Search found 86 matches

by jpringle
Mon Jul 08, 2019 8:23 am
Forum: ROMS Discussion
Topic: Alongshore currents with periodic alongshore boundaries
Replies: 9
Views: 734

Re: Alongshore currents with periodic alongshore boundaries

Aryan -- I just want to amplify a point that Sasha made above, for it is important to understanding the dynamics of your case. An alongshore current in a periodic domain must be maintained by forcing; anything else is inconsistent. Why? what is an alongshore periodic domain? one in which there are n...
by jpringle
Fri Apr 26, 2019 7:04 pm
Forum: ROMS Discussion
Topic: example lightweight isosurface plotting code in python
Replies: 0
Views: 356

example lightweight isosurface plotting code in python

Dear all -- I hope someone finds this usefull. I wanted to plot some iso-surfaces in 3D with ROMS data without re-gridding it to a rectangular grid or some such silliness. There are many heavy-weight environments that can do all sorts of cool things like that (paraview, vapor, yt) -- but getting the...
by jpringle
Tue May 15, 2018 11:57 pm
Forum: ROMS Discussion
Topic: cold water creeping upwards along topography
Replies: 3
Views: 705

Re: cold water creeping upwards along topography

In your sections, the bathymetry has severe stair-stepping (discontinuities). Is that real?

Also, is there any along-isobath flow which could be driving a bottom Ekman transport?

Jamie
by jpringle
Fri Apr 27, 2018 5:37 pm
Forum: ROMS Discussion
Topic: faster MPI on single computer / -bind-to core /Ubuntu 18.04
Replies: 0
Views: 732

faster MPI on single computer / -bind-to core /Ubuntu 18.04

Dear all -- I hope some of you find this useful. I am running ROMS on a dual processor 32 core AMD EPYC machine. I noticed on the latest version of Ubuntu my smaller machines showed good improvement with ROMS runs with openMP parallelization. So I upgraded the big machine to Ubuntu 18.04, and my ROM...
by jpringle
Wed Mar 14, 2018 3:20 pm
Forum: ROMS Tools and Techniques
Topic: Error of installing PyCNAL on conda
Replies: 11
Views: 2399

Re: Error of installing PyCNAL on conda

Dear All, The errors of the type Warning: distutils distribution has been initialized, it may be too late to add an extension _interp Warning: distutils distribution has been initialized, it may be too late to add an extension _obs_interp are a bit of a red herring. You can make the codes work by co...
by jpringle
Tue Feb 27, 2018 5:17 pm
Forum: ROMS Problems
Topic: excess mixing in k-epsilon GLS mixing; bug or misconfigured?
Replies: 8
Views: 2051

Re: excess mixing in k-epsilon GLS mixing; bug or misconfigu

Thanks to John Wilkin, John Warner, Nirnimesh Kumar, the excellent Warner et al. 2005 Ocean Modeling paper on mixing schemes in ROMS and the excellent note by Malcolm Scully (https://www.myroms.org/forum/viewtopic.php?f=17&t=2310&p=8441&hilit=malcolm+scully#p8458 ), I have run this issue down. In su...
by jpringle
Mon Feb 26, 2018 2:12 pm
Forum: ROMS Problems
Topic: excess mixing in k-epsilon GLS mixing; bug or misconfigured?
Replies: 8
Views: 2051

Re: excess mixing in k-epsilon GLS mixing; bug or misconfigu

Both in John Wilkin's reply and in some private emails, I have received some good hints related to minimum turbulence level parameters in the mixing scheme. I shall investigate and compare to the primary literature for this scheme in the next few days, and will post a summary here soon. Thanks for t...
by jpringle
Sat Feb 24, 2018 10:48 pm
Forum: ROMS Problems
Topic: excess mixing in k-epsilon GLS mixing; bug or misconfigured?
Replies: 8
Views: 2051

Re: excess mixing in k-epsilon GLS mixing; bug or misconfigu

ALT_BAK is 1.0d-6 for both T and S, so much less than observed... ¯\_(ツ)_/¯
by jpringle
Fri Feb 23, 2018 7:52 pm
Forum: ROMS Problems
Topic: excess mixing in k-epsilon GLS mixing; bug or misconfigured?
Replies: 8
Views: 2051

Re: excess mixing in k-epsilon GLS mixing; bug or misconfigu

I was asked offline why I expected the diffusion of temperature to be slower than ROMS's k-epsilon in the ocean -- why did I think the GOTM k-epsilon, ROMS MY25 and ROMS LMD was closer to the truth? In this stratified ocean, with no horizontal gradients of density and no forcing, there is no flow. F...
by jpringle
Thu Feb 22, 2018 7:17 pm
Forum: ROMS Problems
Topic: excess mixing in k-epsilon GLS mixing; bug or misconfigured?
Replies: 8
Views: 2051

excess mixing in k-epsilon GLS mixing; bug or misconfigured?

Dear all -- I think I have stumbled across evidence of a bug in the GLS vertical mixing scheme in ROMS, at least for the k-epsilon scheme. It remains possible that I am just doing something stupid. I find that under the k-epsilon scheme vertical stratification diffuses away much more quickly than un...
by jpringle
Wed Jan 31, 2018 9:26 pm
Forum: ROMS Bugs
Topic: bug in ana_psource with openMP
Replies: 0
Views: 775

bug in ana_psource with openMP

I am not well versed in openMP programming -- but I think I found a bug where ana_psource initializes the tracer input. I was having problems with different runs of my code producing wildly different answers from run to run under openMP. It did not do this when run in a single thread and when run un...
by jpringle
Wed Jan 31, 2018 4:37 pm
Forum: ROMS Bugs
Topic: bug in ana_psource.h with analytical initial conditions
Replies: 0
Views: 710

bug in ana_psource.h with analytical initial conditions

I think I found a bug in the ana_psource.h when the model is initialized with ana_initial.h. In this case, the analytical forcing files are invoked in analytical.F before the first time step of integration as part of initializing the u, v etc fields. When this is done, the variable iic(ng) is 0. In ...
by jpringle
Fri Dec 15, 2017 5:45 pm
Forum: ROMS Problems
Topic: Compiling ROMs in Ubuntu
Replies: 7
Views: 1532

Re: Compiling ROMs in Ubuntu

Mark --

Ah -- I see -- I had not defined "USE_MY_LIBS" and so it ignored the changes I made to NF_CONFIG and NETCDF_INCDIR in my build.bash. I had made the changes, and never tested if it worked without them.


Cheers,
Jamie
by jpringle
Thu Dec 14, 2017 2:21 pm
Forum: ROMS Problems
Topic: Compiling ROMs in Ubuntu
Replies: 7
Views: 1532

Re: Compiling ROMs in Ubuntu

I have recently compiled ROMS on a bunch of ubuntu machines for benchmarking and production use, with versions 16.04, 17.04 and 17.10 (I recommend skipping 17.04). In all cases it is trivial to get ROMS going. Just install the following packages (which include the MPI packages, and you can compile a...
by jpringle
Wed Dec 06, 2017 7:46 pm
Forum: ROMS Benchmarks
Topic: Benchmarking Epyc, Ryzen, and Xeon: Tyranny of Memory
Replies: 5
Views: 3611

Re: Benchmarking Epyc, Ryzen, and Xeon: Tyranny of Memory

Wayne -- A couple of things. To get the model to run on my Threadripper 1950x with only 8 threads, I used the environmental variable omp_num_threads. I suspect, based on my earlier post, that the speed of ROMS on this kind of system is limited by memory bandwidth (see Sasha's long thread on this tha...
by jpringle
Mon Dec 04, 2017 12:44 am
Forum: ROMS Benchmarks
Topic: Benchmarking Epyc, Ryzen, and Xeon: Tyranny of Memory
Replies: 5
Views: 3611

Re: Benchmarking Epyc, Ryzen, and Xeon: Tyranny of Memory

Wayne-- This configuration seems reasonable -- but I have not experimented with the intel compilers yet. At some point I will have one of my students install the student version and let people know. If you would like to benchmark my threadripper system, let me know via email. On the 1920x (12 cores)...
by jpringle
Sat Oct 07, 2017 1:35 pm
Forum: ROMS Problems
Topic: Docker container for ROMS?
Replies: 7
Views: 3209

Re: Docker container for ROMS?

A naive question. For multi-threaded or multi-process programs like ROMS, is there any significant performance penalty for using something like docker?

Jamie
by jpringle
Tue Sep 12, 2017 6:14 pm
Forum: ROMS Benchmarks
Topic: Benchmarking Epyc, Ryzen, and Xeon: Tyranny of Memory
Replies: 5
Views: 3611

Benchmarking Epyc, Ryzen, and Xeon: Tyranny of Memory

Dear all -- I hope some of you find this useful; I have been researching purchasing a new modeling server, and the results should be interesting to those trying to optimize the performance on their own machines, or are thinking of purchasing new machines. There are a number of new architectures that...
by jpringle
Wed Jul 26, 2017 2:37 pm
Forum: ROMS Benchmarks
Topic: Ryzen 1800x Benchmarking and memory bandwidth
Replies: 2
Views: 1776

Re: Ryzen 1800x Benchmarking and memory bandwidth

Sacha and All-- A couple of things. First, the AMD Ryzen has a dual memory channels, so is has less memory bandwidth than the x99 Intel boards. Compared to older AMD processors, the L1 and L2 cache's are private to each core, but the L3 cache is shared amoung 4 cores. But see below for more on this,...
by jpringle
Tue Jul 25, 2017 9:43 pm
Forum: ROMS Benchmarks
Topic: Ryzen 1800x Benchmarking and memory bandwidth
Replies: 2
Views: 1776

Ryzen 1800x Benchmarking and memory bandwidth

Dear all -- IF YOU ARE INTERESTED IN THIS POST, PLEASE ALSO SEE: https://www.myroms.org/forum/viewtopic.php?f=29&t=4665 I hope some of you find this helpful. I needed a computer for a new graduate student to run models and do data analysis. For 1500$ I built a Ryzen 1800x box. Since this is a new an...
by jpringle
Tue May 16, 2017 2:02 pm
Forum: ROMS Discussion
Topic: Cheap Ryzen modeling setup
Replies: 0
Views: 684

Cheap Ryzen modeling setup

Dear all -- I need to build/acquire a linux box for a new graduate student for process oriented ROMS modeling and ocean model data analysis, with a side of embarrassingly parallel ecological modeling. I have a budget of 1500 (excluding the massive pile of disks for data storage). I am wondering if a...
by jpringle
Mon Nov 21, 2016 8:37 pm
Forum: Job Opportunities
Topic: Funding for graduate student
Replies: 0
Views: 2276

Funding for graduate student

I have funding available for graduate students at the University of New Hampshire to study the interaction of Western Boundary Currents and continental shelf flows. The applicant must posses strong quantiative skills, with a major in the sciences, mathematics or engineering. Applicants with either M...
by jpringle
Thu Sep 15, 2016 1:48 pm
Forum: ROMS Discussion
Topic: Full vorticity equations
Replies: 5
Views: 2472

Re: Full vorticity equations

I do not know if this helps, but attached is a calculation of relative and potential vorticity that exactly parallels the code in Vorticity.F, but implemented in python. It calculates both 3D and shallow water vorticity. Please look at the function defineVorticity() for the calculation. I have inclu...
by jpringle
Wed Dec 02, 2015 12:49 pm
Forum: ROMS Bugs
Topic: issue with coarse2fine.m
Replies: 3
Views: 2144

Re: issue with coarse2fine.m

It would be easier to debug if you printed out what the attribute name is. You could add an fprint by line 112 of nc_create, and print out what aname is. This might provide insight.

Cheers,
Jamie
by jpringle
Thu Oct 22, 2015 3:25 pm
Forum: ROMS Discussion
Topic: Rivers in nested grids
Replies: 2
Views: 959

Re: Rivers in nested grids

While waiting for some other runs to complete, I did some simple test cases with nested grids, and can confirm that what John said is true.

Jamie
by jpringle
Mon Oct 12, 2015 12:37 am
Forum: ROMS Discussion
Topic: Rivers in nested grids
Replies: 2
Views: 959

Rivers in nested grids

Dear all -- I am having some trouble with nesting and river inflows. I have justed started to implement rivers entering into my domain. Some rivers enter where the fine grid overlaps the coarse grid. When I run the model with nesting, it blows up quickly. When I run with rivers in just coarse grid (...
by jpringle
Wed Sep 09, 2015 8:51 pm
Forum: ROMS Problems
Topic: Bug in large spherical nested run?
Replies: 5
Views: 2151

Re: Bug in large spherical nested run?

Just to update -- the discrepancy in the area of grid cells between the fine and coarse grids was largely caused by an inconsistency between mat2roms_mw and coarse2fine. The former used sw_dist to compute distance between grid points, the later used gcircle. sw_dist uses the "plain sailing" method t...
by jpringle
Wed Sep 09, 2015 1:45 pm
Forum: ROMS Problems
Topic: Bug in large spherical nested run?
Replies: 5
Views: 2151

Re: Bug in large spherical nested run?

The area of the 9 rho cells of the fine grid is 0.144% greater than the area of the associated coarse grid rho cell, with a very weak dependency on latitude. This is of the same order of magnitude of the discrepancy of mass flux at the eastern boundary. I am investigating the origin of this issue. I...
by jpringle
Tue Sep 08, 2015 7:29 pm
Forum: ROMS Problems
Topic: Bug in large spherical nested run?
Replies: 5
Views: 2151

Re: Bug in large spherical nested run?

Hernan -- I will compare the averaged metrics tomorrow, when I have time to code. A question and two points first. 1) It is a curvilinear spherical grids -- the delta-latitude and delta-longitudes are both constant, and the grid is north/south and east/west aligned. 2) There is no wind, so the wind ...
by jpringle
Tue Sep 08, 2015 4:06 pm
Forum: ROMS Bugs
Topic: bug in check_massflux in nesting.F
Replies: 2
Views: 2135

Re: bug in check_massflux in nesting.F

Hernan -- I have posted the information you want in viewtopic.php?f=17&t=3957 ; I did not put it as a bug yet since I have not isolated the exact cause.

Jamie
by jpringle
Tue Sep 08, 2015 4:04 pm
Forum: ROMS Problems
Topic: Bug in large spherical nested run?
Replies: 5
Views: 2151

Bug in large spherical nested run?

NEGLECT THIS MESSAGE -- THE PROBLEM WAS NOT WHERE I SUSPECTED IT WAS HERE. THERE IS SOME USEFUL INFORMATION BELOW ABOUT AREA CALCULATIONS WITH VARIOUS GRID PACKAGES, SO I AM NOT DELETING IT. I have been debugging on and off for several weeks what appears to be a bug (or my stupidity) in nesting in ...
by jpringle
Sat Aug 29, 2015 7:48 am
Forum: ROMS Bugs
Topic: bug in check_massflux in nesting.F
Replies: 2
Views: 2135

bug in check_massflux in nesting.F

In check_massflux in nesting.F, the variable ng in # ifdef NESTING_DEBUG IF (DOMAIN(ng)%SouthWest_Test(tile)) THEN IF (Master) THEN WRITE (300,10) 'Western Boundary Mass Fluxes: ', & & cr, dg, rg, iif(rg), iic(rg), INT(time(rg)) END IF END IF ! # endif should be "ngf". "ng" is not defined in this su...
by jpringle
Tue Aug 18, 2015 2:53 pm
Forum: ROMS Bugs
Topic: Bug in nesting when MASKING not defined
Replies: 1
Views: 1486

Bug in nesting when MASKING not defined

In the latest ROMS, the model does not compile when NESTING is defined but MASKING is not. The error is minor; mask_hweights is always defined at the top of nesting.F even when MASKING is on. The fix is straightforward: *** nesting.F_old 2015-08-18 10:49:28.000000000 -0400 --- nesting.F 2015-08-18 1...
by jpringle
Mon Aug 17, 2015 9:53 pm
Forum: ROMS Bugs
Topic: Bug in fine2coarse.m for nesting
Replies: 6
Views: 2415

Re: Bug in fine2coarse.m for nesting

My original edits to fine2coarse.m, and the "official" version on the Subversion repository, contain an error in which the curvilinear metrics dmde and dndx are not written to the coarse grid. Since those fields are defined in c_grid(), the grid file has fill values for those metrics. The fixed code...
by jpringle
Mon Aug 17, 2015 5:46 pm
Forum: ROMS Discussion
Topic: mat2roms with modern matlab
Replies: 1
Views: 987

mat2roms with modern matlab

Dear all -- I would like to create a ROMS grid file from a grid of h at longitude and latitude points. In the past this was possible with mat2roms_rps.m ( https://github.com/rsignell-usgs/seagrid/blob/master/seagrid/mat2roms_rps.m ) Unfortunately, the code I can find on the web for this uses Chuck D...
by jpringle
Thu Aug 13, 2015 5:40 pm
Forum: ROMS Bugs
Topic: contact.m issue with fine grid on border of coarse grid
Replies: 2
Views: 2188

Re: contact.m issue with fine grid on border of coarse grid

Ah... I noticed in an email from John Wilkins that he told me We are taking this a step at a time. As you say, presently the Matlab tools have been written assuming the nest is wholly within the parent, but the ROMS design anticipates the day that the contact file can allow a nest to cross the paren...
by jpringle
Wed Aug 12, 2015 6:33 pm
Forum: ROMS Bugs
Topic: contact.m issue with fine grid on border of coarse grid
Replies: 2
Views: 2188

contact.m issue with fine grid on border of coarse grid

Dear all -- I just want to document a bug in contact.m, and to ask if anyone has succeed in putting a refined grid next to a model boundary? I am using the latest version of the matlab tools, from SVN revision 722. I create a coarse resolution grid, which I have attached to this post. I then create ...
by jpringle
Tue Jul 21, 2015 10:30 am
Forum: ROMS Bugs
Topic: Bug in fine2coarse.m for nesting
Replies: 6
Views: 2415

Re: Bug in fine2coarse.m for nesting

My fine2coarse code does not set either the coarse_factor or refine_factor attributes of either grid; see https://www.myroms.org/forum/viewtopic.php?f=1&t=3698&p=14962#p14962 ; I am not sure fine2coarse is a good place to do so, and will not be able to do so until I have a better understanding of th...
by jpringle
Tue Jul 21, 2015 7:50 am
Forum: ROMS Usage
Topic: How to generate and use composite grids?
Replies: 16
Views: 5905

Re: How to generate and use composite grids?

Hernan & Kate -- Kate -- to start to get things to work, I have had to add the refine_factor attributes by hand. My efforts have been interrupted by my vacation, but will pick up in two weeks or so. I am not sure if I will end up going fine2coarse or coarse2fine, then edit the bathymetry in the resu...
by jpringle
Thu Jul 02, 2015 6:02 pm
Forum: ROMS Bugs
Topic: Bug in fine2coarse.m for nesting
Replies: 6
Views: 2415

Re: Bug in fine2coarse.m for nesting

Attached is a corrected fine2coarse.m, a testing code, a file with grid information for it to read, and a little routine to plot grids. The testing harness expects the rest of the ROMS Matlab tools to be in the path. Please make sure you are running the provided fine2coarse.m, and not the one that c...
by jpringle
Thu Jul 02, 2015 3:28 pm
Forum: ROMS Bugs
Topic: Bug in ana_grid.h for BENCHMARK
Replies: 0
Views: 1556

Bug in ana_grid.h for BENCHMARK

There is a bug in the definition of lonp,latp,lonr,latr,lonu,latu and lonv,latv in ana_grid.h for the benchmark case. It does not affect the solution, since the metric definitions are correct. However, it can make interpreting plots difficult, and will cause errors if this analytical grid is then pr...
by jpringle
Thu Jul 02, 2015 3:25 pm
Forum: ROMS Bugs
Topic: Bug in fine2coarse.m for nesting
Replies: 6
Views: 2415

Re: Bug in fine2coarse.m for nesting

Before anyone else spends time on this, I am working on fixing this code. I will let people know when a working version exists and has been tested.

Jamie
by jpringle
Tue Jun 30, 2015 9:31 pm
Forum: ROMS Bugs
Topic: Bug in fine2coarse.m for nesting
Replies: 6
Views: 2415

Bug in fine2coarse.m for nesting

I am developing a new modeling setup with a simple nested grid configuration. Following Hernan's advice, I am starting from a full domain fine grid and extracting the coarse grid from it. However, the fine2coarse.m downloaded from the SVN repository as of this morning is completely broken (SVN revis...
by jpringle
Fri May 22, 2015 3:52 pm
Forum: ROMS Bugs
Topic: bug in ana_dqdsst.F
Replies: 6
Views: 3227

Re: bug in ana_dqdsst.F

Agree.
by jpringle
Fri May 22, 2015 1:23 pm
Forum: ROMS Bugs
Topic: bug in ana_dqdsst.F
Replies: 6
Views: 3227

Re: bug in ana_dqdsst.F

John -- Thanks. You are right, the inclusion of the surface layer depth in the formulation is deeply problamatic. However, it is a science issue not a programming issue. In this code we prescribe the surface heat flux as a function of SST. Thus the time rate of change of temperature is set by the ra...
by jpringle
Thu May 21, 2015 1:46 pm
Forum: ROMS Bugs
Topic: bug in ana_dqdsst.F
Replies: 6
Views: 3227

Re: bug in ana_dqdsst.F

Dear Zhang -- You are correct. My code is correct, but the comments are wrong. The comments should be changed to ! !----------------------------------------------------------------------- ! Set surface heat flux sensitivity to SST (m/s). !-------------------------------------------------------------...
by jpringle
Wed May 20, 2015 3:58 pm
Forum: ROMS Bugs
Topic: bug in ana_dqdsst.F
Replies: 6
Views: 3227

bug in ana_dqdsst.F

Dear Hernan et al -- I think I have found a bug in ana_dqdsst.F. The stub code from the most recent model version on subversion reads: ! !----------------------------------------------------------------------- ! Set surface heat flux sensitivity to SST (m/s/degC). !----------------------------------...
by jpringle
Tue May 12, 2015 3:39 pm
Forum: ROMS Installation
Topic: OSX ./build.bash problems (upwelling test case).
Replies: 15
Views: 10510

Re: OSX ./build.bash problems (upwelling test case).

Old thread, but I hope this helps someone. You can run ROMS on OS X/mac using macports to install all the libraries. But was noted above, the netcdf is a bit tricky. To get it to work, you must specify the variant of netcdf-fortran to install that is consistent with your fortran compiler. To do this...
by jpringle
Sat May 09, 2015 3:29 pm
Forum: ROMS Discussion
Topic: recent compiler benchmarks 2015
Replies: 0
Views: 718

recent compiler benchmarks 2015

Dear ROMS runners -- I am starting a ROMS project after a hiatus. Has anyone benchmarked compilers for Intel architectures recently (i.e. gfortran 4.9 or 5, and recent Intel compilers)? On other codes of mine, the gfortran compiler has become much faster. I wonder if the same is true for ROMS? It wo...
by jpringle
Mon Apr 20, 2015 1:14 pm
Forum: ROMS Discussion
Topic: Problems with unforced model -- unrealistic circulation
Replies: 9
Views: 2226

Re: Problems with unforced model -- unrealistic circulation

When you are testing for the effects of pressure gradient error and topography, I would set all the boundaries to closed. I am worried about how the currents are reacting to both the northern and southern boundaries. I would not be surprised if the currents were substantially less if the boundaries ...
by jpringle
Wed Jan 21, 2015 7:04 pm
Forum: Job Opportunities
Topic: Student funding available, University of New Hampshire
Replies: 0
Views: 2523

Student funding available, University of New Hampshire

I have funding available for graduate students at the University of New Hampshire to study the interaction of Western Boundary Currents and continental shelf flows. The applicant must posses strong quantiative skills, with a major in the sciences, mathematics or engineering. Applicants with either M...
by jpringle
Thu May 29, 2014 8:31 pm
Forum: ROMS Problems
Topic: ocean_frc.nc and KPP mixing
Replies: 1
Views: 899

ocean_frc.nc and KPP mixing

I must be doing something silly, but it is escaping me. I have just turned on the LMD_* options to implement KPP mixing. I have ANA_STFLUX and ANA_SMFLUX defined, which should give me tracer fluxes and momentum fluxes. Temperature is the only tracer (there is no salinity). When I turned on the LMD_*...
by jpringle
Fri May 24, 2013 3:09 pm
Forum: ROMS Discussion
Topic: Particle tracking, and differences between AGRIF and Rutgers
Replies: 2
Views: 1761

Re: Particle tracking, and differences between AGRIF and Rut

As always, thanks Kate! I will look at tracmass and see how easy it is to incorporate behavior and vertical mixing. LTRANS will require some recoding to recreate w or omega from u and v ARIANE has a series of weird coordinates to specify time and inititial condition that hurt my brain. If anyone nee...
by jpringle
Thu May 23, 2013 8:32 pm
Forum: ROMS Discussion
Topic: Particle tracking, and differences between AGRIF and Rutgers
Replies: 2
Views: 1761

Particle tracking, and differences between AGRIF and Rutgers

Colleagues -- I am trying to do some particle tracking in ROMS output; the model runs were not done by me, and were made with ROMS-AGRIF V3. I have several questions here; I am also asking them on the AGRIF forum. 1) Has anyone used LTRANS v2 with AGRIF? 2) Is the vertical stretching and transform i...
by jpringle
Mon Dec 17, 2012 12:50 am
Forum: Job Opportunities
Topic: PhD student position at National University of Singapore
Replies: 1
Views: 2216

Re: PhD student position at National University of Singapore

This is the middle of the Christmas vacation season in most of Europe and the Americas -- perhaps reposting this in a month or two might get more of a response if you are interested in students from here...

cheers,
Jamie
by jpringle
Tue Oct 25, 2011 1:12 pm
Forum: ROMS Discussion
Topic: NONLIN_EOS in upwelling example creates velocities
Replies: 6
Views: 2212

Re: NONLIN_EOS in upwelling example creates velocities

This comment is orthogonal to Sasha's comment -- and his certainly the more interesting of the two. However, it is worth noting that if you have stratification over a sloping bottom, in the presence of vertical mixing, you will have an adjustment of the density near the bottom. If the mixing were is...
by jpringle
Sun Jul 31, 2011 6:23 pm
Forum: ROMS Installation
Topic: Netcdf 3.6.3 problem
Replies: 7
Views: 2244

Re: Netcdf 3.6.3 problem

Dear Linda--

It appears that it passes the fortran tests, and fails the C++ tests. Since you only need the fortran libraries for ROMS, it seems like you should be good to go once you install it.

Cheers,
Jamie Pringle
by jpringle
Wed May 11, 2011 2:28 pm
Forum: ROMS Problems
Topic: Poor-man's super-(mini?)-computer revisited in 2011? Advice?
Replies: 0
Views: 1000

Poor-man's super-(mini?)-computer revisited in 2011? Advice?

Dear Colleagues -- For the last 6 years, my ocean modeling needs have been well met by a 6 node cluster; each node a dual Opteron-250 with a single core for a total of 12 cores. This system has enough power to meet my modest process-oriented modeling needs; typical runs for me have a grid size of 38...
by jpringle
Tue Mar 08, 2011 2:11 pm
Forum: ROMS Sediment
Topic: diagnosing vertical coordinate from history/grid files
Replies: 8
Views: 5984

Re: diagnosing vertical coordinate from history/grid files

Kate, Sasha & Hernan--

Thanks for your replies, they have been very helpful.

Cheers,
Jamie
by jpringle
Mon Mar 07, 2011 4:42 pm
Forum: ROMS Sediment
Topic: diagnosing vertical coordinate from history/grid files
Replies: 8
Views: 5984

diagnosing vertical coordinate from history/grid files

Hi all -- I have a simple question; I fear perhaps the answer is not so simple. I am involved in a couple of efforts to read in ROMS history and grid files, and either plot them or compute other products from them (e.g. Lagrangian particle paths). I have several questions 1) What is the best way to ...
by jpringle
Thu Aug 14, 2008 6:32 pm
Forum: ROMS Information
Topic: ROMS, the Cell Processor, and other exotic architecture
Replies: 1
Views: 1829

ROMS, the Cell Processor, and other exotic architecture

Hi all- Several people at my university are trying to purchase a computer cluster with either IBM's Cell Processor (same as in the Sony Playstation) or with many GPUs to use as co-processors. Has anyone tried to modify the ROMS code to take advantage of these exotic (for now) architectures, and what...
by jpringle
Sat May 17, 2008 2:48 pm
Forum: ROMS Discussion
Topic: Left side of the upwelling example
Replies: 3
Views: 1802

Carl- The upwelling code is define to use a constant value of vertical mixing, as you can tell from this code in upwelling.h #if defined GLS_MIXING || defined MY25_MIXING # define KANTHA_CLAYSON # define N2S2_HORAVG #else # define ANA_VMIX #endif and by noting that neither GLS_MIXING or MY25_MIXING ...
by jpringle
Mon Jan 07, 2008 1:38 am
Forum: ROMS Tools and Techniques
Topic: A question about the gridgen
Replies: 7
Views: 3521

As evidenced by my silly answer above, I had not run into this problem with the simple domains of my application, so I had not ever worried how to solve this problem. I have thus never implemented a solution. When I have to, I will, but if someone beats me to it, I would be happy to incorporate thei...
by jpringle
Sat Jan 05, 2008 3:05 am
Forum: ROMS Tools and Techniques
Topic: A question about the gridgen
Replies: 7
Views: 3521

I don't know if this is the issue, but when I was testing Pavel's gridgen, it occasionally threw up nan's if my domain was perfectly rectangular, but if I moved one of the corners by even an infinitesimal amount, the nan's went away. This was a flakey problem, that only occured for certain resolutio...
by jpringle
Sun Sep 09, 2007 4:15 pm
Forum: ROMS Problems
Topic: How to increase ROMS parallel efficiency
Replies: 5
Views: 1948

Roughly, the efficiency of the parallelization is reduced by the following * Slow interconnects *Small tiles, so that there is a lot of communications (which scales as the perimeter of tile) for each bit of internal computation in the tile (which scales as the number of gridpoints in the tile). Your...
by jpringle
Fri Sep 07, 2007 1:50 am
Forum: ROMS Problems
Topic: ROMS2.3 background running problem under PGI + MPI
Replies: 4
Views: 1551

Try putting the model run with a shell script, executing the shell script, and then logging out.

Our you can use the "screen" utility, which lets you disconnect from an active shell session, and reconnect to it later.

Cheers,
Jamie
by jpringle
Fri Sep 07, 2007 1:48 am
Forum: ROMS Problems
Topic: How to increase ROMS parallel efficiency
Replies: 5
Views: 1948

The efficiency of ROMS in parallel mode is a strong function of 1) the grid size 2) the interconnect speed 3) the configuration of MPI, and 4) the configuration of the model (parameters such as NDTFAST can make a big difference). It is hard to answer a question such as yours with no knowledge of the...
by jpringle
Wed May 09, 2007 2:31 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34376

I have a matlab code that calls gridgen and allows you to specify multiple points along each edge, and to specify (roughly) a spatially variable resolution within the model domain. It works well for me, and is reasonably well documented. One caution, however -- if you have a very high-resolution coa...
by jpringle
Tue Feb 27, 2007 2:52 pm
Forum: ROMS Discussion
Topic: Inflow-Outflow options for reservoirs
Replies: 12
Views: 3875

Dmitry-

I would be happy to, but I cannot find your email address. You can find my contact info at my web page, http://oxbow.sr.unh.edu .

Cheers,
Jamie
by jpringle
Sun Feb 25, 2007 3:07 pm
Forum: ROMS Discussion
Topic: Inflow-Outflow options for reservoirs
Replies: 12
Views: 3875

ROMS can handle multiple inflow points. This smells like a subtle coding error. My biggest errors in trying to specify point sources in ROMS have occurred because I calculated the positions in matlab, and did not properly take into account the fact that for array start in fortran at index 0 are offs...
by jpringle
Sat Feb 24, 2007 5:06 pm
Forum: ROMS Discussion
Topic: Inflow-Outflow options for reservoirs
Replies: 12
Views: 3875

Have you turned on the UV_PSOURCE, TS_PSOURCE and ANA_PSOURCE in the cppdefs.h file for your application?

Jamie
by jpringle
Thu Feb 08, 2007 8:27 pm
Forum: ROMS Installation
Topic: ROMS on an Intel Mac with a Core Duo and free compilers
Replies: 1
Views: 1851

ROMS on an Intel Mac with a Core Duo and free compilers

Hi all- I have experimented with running ROMS 2.2 on a iMac 2Ghz Intel Core Duo processor, with 667 MHz DDR2 RAM. I used free compilers installed with fink. As you will see, I suspect that I would do better to use the Intel compiler, but I have not done so since for large runs I use my linux cluste...
by jpringle
Sat Dec 23, 2006 1:56 pm
Forum: ROMS Installation
Topic: ifort and Fedora, again
Replies: 1
Views: 1994

Craig (& others) I have gone through this on numerous systems. The main trick is figuring out how MPI-whatever runs its various sub-jobs on each system. Does it spawn a csh? a sh? Can you specify? Once you do, you can place the ulimit, etc commands in the appropriate .bashrc .cshrc or whatever. To d...
by jpringle
Fri Dec 01, 2006 1:44 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34376

Dear all- If you are using Pavel of CSIRO's gridgen, I have a little chunk of matlab code which allows you to specify the resolution of the grid along the edges of the model domain. If you are interested, mail me. I am not yet distributing it publicly because the rest of my evolving non-interactive ...
by jpringle
Wed Oct 11, 2006 5:04 pm
Forum: ROMS Usage
Topic: geostrophically adjusted initial condition.
Replies: 6
Views: 3471

Thanks a bunch yall. John Wilkin's code worked fine for my use, with minor modifications. It results in a cleaner initialization, and thus is easier for me to explain the initial evolution in my class.

Cheers,
Jamie
by jpringle
Mon Oct 09, 2006 6:31 pm
Forum: ROMS Usage
Topic: geostrophically adjusted initial condition.
Replies: 6
Views: 3471

I am starting a short, semi-idealized run with density features that are only 2-3 times larger than the radius of deformation. As part of the adjustment processes, gravity waves rattle around the domain, and bother the boundary condition. I could get away with a simpler model setup if I did not have...
by jpringle
Mon Oct 09, 2006 4:46 pm
Forum: ROMS Usage
Topic: geostrophically adjusted initial condition.
Replies: 6
Views: 3471

geostrophically adjusted initial condition.

Dear hive mind- Does anyone have a code that takes an initial density field on a ROMS grid (or any other grid) and a level of no motion and uses it to return a geostrophically balanced flow field? It would be nice if it delt with curved grids... It would not be hard to do, but I am hoping to avoid r...
by jpringle
Tue Sep 26, 2006 1:41 pm
Forum: ROMS Discussion
Topic: Understanding T_cline
Replies: 1
Views: 1466

You can find scripts that allow you to experiment with the vertical grid parameters in part of the discussion thread "Stretching parameters - vertical coordinates" on this bulletin board. There is also some discussion of these parameters in the old manual for SCRUM, which can be found at http://mari...
by jpringle
Thu Sep 21, 2006 5:54 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34376

Hi all- I think Kate's problems are, indeed, due to her mexcdf install. Several other folks have used my code without an issue. I am not sure, however, what the issue is, which is less helpful than I would like to be. Also, Kate mentioned This works for ETOPO5, ETOPO2, and now GEBCO, .... If you've ...
by jpringle
Mon Sep 18, 2006 12:33 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34376

Hi everyone- A few weeks ago I had this problem, and I created a matlab code that uses Sakov's grid gen to make a matlab domain, useing Rich P's m_map routines and some code I got from Rich Signell to create ROMS grid files from matlab data. It is relatively primitive right now, but it is easy to us...
by jpringle
Mon Apr 24, 2006 6:12 pm
Forum: ROMS Problems
Topic: How to run ROMS with MPI + OpenPBS with every processors?
Replies: 2
Views: 3442

Hi- I do not recognize your particular error message. However, it smells like a problem in the configuration of your mpi system. You should certainly be able to run one part of your job on each processor. However, if you are having troubles running the code, you should try getting MPI to work on sim...
by jpringle
Mon Nov 07, 2005 3:05 pm
Forum: ROMS Problems
Topic: Blow-up
Replies: 3
Views: 2489

John- You would be able to handle a freshwater wedge with a small vertical resolution in a layer model, like those from FSU, in which the depth of the layers can vary in time. However, in a model like ROMS where the level positions are fixed in time, you must have about six or more levels IN your th...
by jpringle
Fri Oct 07, 2005 8:23 pm
Forum: ROMS Benchmarks
Topic: Benchmarks
Replies: 31
Views: 22170

infiniband vrs. gigabit

Hi all-- I wondered if the varying results people get when they try to understand the relative importance of the interconnects could have to do with the relative importance of the 2D timestepping (lots of little messages) vrs. the 3D timesteps (fewer, larger messages). So I ran the benchmark1 test w...
by jpringle
Thu Jun 30, 2005 7:57 pm
Forum: ROMS Benchmarks
Topic: Benchmarks
Replies: 31
Views: 22170

Dual core/dual processor Opteron 275 benchmarks

Hi all-- Courtesy of Western Scientific Inc, I benchmarked ROMS 2.2 on a dual processor, dual core Opteron 275 rig. These chips have two processing cores per chip, so a workstation with two processor chips will appear to Linux to have four processors. The rig I tested had the following specs: 1) 8GB...
by jpringle
Sun May 15, 2005 8:06 pm
Forum: ROMS Benchmarks
Topic: Benchmarks
Replies: 31
Views: 22170

dual core benchmarks

Has anyone used the standard benchmark cases (for examples, those in Rich Signell's benchmarks above) to exam the speed of the dual core operteron processors that AMD has recently released? For the problem I have in mind, I plan to be running on a 5 or 6 node linux cluster, with each node haveing tw...
by jpringle
Sun May 15, 2005 8:04 pm
Forum: ROMS Discussion
Topic: Interconnect speed for MPI: Gigabit, Myrinet and Infiniband
Replies: 5
Views: 4017

Dual core benchmarks

Has anyone used the standard benchmark cases (for examples, those in Rich Signell's benchmarks above) to exam the speed of the dual core operteron processors that AMD has recently released? For the problem I have in mind, I plan to be running on a 5 or 6 node linux cluster, with each node haveing tw...