[Go-essp-tech] Status of Gateway 2.0 (another use case)
Bryan Lawrence
bryan.lawrence at ncas.ac.uk
Thu Dec 15 12:14:32 MST 2011
Hi Jennifer
With due respect, it's completely unrealistic to expect modelling groups not to want to have multiple versions of some datasets ... that's just not how the world (and in particular, modelling workflow) works. It has never been thus. There simply isn't time to look at everthing before it is released ... if you haave a problem with that, blame the government folk who set the IPCC timetables :-) (Maybe your comment was somewhat tongue in cheek, but I feel obliged to make this statement anyway :-).
Also, with due respect, please don't "replace files with newer versions" ... we absolutely need folks to understand the idea of processing with one particular version of the data, and understanding the provenance of that, so that they understand if the data has changed, they may need to re-run the processing.
I'm sure this doesn't apply to you, but for too long our community has had a pretty cavalier attitude to data provenance! CMIP3 and AR4 was a "dogs breakfast" in this regard ...
(And I too am very grateful that you are laying out your requirements in some detail :-)
Cheers
Bryan
>
> On Dec 15, 2011, at 11:22 AM, Estanislao Gonzalez wrote:
>
> > Hi Jennifer,
> >
> > I'll check this more carefully and see what can be done with what we have (or minimal changes), thought the multiple versions is something CMIP3 hasn't worried about, files just got changed or deleted, cmip5 add a two figure factor to that since there are many more institutions and data... but it might be possible.
> At the moment, I have no good ideas for how to solve the problem of replacing files in my local CMIP5 collection with newer versions if they are available. My strategy at this point is to get the version that is available now and not look for it again. If any data providers are listening, here is my plea:
> ==> Please don't submit new versions of your CMIP5 data. Get it right the first time! <==
> :-)
>
> >
> > In any case I wanted just to thank you very much for the detailed description, it is very useful.
> I'm glad you (and Steve Hankin) find my long emails helpful.
> --Jennifer
>
> >
> > Regards,
> > Estani
> >
> > Am 15.12.2011 14:52, schrieb Jennifer Adams:
> >>
> >> Hi, Estanislao --
> >> Please see my comments inline.
> >>
> >> On Dec 15, 2011, at 5:47 AM, Estanislao Gonzalez wrote:
> >>
> >>> Hi Jennifer,
> >>>
> >>> I'm still not sure how is Lucas change in the API going to help you Jennifer. But perhaps it would help me to fully understand your requirement as well as your use of wget when using the FTP protocol.
> >>>
> >>> I presume what you want is to crawl the archive and get file from a specific directory structure?
> >>> Maybe it would be better if you just describe briefly the procedure you've been using for getting the CMIP3 data so we can see what could be done for CMIP5.
> >>>
> >>> How did you find out which data was interesting?
> >> COLA scientists ask for a specific scenario/realm/frequency/variable they need for their research. Our CMIP3 collection is a shared resource of about 4Tb of data. For CMIP5, we are working with an estimate of 4-5 times that data volume to meet our needs. It's hard to say at this point whether that will be enough.
> >>
> >>> How did you find out which files were required to be downloaded?
> >> For CMIP3, we often referred to http://www-pcmdi.llnl.gov/ipcc/data_status_tables.htm to see what was available.
> >>
> >> The new version of this chart for CMIP5, http://cmip-pcmdi.llnl.gov/cmip5/esg_tables/transpose_esg_static_table.html, is also useful. An improvement I'd like to see on this page: the numbers inside the blue boxes that show how many runs there are for a particular experiment/model should be a link to a list of those runs that has all the necessary components from the Data Reference Synatax so that I can go directly to the URL for that data set. For example,
> >> the BCC-CSM1.1 model shows 45 runs for the decadal1960 experiment. I would like to click on that 45 and get a list of the 45 URLs for those runs, like this:
> >> http://pcmdi3.llnl.gov/esgcet/dataset/cmip5.output1.BCC.bcc-csm1-1.decadal1960.day.land.day.r1i1p1.html
> >> http://pcmdi3.llnl.gov/esgcet/dataset/cmip5.output1.BCC.bcc-csm1-1.decadal1960.day.land.day.r2i1p1.html
> >> ...
> >>
> >>
> >>> How did you tell wget to download those files?
> >> For example: wget -nH --retr-symlinks -r -A nc ftp://username@ftp-esg.ucllnl.org/picntrl/atm/mo/tas -o log.tas
> >> This would populate a local directory ./picntrl/atm/mo/tas with all the models and ensemble members in the proper subdirectory. If I wanted to update with newer versions or models that had been added, I simply ran the same 1-line wget command again. This is what I refer to as 'elegant.'
> >>
> >>
> >>> We might have already some way of achieving what you want, if we knew exactly what that is.
> >> Wouldn't that be wonderful? I am hopeful that the P2P will simplify the elaborate and flawed workflow I have cobbled together to navigate the current system.
> >> I have a list of desired experiment/realm/frequency/MIP_table/variables for which I need to grab all available models/ensembles. Is that not enough to describe my needs?
> >>
> >>>
> >>> I guess my proposal of issuing:
> >>> bash <(wget http://p2pnode/wget?experiment=decadal1960&realm=atmos&time_frequency=month&variable=clt -qO - | grep -v HadCM3)
> >> Yes, this would likely achieve the same result as the '&model=!name' that Luca implemented. However, I believe the documentation says that there is a limit of 1000 to the number of wgets that p2pnode will put into a single search request, so I don't want to populate my precious 1000 results with wgets that I'm going to grep out afterwards.
> >>
> >> --Jennifer
> >>
> >>
> >>>
> >>> was not acceptable to you. But I still don't know exactly why.
> >>> It would really help to know what you meant by "elegant use of wget".
> >>>
> >>> Thanks,
> >>> Estani
> >>>
> >>>
> >>> Am 14.12.2011 18:44, schrieb Cinquini, Luca (3880):
> >>>>
> >>>> So Jennifer, would having the capability of doing negative searches (model=!CCSM), and generate the corresponding wget scripts, help you ?
> >>>> thanks, Luca
> >>>>
> >>>> On Dec 14, 2011, at 10:38 AM, Jennifer Adams wrote:
> >>>>
> >>>>> Well, after working from the client side to get CMIP3 and CMIP5 data, I can say that wget is a fine tool to rely on at the core of the workflow. Unfortunately, the step up in complexity from CMIP3 to CMIP5 and the switch from FTP to HTTP trashed the elegant use of wget. No amount of customized wrapper software, browser interfaces, or pre-packaged tools like DML fixes that problem.
> >>>>>
> >>>>> At the moment, the burden on the user is embarrassingly high. It's so easy to suggest that the user should "filter to remove what is not required" from a downloaded script, but the actual pratice of doing that in a timely and automated and distributed way is NOT simple! And if the solution to my problem of filling in the gaps in my incomplete collection is to go back to clicking in my browser and do the whole thing over again but make my filters smarter by looking for what's already been acquired or what has a new version number … this is unacceptable. The filtering must be a server-side responsibility and the interface must be accessible by automated scripts. Make it so!
> >>>>>
> >>>>> By the way, the version number is a piece of metadata that is not in the downloaded files or the gateway's search criteria. It appears in the wget script as part of the path in the file's http location, but the path is not preserved after the wget is complete, so it is effectively lost after the download is done. I guess the file's date stamp would be the only way to know if the version number of the data file in question has been changed, but I'm not going to write that check into my filtering scripts.
> >>>>>
> >>>>> --Jennifer
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Jennifer M. Adams
> >>>>> IGES/COLA
> >>>>> 4041 Powder Mill Road, Suite 302
> >>>>> Calverton, MD 20705
> >>>>> jma at cola.iges.org
> >>>>>
> >>>>>
> >>>>>
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> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>
> >> --
> >> Jennifer M. Adams
> >> IGES/COLA
> >> 4041 Powder Mill Road, Suite 302
> >> Calverton, MD 20705
> >> jma at cola.iges.org
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >> GO-ESSP-TECH at ucar.edu
> >> http://mailman.ucar.edu/mailman/listinfo/go-essp-tech
> >
> >
>
> --
> Jennifer M. Adams
> IGES/COLA
> 4041 Powder Mill Road, Suite 302
> Calverton, MD 20705
> jma at cola.iges.org
>
>
>
>
--
Bryan Lawrence
University of Reading: Professor of Weather and Climate Computing.
National Centre for Atmospheric Science: Director of Models and Data.
STFC: Director of the Centre for Environmental Data Archival.
Ph: +44 118 3786507 or 1235 445012; Web:home.badc.rl.ac.uk/lawrence
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