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Dear Jamie and Charles (a couple of questions for you),<br>
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<div dir="ltr" align="left"><span class="994545009-29102010"><font
color="#0000ff" face="Arial" size="2">Hello Karl,</font></span></div>
<div dir="ltr" align="left"><span class="994545009-29102010"></span> </div>
<div dir="ltr" align="left"><span class="994545009-29102010"><font
color="#0000ff" face="Arial" size="2">I think the
recommended way to 'turn off' ext_cell_measures is to make a
call to cmor.set_variable_attribute(varid,
'ext_cell_measures', ''). Is that right? We are very
tempted to do this for all variables - so basically
overriding the MIP tables. How big a problem do you think
this will be for data users - our grid is pretty straight
forward and users can calculate cell_areas from the
latitudes.</font></span></div>
</blockquote>
<br>
Yes, if the cell areas stored in areacella are not appropriate for a
particular field, and the requested output tables say that
ext_cell_measure includes areacella, then you should call the set
attribute function to reset ext_cell_measures="". Isn't that right
Charles?<br>
<br>
Why are you tempted to turn off the ext_cell_measures for all
variables? Then your output won't conform to the CMIP5
requirements.<br>
<br>
In the latest CMOR tables, I have removed ext_cell_measures from all
the variables that we don't expect always to be on the standard mesh
(i.e., on the grid for which areacella is correct). This includes
velocities and transports and closely related fields, which are
sometimes staggered relative to areacella. I would still be
interested in hearing a clear explanation for why there are
additional fields carried on a completely different grid. <br>
<br>
If users must compute the cell areas for only your grid, and for all
others they simply read the areacella field in, then you are
creating a special case that is completely unnecessary.<br>
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<div dir="ltr" align="left"><span class="994545009-29102010"></span> </div>
<div dir="ltr" align="left"><span class="994545009-29102010"><font
color="#0000ff" face="Arial" size="2">That aside, doesn't
the approach of providing alternative grid areas need more
discussion?</font></span></div>
<div dir="ltr" align="left"><span class="994545009-29102010"></span> </div>
<div dir="ltr" align="left"><span class="994545009-29102010"><font
color="#0000ff" face="Arial" size="2"> 1. how should we
produce these. The most natural approach I can think of is
to modify the fx MIP tables to add in areacellb (or whatever
we choose to call it) and then output through CMOR - this
will maximise the chance of consistency between different
grid area files for any one model. </font></span></div>
<div dir="ltr" align="left"><span class="994545009-29102010"></span> </div>
<div dir="ltr" align="left"><span class="994545009-29102010"><font
color="#0000ff" face="Arial" size="2"> 2. how should we
reference these additional areas from a variable.? I could
call cmor.set_variable_attribute(varid, 'ext_cell_measures',
'areacellb') - but in the tests I've done on CMOR 2.4 this
only does half the job: it puts the appropriate
ext_call_measures attribute into the file, but does nothing
with associatedFiles.</font></span></div>
</blockquote>
I don't think it is a high priority to standardize this
immediately. We will want CMOR to place the fields in the
subdirectory fx, so I need to check with Charles whether this
requires the variable to appear in table fx. If not, I would
probably build an entirely new table similar to fx, but with only
the additional variables. This way you won't have to modify your
table if a new fx table comes out. As for referencing these
additional area variables, I think if you include area:
<area_name> in the ext_cell_measures attribute, then if CMOR
isn't already doing this, Charles can modify construction of
associated_files to include something following the template
"<area_name>:
<area_name>_fx_IPSL-CM5_historical_r0i0p0.nc" What do you
think, Charles?<br>
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<div><span class="994545009-29102010"><font color="#0000ff"
face="Arial" size="2">Clearly these may have been things you
were going to cover - but ran out of time to, in which case
sorry.</font></span></div>
<div><span class="994545009-29102010"></span> </div>
<div><span class="994545009-29102010"><font color="#0000ff"
face="Arial" size="2">I think another scenario that still
needs some thought is one where a data provider has
submitted data and published it in ESG. They then realise
they made a mistake - they should have turned
ext_cell_measures off, but didn't (or visa-versa). What
happens in this case? (We have kind of done this in that we
have send data with incorrect cell_measures to the BADC -
but have caught the issue before ingestion into ESG - I
don't believe we will always be this lucky). You'll
probably see through why I'm asking this question about
meta-data updates again now, so I may as well be explicit...
If we choose to turn off ext_cell_measures for all our
diagnostics on this initial submission - what are our
options for recovering from this if we later found the
decision to submit without ext_cell_measures was making our
data hard to use?</font></span></div>
</blockquote>
<br>
Please don't turn off ext_cell_measures (in general). I think you
could easily write a script to remove the cell_measures attribute
using netCDF tools, but adding it would require rewriting the entire
file.<br>
<br>
Best regards,<br>
Karl<br>
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<div><span class="994545009-29102010"></span> </div>
<div><span class="994545009-29102010"></span><font face="Arial"><font
color="#0000ff"><font size="2">J<span
class="994545009-29102010">amie</span></font></font></font><br>
</div>
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<hr tabindex="-1"> <font face="Tahoma" size="2"><b>From:</b>
Karl Taylor [<a class="moz-txt-link-freetext" href="mailto:taylor13@llnl.gov">mailto:taylor13@llnl.gov</a>] <br>
<b>Sent:</b> 29 October 2010 02:15<br>
<b>To:</b> Bentley, Philip<br>
<b>Cc:</b> V. Balaji; <a class="moz-txt-link-abbreviated" href="mailto:martin.juckes@stfc.ac.uk">martin.juckes@stfc.ac.uk</a>;
<a class="moz-txt-link-abbreviated" href="mailto:go-essp-tech@ucar.edu">go-essp-tech@ucar.edu</a>; <a class="moz-txt-link-abbreviated" href="mailto:cmor@lists.llnl.gov">cmor@lists.llnl.gov</a>;
<a class="moz-txt-link-abbreviated" href="mailto:Kyle.Olivo@noaa.gov">Kyle.Olivo@noaa.gov</a>; Doutriaux, Charles; Kettleborough,
Jamie<br>
<b>Subject:</b> Re: [Go-essp-tech] CMOR and cell_measures
issues<br>
</font><br>
</div>
<font face="Times New Roman">Dear all,<br>
<br>
I meant to try to address all the stuff in this discussion,
but won't have time today. This email is just to say that I
think we should insist that the cell_area files (areacella and
areacello) be placed in the archive, even if there are also
gridspec files. The ext_cell_measures attribute should also
be included for fields that are on the "standard" grid (i.e.,
the one with the cell areas stored in areacella or
areacello). If there are other fields for which the standard
areas are inappropriate and where your scientists think it is
important to provide cell areas, then I recommend that you
create specially named variables and place them in the "fx"
subdirectories. For variables not on the "standard" grid
(i.e., the grid of areacella or areacello), you should "turn
off" the ext_cell_measures attribute.<br>
<br>
I don't expect most groups to produce gridspec files, so most
analysts will be looking for areas in the areacella and
areacello variables, not the gridspec files. This is why you
should write the areacella and areacello files even if you
also write the gridspec files.<br>
<br>
Also, could you please explain why you prefer not to duplicate
the "fx" fields in each experiment's directory tree. <br>
<br>
Best regards,<br>
Karl<br>
</font><br>
On 10/25/10 7:12 AM, Bentley, Philip wrote:
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<pre wrap="">Hi Balaji,
</pre>
<blockquote type="cite">
<pre wrap="">Phil, I'm very impressed that Had will have gridspec files,
is this a done deal? I've been so pessimistic about this that
I was wondering if even we should do one ourselves.
</pre>
</blockquote>
<pre wrap="">Nope, not a done deal yet :-(
In line with the CMIP5 expt design doc, we don't really need to provide
gridspec files since all our model output is on either regular or
uniform grids (i.e. simple cartesian product of lat & long).
However, this whole cell_measures business prompted me to revisit the
gridspec tools and output, which reminded me that the gridspec netcdf
files include a cell area variable. Which in turn means we wouldn't need
to provide a separate file (or files) for cell areas. Hence we could
drop the ext_cell_measures attribute from our CMIP5 output files.
Using the gridspec tools may be a quick and easy way for us to provide
cell area info if we need to.
Caveat: from a quick glance it looks like the netcdf files produced by
the gridspec tools are not CF compliant. Is this is an issue? Presumably
it is if we want all the data in the CMIP5 archive to be CF compliant.
(NB: it could be I'm not running with the very latest version of the
tools - but I couldn't see a more recent version on the gfdl web site).
</pre>
<blockquote type="cite">
<pre wrap="">You know of course that gridspec says you can supply
</pre>
<blockquote type="cite">
<pre wrap="">gridspec_fx_HadGEM2-ES_atm_pgrid.nc
gridspec_fx_HadGEM2-ES_atm_ugrid.nc
gridspec_fx_HadGEM2-ES_atm_vgrid.nc
gridspec_fx_HadGEM2-ES_atm_uvgrid.nc
</pre>
</blockquote>
<pre wrap="">as one single supergrid...
</pre>
</blockquote>
<pre wrap="">If I could figure out how to output all 7 or 8 atm/ocn (sub-)grids to a
single netcdf file I would, but the available documentation (e.g. for
make_hgrid) isn't clear on this point. Sorry, that's probably just me
being dumb! But if there is updated documentation then please point me
to it. If necessary I could concatenate variables afterwards using NCO
tools.
Right now I'm trying to figure out how to create a gridspec file for our
HadGEM2 ocean model, which uses a stretched (i.e. tartan/plaid) grid:
longitudes are evenly spaced, latitudes vary from 1 deg to 1/3 deg.
(Looks like I need to use the --my_grid_file option to supply the
lat/long coords).
</pre>
<blockquote type="cite">
<pre wrap="">But if you're doing gridspec at all, I will concede this
point:-). Let's both do these separate gridspecs for now.
</pre>
</blockquote>
<pre wrap="">Works for me.
I think we're suffering from 'early-adopter syndrome' :-/
Cheers,
Phil
</pre>
<blockquote type="cite">
<pre wrap="">Bentley, Philip writes:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Karl,
A somewhat belated follow-up question in connection with
</pre>
</blockquote>
<pre wrap="">this proposal
</pre>
<blockquote type="cite">
<pre wrap="">(and with some slight overlap with Jamie's email which
</pre>
</blockquote>
<pre wrap="">crossed on the
</pre>
<blockquote type="cite">
<pre wrap="">ether)...
As things stand the files named in the 'associated_files' attribute
appear thus (using our RCP 4.5 simulation as an example):
"... gridspecFile: gridspec_fx_HadGEM2-ES_rcp45_r0i0p0.nc areacella:
areacella_fx_HadGEM2-ES_rcp45_r0i0p0.nc"
Are the <expt_id>_<rip> parts (i.e. 'rcp45_r0i0p0.nc' ) actually
required? AFAIK, our gridspec/cellarea files will not
</pre>
</blockquote>
<pre wrap="">change from one
</pre>
<blockquote type="cite">
<pre wrap="">simulation to the next using the same model (HadGEM2-ES in
</pre>
</blockquote>
<pre wrap="">this case).
</pre>
<blockquote type="cite">
<pre wrap="">Since, like most centers, we will be running large numbers of
simulations using the same model, it looks like we would need to
create numerous duplicates of the gridspec/cellarea files -
</pre>
</blockquote>
<pre wrap="">or lots of
</pre>
<blockquote type="cite">
<pre wrap="">symlinks
- in order to for these references to make sense. Unless you are
planning to manage that on our behalf somehow...?
I think our 4 gridspec files for the HadGEM2 atm grids are
</pre>
</blockquote>
<pre wrap="">likely to
</pre>
<blockquote type="cite">
<pre wrap="">be called something like...
gridspec_fx_HadGEM2-ES_atm_pgrid.nc
gridspec_fx_HadGEM2-ES_atm_ugrid.nc
gridspec_fx_HadGEM2-ES_atm_vgrid.nc
gridspec_fx_HadGEM2-ES_atm_uvgrid.nc
So without any simulation-specific info. (There would also be files
for the ocean grids)
As it happens the gridspec files contain grid cell areas,
</pre>
</blockquote>
<pre wrap="">so I'm now
</pre>
<blockquote type="cite">
<pre wrap="">wondering if we'd even supply both?
I'd be interested to hear your thoughts on this. I may be
mis-understanding something/everything :-)
Regards
Phil
</pre>
</blockquote>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
</blockquote>
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