[Go-essp-tech] Incorrect use of missing value in some MRI ocean data -- correction

Mon Dec 5 11:39:52 MST 2011

Hello Karl,

Seiji (from MRI) suggested people use sea-area fraction"sftof": I think "areacello" (standard name "cell_area") refers to the actual grid cell, which may be be partially or completely land. "volcello" (standard name "ocean_volume") doesn't have a definition in the current standard name table -- but from the name I would expect to refer to the volume of ocean, so that should be OK for the height dependent fields,

cheers,
Martin

________________________________
From: Karl Taylor [taylor13 at llnl.gov]
Sent: 05 December 2011 18:21
To: Juckes, Martin (STFC,RAL,RALSP)
Cc: go-essp-tech at ucar.edu; Parton, Graham (STFC,RAL,RALSP); cmip5-users at jiscmail.ac.uk
Subject: Re: [Go-essp-tech] Incorrect use of missing value in some MRI ocean data -- correction

Hi Martin,

You're quite right.  It states:

"2. Unless otherwise specified, the ocean and sea-ice output (including Oclim, Oyr, Omon, and OImon) represents a mean over only the sea portion of each grid cell (i.e., it is interpreted as "where ocean over ocean"), and a value of 0.0 should be reported where the sea fraction is 0."

I'm can't recall whether this specification was the result of some requirement, or if it was simply a mistake.  Thinking about it now, I think the recommendation should have been to set it to the "missing" value, not 0.0, since over land the values are undefined.

Given that some groups will follow the specified rule, and others will put in the missing value for land points, users would be advised to obtain the areacello variable (or volcello) which should be set to 0.0 where there is no ocean.

Any other ideas?

Best regards,
Karl

On 12/5/11 9:45 AM, martin.juckes at stfc.ac.uk<mailto:martin.juckes at stfc.ac.uk> wrote:

Hello Karl,

In the following:
http://cmip-pcmdi.llnl.gov/cmip5/docs/standard_output.xls, sheet "general", column A, row 15 and 17.

It says "the value 0.0 should be reported where the sea fraction is 0",

regards,
Martin

________________________________
From: Karl Taylor [taylor13 at llnl.gov<mailto:taylor13 at llnl.gov>]
Sent: 05 December 2011 16:42
To: Juckes, Martin (STFC,RAL,RALSP)
Cc: go-essp-tech at ucar.edu<mailto:go-essp-tech at ucar.edu>; Parton, Graham (STFC,RAL,RALSP); cmip5-users at jiscmail.ac.uk<mailto:cmip5-users at jiscmail.ac.uk>
Subject: Re: [Go-essp-tech] Incorrect use of missing value in some MRI ocean data -- correction

Dear Martin and all,

For 3-d ocean fields like thetao, I think the missing value (not 0.0) should invariably be assigned to all land grid cells and for grid cells below the bottom of the ocean.  I can't find where in the document pointed to below it says otherwise.  I would like to correct the document, so please tell me where it needs revision.

thanks,
Karl

On 12/4/11 8:07 PM, martin.juckes at stfc.ac.uk<mailto:martin.juckes at stfc.ac.uk><mailto:martin.juckes at stfc.ac.uk><mailto:martin.juckes at stfc.ac.uk> wrote:

I owe MRI an apology -- the use of zero instead of a missing value is in fact recommended in (http://cmip-pcmdi.llnl.gov/cmip5/docs/standard_output.xls),

regards,
Martin
________________________________________
From: Juckes, Martin (STFC,RAL,RALSP)
Sent: 04 December 2011 08:45
To: go-essp-tech at ucar.edu<mailto:go-essp-tech at ucar.edu><mailto:go-essp-tech at ucar.edu><mailto:go-essp-tech at ucar.edu>; Parton, Graham (STFC,RAL,SSTD); cmip5-users at jiscmail.ac.uk<mailto:cmip5-users at jiscmail.ac.uk><mailto:cmip5-users at jiscmail.ac.uk><mailto:cmip5-users at jiscmail.ac.uk>
Cc: Pascoe, Stephen (STFC,RAL,RALSP)
Subject: Incorrect use of missing value in some MRI ocean data.

Hello,

It has come to light that some MRI ocean data has land grid points set to zero rather than to the declared missing value. This is likely to confuse some applications reading and plotting the data -- I've notified Seiji Yukimoto at MRI,

sincerely,
Martin
________________________________________
From: Dennis Shea [shea at ucar.edu<mailto:shea at ucar.edu><mailto:shea at ucar.edu><mailto:shea at ucar.edu>]
Sent: 03 December 2011 19:45
To: Zhang Tao
Cc: Juckes, Martin (STFC,RAL,RALSP); haley at ucar.edu<mailto:haley at ucar.edu><mailto:haley at ucar.edu><mailto:haley at ucar.edu>; Gary Strand; Karl Taylor
Subject: Re: [ncl-talk] How to regrid CMIP5 ocean temp. data to regular 1X1 grid

CMIP5 users beware!   :-(

---

The first rule of data processing is to 'look at the data.'

The problem is *not* with the cdo. Rather the source data file
from CMIP5 has incorrect information. I read the  surface level

   a   =
addfile("thetao_Omon_MRI-CGCM3_piControl_r1i1p1_230101-230102.lite.nc","r")
   ta  = a->thetao(0,0,:,:)

   printVarSummary(ta)
   printMinMax(ta,0)

The variable has the following attributes

   missing_value :      1e+20
   _FillValue : 1e+20

I counted the number of number of _FillValue (nmsg1) and the
min/max temperatures.

(0)     Sea Water Potential Temperature: min=0   max=303.924
(0)     nmsg1=0

Obviously, a temperature of 0 is physically not correct. I printed
the array. No missing values (1e20) were encountered. What about land?
The actual _FillValue (missing_value) is 0.0. In an NCL
script I reset to 0.0

   ta at _FillValue = 0.0

I counted the _FillValue and the min/max

(0)     nmsg2=42671
(0)     Sea Water Potential Temperature: min=271.293   max=303.924

The temperature range is much more reasonable.

So the cdo treated the original 0.0 as valid values rather than
_FillValue. I used the NCO operator, ncatted, to create a copy of the
original source file but altered the _FillValue to 0.0

%> ncatted -O -h -a _FillValue,thetao,o,f,0
thetao_Omon_MRI-CGCM3_piControl_r1i1p1_230101-230102.lite.nc
thetao_Omon_MRI_FillValue.nc

Then ran the cdo to generate the weights

%> cdo genbil,r360x180 thetao_Omon_MRI_FillValue.nc
thetao_Omon_MRI_bilwgt.nc

Then did the remap

%> cdo remap,r360x180,thetao_Omon_MRI_bilwgt.nc
thetao_Omon_MRI_FillValue.nc thetao_Omon.r360x180.nc

I works!!

See: http://www.cgd.ucar.edu/~shea/TaoZhang.png

D

On 12/2/11 4:12 PM, Zhang Tao wrote:

Dennis,

I have attached 3 plots for you to take a look. MPI.pdf is the results
from MPI model, I use "cdo remapbil,ll1deg_grid.nc <input file> <output
file> " to get it.

I plot out the contour and shaded plots of MRI-CGCM3 which is obtained
from your command. clearly, the following command does not work
well with this model. I use "cdo remapbil,ll1deg_grid.nc <input file>
<output file> " for this model, similar results are obtained. There are
lots of unrealistically points in the land.

Tao

%> cdo genbil,r360x180
thetao_Omon_MRI-CGCM3_piControl_r1i1p1_230101-230102.lite.nc
thetao_Omon_MRI_bilwgt.nc

&> cdo remap,r360x180,thetao_Omon_MRI_bilwgt.nc
thetao_Omon_MRI-CGCM3_piControl_r1i1p1_230101-230102.lite.nc
thetao_Omon.r360x180.nc

On 12/2/11 3:49 PM, Dennis Shea wrote:

%> cdo genbil,r360x180
thetao_Omon_MRI-CGCM3_piControl_r1i1p1_230101-230102.lite.nc
thetao_Omon_MRI_bilwgt.nc

&> cdo remap,r360x180,thetao_Omon_MRI_bilwgt.nc
thetao_Omon_MRI-CGCM3_piControl_r1i1p1_230101-230102.lite.nc
thetao_Omon.r360x180.nc

ftp ftp.cgd.ucar.edu<ftp://ftp.cgd.ucar.edu><ftp://ftp.cgd.ucar.edu><ftp://ftp.cgd.ucar.edu>
anonymous
email
cd pub/shea/ZhangTao
prompt
mget *
quit

=================
10997404 Dec 2 15:46 thetao_Omon_MRI_bilwgt.nc
1050660 Dec 2 15:47 thetao_Omon.r360x180.nc

Hope it worked.

I'm outta her!

D

On 12/02/2011 03:00 PM, Zhang Tao wrote:

Dennis,

Could you write down the detailed CDO command to remap Japanese model?
I can make a test.

Thanks,
Tao

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