[Go-essp-tech] Reasoning for the use of symbolic links in drslib
Karl Taylor
taylor13 at llnl.gov
Wed Sep 21 16:18:54 MDT 2011
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(i.e., "latest") version of a dataset, or has been withdrawn or replaced.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>.<modeling
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 dayStephen 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 <mailto:go-essp-tech at ucar.edu>;esg-node-dev at lists.llnl.gov <mailto: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 <mailto: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.
>
>
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