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<DIV dir=ltr align=left><SPAN class=906461817-02112010><FONT color=#0000ff
size=2 face=Arial>Hello Karl,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=906461817-02112010><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=906461817-02112010><FONT color=#0000ff
size=2 face=Arial>Thanks for the clarification - before we make a final decision
on which variables to include cell_measures for we'll take into account
what you have said here.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=906461817-02112010><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=906461817-02112010><FONT color=#0000ff
size=2 face=Arial>The variables that we have problems with (the diagnostics that
are neither velocities/transports or on the primary mesh) I think are the
time mean pressure level diagnostics. Without looking at the
actual meshes and MIP tables to confirm I think this
includes things like ta, zg from Amon and day tables, and
ta from 6hrPlev. How important is it that users can
(easily) take area means of these pressure level
diagnostics? </FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=906461817-02112010><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=906461817-02112010><FONT color=#0000ff
size=2 face=Arial>I'm still unclear what our options are if we submit data that
we later find has inappropriate meta-data. Any thoughts on
this?</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=906461817-02112010><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=906461817-02112010><FONT color=#0000ff
size=2 face=Arial>Jamie</FONT></SPAN></DIV><BR>
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<FONT size=2 face=Tahoma><B>From:</B> Karl Taylor [mailto:taylor13@llnl.gov]
<BR><B>Sent:</B> 01 November 2010 18:19<BR><B>To:</B> Kettleborough,
Jamie<BR><B>Cc:</B> Bentley, Philip; V. Balaji; martin.juckes@stfc.ac.uk;
go-essp-tech@ucar.edu; cmor@lists.llnl.gov; Kyle.Olivo@noaa.gov; Doutriaux,
Charles<BR><B>Subject:</B> Re: [Go-essp-tech] CMOR and cell_measures
issues<BR></FONT><BR></DIV>
<DIV></DIV><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:
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<DIV dir=ltr align=left><SPAN class=558304916-01112010><FONT color=#0000ff
size=2 face=Arial>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
size=2 face=Arial>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
size=2 face=Arial>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
size=2 face=Arial>Jamie</FONT></SPAN></DIV>
<DIV><SPAN class=558304916-01112010></SPAN> </DIV>
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<FONT size=2 face=Tahoma><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>
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<DIV dir=ltr align=left><SPAN class=994545009-29102010><FONT
color=#0000ff size=2 face=Arial>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 size=2 face=Arial>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><FONT
color=#0000ff size=2 face=Arial>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 size=2 face=Arial> 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 size=2 face=Arial> 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 size=2
face=Arial>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 size=2
face=Arial>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><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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<FONT size=2 face=Tahoma><B>From:</B> Karl Taylor [<A
class=moz-txt-link-freetext href="mailto:taylor13@llnl.gov"
moz-do-not-send="true">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"
moz-do-not-send="true">martin.juckes@stfc.ac.uk</A>; <A
class=moz-txt-link-abbreviated href="mailto:go-essp-tech@ucar.edu"
moz-do-not-send="true">go-essp-tech@ucar.edu</A>; <A
class=moz-txt-link-abbreviated href="mailto:cmor@lists.llnl.gov"
moz-do-not-send="true">cmor@lists.llnl.gov</A>; <A
class=moz-txt-link-abbreviated href="mailto:Kyle.Olivo@noaa.gov"
moz-do-not-send="true">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="">
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