Ocean Modeling Discussion

hetland

We are looking for a postdoc to look at regional coupled air-sea modeling for our new offshore wind energy earthshot project, ACE-FWIC. For information about the Energy Earthshot initiative, see: https://www.energy.gov/energy-earthshots-initiative For more details on the project, see: https://www ...

hetland

The Atmospheric, Climate, and Earth Systems Division at Pacific Northwest National Laboratory (PNNL) seeks a postdoctoral research associate to work on nesting the Regional Ocean Modeling System (ROMS) within the ocean component (MPAS-O) of a global climate model (E3SM). The successful candidate ...

hetland

You can find a very recent version in the octant tree. They are basically mirrored here:

https://github.com/hetland/octant/tree/master/external

I assume since you got octant, you can also get this.

hetland

You can find it here: https://code.google.com/p/gridgen-c/ But you need a few more things to compile it. All of the relevant links are: https://code.google.com/p/gridgen-c/ https://code.google.com/p/gridutils-c/ https://code.google.com/p/nn-c/ https://code.google.com/p/csa-c/ You're welcome, -Rob

hetland

Frist of all, the version of octant on googlecode is very old, and should be considered obsolete. I have migrated the codebase to github. You can find it here: https://github.com/hetland/octant Some recent changes include pulling some of the compiled code out so that it is easier to install. Notably ...

hetland

Did you make either package before using it? You need to do something like this: python setup.py build sudo python setup.py install In order for the C-libraries to be built, and to install everything in the right place. If you did this, then your build is failing somewhere, and you need to look at ...

hetland

Which pyroms?

hetland

Texas A&M University, Department of Oceanography seeks to hire a Postdoctoral Research Associate in Coastal Ocean Hydrodynamic Modeling, starting as soon as possible . The appointment is for 12 months, with an additional funding of at least one year available upon satisfactory performance. The ...

hetland

The googlecode version of octant is deprecated. You should use the one on github: https://github.com/hetland/octant You can download it using the command: git clone https://github.com/hetland/octant.git For this version, I separated out the gridgen stuff, so it should be much easier to install. -Rob ...

hetland

There are a number of reasons for this discrepancy. First of all, what does the data represent? A climatology? A synoptic cruise? At what level were the salinities measured (usually a few meters depth for standard hydrography)? As for errors in the model, the differences you show are too far away ...

hetland

Can you give a more specific error? I think this is a very easy fix -- just changing one line of an import. But we need to know which file is the problem.

hetland

I am not sure how to specify the data in the forcing file. I have the following but I am not sure if it is correct, do I need to have river_Vshape? And should I have a transport value for each time and river? [/code] Yes, and yes. I am not sure if there is a 'default' Vshape, but I think it is best ...

hetland

Here is a (slightly old) python script that will give you some guidance in making river forcing files. Also, if you don't see the rivers at all, you need to back up some steps. Make sure you can get the RIVERPLUME test case to work, and then work from there. Make sure you are compiling the code you ...

hetland

All ROMS applications can take forcing and bathymetry (and other) information from either an analytical file (look in the Analytical directory for many, many examples) or from a netCDF file. The variables, in the end, are the same to ROMS, it is just a matter of whether they are defined by FORTRAN ...

hetland

Texas A&M University, Department of Oceanography seeks to hire a Postdoctoral Research Associate in Coastal Ocean Hydrodynamic Modeling, starting as soon as possible . The appointment is for 12 months, with an additional funding of at least one year available upon satisfactory performance. This ...

hetland

I'm not sure what is going on. Since you can import netCDF4 by hand, it seems like that is all fine. You can try to find where pypurene is loaded in pyroms (it will be in a try/except block), and hardwire in a netcdf4 import. I don't think that the latest version of octant does this, though. You may ...

hetland

Your noise looks like Rossby waves (note the pattern that the noise is least at the equator, and seems to be propagating faster to the south). I suspect that you have some strangeness at your open boundaries that is causing this noise.

What are your OBCs?

hetland

I suspect that your netcdf build actually built netcdf3 libraries. Double check the include and library dirs. Look at the output of configure and make.

Also, DAP support is built into the netCDF4 libraries, not HDF. So there should be no problem there.

hetland

I usually do something like this to fill in undefined values (assuming you use masked arrays for your variables): grd.dx = grd.dx.filled( grd.dx.mean() ) grd.dy = grd.dy.filled( grd.dy.mean() ) grd.dndx = grd.dndx.filled( grd.dndx.mean() ) grd.dmde = grd.dmde.filled( grd.dmde.mean() ) grd.angle ...

hetland

Right... After looking at the octant code - it seems that it does not save sigmas to disk (Rob?). If you are using a later version of octant that calls the gridgen libraries directly (instead of a straight command line call to gridgen), no files are saved. I think this is what you are using, so you ...

hetland

Well, since you can get octant.gridgen to work (I assume the output of the square looked sensible?), then it must be the gridgen library. I still suspect this might be a 32/64 bit issue. There are many options to put into griggen to tell how many times to itterate, for example. You can try to modify ...

hetland

Can you see if your code works with a square, that is x = [1, 0, 0, 1] y = [1.1, 1.0, 0., 0.] beta = [1, 1, 1, 1] That way you can isolate the problem to the gridgen library. Also, I seem to remember some issues with compiling the gridgen library with 64 bit. I have found that 32 bit python, numpy ...

hetland

The mixing value for salinity is used for all passive tracers, as this represents the mixing of actual molecules. Heat can be transferred without moving molecules around.

hetland

Texas A&M University, Department of Oceanography seeks to hire a Postdoctoral Research Associate in Coastal Ocean Hydrodynamic Modeling, starting September 1, 2010 or sooner if possible. The appointment is for 12 months , with an additional 12 months of funding available upon satisfactory ...

hetland

I think it is important to understand if you have a propagating or standing wave. Usually, this boils down to large vs. small domains, respectively. I usually just specify sea-level on my boundaries for small domains, since the tides at my boundaries have both the incoming and outgoing waves in ...

hetland

There is a known issue with openmpi that gives an error like this. I used version openmpi-1.2.8 and got this error (this is the version that ships with the latest version of rocks, so you probably have this, or older..). This flag helped: -mca mpi_leave_pinned 0 as in: /usr/mpi/gcc/openmpi-1.2.8/bin ...

hetland

I think that the current logic is flexible enough to allow you to manipulate the I/O in a satisfactory way. The code is not flexible, it is broken. It does not do what is expected for the obvious cases. There is absolutely no reason that this simple subroutine should be so complicated that it ...

hetland

Texas A&M University, Department of Oceanography seeks to hire a Postdoctoral Research Associate in Coastal Ocean Hydrodynamic Modeling, starting September 1, 2009. The appointment is for 24 months . Primary responsibilities include assessing and improving a hydrodynamic model of surface currents ...

hetland

Pavel moved to Norway, and his web site was taken down by CSIRO. You can find his codes here:

http://code.google.com/p/octant/source/ ... ant/extern

Get it with a command like this:

svn checkout http://octant.googlecode.com/svn/trunk/octant/extern sakov

-Rob

hetland

It seems the new(?) UV_U3ADV_SPLIT does not work in 2D applications. It expects a tracer variable to be set, which of course does not exist.

hetland

I can't see why it would depend on application. I guess it would depend on hardware, compiler, etc. The previous benchmark explicitly left out i/o, so as only to test the computational engine. For an i/o benchmark, we would need a very very large domain that did as little computation as possible ...

hetland

For what it's worth, I have seen this exact sort of behavior. Sometimes, I need to decrease the timestep, but sometimes, I just need to restart the run, and it sails through the previous crash without any problems. I usually don't even see any problems in the history file that suggests that a ...

hetland

I can't think of a single good reason not to use _FillValue. I've wondered for years why ROMS does not do this (but have been too lazy to write the wrapper). Other models, like GETM, do this, and suffer no ill effects. And it makes quick looks in ncview much nicer. Note, the values in the model ...

hetland

I would use gfortran (found here: http://r.research.att.com/tools/ ) instead of g95. I experimented with a number of gnu fortran variants on Mac OS X a while ago, and gfortran is definately the way to go. Here are some instructions for compiling all the stuff you need using ifort and gfortran: http ...

hetland

This problem is due to the changes in the netCDF4 API. Basically, the multifile support has been folded into the regular netCDF4 object. In other words, there is no more MFNetCDF4. I would recommend that you use the newer package (that has already fixed this bug) called octant. It is very similar to ...

hetland

Usually temporary environmental variable definitions go before the command (e.g., ./configure). Look at the script to make sure it is using the right fortran compiler. Also, try a which ifort command to make sure you are using the one you think (you will have to follow a few softlinks to get to the ...

hetland

Versions? Which ifort, which netcdf?

hetland

I mean 10.1.012, of course...

I have edited the above posts so that no one will ever know I was wrong. Sneaky, eh?

hetland

Inspired by some of the other build scripts I have seen using either the C shell or bash, I have made a python script that does the same. I feel the advantage of this script is that the options are more flexible -- it is easier to have more logic in a real programing language than a shell script ...

hetland

For the record, here are some build notes for netcdf and openmp on Leopard. I used ifort 10.1.012 and gfortran 4.3.0. Nothing too surprising here, but I finally decided to write all this down after I kept on forgetting which options needed to be specified. Notes for making netcdf3 and netcdf4 ...

hetland

I had exactly the same problem. The solution appears to be to get the latest version of the compiler (10.1.012). Intel has had some pretty sever problems with Leopard, and I'm not sure whether to blame Apple or Intel. Either way, it has not been good. See: http://softwarecommunity.intel.com/isn ...

hetland

OK, so Jacapo sent me the movie (that I made... but lost... now have again..). I put it back on my website; get it here:

http://pong.tamu.edu/~rob/movies/roms_project.mov

hetland

Indeed it is not there. At all. I checked... This is a bit embarrassing, but I hope that somebody downloaded a copy and can send it back to me again. Or, better, put it on the myroms website. However, in the worst case, I will redo the movie. The first was done in one take, and (as you can see by ...

hetland

Running a number of separate appendage grids may have advantages in some particular cases -- in particular, a long estuary attached to a coastal sea. However, in the long run, I would rather see ROMS do something more like GETM. GETM allows you to ignore tiles that are completely land. Presently ...

hetland

You need to specify values for everything where there is a NaN. Gridgen simply does not define the grid here, and they are not water points, so you just need to fill them in with values that do no harm. First, you need to set your mask to include the NaNs (and possibly other points if you have a ...

hetland

The first thing to do is take a look in the analytical section of the code (now, Functionals/ana_psource.h). All of the variables that are described there need to be set. It will be more clear what each variable does when you see how it is specified in the analytical code. Perhaps the least clear ...

hetland

I recently made a movie for a student on how to download roms via svn and create a project. I would like to say it is 'little' but it is 28 min and 200 megs... but perhaps you might still find it useful:

http://pong.tamu.edu/~rob/?p=98

hetland

The way to include tides in a painless way is to use a FLATHER/CHAPMAN combination, then specify the climatological sea surface height with tides in it. Thus your cpp options for an eastern open boundary with tides would look like this: #define EAST_FSCHAPMAN #define EAST_M2FLATHER #define EAST ...

hetland

There is not much to think about, as the release of tagged versions is done often for many open source software projects. This is how it goes: Official release versions (in the future, of course) are nothing more than snapshots of the svn repository. These are usually tagged in the svn repository ...

hetland

This short suite of benchmarks was done on a cluster of 2.0 GHz Duel Opterons. The cluster has eight nodes, two processors per node, and two cores per processor for a total of 16 actual CPUs and 32 kind-of CPUs. The nodes are connected with Infiniband. The total cost of the cluster was about 40K ...

hetland

Another thing to try is to move the points one further into the interior in analytical.F. Since this specifies the transport on a cell face, you will see your flux as a source of bouyancy on one side of the source, and a sink on the other. This will help you diagnose if the points are in the right ...

hetland

Perhaps your source point indicies are one off? Make sure they are on the edge of the domain interior, and not a point off..

-r

hetland

If you hate fink as much as I do (I _really_ hate fink), you can also install gfortran very easily from the binary distribution found at

http://hpc.sourceforge.net

I have used these versions successfully for a few years now.

-r

hetland

NOTE: THIS SECTION USED TO BE ABOUT PYROMS, WHICH HAS CEASED DEVELOPMENT. PLEASE USE OCTANT INSTEAD. I have started to create a tool suite for working with ROMS in python, called octant. You can get the source and see other project resources at http://octant.google.com/ This package is based on ...

hetland

Given that roms_sed is maintained with subversion (as is all the stuff on google code, and newer sourceforge projects), I thought I would share the best subversion book I have found yet: http://svnbook.red-bean.com There are others that are almost as good, but this one does a good job describing ...

hetland

Regarding MPI on the Mac, I got this note from Enrique Rob, I can't seem to be able to log on to the forum. Anyway, I have ROMS compiled on my new Mac Quad PRO using mpich2 and g95. e. ____________________________ Enrique Curchitser Institute of Marine and Coastal Sci. 71 Dudley Rd New Brunswick, NJ ...

hetland

Well, I already know that it ..works.. if you fill in pm and pn with non-zeros. I don't know if the solution is sensitive to the fill value. I suspect that it can really only come in through the viscous/diffusive terms, if at all. Rather than try the empirical approach, and see what happens with ...

hetland

I am working more on using Sakov's gridgen utility for ROMS grids. The output of this utility only returns 'wet' cells, that is, there is no information about the grid at all in some locations. Generally, this is not a problem -- these points would be masked anyways. However, it leads me to the ...

hetland

I have worked on this (a bit), and Brian Powel has worked on this more. Right now, we have both been unsuccessful at getting this to work with MPI. If you figure it out, let us know. I would start with LAMMPI, as they say they now have Mac compatible libraries available.

Good luck,

hetland

There is a parallel bug in roms-2.2 (and beyond, I think) which does not correctly read in point winds for parallel cases. Here is the fix to Nonlinear/set_data.F: ! ! If input point surface winds, rotate to curvilinear grid. ! IF (.not.Linfo(1,idUair,ng)) THEN DO j=MIN(Jstr-1,JstrR),JendR ...

hetland

I have also see people hack in an addition to the momentum equation one cell in from the source. That way, if you have a straight coastline, you can still have a river that comes in at an angle. However, I would not recommend this. If you really want to resolve the details of the circulation field ...

hetland

Did you install XTools? Did you get the latest version from the Developer Connection? As you probably know, gcc does not come installed by default on a Mac. Also, there have been pretty significant changes recently between gcc4.0 and gcc4.1. Make sure you are running gcc 4.1: $ gcc --version i686 ...

hetland

I've found that I need to copy libc or libc++ to a place the linker can find. This was a particular problem when the new macs updated to gcc4. See if you can find libc, and if it's not already in /usr/lib, put a copy there.

hetland

If your features are only 2-3 times the deformation radius, your flow field might not be all that geostrophic. I would think about spinning up diagnostically, to get a cyclostrophic/geostrophic/QG (or whatever) balance that better matches your density field *and* the physics at the scales you are ...

hetland

Below is an ncdump -h of a minimalist grid, created with gridgen so land points are not defined, that works in roms. I did linear interpolation on a retangular grid (i.e., using gridpoint values for x and y) of all the values, so that all of the values were defined everywhere, but just not used by ...

hetland

I have had much success on linux machines, after increasing the stack size by applying ulimit -s unlimited I think the heap is typically unlimited (or very large) by default on most linux distributions. The BENCHMARK cases are good to see how well you can deal with very large domains. Unfortunately ...

hetland

All I have made a gridgen wrapper for python. This is not too terribly different from using gridgen from the command line, but it does keep everything in one place. You can get it with subversion using the command svn co http://pong.tamu.edu/svn/python/trunk/gridgen gridgen You can browse the code ...

hetland

MATLAB is presently the defacto standard in analysis of ROMS model output. This is in part because MATLAB is the standard analysis tool for observational oceanogrpahy (although not always), but mostly because of the hurculean efforts of Rich Signell (with much help from Chuck Denham and John Evans ...

hetland

If this still works the same way it did when we first put tides in, all the _TIDES routines do is add the appropriate high-frequency signals to the low-frequency climatology signals. So, what you need to specify depends on how you set up your open boundary conditions. I would reccoment the CHAPMAN ...

hetland

You also need to make sure that you specify *all* of the other tracer variables in your river inflow values. Like, if you are running an NPZD model, you need to specify phytoplankton (et al.) as well. There may be a way to make ROMS default to a zero tracer value, but this is not the way it is set ...

hetland

I know that we have all developed little hacks in matlab to deal with structured grids, in particular, roms output. I have tried to make a few very simple, minimalist functions that do the things I find myself doing all the time. The goal is to have each function be simple enough that you do not ...

hetland

2.1 has subroutines that have been fixed (for example the wieghts for the 2D stepping) and typos (e.g., #ifdef CANUTO_A || CANUTO_B). Why not fix these things in the standard releases so that everybody doesn't need to discover these things for themselves (or reapply them each time they start from ...

hetland

Subversion seems to be the hippest CVS replacement, and many thought it should be used for the Linux source code (which used BitKeeper, until recently...). In the discussions on slashdot about replacing BitKeeper, I found some comments about monotone that seemed positive, so I checked it out and ...

hetland

Often, I find that I want to run roms over some set of parameters. The best way to do this is to make critical parameters dependent on the USER parameters in the roms.in file. I have written a program in python which does just this, automatically. The program, pspace.py , creates a series of input ...

hetland

I think we sould consider using some sort of version control system for distributing ROMS. This would be useful, because users could fix bugs in the code, and the code that we download could also be bug free. The second thing is a big deal for me. Every time I want to start over with ROMS, I need to ...

hetland

Yes, that did it. Youv'e saved me an afternoon with the debugger.

Thanks,

-Rob.

hetland

The trick above worked fine to get the input files read. I rebuilt netcdf with xlf (various different ways and versions), but I still get errors that DEF_VAR can't write. E.g., [...] DEF_VAR - unable to define variable: xl in NetCDF file: ocean_his.nc [...] Obviously the code compiles error free ...

hetland

How about Australia? (Or is that covered by 'Asia'?)

hetland

First of all, I was unclear when I said unphysical numbers. I meant local values of the outflow speed and Froude number not matching measured values but otherwise physically consistent, rather than numerical dispersion (i.e., the very high salinity). These slightly elevated values of salinity near ...

hetland

The Mississippi Delta is like a leaky sponge, with a few cuts in it. Southwest Pass (the major outflow) is resolved with three horizontal points, (slightly less than 1 km wide each), and it carries about 1/3 of the total flow. Maximum transports are about 4000 m3/s, and velocities in the vicinity of ...

hetland

Rivers are a boundary condition within the model. As such, they should be formed just like any other boundary condition -- in a way that is numerically sound and physically consistent. That said, a river boundary condition should look like river flow, especially if this is put at the head of some ...

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