that setting of TS_MPDATA -- I guess the "find" on my browser doesn't work on these discussion pages.

Are you specifying a point source in a cell surrounded by ocean? I don't think it's designed to work that way -- the flux needs to come in through a wall between land and sea ...

rsignell

Are you defining TS_MPDATA so that you use the MPDATA scheme for advection of tracer? If not, it's not surprising that you would get negative concentrations 1 grid cell upstream from a point source.

rsignell

Michele,

I hadn't heard of esvn, so I checked out the web site and it looked like development on this stopped about a year ago.

We've had good luck with SmartSVN, a cross-platform Java GUI SVN client. The Foundation version is free, trivial to install, robust and relatively easy to use. You can ...

rsignell

Mark,

We agree that a test suite is a great idea for ROMS! Sachin Bhate, who is working on ROMS software tools under the NOPP Community Sediment Transport Project, has been working on just such a regression testing script (using Perl) to run a list of test cases in scalar, openmp and mpi modes ...

rsignell

Okay, I see from Hernan's post in the ROMS bugs discussion that the Trac site for ROMS does exist:

https://www.myroms.org/projects/src

Thanks Hernan & David!

If you haven't already checked out the capabilities on "browse source", it really is nice.

Should we submit bugs now as "new ticket" on ...

rsignell

I definitely think having Trac available for the Roms_rutgers SVN repository would be a good idea. There is already a Trac system at myroms.org for the ROMS CSTM repository, and it's proven very useful. At the very least, it's a great way to browse the source, examine recent code changes, and ...

rsignell

Barbara,

I increased the size to 1200x1200 and recompiled. If you replace your win32 mex files with these, does it work?

http://stellwagen.er.usgs.gov/rps/share ... d_mex2.zip

-Rich

rsignell

Bert,

Yes, it now appears my statements above about Delft3D and MORFAC could be in error, and that the non-conservative nature of the sediment I experienced was likely related to another bug that was fixed (although I still need to find time to go back and check).

After some offline discussion ...

rsignell

I first realized this problem with MORPHFAC and limited sediment during Delft3D runs where I started growing large sand banks on either side of a tidal headland where the sand had been completely eroded at the headland tip. I found I was generating huge amounts of sand (beach replenishment folks ...

rsignell

OpenMP works remarkably well and I can get perfect scaling,
and overall excellent performance: my CoreDuo 1.83GHz laptop yields about 80%
performance of a dual-Opteron machine (with single cores).

Sasha,

Just curious -- are you running Windows or Linux on this laptop? And would you expect OS ...

rsignell

When BULK_FLUXES is defined, the default "measurement" height for temperature, humidity and wind are all set to 10 m, as Jacopo mentioned.

Yet it seems likely that most people using BULK_FLUXES are using met model output, which typically outputs temperature and humidity at 2 m, and wind at 10 m, as ...

rsignell

Ivica's question got me wondering:

It looks like the XXXX_M2REDUCED option will allow you to specify elevation at the open boundary and have the depth-averaged velocity at the open boundary determined by the reduced physics approximation.

It should also be possible to specify depth-averaged ...

rsignell

Dear Kate, Rich, and all,

I am just wondering: sometime ago, back in February 2004 Hernan asked me to revise mex-function interface and fortran code "mexsepeli" in order to enable it to work on Linux platform and being called from Matlab on Linux. Which I succeeded to do. I knew that it was needed ...

rsignell

Neil,

Can you put the problematic coast, bathy and seagrid file somewhere so I can take a look?

Thanks,
Rich

rsignell

Sandro,

Several comments on the above problems:

1) Presto: Seagrid depends on Presto, and we therefore supplied Presto as a subdirectory of the Seagrid distribution. This version should be in the matlab path, not some other version of Presto. It should not matter where it is in the path unless ...

rsignell

So is Seagrid making bad grids for people? We need to know that and replace it. Personally, I have never gotten it to really work and always go back to my nasty old fortran code that no one else will touch. :twisted:

Seagrid doesn't make bad grids. People make bad grids. :wink:

Seriously, I and ...

rsignell

I'am using seagrid with Matlab 7 in windows envirnoment. I get it to work, together with mexnc and NetCDF_Toolbox. All the seagrid test's are fine and Its seems to work all cool, but when I try to convert a file to NetCDF using the function seagrid2roms I get this error...
seagrid2roms works fine ...

rsignell

When I tried installing the newer seagrid version, I had trouble with the mex stuff and recieved the following advice from a kind person who no longer wishes to be bothered by Seagrid questions:
"The "SeaGrid" PCWIN mex-files have rarely worked, or never, and I have recommended that users invoke ...

rsignell

I know of two ways to make grids: the nasty old Fortran way and the sexy Matlab way. I managed to download mexnc and seagrid onto one of their LInux boxes and could not get it to work. Since I came home, I also tried on my IBM and Linux boxes and failed there too. The very latest Seagrid download ...

rsignell

ROMS gang,

I was disturbed by this Monday's ROMS discussion summary announcement that
"There were not topics discussed this week." and was thinking about ways to make the ROMS forum more active.

I'm pretty sure that there were some people who had ROMS issues to discuss last week, but rather than ...

rsignell

Kieran,

This is very cool and in my opinion, *definitely* worth continuing!

I'm including a link to the zip file you sent me that demonstrates what you did:

http://stellwagen.er.usgs.gov/rps/share/xml.zip

And here's a little screen grab, just to get people jazzed on the concept:

https://www ...

rsignell

I asked Dave Robertson the same thing and this was his reply:

You can reach each person's presentation through the agenda:

http://www.myroms.org/index.php?page=ROMS_2005_agenda

Each talk has a PPT or PDF link.

The directory where the actual files are located is:

http://www.myroms.org/Workshops ...

rsignell

Is this site still operational?
I tried just now and got "dati mancati" for everything.

Are there any other sites where ROMS is running operationally?

rsignell

I think there is a problem with ROMS 2.2 in the way that the variable Awave is handled.

Awave is used as wave amplitude in the BBL routines such as SG_BBL.H to calculate the wave orbital velocity amplitude (if SWAN is not used):

# ifdef SWAN
Ub(i,j)=ABS(Ub_swan(i,j))+eps
Ab(i,j)=Ub(i,j)/Fwave ...

rsignell

Want to compile ROMS faster with little affect on the run time?

Ruoying He heard me complain about the length of time ROMS 2.2 was taking to compile on my Linux box with the Intel Fortran Compiler (5 minutes using *both* of my 3Ghz Zeon Processors!) and told me to compile with "-O2" instead of "-O3 ...

rsignell

I'd like to see variables intended for HISTORY, AVERAGES or TIME SERIES files to ALL be controlled from the ocean.in file.

I just realized that in my recently completed run, I don't have the wind stress in the NetCDF averages file because I forgot to compile the code with #define AVERAGES_FLUXES in ...

rsignell

Applications are being accepted for the following modeling support positiion at
the NATO Undersea Research Centre in La Spezia Italy.

You MUST have citizenship of a NATO country to apply for this positon.

Instructions for application can be found at

< http://www.nurc.nato.int/employ/vacancies ...

rsignell

Elad,

As you can see from the benchmark results at
http://cove.whoi.edu/~rsignell/roms/bench
I had no problem running ROMS on AMD with Intel Fortran 8.1.

I used

FFLAGS="-ip -O2 -xW"

if that is useful.

Are you using OpenMP or MPI? If MPI, could it be that you are using LAM compiled with PGI ...

rsignell

Constantinos,

When I get some time I will try to understand fully the meaning of your post -- you clearly know a lot more about this stuff than I do! However, I thought it would be of interest to point out that the BENCHMARK1 ROMS test case has been run on dual-Opteron 250 clusters with both ...

rsignell

To follow up the post I made last month, I've uploaded a updated spreadsheet of benchmark data for BENCHMARK1 and also our ADRIA02 Adriatic Sea run (with non-parallel I/O) to:

http://cove.whoi.edu/~rsignell/roms/bench/

Additions to this list are an 8-way Opteron Server and a Dual-Opteron cluster ...

rsignell

The interconnect used between nodes on a cluster can be the limiting factor in performance for bandwidth-limited models like ROMS. This was certainly impressed upon me during some ROMS benchmarking I did recently that I will post shortly.

I wasn't aware, however, of just how big the difference in ...

rsignell

As Sasha pointed out before, there is an amazing difference between F90 compilers, and picking the “best compiler” can depend on the problem you are trying to run. Proof of this is at the Polyhedron 2004 F90 Benchmarks site, where they show difference in performance on 10 different F90 programs ...

rsignell

5 step program to a blissful DODS/OpenDAP life

Get Inspired: Grab the mexnc_dap binary for your platform and Matlab version and the latest netcdf_toolkit from here and then get the test Matlab script "get_roms_dap.m" from here . Make sure that "which mexnc" points to your new OpenDAP-enabled ...

rsignell

Here's what I've got so far for the ROMS "BENCHMARK1" test: (ROMS/TOMS 2.1 - Benchmark Test, Idealized Southern Ocean Resolution, Grid 01: 0512x0064x030): All time are "wall clock" on otherwise idle systems. The tiling was 1x2, 1x4, 2x4, 4x4 for the 2, 4, 8 and 16 processor runs, respectively.

16 ...

rsignell

ROMS Chiefs,

IMHO, listing affiliations on the ROMS logo (Rutgers, UCLA, U Colorado, etc) is a bad idea. One of the great things about ROMS is that it truly feels like a community model, where ideas and contributions are rapidly incorporated into something that feels like "ours". Even it's name ...

rsignell

Senior/Principal Scientist, NATO Undersea Research Centre, Grade A3/A4

The NATO Undersea Research Centre, located in La Spezia Italy, is seeking applications for a position in Air-Sea Interaction. The successful candidate will spearhead Centre efforts to investigate the effects of air-sea ...

rsignell

John's question on time convention brings up a point that I think is important for the ROMS community, and I'd be interested in hearing what others have to say.

Here's my take on handling time:

Because the world did not agree on a calendar until after 1753, it is very dangerous to use any date ...

rsignell

ROMS gang,

From a quick Google Search it seems there are at least 3 sites from which one can download a draft PDF version of a "ROMS" paper, written by Shchepetkin and McWilliams:

[PDF] The Regional Oceanic Modeling System: A Split-Explicit, Free ...
File Format: PDF/Adobe Acrobat - View as HTML ...

rsignell

ROMS community,

If the policy *is* for "NON COMMERCIAL USE ONLY", I think the policy should be reexamined!

We would benefit from commercial use of ROMS in at least two ways:

1) The ROMS community would benefit from a larger user base, and therefore bugs would be found faster, and we would obtain ...

rsignell

To create a better initialization field from our Adriatic CTD data, I was thinking about taking the OA'd field, and running the model forward for a couple of days with the observed (weak) wind forcing but strongly nudging back to the initial field along the sections of initial CTD data.

The reason ...

rsignell

I can't seem to find an archive of the ROMS mailing list. Am I overlooking it somewhere

-Rich Signell

rsignell

Too bad I heard about this later rather than sooner. In my opinion you should always use the F90 compiler on the IBM (xlf90,xlf90_r, etc). Might have saved them some time and trouble. Scaling at 11 out of 16 pe's is about as much as can be expected on this system.

Rich

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