Ocean Modeling Discussion

andres

Hi Jamie, Here at University of Concepcion we have the following approach. There is a course called Applied Ocean Modelling mostly for advanced undergraduates and the rare desperate graduate student whose advisor told her/him to add a chapter with a numerical model in their thesis. The objective is ...

andres

Hi,

I am looking for examples of operational ocean forecasting systems with atmosphere and/or wave coupling. Any info is appreciated.

andres

What is the advantage on moving the code from python2.7 to python 3?

andres

The datasets for roms/croco_tools are in

http://www.croco-ocean.org/download/datasets/

andres

Hi MIDHILAVARNAV,

These tools are used with ROMS_AGRIF/CROCO code, please post your questions here:

https://gforge.inria.fr/forum/forum.php?forum_id=3526

Please post there the crocotools_param.m or romtools_param.m file that you use.

andres

Hi MIDHILAVARNAV, These tools are used with ROMS_AGRIF/CROCO code, please post your questions here: https://gforge.inria.fr/forum/forum.php?forum_id=3526 Do you have these files in your COADS05 directory? airdens.cdf precip.cdf shortrad.cdf tauy.cdf emp.cdf qsea.cdf sss.cdf u3.cdf longrad.cdf rh.cdf ...

andres

Please check the link at https://www.researchgate.net/job/903618_Postdoctoral_Position-Plankton_Oceanography Key part is: "Skilled candidates in physical-biological modelling as well as a general knowledge of the key functional groups of the plankton (i. e. bacteria, phytoplankton, zooplankton) will ...

andres

Hi,

I would be very interested in our Dockerfile for ROMS. I am currently using Virtual Machines for teaching, this seems a good alternative, Let's talk...

andres

I've once heard a similar comment about the -O3 flag, from the IT manager of a modeling group, he was describing it as "aggressive paralelization". Any experience between -O3 and -O2 ? In the last ROMS_AGRIF (3.1.1) and CROCO the default flags for gfortran are FFLAGS1="-O3 -fdefault-real-8 -fdefault ...

andres

Dear all, The chilean science council (CONICYT) has opened the 2018 call for PostDocs. http://www.conicyt.cl/fondecyt/2016/09/06/concurso-postdoctorado-2018/ the deadline is August 28th, 2017. Those who have obtained (or will) their PhD degree between 01/01/2014 and 30/08/2017 are eligible to apply ...

andres

I think the tzplot file is just a contour plot for your data. Since the model is 1D
you can set depth in the Y-axis and time in the X-axis.

andres

Hi,

We are using roms1d. I've attached the version we use which compiles ok in a Linux machine (Ubuntu)

Hope this helps,

andres

Hi,

Please take a loot at this. It is built for ROMS_AGRIF as it uses a NetCDF file with a SST climatology (Pathfinder) that comes as default in ROMSTOOLS. The code runs in Octave, so you might need some minor modifications, in particular for the histogram plot I think.

Hope it helps.

andres

Hi, This system is for the ROMS_AGRIF version, but to start is as good as any other. For professional development, it might depend on your application. The md5 files are used to verify the integrity of the ISO file after a download. The version number has been arbitrary, and confusing, so we will ...

andres

Besides the historical approach, there is some interesting work done in that line on climate models Knutti, Reto, David Masson, and Andrew Gettelman. "Climate model genealogy: Generation CMIP5 and how we got there." Geophysical Research Letters (2013). is is based on performance comparison, which ...

andres

An option is to export the surface velocities into GNOME (and also surface winds from WRF, for example). There are some examples in Youtube. There is some file exporting to do, including the coastline, but is not too hard. You should consider also the AMIGO software (both free from NOAA) to study ...

andres

Hi, Can you post an image the mask of your domain? It might be that there are no data in the WOA files for your area of interest. What is your domain and resolution? (post also the file romstools_param.m) Hi all, I'm using the ROMS TOOLS Package to produce my own initial and boundary file. I've ...

andres

Hi, I think the problem was your fortran pre-processor (fpp). Your path was not well defined so you couldn't find it. As you found, this solves that problem source /opt/intel/bin/ifortvars.csh ia32 it is better if you put it in your .bashrc file. Thank God~Thank everyone.It finally works.I put ...

andres

Please post your romstools_param.m to understand the problem.

My guess is that the roms_grd.nc file was created and there is a problem plotting the domain. Check if you can find the roms_grd.nc file in the ROMS_FILES directory. If there is one, at least you can continue with your simulation.

andres

Hi, Our wiki server died and all the documentation was lost. Try to contact me in Skype (username: andres_udec) to explain you how it works. Hi Andres Sepulveda, I am working on ROMS application in the Mediterranean sea. I need to modify manually the bathymetry after smoothing to reach the required ...

andres

For what I understand, AWS is a bunch of dual Quadcore-CPUs with a lot of memory and disk space. A problem is that they are connected with Gigabit cables and not Infiniband. It would be good to know if the chance to use a lot of cores compensates the "slow" communication between computing nodes.

andres

Hi, We developed a tool to modify the depth in the roms_grd.nc file generated by ROMSTOOLS. For the moment it just changes the value of a specific matrix and leaves everything else as it is, which most probably is a bad idea, but here is the code for you to improve it. It is based on a previous idea ...

andres

Hi Kate, Thanks for the idea. I need to add git first! After a quick check in the development laptop (mine, of course) seems I need several of the packages (scipy, matplotlib, basemap, ipython, ...) Current python version is 2.6.5 and numpy 1.3.0 I remember reading on your blog about using a virtual ...

andres

Hi all, We are developing a live DVD with ROMS and a bunch of tools pre-installed, primarily as a tool to help teaching numerical modelling. The idea is to bypass most of the installation, compilation, and dependencies problems and focus on the numerical code itself. It could be used to deploy all ...

andres

Hi, I am looking for information on guidelines used to evaluate numerical models (for coastal ocean or lakes) that are part of an environmental study. Documents similar to STOWA/RIZA, 1999, Smooth Modeling in Water Management, Good Modelling Practice Handbook but that are used by government or ...

andres

Hi, I am interested in modeling the sediment input of a river. From the test cases ocean_estuary_test.in, lake_signell.in, sed_test.in, test_chan.in, test_head.in and adria02.in seems to include this ( Nbed > 0 ). Has any of those been described/used in more detail in a publication? Any advise is ...

andres

The Geophysics Department at University of Concepción (DGEO) together with the Center for Advanced Research in Arid Zones (CEAZA) seeks a postdoctoral scholar in Ocean Modeling. Qualifications: Ph.D degree, preferably in physical oceanography. Matlab/Octave skills and experience with ROMS are needed. ...

andres

Hi, improvechen Seems you have a confusion between OPENMP and MPI To use mpi you have to compile the mpich2 code indicating that you will use the intel fortran compiler. This will generate the mpif90 executable that you have to use in the jobcomp file to compile the ROMS_AGRIF code, set LINUX_FC ...

andres

This is a classic operation. Everybody has different scripts. Mine are available from http://www.liga.ens.fr/~dutour/Roms_Interpolation/ . The idea is to interpolate from the history file (or from stations if prefered) to the boundary points and then create a boundary forcing file. Thank you for ...

andres

Hi, I've read there are tools to create the boundary conditions for a small domain using a previous run of ROMS of a larger domain. I've used nestgui from ROMSTOOLS to create the smaller domain and the initial and forcin files, but seems I can use it to extract the information from the his or avg ...

andres

kate wrote:Many of us have done off-line nesting, in which you compute the larger domain first, then extract boundary conditions from it for the smaller domain. What are your exact needs?

Hi Kate,

What routines do you use to do that? They could be useful for already run scenarios...

Andres

andres

It is possible to do in the ROMS_AGRIF version, at least.

Please get the code and manual at

http://roms.mpl.ird.fr/

Regards,

Andres

andres

Hi,

Can you send the screen output?

size wrote:hi rakeshthp
i am very newer of roms and i use ifort too. Can you tell which part of jobcomp I should modify to go through this problem?

andres

The Geophysics Department at University of Concepción (DGEO) together with the Center for Advanced Research in Arid Zones (CEAZA) seeks a postdoctoral scholar in Data Assimilation/Ocean Modeling. Qualifications: Ph.D degree, preferably in physical oceanography, knowledge of data assimilation ...

andres

Hi all, Just an announcement to release a beta version of EDITBATHYMETRY, a program we wrote to modify a bathymetry file to better represent depth near coastal areas. It was inspired by the editmask tool (Andrey Shcherbina) and also by ROMS_TOOLS (Pierrick Penven et al). Please take a look at the ...

andres

The Geophysics Department at University of Concepcion together with the Center for Advanced Research in Arid Zones seeks a postdoctoral scholar in Physical Oceanography/Ocean Modeling. Qualifications: Ph.D degree, preferably in physical oceanography. Knowledge of mesoscale ocean dynamics ...

andres

Hi, seems you forgot to reload the netcdf toolbox. For Romstools this is usually done with the start command.

Cheers,

Andres

andres

Hi, A couple of questions: Do you have a close boundary? (Could you post a figure of your domain? ) What is the spatial resolution you are using? The first thing I always try is to decrease the time step by half until it works. If it never works, then check other details. Please try this first ...

andres

Hi, It would be easier for me to help you if you install the Intel Fotran Compiler (is the one I use)... Andres Hi there... cpp is installed by default on my system. I'm using Open SUSE 10.3.. i typed which cpp at command prompt. I got the following output: /usr/bin/cpp i think it can be compiled ...

andres

Hi, Could you tell me the output, at the Matlab prompt, of >> which dim My first guess would be that you are not loading completly the netcdf implementation. In my machine what I get is: >> which dim /storage3/ROMS/Roms_tools/netcdf_matlab/@ncatt/dim.m % ncatt method Regards, Andres

andres

my system is having gfortran compiler.. i tried all 4 combinations that is given in jobcomp.. i.e. ifort, f99 or something... Hi. you need to modify a line at the top of the jobcomp (near line 25) declaring which fortran compiler do you use. Seems jobcomp does not include yet gfortran as an option ...

andres

Hi Hi.. I got this message.. > locate fpp /usr/bin/diffpp /usr/bin/dprofpp /usr/share/man/man1/diffpp.1.gz /usr/share/man/man1/dprofpp.1.gz /windows/C/Perl/html/bin/dprofpp.html which part of jobcomp file do i need to change..??? The problem now is not a modification of the jobcomp file. Seems you ...

andres

Hi Rakesh, You have to modify jobcomp to point where is in your system the fortran pre processor, fpp. What fortran processor do you have in your system? Have you installed the Intel fortran compiler? What do you get if you type locate fpp at the shell? Regards, Andres :> tcsh jobcomp I got the ...

andres

Cecilia,

Hola! You can try

http://www.brest.ird.fr/Roms_tools/

It is based on Matlab. It helps to generate the file for ROMS_AGRIF but I think it will work also for ROMS 3.0 (anyone knows for shure?)

Andres

andres

Hi,

Does anyone has a Matlab script ro read the GEBCO bathymetry data for a certain region? I can´t load the whole dataset in my machine...

Thank you,

Andres

andres

What is the time of your initial conditions and what are the times listed in the boundary file? From roms_ini.nc tstart = 36524 tend = 36524 scrum_time = 3155673600 From the roms_bry.nc bry_time = 36849.0208333334, 36859.0208333334, 36869.0208333334, 36879.0208333334, 36889.0208333334, 36899 ...

andres

A solution I have seen for this is to set your run to be, for example, one month long, and the do an external script (csh) that copies the rst file into the ini file, moves it to rst_Y1M1 and runs again the code. There is a bacth file in the Roms_tools package that you can use as an example. Andres

andres

Hi, I want to do a hindcast run using Roms_Agrif v1.2 and SODA data which is saved into monthly files When I try to run the coe I get the following error. SET_CYCLE ERROR: non-cycling regime, but model time exeeds time of the last available data record for variable: bry_time TDAYS = 0.3652E+05 TLAST ...

andres

No problem! Well, a couple. It will be in spanish and where... Is there a Wiki installed in Rutgers server? I could ask for space in our deparment's server, if it's ok. Andres andres wrote: Quite a good idea. My students are building a notes on the class I teach using wiki and it is sometimes ...

andres

Quite a good idea. My students are building a notes on the class I teach using wiki and it is sometimes surprising the quality and dedication they put in the contributions. The point is new/recent/intermediate users can learn from trying to explain how tu use ROMS Andres Hi, I am a really new user ...

andres

Hi Kate, Where can I find xcoast? Andres I've got a new version here. The old one is probably still at Rutgers somewhere, but was giving way too many warnings from modern gcc. Hi Kate, Thank your for the program. Seems it needs the world_int.cst file, which I can't access from http://marine.rutgers ...

andres

kate wrote:Thanks for the pointer to a new toy! It works with xcoast about as well as my old Fortran codes.

Hi Kate,
Where can I find xcoast?

Andres

andres

Hi, I am using the Matlab package Roms_tools to start a climatological run for my study area. The model version is ROMS_AGRIF v1.1, and in roms.in I've set NTIMES so each run is of one month >> time_stepping: NTIMES dt[sec] NDTFAST NINFO >> 2880 900 45 1 >> restart: NRST, NRPFRST / filename >> 2880 ...

andres

Hi,

How do I split the NetCDF output files (roms_his.nc).

I would like to have several files rather that a huge one.

Thanx,

Andres

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