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<font face="Times New Roman">Hi Jamie,<br>
<br>
I'm arguing that given that cell_measures (or ext_cell_measures)
will *not* appear in files containing fields most likely to be
carried on a mesh different from the "primary" mesh (because I've
removed those from the requested output table, and hence the CMOR
tables), I think it is better to *assume* the remaining variables
are on the "primary" mesh. I would be surprise if more than 1% of
the variables written will have cell_measures pointing to an
incorrect area field. If it does, I assume the area variable will
have different latxlon dimensions than the variable itself, so it
will be difficult for a user to mistakenly apply the areas.<br>
<br>
So rather than advocate completeness over correctness, I'd say I'm
advocating "almost perfect" versus "perfect".<br>
<br>
If the number of offending cases is much larger than I'm
imagining, please let me know.<br>
<br>
Best regards,<br>
Karl<br>
</font><br>
On 11/1/10 10:09 AM, Kettleborough, Jamie wrote:
<blockquote
cite="mid:E51EDFEBF10BE44BB4BDAF5FC2F024B90250C30B@EXXMAIL02.desktop.frd.metoffice.com"
type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<meta name="GENERATOR" content="MSHTML 8.00.6001.18975">
<div dir="ltr" align="left"><span class="558304916-01112010"><font
color="#0000ff" face="Arial" size="2">Hello Karl,</font></span></div>
<div dir="ltr" align="left"><span class="558304916-01112010"></span> </div>
<div dir="ltr" align="left"><span class="558304916-01112010"><font
color="#0000ff" face="Arial" size="2">thanks for this
reply. Putting aside the issue of whether this is really
ext_cell_measures or cell_measures then I think, given the
resources we have locally, we have to make a choice of
correctness vs completeness. The reason we are tempted to
turn off ext_cell_measures is it is the least effort way we
can see of submitting data that is correct. I think you are
suggesting going for completness - even if we risk
submitting some data with ext_cell_measures that is
incorrect. Obviously this is *my* interpretation of what
you are saying. Yes we can go for both correctness and
completeness, but this will take us some effort - we need an
exta component in our system that can recognise which cell
areas to assign to which variables (with minimum error) -
and we (like everyone) have lots of demands on our effort at
the moment - and we have to make judgements about where to
prioritise. (This isn't supposed to be a sob story - just
trying to explain why we are tempted...)</font></span></div>
<div dir="ltr" align="left"><span class="558304916-01112010"></span> </div>
<div dir="ltr" align="left"><span class="558304916-01112010"><font
color="#0000ff" face="Arial" size="2">Would you recommend
'completeness' over 'correctness' - have I interpreted you
correctly? What are the options for correcting incorrect
meta-data once data is ingested into ESG?</font></span></div>
<div dir="ltr" align="left"><span class="558304916-01112010"></span> </div>
<div dir="ltr" align="left"><span class="558304916-01112010"><font
color="#0000ff" face="Arial" size="2">Jamie</font></span></div>
<div><span class="558304916-01112010"></span> </div>
<div dir="ltr" align="left"><br>
</div>
<blockquote style="border-left: 2px solid rgb(0, 0, 255);
padding-left: 5px; margin-left: 5px; margin-right: 0px;"
dir="ltr">
<div dir="ltr" class="OutlookMessageHeader" align="left"
lang="en-us">
<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 21:36<br>
<b>To:</b> Kettleborough, Jamie<br>
<b>Cc:</b> Bentley, Philip; 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<br>
<b>Subject:</b> Re: [Go-essp-tech] CMOR and cell_measures
issues<br>
</font><br>
</div>
Dear Jamie and Charles (a couple of questions for you),<br>
<blockquote
cite="mid:E51EDFEBF10BE44BB4BDAF5FC2F024B90250C2FB@EXXMAIL02.desktop.frd.metoffice.com"
type="cite">
<meta name="GENERATOR" content="MSHTML 8.00.6001.18939">
<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>
<blockquote
cite="mid:E51EDFEBF10BE44BB4BDAF5FC2F024B90250C2FB@EXXMAIL02.desktop.frd.metoffice.com"
type="cite">
<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>
<blockquote
cite="mid:E51EDFEBF10BE44BB4BDAF5FC2F024B90250C2FB@EXXMAIL02.desktop.frd.metoffice.com"
type="cite">
<div><span class="994545009-29102010"></span> </div>
<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>
<blockquote
cite="mid:E51EDFEBF10BE44BB4BDAF5FC2F024B90250C2FB@EXXMAIL02.desktop.frd.metoffice.com"
type="cite">
<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>
<blockquote style="border-left: 2px solid rgb(0, 0, 255);
padding-left: 5px; margin-left: 5px; margin-right: 0px;"
dir="ltr">
<div dir="ltr" class="OutlookMessageHeader" align="left"
lang="en-us">
<hr tabindex="-1"> <font face="Tahoma" size="2"><b>From:</b>
Karl Taylor [<a moz-do-not-send="true"
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 moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:martin.juckes@stfc.ac.uk">martin.juckes@stfc.ac.uk</a>;
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:go-essp-tech@ucar.edu">go-essp-tech@ucar.edu</a>;
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:cmor@lists.llnl.gov">cmor@lists.llnl.gov</a>;
<a moz-do-not-send="true"
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:
<blockquote
cite="mid:E51EDFEBF10BE44BB4BDAF5FC2F024B9036364A5@EXXMAIL02.desktop.frd.metoffice.com"
type="cite">
<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>
</blockquote>
</blockquote>
</blockquote>
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