[Go-essp-tech] Reasoning for the use of symbolic links in drslib
V. Balaji
V.Balaji at noaa.gov
Fri Sep 23 09:00:21 MDT 2011
I'd like to assume, optimistically, that the number of files that have
non-latest status (i.e been superseded or retracted) is going to be very
small compared to the total number of files on the system.
In that case, perhaps it would be more efficient for the additional text
file proposed by Karl to list only those files that have been superseded
and should _not_ be downloaded, thus only the non-latest rather than the
latest.
Additionally it should be possible to set a flag in THREDDS that marks
those files as non-latest, and then have some behaviour from the UI,
like a warning popup, signalling that an alternate file is to be
downloaded instead.
Even more basic, we can return to the filesystem directory (which is
the *original* data catalog, using a software artifact developed in
1969 or so... we should all be so lucky as to create a data structure
that's used 40 years from now...) and signal a file as non-latest by
simply flipping its read bit (chmod a-r).
PS. I am glad we have consensus on checksums, but I'd like to hear
comments on Karl's proposal on how to enforce this requirement on
already catalogued files, pulled out and re-quoted here
> P.S. to weigh in on another issue, I think it *will* be
> essential to require, as part of ESG publication that the check-sum be
> recorded (in the THREDDS catalog, if I'm not mistaken). We haven't
> asked groups to republish data conforming to this new requirement
> because I want to make sure that any other required alterations in the
> configuration of the publisher are also communicated, so we only have to
> ask groups to republish once. Note also that if my "alternative"
> approach outlined above is adopted, the checksums could either be gotten
> from the catalog (if they were computed and stored there) or be
> calculated by drslib itself; there would be no need to republish data to
> ESG
Is Karl's proposed design ok? Look for it in THREDDS, if not found,
have drslib or something add it in.
Thanks,
Kettleborough, Jamie writes:
> Hello Karl,
>
> thanks for responding on this and making the user view much more
> explicit. And thanks for the note on the checksum - its good to know
> this is close to being 'required'.
>
> I also agree that the risk to CMIP5 (and the model contribution to IPCC
> AR5) due to data access problems is sufficiently high that simple
> (non-general) solutions that can be delivered quickly are needed. I
> think that many of the early CMIP5/working group 1 users are happy to
> take some of the responsibility for filtering which data they need,
> q.c., etc on themselves. So this user base can toleterate simpler
> solutions. This may not apply to working groups 2, 3... I don't know.
> Later studies of working group 1 may need richer model meta-data.
>
> Some questions /comments on your proposal:
>
> 1. I think the list files are derivable from the thredds catalogue
> entries for the publication version dataset (if they all contained the
> checksums) - I think you suspect this. In a sense (I think) they are a
> reformatting of the thredds catalogues into a form more parsable by
> users. If it can be achieved in time then I think its safer to get the
> checksums in the thredds cataloges and derive any other format from
> there.
> 2. do you think you would expose these list files through http? You
> mention gridFTP but how soon do you think gridFTP will be available for
> the users that need it...
> a. I'm not sure how many have data available through gridFTP
> (http://esgf.org/wiki/Cmip5Status/ArchiveView suggest not many?)
> b. I'm not sure how many users will have gridFTP clients (or maybe
> you can use a standard ftp client?)
> 3. Do you need to capture this idea of 'latest' in the user view, or can
> the user work this out based on the version number?
> a. including 'latest' makes is easier for users as it takes one bit
> of responsibility away from them
> b. but you may be introducing an inconsistency between the thredds
> interface (which doesn't really expose this idea of latest), and the
> more file based interface).
> c. this exposure of 'latest' may be a minor point, (but its ringing
> alarm bells with me).
> 4. I don't think you need time sample do you - isn't that in the file
> name?
> 5. what is the full path to the file - the one visible through gridFTP,
> or through the thredds file server or what?
> 6. an addition - but in the same vain of simplicity, can we have an easy
> to parse list of servers that hold CMIP5 data available via http. In
> the first instance this could be populated by hand. It could be as
> simple as a csv file - server,pki_status.
>
> I'm afraid I haven't had time to think about all the issues around hard
> links, soft links and tape storage - and there may be more major issues
> there.
>
> Jamie
>
>
> ________________________________
>
> From: Karl Taylor [mailto:taylor13 at llnl.gov]
> Sent: 21 September 2011 23:19
> To: stephen.pascoe at stfc.ac.uk
> Cc: gavin at llnl.gov; Kettleborough, Jamie; go-essp-tech at ucar.edu;
> esg-node-dev at lists.llnl.gov
> Subject: Re: [Go-essp-tech] Reasoning for the use of symbolic
> links in drslib
>
>
> Hi Stephen and all,
>
> I would add another requirement (or is this part of 4?):
>
> 5. A user (as opposed to a data provider or a "replicator" or a
> data center data manager) should be able to determine (through an
> automated scripted process) whether a file previously downloaded is in
> the current (i.e., "latest") version of a dataset, or has been
> withdrawn or replaced.
>
> To meet all the requirements in a practical way in the next few
> weeks, I'll suggest an alternative approach: We could use drsLib to
> create the DRS directory structure, but populate the lowest level (where
> the files would normally be found) with a single text file (referred to
> subsequently as the "listing file") containing the following
> information:
>
> the publication-level dataset version THREDDS id, which is:
> <activity>.<product>.<institute>.<model>.<experiment>.<frequency>.<model
> ing realm>.<MIP table>.<ensemble member>.<version number>
> plus the <variable name>
> followed by a table with:
> filename time units time of 1st time sample
> time of last time sample full path to file tracking_id
> checksum
> ---------- ------------ ----------------------------
> ----------------------------- ------------------- -------------
> ----------
> file1
> file2
> .
> .
> .
> fileN
>
> The "listing file" would be stored twice for the latest version
> of each dataset: once under the numbered version subdirectory and
> *also* under the generically labeled "latest" directory. [This is so a
> user interested in the latest version can find it without knowing its
> actual number.] By the way the time information included in the list
> might not be absolutely essential, but it could be helpful for those
> only wanting to download specific time-segments of an integration.
>
> I realize this is not a particularly elegant approach, but if
> users were given access to the drs directory structure (say, through
> gridftp), they could run a script that navigated directly to a variable
> of interest (based on the DRS directory structure specifications) and
> download the "listing file" stored there. Then, the "latest" listing
> file could be compared to the older "listing file" (previously
> downloaded by the user) to determine whether a new version was available
> (by simply comparing the <version numbers> stored in the THREDDS ID).
> If the user didn't have the most recent version, he could then compare
> the two "listing files" (old and new) to determine which files were new
> and which (if any) had been eliminated.
>
> At that point, the user could generate a local copy of the
> latest version by moving/deleting files not found in the latest "listing
> file" and by downloading (using, for example, gridftp) only the new
> files.
>
> I bet that in a single day Stephen could enhance drslib to
> produce these list files, rather than creating the symbolic links to the
> actual file locations as it currently does. Note that if the actual
> files were moved into new directories sometime in the future, a utility
> would have to be written to modify all the "list files" to point to the
> new file locations (but that's also true of the symbolic links, I think)
>
> Also note that creation of a new version would *not* require
> changing any of the existing "list files" (except the list file in the
> "latest" directory would be removed). A new version subdirectory would
> have to be created and for each variable in the dataset, the new "list
> file" for that version would have to be generated (and copied also to
> "latest").
>
> I'll be interested in your response to this idea and trust that
> any time spent thinking about it is warranted (i.e., that this is not a
> completely stupid suggestion). Will it meet all of Stephen's needs?
> Are there any other solutions to the data users' troubles in obtaining
> data, which we can implement in the next few weeks (since that should be
> our goal here).
>
> My primary interest is in making CMIP5 data easily obtainable by
> users (which appears not to be the case at present), and to allow users
> to write scripts to troll for new data they are interested in and
> discover any new versions of data that should replace the old. This is
> not meant to be a general solution to all of the possible ESG
> applications. Also, I'm guessing that a similar approach could be
> followed where instead of reading the "list files", one read the
> catalogs, but I doubt that this would be as easy for the typical user to
> do.
>
> Best regards,
> Karl
>
> P.S. to weigh in on another issue, I think it *will* be
> essential to require, as part of ESG publication that the check-sum be
> recorded (in the THREDDS catalog, if I'm not mistaken). We haven't
> asked groups to republish data conforming to this new requirement
> because I want to make sure that any other required alterations in the
> configuration of the publisher are also communicated, so we only have to
> ask groups to republish once. Note also that if my "alternative"
> approach outlined above is adopted, the checksums could either be gotten
> from the catalog (if they were computed and stored there) or be
> calculated by drslib itself; there would be no need to republish data to
> ESG
>
>
> On 9/20/11 2:35 PM, stephen.pascoe at stfc.ac.uk wrote:
>
> Hi All,
>
>
>
> Lots of good discussion here and sorry I've been keeping
> quiet. I want to remind ourselves of the requirements I laid out in the
> wiki page
>
>
>
> 1. It should allow data from multiple versions to be
> kept on disk simultaneously.
>
> 2. It should avoid storing multiple copies of files that
> are present in more than one version.
>
> 3. It should be straightforward to copy dataset changes
> (i.e. differences between versions) between nodes to allow efficient
> replication.
>
> 4. It should rely only on the filesystem so that generic
> tools like FTP could be used to expose the structure if necessary.
>
>
>
> In my view we should address these directly. Are they
> needed? Which are the most important?
>
>
>
> Gavin said about catalogs
>
> > you can quickly and easily inspect catalog_v1 and
> catalog_v2 to find what the changes are.
> > This all answers the question of "WHAT" (to
> download)... the other question of "HOW" is a different, but related
> story.
> > The trick is to not conflate the two issues which is
> what filesystem discussions do. .
>
>
>
> But THREDDS conflates the two as well! A THREDDS
> catalog contains descriptions of service endpoints that are not
> independent of the node serving the data (the "HOW"). Maybe we should
> have developed a true catalog format but that is not where we are now.
> The replication client use THREDDS catalogs in this way but when I last
> looked it was completely unaware of versions -- i.e. it won't help with
> #3.
>
>
>
> I don't see how Gavin's point addresses any of the
> requirements above. Even if we ditch #4, which I expect Gavin would
> argue for, it doesn't directly solve the problem for #1-#3 either.
>
>
>
> Briefly on some other points that have been made...
>
>
>
> Balaji, some archive tools maybe can detect 2 paths
> pointing to the same filesystem inode but both Estani and I have
> enquired with our backup people and they say hard links must be avoided.
> I am happy to include a hard-linking option in drslib though. I've
> created a bugzilla ticket for it.
>
>
>
> Karl, I think putting real files in "latest" is
> equivalent to putting real files in the latest "vYYYYMMDD" directory.
> The directories can be renamed trivially on upgrade but you still have
> the same problems as the wiki page says.
>
>
>
> I'm sure there were other points but I've lost track.
> Checksums will have to wait for another email.
>
>
>
> Cheers,
>
> Stephen.
>
>
>
>
>
> ---
>
> Stephen Pascoe +44 (0)1235 445980
>
> Centre of Environmental Data Archival
>
> STFC Rutherford Appleton Laboratory, Harwell Oxford,
> Didcot OX11 0QX, UK
>
>
>
> From: go-essp-tech-bounces at ucar.edu
> [mailto:go-essp-tech-bounces at ucar.edu] On Behalf Of Gavin M. Bell
> Sent: 20 September 2011 17:26
> To: Kettleborough, Jamie
> Cc: go-essp-tech at ucar.edu; esg-node-dev at lists.llnl.gov
> Subject: Re: [Go-essp-tech] Reasoning for the use of
> symbolic links in drslib
>
>
>
> Jamie and friends.
>
> You've answered your own questions :-)...
> It is the catalog where these checksums (and other
> features) are recorded.
> And thus using the catalog you can see what has changed.
> There is a new catalog for every version of a dataset.
> Given that...
> you can quickly and easily inspect catalog_v1 and
> catalog_v2 to find what the changes are.
> This all answers the question of "WHAT" (to download)...
> the other question of "HOW" is a different, but related story.
> The trick is to not conflate the two issues which is
> what filesystem discussions do. When talking about filesystems you are
> stipulating the what but implicitly conflating the HOW because you are
> implicitly designing for tools that intrinsically use the filesystem.
> It is a muddying of the waters that doesn't separate the two concerns.
> We need to deal with these two concepts independently in a way that does
> not limit the system or cause undo burden on institutions by requiring
> a rigid structure.
>
> As I mentioned... it's not the filesystem we need to
> look at... it's the catalogs.
>
> just my $0.02 - I'll stop flogging this particular
> horse... but I hope I have done a better job expressing the issues and
> where the solution lies (IMHO).
>
> On 9/20/11 8:14 AM, Kettleborough, Jamie wrote:
>
> Hello Balaji,
>
> I agree - getting all nodes to make the checksums
> available would be a
> good thing. It gives you both the data integrity check
> on download, and
> the ability to see what files really have changed from
> one publication
> version to the next.
>
> I don't know how hard it is to do this, particularly for
> data that is
> already published.
>
> Jamie
>
>
> -----Original Message-----
> From: V. Balaji [mailto:V.Balaji at noaa.gov]
> Sent: 20 September 2011 16:01
> To: Kettleborough, Jamie
> Cc: Karl Taylor; go-essp-tech at ucar.edu;
> esg-node-dev at lists.llnl.gov
> Subject: Re: [Go-essp-tech] Reasoning for the
> use of symbolic
> links in drslib
>
> If nodes can currently choose to record
> checksums or not, I'd
> strongly recommend this be a non-optional
> requirement.. how
> could anyone download any data with confidence
> without being
> able to checksum?
>
> You can of course check timestamps and filesizes
> and so on,
> but you have to consider those optimizations...
> a fast option
> for the less paranoid to avoid the sum
> computation, which has
> to be the gold standard.
>
> "Trust but checksum".
>
> Kettleborough, Jamie writes:
>
>
> Hello Karl, everyone,
>
>
> For replicating the latest version, I
> agree that your alternate
> structure poses difficulties (but it
> seems like there must
>
> be a way to
>
> smartly determine whether the file you
> already have a file
>
> and simply
>
> need to move it, rather than bring it
> over again).
>
>
> Doesn't every user (not just the
> replication system) have
>
> this problem:
>
> they want to know what files have
> changed (or not changed) at a new
> publication version. No one wants to be
> using band width
>
> or storage
>
> space to fetch and store files they
> already have. How is a user
> expected to know what has really
> changed? Estani mentions
>
> check sums
>
> - OK, but I don't think all nodes expose
> them (is this
>
> right?). You
>
> may try to infer from modification dates
> (not sure, I
>
> haven't look at
>
> them that closely). You may try to
> infer from the
>
> TRACKING_ID - but
>
> I'm not sure how reliable this is (I can
> imagine scenarios where
> different files share the same
> TRACKING_ID - e.g. if they have been
> modified with an nco tool).
>
> Is there a recommended method for users
> to understand what *files*
> have actually changed when a new
> publication version appears?
>
> Thanks,
>
> Jamie
>
>
>
> --
>
> V. Balaji Office:
> +1-609-452-6516
> Head, Modeling Systems Group, GFDL Home:
> +1-212-253-6662
> Princeton University Email:
> v.balaji at noaa.gov
>
>
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>
>
>
>
>
> --
> Gavin M. Bell
> --
>
> "Never mistake a clear view for a short distance."
> -Paul Saffo
>
>
>
> --
> Scanned by iCritical.
>
>
>
--
V. Balaji Office: +1-609-452-6516
Head, Modeling Systems Group, GFDL Home: +1-212-253-6662
Princeton University Email: v.balaji at noaa.gov
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