Search found 120 matches

by rsignell
Tue May 22, 2018 10:57 am
Forum: ROMS Installation
Topic: Anyone tried running ROMS on HPC Cloud (e.g. Amazon)?
Replies: 8
Views: 5982

Re: Anyone tried running ROMS on HPC Cloud (e.g. Amazon)?

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 Infin...
by rsignell
Wed Dec 06, 2017 1:05 pm
Forum: Meetings/Workshops
Topic: 15th International Estuarine and Coastal Modeling Conference
Replies: 0
Views: 1092

15th International Estuarine and Coastal Modeling Conference

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 world...
by rsignell
Thu Oct 12, 2017 10:08 am
Forum: ROMS Problems
Topic: Docker container for ROMS?
Replies: 7
Views: 3239

Re: Docker container for ROMS?

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 fa...
by rsignell
Tue Oct 03, 2017 11:22 am
Forum: ROMS Problems
Topic: Docker container for ROMS?
Replies: 7
Views: 3239

Docker container for ROMS?

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
by rsignell
Fri Jun 09, 2017 8:15 pm
Forum: ROMS Tools and Techniques
Topic: Using NCO's "ncregrid" to regrid ROMS output?
Replies: 0
Views: 1114

Using NCO's "ncregrid" to regrid ROMS output?

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?
by rsignell
Wed Feb 15, 2017 2:21 pm
Forum: ROMS Tools and Techniques
Topic: SEAGRID.m with MATLAB R2014b
Replies: 12
Views: 11882

Re: SEAGRID.m with MATLAB R2014b

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!
by rsignell
Fri Sep 09, 2016 1:49 pm
Forum: ROMS Tools and Techniques
Topic: vertical section of a roms output variable
Replies: 4
Views: 2547

Re: vertical section of a roms output variable

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....
by rsignell
Thu Sep 08, 2016 1:09 pm
Forum: ROMS Tools and Techniques
Topic: vertical section of a roms output variable
Replies: 4
Views: 2547

Re: vertical section of a roms output variable

I have a simple Jupyter notebook example using matplotlib here, does that help?
https://github.com/rsignell-usgs/notebo ... ture.ipynb
by rsignell
Thu Jul 14, 2016 4:55 pm
Forum: ROMS Tools and Techniques
Topic: standard_name for U,V current components
Replies: 6
Views: 3991

Re: standard_name for U,V current components

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 list he...
by rsignell
Thu Jul 07, 2016 5:53 pm
Forum: Job Opportunities
Topic: Oceanographer support position at USGS Woods Hole
Replies: 0
Views: 8101

Oceanographer support position at USGS Woods Hole

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.usajobs....
by rsignell
Mon Feb 29, 2016 10:38 am
Forum: Meetings/Workshops
Topic: Reminder: ECM14 Abstracts due Friday!
Replies: 0
Views: 4818

Reminder: ECM14 Abstracts due Friday!

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 an...
by rsignell
Tue Dec 15, 2015 6:55 pm
Forum: Meetings/Workshops
Topic: Call for Abstracts: ECM14, Jun 13-15, 2016
Replies: 0
Views: 1782

Call for Abstracts: ECM14, Jun 13-15, 2016

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 results...
by rsignell
Thu Oct 01, 2015 4:21 pm
Forum: Job Opportunities
Topic: Experienced ROMS user to transition HAB model to NOAA
Replies: 0
Views: 3180

Experienced ROMS user to transition HAB model to NOAA

"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 interdiscipl...
by rsignell
Thu Oct 02, 2014 1:37 am
Forum: ROMS Installation
Topic: NCO script to average (u,v) to rho points and rotate to E/W?
Replies: 3
Views: 2698

Re: NCO script to average (u,v) to rho points and rotate to

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.
by rsignell
Wed Oct 01, 2014 4:29 pm
Forum: ROMS Installation
Topic: NCO script to average (u,v) to rho points and rotate to E/W?
Replies: 3
Views: 2698

NCO script to average (u,v) to rho points and rotate to E/W?

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. ;-)
by rsignell
Mon Jun 30, 2014 2:10 pm
Forum: ROMS Tools and Techniques
Topic: where can i download RPSstuff?
Replies: 4
Views: 1354

Re: where can i download RPSstuff?

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...
by rsignell
Thu Jun 26, 2014 6:53 pm
Forum: ROMS Tools and Techniques
Topic: where can i download RPSstuff?
Replies: 4
Views: 1354

Re: where can i download RPSstuff?

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). ...
by rsignell
Thu Jun 26, 2014 11:09 am
Forum: ROMS Discussion
Topic: tidal analysis of large output files
Replies: 22
Views: 6581

Re: tidal analysis of large output files

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://g...
by rsignell
Thu Jun 19, 2014 3:08 pm
Forum: ROMS Discussion
Topic: tidal analysis of large output files
Replies: 22
Views: 6581

Re: tidal analysis of large output files

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?
by rsignell
Thu Jun 19, 2014 1:04 pm
Forum: ROMS Discussion
Topic: tidal analysis of large output files
Replies: 22
Views: 6581

Re: tidal analysis of large output files

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 ; variables: do...
by rsignell
Mon Jun 09, 2014 8:31 pm
Forum: Job Opportunities
Topic: US/NOAA GLERL Modeling and Forecasting Group Lead
Replies: 0
Views: 1914

US/NOAA GLERL Modeling and Forecasting Group Lead

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 responsible...
by rsignell
Tue Aug 27, 2013 10:42 am
Forum: ROMS Installation
Topic: pyroms installation
Replies: 4
Views: 3878

Re: pyroms installation

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 started...
by rsignell
Mon Apr 22, 2013 6:49 pm
Forum: Meetings/Workshops
Topic: Abstract Call: ECM13 Conference, Nov 4-6, San Diego USA
Replies: 0
Views: 2381

Abstract Call: ECM13 Conference, Nov 4-6, San Diego USA

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 latest...
by rsignell
Fri Sep 14, 2012 12:01 pm
Forum: ROMS Tools and Techniques
Topic: how to use seagrid to Locally Add Mesh Density
Replies: 7
Views: 2759

Re: how to use seagrid to Locally Add Mesh Density

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 inter...
by rsignell
Thu Jun 21, 2012 10:59 am
Forum: ROMS Tools and Techniques
Topic: netcdf4-python
Replies: 7
Views: 4278

Re: netcdf4-python

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 M...
by rsignell
Fri Jun 01, 2012 9:00 pm
Forum: ROMS Problems
Topic: error in read_srtm30plus.m script ....
Replies: 5
Views: 3567

Re: error in read_srtm30plus.m script ....

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 look...
by rsignell
Fri Mar 02, 2012 2:45 pm
Forum: ROMS Installation
Topic: Anyone tried running ROMS on HPC Cloud (e.g. Amazon)?
Replies: 8
Views: 5982

Anyone tried running ROMS on HPC Cloud (e.g. Amazon)?

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 in...
by rsignell
Thu Nov 17, 2011 11:31 am
Forum: ROMS Tools and Techniques
Topic: Anyone tried 3D visualization of ROMS output using Mayavi?
Replies: 5
Views: 3751

Re: Anyone tried 3D visualization of ROMS output using Mayav

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
by rsignell
Tue Nov 15, 2011 9:51 pm
Forum: ROMS Tools and Techniques
Topic: Anyone tried 3D visualization of ROMS output using Mayavi?
Replies: 5
Views: 3751

Anyone tried 3D visualization of ROMS output using Mayavi?

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_...
by rsignell
Mon Oct 10, 2011 5:17 pm
Forum: ROMS Discussion
Topic: Delft3D grids to NetCDF
Replies: 7
Views: 3051

Re: Delft3D grids to NetCDF

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's...
by rsignell
Mon May 23, 2011 11:06 am
Forum: Meetings/Workshops
Topic: Reminder: Coastal Ocean Modeling GRC deadline is May 29th!
Replies: 0
Views: 1457

Reminder: Coastal Ocean Modeling GRC deadline is May 29th!

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 conferen...
by rsignell
Thu Jun 17, 2010 8:49 pm
Forum: ROMS Discussion
Topic: Simple method for calculating Numerically Induced Mixing
Replies: 2
Views: 1451

Re: Simple method for calculating Numerically Induced Mixing

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 t...
by rsignell
Tue Jun 15, 2010 7:26 pm
Forum: ROMS Discussion
Topic: Simple method for calculating Numerically Induced Mixing
Replies: 2
Views: 1451

Simple method for calculating Numerically Induced Mixing

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...
by rsignell
Wed Jun 02, 2010 12:55 am
Forum: ROMS Tools and Techniques
Topic: Problem with the MATLAB R2009a version (7.8.0) and Netcdf
Replies: 3
Views: 3296

Re: Problem with the MATLAB R2009a version (7.8.0) and Netcdf

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 Ne...
by rsignell
Mon Nov 30, 2009 2:26 pm
Forum: Meetings/Workshops
Topic: EGU May 2-7, 2010 Vienna: Ocean Modeling Special Session
Replies: 0
Views: 1715

EGU May 2-7, 2010 Vienna: Ocean Modeling Special Session

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, I...
by rsignell
Thu Sep 24, 2009 11:57 am
Forum: Job Opportunities
Topic: Three Job Opportunities at the Naval Research Laboratory
Replies: 1
Views: 3455

Re: Three Job Opportunities at the Naval Research Laboratory

Charlie Barronvia, Richard Allardvia, and Patrick Hoganvia?

I had no idea so many Italians worked at NRL! ;-)

-Rich
by rsignell
Tue Jul 28, 2009 6:20 pm
Forum: ROMS Tools and Techniques
Topic: Is it mandatory to get bathymetry from the net??
Replies: 4
Views: 1619

Re: Is it mandatory to get bathymetry from the net??

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 ...
by rsignell
Tue Jul 28, 2009 6:15 pm
Forum: ROMS Tools and Techniques
Topic: SEAGRID use
Replies: 9
Views: 4016

Re: SEAGRID use

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 segmen...
by rsignell
Thu Jun 25, 2009 11:58 am
Forum: ROMS Problems
Topic: what's wrong with the seagrid spacer?
Replies: 12
Views: 2622

Re: what's wrong with the seagrid spacer?

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 Sea...
by rsignell
Thu Jun 25, 2009 2:24 am
Forum: ROMS Problems
Topic: what's wrong with the seagrid spacer?
Replies: 12
Views: 2622

Re: what's wrong with the seagrid spacer?

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.
by rsignell
Tue Jun 23, 2009 4:20 pm
Forum: ROMS Problems
Topic: what's wrong with the seagrid spacer?
Replies: 12
Views: 2622

Re: what's wrong with the seagrid spacer?

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 b...
by rsignell
Tue Feb 10, 2009 2:34 am
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

Re: Grid generation

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... :)
by rsignell
Tue Feb 10, 2009 12:20 am
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

Re: Grid generation

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
by rsignell
Mon Feb 09, 2009 3:22 am
Forum: ROMS Benchmarks
Topic: Parallel I/O benchmarks?
Replies: 13
Views: 5511

Parallel I/O benchmarks?

Hernan, do you have benchmark tests that illustrate the performance increases with the new NetCDF4 parallel I/O?
by rsignell
Fri Feb 06, 2009 7:50 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

Re: Grid generation

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 requi...
by rsignell
Fri Feb 06, 2009 4:34 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

Re: Grid generation

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
by rsignell
Fri Feb 06, 2009 2:37 pm
Forum: ROMS Usage
Topic: struggling for sharp halocline
Replies: 9
Views: 6756

Re: struggling for sharp halocline

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, whi...
by rsignell
Thu Feb 05, 2009 2:18 am
Forum: ROMS Usage
Topic: struggling for sharp halocline
Replies: 9
Views: 6756

Re: struggling for sharp halocline

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...
by rsignell
Tue Nov 25, 2008 11:22 pm
Forum: ROMS Sediment
Topic: MUD, SAND and BEDLOAD
Replies: 0
Views: 1451

MUD, SAND and BEDLOAD

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 the ha...
by rsignell
Tue Nov 25, 2008 3:22 pm
Forum: ROMS Discussion
Topic: NetCDF4 compression for ROMS output files
Replies: 7
Views: 3589

Re: NetCDF4 compression for ROMS output files

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 ...
by rsignell
Tue Nov 25, 2008 2:50 am
Forum: ROMS Discussion
Topic: NetCDF4 compression for ROMS output files
Replies: 7
Views: 3589

Re: NetCDF4 compression for ROMS output files

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 (bu...
by rsignell
Tue Nov 04, 2008 2:45 pm
Forum: ROMS Discussion
Topic: NetCDF4 compression for ROMS output files
Replies: 7
Views: 3589

NetCDF4 compression for ROMS output files

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? Another ...
by rsignell
Thu Oct 30, 2008 11:52 am
Forum: ROMS Discussion
Topic: Adding a state variable to ROMS
Replies: 1
Views: 702

Adding a state variable to ROMS

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
by rsignell
Tue Oct 28, 2008 1:06 pm
Forum: ROMS Discussion
Topic: "missing_value" for masked regions in NetCDF output files?
Replies: 16
Views: 3934

Re: "missing_value" for masked regions in NetCDF output files?

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) global...
by rsignell
Fri Oct 24, 2008 3:46 pm
Forum: ROMS Discussion
Topic: "missing_value" for masked regions in NetCDF output files?
Replies: 16
Views: 3934

Re: "missing_value" for masked regions in NetCDF output files?

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 multiplyi...
by rsignell
Fri Oct 24, 2008 2:15 am
Forum: ROMS Discussion
Topic: "missing_value" for masked regions in NetCDF output files?
Replies: 16
Views: 3934

Re: "missing_value" for masked regions in NetCDF output files?

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 ...
by rsignell
Wed Oct 22, 2008 9:08 pm
Forum: ROMS Discussion
Topic: "missing_value" for masked regions in NetCDF output files?
Replies: 16
Views: 3934

Re: "missing_value" for masked regions in NetCDF output files?

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 fo...
by rsignell
Wed Oct 22, 2008 2:00 pm
Forum: ROMS Discussion
Topic: "missing_value" for masked regions in NetCDF output files?
Replies: 16
Views: 3934

"missing_value" for masked regions in NetCDF output files?

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 handle...
by rsignell
Tue Aug 19, 2008 3:53 pm
Forum: ROMS Discussion
Topic: Operating ROMS nowcast/forecast models
Replies: 3
Views: 1356

Operating ROMS nowcast/forecast models

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
by rsignell
Tue Aug 19, 2008 3:35 pm
Forum: Job Opportunities
Topic: Engineer or Scientist Position at ASA, Inc.
Replies: 0
Views: 1261

Engineer or Scientist Position at ASA, Inc.

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 client...
by rsignell
Tue Aug 19, 2008 3:26 pm
Forum: Job Opportunities
Topic: Data Assimilation Scientist position at NURC (NATO, Italy)
Replies: 1
Views: 1704

Data Assimilation Scientist position at NURC (NATO, Italy)

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 ass...
by rsignell
Tue Aug 12, 2008 11:49 am
Forum: ROMS Discussion
Topic: two way nesting
Replies: 2
Views: 1192

Re: two way nesting

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 nestin...
by rsignell
Wed Jun 18, 2008 3:41 pm
Forum: ROMS Information
Topic: NetCDF subsetter for Global and Regional Bathymetry Data
Replies: 0
Views: 1644

NetCDF subsetter for Global and Regional Bathymetry Data

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 Servic...
by rsignell
Tue Jun 03, 2008 10:44 am
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

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 the ...
by rsignell
Mon Jun 02, 2008 3:05 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

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
by rsignell
Thu Apr 10, 2008 8:41 pm
Forum: ROMS Information
Topic: What is the output of DIAGNOSTICS_TS/UV?
Replies: 6
Views: 4325

Re: What is the output of DIAGNOSTICS_TS/UV?

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't s...
by rsignell
Fri Mar 28, 2008 1:00 am
Forum: ROMS Problems
Topic: MexNC, NetCDF and Matlab?
Replies: 2
Views: 2257

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 pa...
by rsignell
Mon Feb 11, 2008 8:52 pm
Forum: ROMS Tools and Techniques
Topic: Tidal filtering of output files
Replies: 3
Views: 2815

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 wi...
by rsignell
Wed Dec 19, 2007 11:06 pm
Forum: ROMS Sediment
Topic: questions about test cases posted on USGS webpage
Replies: 2
Views: 2059

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 ...
by rsignell
Thu Oct 25, 2007 10:27 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

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 ...
by rsignell
Wed Oct 10, 2007 11:10 am
Forum: ROMS Tools and Techniques
Topic: is the coastline data requisites for the Seagrid?
Replies: 3
Views: 2518

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
by rsignell
Thu Aug 16, 2007 1:00 pm
Forum: ROMS Discussion
Topic: Bulk fluxes, surface-relative winds and gustiness
Replies: 12
Views: 5789

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 curr...
by rsignell
Wed Aug 15, 2007 2:58 pm
Forum: ROMS Discussion
Topic: Bulk fluxes, surface-relative winds and gustiness
Replies: 12
Views: 5789

Re: Bulk fluxes, surface-relative winds and gustiness

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 ! Compute g...
by rsignell
Tue Aug 14, 2007 3:47 pm
Forum: ROMS Discussion
Topic: Bulk fluxes, surface-relative winds and gustiness
Replies: 12
Views: 5789

Bulk fluxes, surface-relative winds and gustiness

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/wc...
by rsignell
Fri Jul 20, 2007 12:02 pm
Forum: ROMS Bugs
Topic: a bug(typo) in Linux-gfortran.mk
Replies: 4
Views: 1955

Re: a bug(typo) in Linux-gfortran.mk

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 wa...
by rsignell
Tue Jul 10, 2007 11:59 am
Forum: ROMS Bugs
Topic: Minus values of sediment next to sediment point sources
Replies: 18
Views: 6341

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 code ...
by rsignell
Tue Jul 10, 2007 11:49 am
Forum: ROMS Installation
Topic: different result obtained with different versions of pgi
Replies: 5
Views: 1977

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 machin...
by rsignell
Tue Jul 03, 2007 10:41 am
Forum: ROMS Bugs
Topic: Minus values of sediment next to sediment point sources
Replies: 18
Views: 6341

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, d...
by rsignell
Tue Jul 03, 2007 8:38 am
Forum: ROMS Bugs
Topic: Minus values of sediment next to sediment point sources
Replies: 18
Views: 6341

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.
by rsignell
Fri May 18, 2007 10:59 am
Forum: ROMS Installation
Topic: About subversion
Replies: 2
Views: 1810

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 see ...
by rsignell
Mon May 14, 2007 1:32 pm
Forum: ROMS Source
Topic: Test suite
Replies: 6
Views: 5114

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, and ...
by rsignell
Fri May 04, 2007 6:29 pm
Forum: ROMS Discussion
Topic: Collaboration, releases, SVN, Trac, flavors of ROMS...
Replies: 11
Views: 11342

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 the Tr...
by rsignell
Wed May 02, 2007 10:49 am
Forum: ROMS Discussion
Topic: Collaboration, releases, SVN, Trac, flavors of ROMS...
Replies: 11
Views: 11342

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 compar...
by rsignell
Fri Mar 23, 2007 9:18 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

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
by rsignell
Wed Feb 14, 2007 2:14 pm
Forum: ROMS Sediment
Topic: SEDMORPH parameters
Replies: 16
Views: 7651

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 with ...
by rsignell
Tue Feb 13, 2007 2:37 pm
Forum: ROMS Sediment
Topic: SEDMORPH parameters
Replies: 16
Views: 7651

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 wou...
by rsignell
Thu Jan 25, 2007 1:49 pm
Forum: ROMS Installation
Topic: Intel Core 2 Duo processor
Replies: 14
Views: 7404

Re: ROMS on Dual Core

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-depend...
by rsignell
Tue Jan 02, 2007 4:02 pm
Forum: ROMS Problems
Topic: shortwave solar radiation in ROMS surface forcing
Replies: 8
Views: 6711

Default BULK_FLUXES "measurement" heights in mod_s

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 ...
by rsignell
Fri Dec 01, 2006 1:41 pm
Forum: ROMS Usage
Topic: Open Boudary Conditions: Inflow
Replies: 11
Views: 7779

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 velocity...
by rsignell
Fri Dec 01, 2006 3:36 am
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

Re: RE: grid generation

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 ...
by rsignell
Wed Nov 01, 2006 12:26 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

Neil,

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

Thanks,
Rich
by rsignell
Mon Oct 23, 2006 2:26 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

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 there...
by rsignell
Tue Oct 03, 2006 8:47 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

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 man...
by rsignell
Sun Sep 24, 2006 4:19 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

seagrid issues

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 f...
by rsignell
Wed Sep 20, 2006 1:57 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

Re: Seagrid and mex mess

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 th...
by rsignell
Mon Sep 18, 2006 6:49 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34552

Re: Grid generation

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 d...
by rsignell
Tue Jul 11, 2006 2:48 pm
Forum: ROMS Discussion
Topic: How can we make the ROMS forum more active?
Replies: 2
Views: 1752

How can we make the ROMS forum more active?

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 dis...
by rsignell
Tue Jan 10, 2006 10:28 pm
Forum: ROMS Discussion
Topic: XML form of ROMS cppdefs.h
Replies: 2
Views: 2415

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.myroms.o...
by rsignell
Mon Nov 21, 2005 1:11 pm
Forum: Meetings/Workshops
Topic: 2005 ROMS/TOMS Workshop, Final Notice
Replies: 2
Views: 2692

Workshop Presentations

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/ROMS2...
by rsignell
Thu Sep 29, 2005 9:27 am
Forum: Adriatic Sea
Topic: ROMS operational in the Adriatic Sea
Replies: 5
Views: 12222

Operational ROMS in Adriatic Sea still working?

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?
by rsignell
Thu Sep 22, 2005 6:55 pm
Forum: ROMS Bugs
Topic: Inconsistent use of Awave in BULK_FLUX and BBL routines
Replies: 0
Views: 1338

Inconsistent use of Awave in BULK_FLUX and BBL routines

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+eps # ...
by rsignell
Wed Aug 10, 2005 8:04 pm
Forum: ROMS Installation
Topic: Quick tip for Linux Intel Fortran users
Replies: 1
Views: 2088

Quick tip for Linux Intel Fortran users

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"...
by rsignell
Wed Aug 10, 2005 6:14 pm
Forum: ROMS Source
Topic: HIS and AVG output variable selection
Replies: 1
Views: 2886

HIS and AVG output variable selection

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 ...
by rsignell
Mon Jul 11, 2005 8:26 pm
Forum: Job Opportunities
Topic: Modeling Support Position at NATO in La Spezia, Italy
Replies: 0
Views: 2323

Modeling Support Position at NATO in La Spezia, Italy

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.html >...
by rsignell
Tue Jan 04, 2005 5:21 pm
Forum: ROMS Installation
Topic: ROMS on AMD linux pc with ifort 8.1
Replies: 2
Views: 2120

No problem running on AMD with IFORT 8.1

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, but then...
by rsignell
Tue Jan 04, 2005 1:42 pm
Forum: ROMS Discussion
Topic: Interconnect speed for MPI: Gigabit, Myrinet and Infiniband
Replies: 5
Views: 4029

Gigabit vs. Infiniband on the BENCHMARK1 test

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 INFINIB...
by rsignell
Tue Dec 21, 2004 6:34 pm
Forum: ROMS Benchmarks
Topic: Benchmarks
Replies: 31
Views: 22269

Benchmarking update & expanded info

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 wit...
by rsignell
Tue Dec 21, 2004 1:30 pm
Forum: ROMS Discussion
Topic: Interconnect speed for MPI: Gigabit, Myrinet and Infiniband
Replies: 5
Views: 4029

Interconnect speed for MPI: Gigabit, Myrinet and Infiniband

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 th...
by rsignell
Tue Dec 21, 2004 1:11 pm
Forum: ROMS Benchmarks
Topic: Benchmarks
Replies: 31
Views: 22269

What is the best F90 compiler? Check this out!

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 depe...
by rsignell
Fri Nov 19, 2004 8:22 pm
Forum: ROMS Tools and Techniques
Topic: 5 Steps to a Blissful Life with ROMS and DODS/OpenDAP
Replies: 0
Views: 1894

5 Steps to a Blissful Life with ROMS and DODS/OpenDAP

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 mexnc ...
by rsignell
Tue Nov 09, 2004 8:28 pm
Forum: ROMS Benchmarks
Topic: Benchmarks
Replies: 31
Views: 22269

More BENCHMARK1 Results for various Linux & Windows

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 cp...
by rsignell
Wed Sep 15, 2004 12:28 pm
Forum: Meetings/Workshops
Topic: 2004 ROMS/TOMS Workshop T-shirt
Replies: 4
Views: 4254

Listing affiliations on ROMS logo is a bad idea

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, "Re...
by rsignell
Sat May 15, 2004 2:05 pm
Forum: Job Opportunities
Topic: Senior/Principal Scientist, NATO Undersea Research Centre
Replies: 0
Views: 2680

Senior/Principal Scientist, NATO Undersea Research Centre

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 interacti...
by rsignell
Tue May 11, 2004 5:09 pm
Forum: ROMS Discussion
Topic: Model Time Clocks
Replies: 10
Views: 19641

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 (YYYY...
by rsignell
Fri Jan 09, 2004 3:33 pm
Forum: ROMS Information
Topic: The "ROMS" paper?
Replies: 1
Views: 2474

The "ROMS" paper?

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 Pag...
by rsignell
Wed Nov 12, 2003 4:55 pm
Forum: ROMS FAQ
Topic: ROMS licensing
Replies: 1
Views: 4215

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 mor...
by rsignell
Tue Nov 11, 2003 5:09 pm
Forum: ROMS FAQ
Topic: Nudging coefficients from NetCDF file
Replies: 1
Views: 6934

Nudging coefficients from NetCDF file

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 i...
by rsignell
Fri Apr 25, 2003 9:30 pm
Forum: ROMS Information
Topic: New ROMS Web Site
Replies: 1
Views: 2118

Is there an archive of info sent to the ROMS mailing list?

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

-Rich Signell
by rsignell
Wed Feb 26, 2003 4:18 pm
Forum: ROMS Problems
Topic: ROMS on the IBM Regatta
Replies: 1
Views: 1757

Re: ROMS on the IBM Regatta

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