Re: Using my own oceanographic netcdf files

Christina Hernandez

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Mar 22, 2018, 10:18:28 AM3/22/18

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File attachment was too big, so here's a Google Drive link for the netcdf file:

nest_1_20000410000000.nc

Christina Hernandez

Graduate Student

MIT-WHOI Joint Program in Oceanography

Biology Dept- Llopiz Lab

MS #33

508-289-3253

On Thu, Mar 22, 2018 at 10:15 AM, Christina Hernandez <cmh...@columbia.edu> wrote:

Hi all,

I've read all the messages in this thread: https://groups.google.com/d/topic/connectivity-modeling-system-club/XHCjqLvIMeU/discussion

However, I am having issues with using getdata to read in my own netcdf files. These files are from a theoretical model that is basically simulating flow in a rectangular channel with eddies arising due to wind forcing and instabilities at a front. Our project is hoping to look at dispersal kernels at several levels of abstraction (with the most realistic instance being a ROMS model being developed for our study region, along the coast of Central Chile), so I'd like to use CMS for all the runs.

I'm using an older version of CMS, downloaded in 2013. I don't know if any of the code dealing with using non-HYCOM files have been edited since then.

Anyway, I'm attaching my nest_1.nml file and the first oceanographic file. Can anyone tell me if getdata will run for them on this or if they spy a mistake? I wrote this nest file myself (in R) using hydrodynamic output that a collaborator gave me, and I've checked the names of the variables several times. I still get the error:
fortran runtime error: Cannot match namelist object name "lon"

Thanks!
Chrissy

Christina Hernandez
Graduate Student
MIT-WHOI Joint Program in Oceanography
Biology Dept- Llopiz Lab
MS #33
508-289-3253

nest_1.nml

Robin F

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Mar 22, 2018, 10:40:54 AM3/22/18

to Christina Hernandez, connectivity-modeling-system-club

Hi Christina,

You don’t need to use getdata when dealing with your own nc files.

Instead, format the nest files in the exact same way as in the cms example (order of dimensions, direction of the dimensions, etc), create a folder "/expt/expt_myexptname/nests" and put them in the folder.

You may also have to split your nest files into (1) nest_1_20000410000000u.nc and (2) nest_1_20000410000000v.nc, with a single u or v component in each u or v nest files.

It is a bit more complicated than using standard HYCOMS or ROMS data but it does work ;)
If you have more questions I can try to help you, I have done it in the past with my own files.

Good luck,

> Le 22 mars 2018 à 10:18, Christina Hernandez <cmh...@columbia.edu> a écrit :
>
> File attachment was too big, so here's a Google Drive link for the netcdf file:

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Dr. Robin Faillettaz
——————————————————————

Postdoctoral Research Fellow
University of Miami
Rosenstiel School of Marine & Atmospheric Science
4600 Rickenbacker Causeway, Miami, FL 33149-1098, USA
Tel: (US) +1-702-910-0380; (FR) +33-6-84-91-43-33
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Robin.Fa...@univ-lille1.fr

Christina Hernandez

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Apr 16, 2018, 12:07:56 PM4/16/18

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Sorry, attachments didn't work. They are here:

https://drive.google.com/open?id=1Vl8QWQyryAPXTxBdtqUJGq59zlZZuiWm

Christina Hernandez

Graduate Student

MIT-WHOI Joint Program in Oceanography

Biology Dept- Llopiz Lab

MS #33

508-289-3253

On Mon, Apr 16, 2018 at 11:59 AM, Christina Hernandez <cmh...@columbia.edu> wrote:

Hey Robin,

So I have tried a few times now to get CMS to run with idealized model output. Attached is one of the hydrodynamic files, and the nest_1.nml file.
When I run CMS with the file as attached, with [u, v, w] all in one file, it says "NETCDF variable not found" but it doesn't tell me which variable is not found. When I run CMS with [u, v, w] in separate files with u/v/w/ appended to the filename, it says that it can't find the nest_1_20000605000000.nc file.

Do you have any other tips?

Thanks,
Chrissy

Christina Hernandez
Graduate Student
MIT-WHOI Joint Program in Oceanography
Biology Dept- Llopiz Lab
MS #33
508-289-3253

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--

Dr. Robin Faillettaz
——————————————————————

Postdoctoral Research Fellow
University of Miami
Rosenstiel School of Marine & Atmospheric Science
4600 Rickenbacker Causeway, Miami, FL 33149-1098, USA
Tel: (US) +1-702-910-0380; (FR) +33-6-84-91-43-33
Robin.Fa...@gmail.com

Robin.Faillettaz@univ-lille1.fr

Juan Faundez

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Jun 26, 2018, 10:32:09 AM6/26/18

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Dear All,

I have my own oceanographic data from CROCO (ROMS-AGRIF). Such as Christina i couldnt match my variable names into my data.nc with the nest_1.nml when I runned ./cms my_data. I runned the example downloaded by getdata getting results, but if I change the dimension or variable names between " " in the input_example/nest_1.nml, anyway cms run.

Then i changed in my own data the variable and dimension names to the same which produced getdata, "Longitude", "Latitude", "Depth" ,"Time", transforming my C-grid to an A-grid and from sigma to z-level (Sorry, but the last two processes i did before change the dimension and variable names, for the first test). Also I'm using Time as the record dimension (UNLIMITED). Then from a "NETCDF variable not found" I passed to a "Error in the netCDF file: expt_mpa/nests/nest_1_20101201000000.nc / NetCDF: Start+count exceeds dimension bound". What i figure out is that the first trouble was due to the wrong dimension names (now solved) and the second one perhaps depend of the dimension order in each variable, where I changed variable("Time","Depth","Latitude","Longitude" ) by variable("Longitude", "Latitude", "Depth" ,"Time"). This last step also didn't work and i got the same last error

I attached my own data (https://drive.google.com/open?id=1Rf6MHM-A2qcPhpTaxxek_mB6e4NeMPPD) and my nest_1.nml. Maybe my trouble come from other places which i cant see yet. I will be very glad if somebody can help me.

Thank you

DATA FROM MATLAB SHOW DIMENSIONS AND SIZES WITH 31 SNAPSHOT

Format:

classic

Dimensions:

Longitude = 155

Latitude = 172

Depth = 40

Time = 31 (UNLIMITED)

Variables:

Longitude

Size: 155x1

Dimensions: Longitude

Datatype: double

Attributes:

long_name = 'Longitude'

units = 'degrees_east'

valid_range = [-82.9167 -70.0833]

Latitude

Size: 172x1

Dimensions: Latitude

Datatype: double

Attributes:

long_name = 'Latitude'

units = 'degrees_north'

valid_range = [-38.9352 -27.026]

Time

Size: 31x1

Dimensions: Time

Datatype: double

Attributes:

long_name = 'Time'

units = 'seconds since 2002-1-17'

Depth

Size: 40x1

Dimensions: Depth

Datatype: double

Attributes:

long_name = 'Depth'

units = 'meter'

valid_range = [0 2000]

zu

Size: 155x172x40x31

Dimensions: Longitude,Latitude,Depth,Time

Datatype: double

Attributes:

long_name = 'zu'

units = 'm/s'

_FillValue = 1.2676506e+30

valid_range = [-0.51724 0.38312]

zv

Size: 155x172x40x31

Dimensions: Longitude,Latitude,Depth,Time

Datatype: double

Attributes:

long_name = 'zv'

units = 'm/s'

_FillValue = 1.2676506e+30

valid_range = [-0.31513 0.64925]

zw

Size: 155x172x40x31

Dimensions: Longitude,Latitude,Depth,Time

Datatype: double

Attributes:

long_name = 'zw'

units = 'm/s'

_FillValue = 1.2676506e+30

valid_range = [-0.00054219 0.00072905]

##########################################################################################

NCDUMP -H SHOWING THE DIMENSION POSITION INSIDE THE VARIABLE WITH 1 SNAPSHOT

dimensions:

Depth = 40 ;

Latitude = 172 ;

Longitude = 155 ;

Time = UNLIMITED ; // (1 currently)

variables:

double Depth(Depth) ;

Depth:long_name = "Depth" ;

Depth:units = "meter" ;

Depth:valid_range = 0., 2000. ;

double Latitude(Latitude) ;

Latitude:long_name = "Latitude" ;

Latitude:units = "degrees_north" ;

Latitude:valid_range = -38.9352378845215, -27.0260391235352 ;

double Longitude(Longitude) ;

Longitude:long_name = "Longitude" ;

Longitude:units = "degrees_east" ;

Longitude:valid_range = -82.9166641235352, -70.0833358764648 ;

double Time(Time) ;

Time:long_name = "Time" ;

Time:units = "seconds since 2002-1-17" ;

double zu(Time, Depth, Latitude, Longitude) ;

zu:long_name = "zu" ;

zu:units = "m/s" ;

zu:_FillValue = 1.2676506e+30 ;

zu:valid_range = -0.517239212989807, 0.383117631077766 ;

double zv(Time, Depth, Latitude, Longitude) ;

zv:long_name = "zv" ;

zv:units = "m/s" ;

zv:_FillValue = 1.2676506e+30 ;

zv:valid_range = -0.315126286007926, 0.64925342798233 ;

double zw(Time, Depth, Latitude, Longitude) ;

zw:long_name = "zw" ;

zw:units = "m/s" ;

zw:_FillValue = 1.2676506e+30 ;

zw:valid_range = -0.000542192161233348, 0.000729051047234748 ;

// global attributes:

:history = "Tue Jun 26 10:14:20 2018: ncks -d Time,0,0 nest_1_20101201000000_mpa.nc nest_1_20101201000000.nc" ;

:NCO = "4.6.8" ;

#################################################################

TEST WITH GETDATA JUST TO READ FILE.NC

./getdata mpa 1

fill_value and velocity_conversion_factor on read 1.26765060E+30 1.00000000

Opening file for reading: expt_mpa/nests/raw/nest_1_20101201000000.nc

Succesfully read data: Longitude

Succesfully read data: Latitude

Succesfully read data: Depth

Starting X Axis index: 1

Ending X Axis index : 155

Starting Y Axis index: 172

Ending Y Axis index : 1

Starting Z Axis index: 1

Ending Z Axis index : 40

Reading data files: 2010-12-1 00:00:00

Error in the netCDF file: expt_mpa/nests/raw/nest_1_20101201000000.nc

NetCDF: Start+count exceeds dimension bound

root@DESKTOP-8RKHT2D:/mnt/c/Users/juanf/Documents/cms/cms-master/expt# ./cms mpa 1

Error in the netCDF file: expt_mpa/nests/nest_1_20101201000000.nc

NetCDF: Start+count exceeds dimension bound

nest_1.nml

Ignasi Vallès Casanova

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Jan 10, 2020, 11:56:17 AM1/10/20

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any solution about that? I'm having similar problem

El dimarts, 26 juny de 2018 16:32:09 UTC+2, Juan Faundez va escriure:

Robin F

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Jan 10, 2020, 1:44:31 PM1/10/20

to Ignasi Vallès Casanova, connectivity-modeling-system-club

Briefly, one work around for the 'variable not found’ error that works most of the time is to run a getdata on your local files. You just have to place them in nests/raw and run ./getdata exptname

The issues 'Start+count exceeds dimension bound' has to be with your file, likely with the dimensions or values you provided when preparing your files.

Good luck.

> Le 10 janv. 2020 à 11:56, Ignasi Vallès Casanova <ignasi...@gmail.com> a écrit :
>
> any solution about that? I'm having similar problem

--

Robin Faillettaz, Ph.D
——————————————————————

Postdoctoral Research Fellow
RECOVER2 project

University of Miami
Rosenstiel School of Marine & Atmospheric Science
4600 Rickenbacker Causeway, Miami, FL 33149-1098, USA
Tel: (US) +1-702-910-0380; (FR) +33-6-84-91-43-33
Robin.Fa...@gmail.com

Robin.Fa...@rsmas.miami.edu

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