[Go-essp-tech] CMOR and cell_measures issues
Karl Taylor
taylor13 at llnl.gov
Tue Nov 2 12:41:00 MDT 2010
Hi Jamie,
Thanks for spending your valuable time attempting to find the best way
to do things (given practical constraints and software limitations).
[By the way, Charles has been at home with a cold for the last few days,
but I expect him back tomorrow to address the issue of grids and
zfactors. Thanks for bringing this issue to our attention. I think
you're right that we need to revise CMOR to handle this.]
Data that has been interpolated in the vertical has already likely
destroyed our ability to calculate accurate global integrals, so if the
areas aren't quite right it probably doesn't matter much.
I'm almost positive that an attribute that is wrong can be removed or
its value can be replaced (as long as the new string is no longer than
the original) *without* actually rewriting the entire file, so flaws
might be fairly easily corrected after the fact.
Best regards,
Karl
On 11/2/10 10:42 AM, Kettleborough, Jamie wrote:
> Hello Karl,
> 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.
> 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?
> I'm still unclear what our options are if we submit data that we later
> find has inappropriate meta-data. Any thoughts on this?
> Jamie
>
> ------------------------------------------------------------------------
> *From:* Karl Taylor [mailto:taylor13 at llnl.gov]
> *Sent:* 01 November 2010 18:19
> *To:* Kettleborough, Jamie
> *Cc:* Bentley, Philip; V. Balaji; martin.juckes at stfc.ac.uk;
> go-essp-tech at ucar.edu; cmor at lists.llnl.gov; Kyle.Olivo at noaa.gov;
> Doutriaux, Charles
> *Subject:* Re: [Go-essp-tech] CMOR and cell_measures issues
>
> Hi Jamie,
>
> 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.
>
> So rather than advocate completeness over correctness, I'd say I'm
> advocating "almost perfect" versus "perfect".
>
> If the number of offending cases is much larger than I'm
> imagining, please let me know.
>
> Best regards,
> Karl
>
> On 11/1/10 10:09 AM, Kettleborough, Jamie wrote:
>> Hello Karl,
>> 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...)
>> 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?
>> Jamie
>>
>> ------------------------------------------------------------------------
>> *From:* Karl Taylor [mailto:taylor13 at llnl.gov]
>> *Sent:* 29 October 2010 21:36
>> *To:* Kettleborough, Jamie
>> *Cc:* Bentley, Philip; V. Balaji; martin.juckes at stfc.ac.uk;
>> go-essp-tech at ucar.edu; cmor at lists.llnl.gov;
>> Kyle.Olivo at noaa.gov; Doutriaux, Charles
>> *Subject:* Re: [Go-essp-tech] CMOR and cell_measures issues
>>
>> Dear Jamie and Charles (a couple of questions for you),
>>> Hello Karl,
>>> 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.
>>
>> 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?
>>
>> Why are you tempted to turn off the ext_cell_measures for all
>> variables? Then your output won't conform to the CMIP5
>> requirements.
>>
>> 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.
>>
>> 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.
>>> That aside, doesn't the approach of providing alternative
>>> grid areas need more discussion?
>>> 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.
>>> 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.
>> 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?
>>> Clearly these may have been things you were going to cover -
>>> but ran out of time to, in which case sorry.
>>> 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?
>>
>> 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.
>>
>> Best regards,
>> Karl
>>> Jamie
>>>
>>> ------------------------------------------------------------------------
>>> *From:* Karl Taylor [mailto:taylor13 at llnl.gov]
>>> *Sent:* 29 October 2010 02:15
>>> *To:* Bentley, Philip
>>> *Cc:* V. Balaji; martin.juckes at stfc.ac.uk;
>>> go-essp-tech at ucar.edu; cmor at lists.llnl.gov;
>>> Kyle.Olivo at noaa.gov; Doutriaux, Charles; Kettleborough,
>>> Jamie
>>> *Subject:* Re: [Go-essp-tech] CMOR and cell_measures issues
>>>
>>> Dear all,
>>>
>>> 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.
>>>
>>> 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.
>>>
>>> Also, could you please explain why you prefer not to
>>> duplicate the "fx" fields in each experiment's directory
>>> tree.
>>>
>>> Best regards,
>>> Karl
>>>
>>> On 10/25/10 7:12 AM, Bentley, Philip wrote:
>>>> Hi Balaji,
>>>>
>>>>> 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.
>>>> 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).
>>>>
>>>>> You know of course that gridspec says you can supply
>>>>>
>>>>>> 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
>>>>> as one single supergrid...
>>>> 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).
>>>>> But if you're doing gridspec at all, I will concede this
>>>>> point:-). Let's both do these separate gridspecs for now.
>>>> Works for me.
>>>>
>>>> I think we're suffering from 'early-adopter syndrome' :-/
>>>>
>>>> Cheers,
>>>> Phil
>>>>
>>>>> Bentley, Philip writes:
>>>>>
>>>>>> Hi Karl,
>>>>>>
>>>>>> A somewhat belated follow-up question in connection with
>>>>> this proposal
>>>>>> (and with some slight overlap with Jamie's email which
>>>>> crossed on the
>>>>>> 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
>>>>> change from one
>>>>>> simulation to the next using the same model (HadGEM2-ES in
>>>>> this case).
>>>>>> 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 -
>>>>> or lots of
>>>>>> 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
>>>>> likely to
>>>>>> 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,
>>>>> so I'm now
>>>>>> 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
>>>>
>>>
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