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From Pouria Pirzadeh <pouria.pirza...@gmail.com>
Subject Re: Creating RTree: no space left
Date Thu, 15 Sep 2016 17:04:05 GMT
@Wail
One quick question:
By any chance do you have some spatial data at a similar scale
(size/cardinality-wise) but with less (ideally without) duplicates ? I am
really curious to know if the core of your loading problem is because of
the size/setting that is being used or because of the duplicates ? (The
fact is we had successfully loaded data at scale into R-Tree indices
before, however with different settings i.e. the amount of data per NC and
IO Device was less, and definitely with much less duplicates (at least in
my experiments) ).

Thanks.
Pouria

On Thu, Sep 15, 2016 at 8:25 AM, Wail Alkowaileet <wael.y.k@gmail.com>
wrote:

> Hi Ahmed and Mike,
>
> @Ahmed
> I actually did a small experiment where I loaded about 1/5 of the data (so
> I can index it) and seems that the R-Tree was really useful for querying
> small regions or neighborhoods.
> I also tried the B-Tree and it was slower than a full scan.
>
> @Mike
> Unfortunately, I cannot still even after anonymization :-)
>
>
> On Wed, Sep 14, 2016 at 11:29 PM, Mike Carey <dtabass@gmail.com> wrote:
>
> > Interesting point, so to speak.  @Wail, any chance you could post a
> Google
> > maps screenshot showing a visualization of the points in this dataset on
> > the underlying geographic region?  (If the dataset is shareable in that
> > anonymized form?)  I would think an R-tree would still be good for
> > small-region geo queries - possibly shrinking the candidate object set
> by a
> > factor of 10,000 - so still useful - and we also do index-AND-ing now, so
> > we would also combine that shrinkage by other index-provided shrinkage on
> > any other index-amenable predicates.  I think the queries are still
> spatial
> > in nature, and the only AsterixDB choices for that are R-tree.  (We did
> > experiments with things like Hilbert B-trees, but the results led to the
> > conclusion that the code base only needs R-trees for spatial data for the
> > forseeable future - they just work too well and in a no-tuning-required
> > fashion.... :-))
> >
> >
> >
> > On 9/14/16 12:49 PM, Ahmed Eldawy wrote:
> >
> >> Looks like an interesting case. Just a small question. Are you sure a
> >> spatial index is the right one to use here? The spatial attribute looks
> >> more like a categorization and a hash or B-tree index could be more
> >> suitable. As far as I know, the spatial index in AsterixDB is a
> secondary
> >> R-tree index which, like any other secondary index, is only good for
> >> retrieving a small number of records. For this dataset, it seems that
> any
> >> small range would still return a huge number of records.
> >>
> >> It is still interesting to further investigate and fix the sort issue
> but
> >> I
> >> mentioned the usage issue for a different perspective.
> >>
> >> Thanks
> >> Ahmed
> >>
> >> On Wed, Sep 14, 2016 at 10:30 AM Mike Carey <dtabass@gmail.com> wrote:
> >>
> >> ☺!
> >>>
> >>> On Sep 14, 2016 1:11 AM, "Wail Alkowaileet" <wael.y.k@gmail.com>
> wrote:
> >>>
> >>> To be exact
> >>>> I have 2,255,091,590 records and 10,391 points :-)
> >>>>
> >>>> On Wed, Sep 14, 2016 at 10:46 AM, Mike Carey <dtabass@gmail.com>
> wrote:
> >>>>
> >>>> Thx!  I knew I'd meant to "activate" the thought somehow, but couldn't
> >>>>> remember having done it for sure.  Oops! Scattered from VLDB, I
> >>>>>
> >>>> guess...!
> >>>
> >>>>
> >>>>>
> >>>>> On 9/13/16 9:58 PM, Taewoo Kim wrote:
> >>>>>
> >>>>> @Mike: You filed an issue -
> >>>>>> https://issues.apache.org/jira/browse/ASTERIXDB-1639. :-)
> >>>>>>
> >>>>>> Best,
> >>>>>> Taewoo
> >>>>>>
> >>>>>> On Tue, Sep 13, 2016 at 9:28 PM, Mike Carey <dtabass@gmail.com>
> >>>>>>
> >>>>> wrote:
> >>>
> >>>> I can't remember (slight jetlag? :-)) if I shared back to this list
> >>>>>>
> >>>>> one
> >>>
> >>>> theory that came up in India when Wail and I talked F2F - his data
> >>>>>>>
> >>>>>> has
> >>>
> >>>> a
> >>>>
> >>>>> lot of duplicate points, so maybe something goes awry in that case.
> >>>>>>>
> >>>>>> I
> >>>
> >>>> wonder if we've sufficiently tested that case?  (E.g., what if there
> >>>>>>>
> >>>>>> are
> >>>>
> >>>>> gazillions of records originating from a small handful of points?)
> >>>>>>>
> >>>>>>>
> >>>>>>> On 8/26/16 9:55 AM, Taewoo Kim wrote:
> >>>>>>>
> >>>>>>> Based on a rough calculation, per partition, each point
field takes
> >>>>>>>
> >>>>>> 3.6GB
> >>>>
> >>>>> (16 bytes * 2887453794 records / 12 partition). To sort 3.6GB, we
> >>>>>>>>
> >>>>>>> are
> >>>
> >>>> generating 625 files (96MB or 128MB each) = 157GB. Since Wail
> >>>>>>>>
> >>>>>>> mentioned
> >>>>
> >>>>> that there was no issue when creating a B+ tree index, we need to
> >>>>>>>>
> >>>>>>> check
> >>>>
> >>>>> what SORT process is required by R-Tree index.
> >>>>>>>>
> >>>>>>>> Best,
> >>>>>>>> Taewoo
> >>>>>>>>
> >>>>>>>> On Fri, Aug 26, 2016 at 7:52 AM, Jianfeng Jia <
> >>>>>>>>
> >>>>>>> jianfeng.jia@gmail.com
> >>>
> >>>> wrote:
> >>>>>>>>
> >>>>>>>> If all of the file names start with “ExternalSortRunGenerator”,
> then
> >>>>>>>> they
> >>>>>>>>
> >>>>>>>> are the first round files which can not be GCed.
> >>>>>>>>> Could you provide the query plan as well?
> >>>>>>>>>
> >>>>>>>>> On Aug 24, 2016, at 10:02 PM, Wail Alkowaileet <
> wael.y.k@gmail.com
> >>>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>> Hi Ian and Pouria,
> >>>>>>>>>
> >>>>>>>>>> The name of the files along with the sizes (there
were 625 one
> of
> >>>>>>>>>> those
> >>>>>>>>>> before crashing):
> >>>>>>>>>>
> >>>>>>>>>> size        name
> >>>>>>>>>> 96MB     ExternalSortRunGenerator8917133039835449370.waf
> >>>>>>>>>> 128MB   ExternalSortRunGenerator8948724728025392343.waf
> >>>>>>>>>>
> >>>>>>>>>> no files were generated beyond runs.
> >>>>>>>>>> compiler.sortmemory = 64MB
> >>>>>>>>>>
> >>>>>>>>>> Here is the full logs
> >>>>>>>>>> <https://www.dropbox.com/s/k2qbo3wybc8mnnk/log_Thu_Aug_
> >>>>>>>>>>
> >>>>>>>>>> 25_07%3A34%3A52_AST_2016.zip?dl=0>
> >>>>>>>>>>
> >>>>>>>>> On Tue, Aug 23, 2016 at 9:29 PM, Pouria Pirzadeh
<
> >>>>>>>>>
> >>>>>>>>>> pouria.pirzadeh@gmail.com>
> >>>>>>>>>>
> >>>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>>> We previously had issues with huge spilled sort
temp files when
> >>>>>>>>>> creating
> >>>>>>>>>>
> >>>>>>>>>> inverted index for fuzzy queries, but NOT R-Trees.
> >>>>>>>>>>> I also recall that Yingyi fixed the issue
of delaying clean-up
> >>>>>>>>>>>
> >>>>>>>>>> for
> >>>
> >>>> intermediate temp files until the end of the query execution.
> >>>>>>>>>>> If you can share names of a couple of temp
files (and their
> sizes
> >>>>>>>>>>> along
> >>>>>>>>>>> with the sort memory setting you have in
> >>>>>>>>>>>
> >>>>>>>>>> asterix-configuration.xml)
> >>>
> >>>> we
> >>>>>>>>>>>
> >>>>>>>>>>> may
> >>>>>>>>>>>
> >>>>>>>>>> be able to have a better guess as if the sort
is really going
> >>>>>>>>>>
> >>>>>>>>> into a
> >>>
> >>>> two-level merge or not.
> >>>>>>>>>>>
> >>>>>>>>>>> Pouria
> >>>>>>>>>>>
> >>>>>>>>>>> On Tue, Aug 23, 2016 at 11:09 AM, Ian Maxon
<imaxon@uci.edu>
> >>>>>>>>>>>
> >>>>>>>>>> wrote:
> >>>>
> >>>>> I think that execption ("No space left on device") is just casted
> >>>>>>>>>>> from
> >>>>>>>>>>> the
> >>>>>>>>>>>
> >>>>>>>>>>> native IOException. Therefore I would be
inclined to believe
> it's
> >>>>>>>>>>>
> >>>>>>>>>>>> genuinely
> >>>>>>>>>>>>
> >>>>>>>>>>> out of space. I suppose the question is
why the external sort
> is
> >>>>>>>>>>>
> >>>>>>>>>> so
> >>>
> >>>> huge.
> >>>>>>>>>>>>
> >>>>>>>>>>> What is the query plan? Maybe that will
shed light on a
> possible
> >>>>>>>>>> cause.
> >>>>>>>>>>
> >>>>>>>>>> On Tue, Aug 23, 2016 at 9:59 AM, Wail Alkowaileet
<
> >>>>>>>>>>>
> >>>>>>>>>>>> wael.y.k@gmail.com
> >>>>>>>>>>>> wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>> I was monitoring Inodes ... it didn't
go beyond 1%.
> >>>>>>>>>>>>
> >>>>>>>>>>>> On Tue, Aug 23, 2016 at 7:58 PM, Wail
Alkowaileet <
> >>>>>>>>>>>>> wael.y.k@gmail.com
> >>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Hi Chris and Mike,
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Actually I was monitoring it to
see what's going on:
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>      - The size of each partition
is about 40GB (80GB in
> total
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> per
> >>>>
> >>>>>      iodevice).
> >>>>>>>>>>>>>>      - The runs took 157GB per
iodevice (about 2x of the
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> dataset
> >>>
> >>>> size).
> >>>>>>>>>>>>>>      Each run takes either of
128MB or 96MB of storage.
> >>>>>>>>>>>>>>      - At a certain time, there
were 522 runs.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> I even tried to create a BTree
Index to see if that happens
> as
> >>>>>>>>>>>>>> well.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> I
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> created two BTree indexes one for
the *location* and one for
> >>>>>>>>>>>> the
> >>>>>>>>>>>>
> >>>>>>>>>>>> *caller
> >>>>>>>>>>>>> *and
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> they were created successfully.
The sizes of the runs didn't
> >>>>>>>>>>>>>
> >>>>>>>>>>>> take
> >>>
> >>>> anyway
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> near that.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Logs are attached.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> On Tue, Aug 23, 2016 at 7:19
PM, Mike Carey <
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> dtabass@gmail.com>
> >>>
> >>>> wrote:
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> I think we might have "file GC issues"
- I vaguely remember
> >>>>>>>>>>>> that
> >>>>>>>>>>>>
> >>>>>>>>>>> we
> >>>>
> >>>>> don't
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> (or at least didn't once upon
a time) proactively remove
> >>>>>>>>>>>>>> unnecessary
> >>>>>>>>>>>>>> run
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> files - removing all of them
at end-of-job instead of at the
> >>>>>>>>>>>>>
> >>>>>>>>>>>> end
> >>>
> >>>> of
> >>>>
> >>>>> the
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> execution phase that uses their
contents.  We may also have
> an
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> "Amdahl
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> problem" right now with our
sort since we serialize phase
> two
> >>>>>>>>>>>>>
> >>>>>>>>>>>> of
> >>>
> >>>> parallel
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> sorts - though this is not a
query, it's index build, so
> that
> >>>>>>>>>>>>>> shouldn't
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> be
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> it.  It would be interesting to
put a df/sleep script on each
> >>>>>>>>>>>>>
> >>>>>>>>>>>> of
> >>>
> >>>> the
> >>>>>>>>>>>>>> nodes
> >>>>>>>>>>>>>> when this is happening - actually
a script that monitors the
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> temp
> >>>>
> >>>>> file
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> directory - and watch the lifecycle
happen and the sizes
> >>>>>>>>>>>>>
> >>>>>>>>>>>> change....
> >>>>
> >>>>> On 8/23/16 2:06 AM, Chris Hillery wrote:
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> When you get the "disk full"
warning, do a quick "df -i" on
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>> the
> >>>
> >>>> device
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> -
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> possibly you've run out of inodes
even if the space isn't all
> >>>>>>>>>>>>>
> >>>>>>>>>>>> used
> >>>>
> >>>>> up.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> It's
> >>>>>>>>>>>>>> unlikely because I don't think
AsterixDB creates a bunch of
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> small
> >>>>
> >>>>> files,
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> but worth checking.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> If that's not it, then can you
share the full exception and
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>> stack
> >>>>
> >>>>> trace?
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Ceej
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> aka Chris Hillery
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> On Tue, Aug 23, 2016
at 1:59 AM, Wail Alkowaileet <
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> wael.y.k@gmail.com>
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>> I just cleared the hard drives
to get 80% free space. I
> still
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> get
> >>>>
> >>>>> the
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> same
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> issue.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> The data contains:
> >>>>>>>>>>>>>>>>> 1- 2887453794 records.
> >>>>>>>>>>>>>>>>> 2- Schema:
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> create type CDRType
as {
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> id:uuid,
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> 'date':string,
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> 'time':string,
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> 'duration':int64,
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> 'caller':int64,
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> 'callee':int64,
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> location:point?
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> }
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> On Tue, Aug 23,
2016 at 9:06 AM, Wail Alkowaileet <
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> wael.y.k@gmail.com
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Dears,
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> I have a dataset of size
290GB loaded in a 3 NCs each of
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> which
> >>>>
> >>>>> has
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> 2x500GB
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> SSD.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> Each of NC has two IODevices
(partitions) in each hard
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> drive
> >>>
> >>>> (i.e
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>> the
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> total is 4 iodevices
per NC). After loading the data,
> each
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Asterix
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> partition occupied 31GB.
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> The cluster has about 50%
free space in each hard drive
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> (approximately
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> about 250GB free
space in each hard drive). However,
> when I
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> tried
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> to
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> create
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> an index of type RTree,
I got an exception that no space
> left
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> in
> >>>
> >>>> the
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> hard
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> drive during the External
Sort phase.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Is that normal ?
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>> --
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>> *Regards,*
> >>>>>>>>>>>>>>>>>> Wail Alkowaileet
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>> --
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>> *Regards,*
> >>>>>>>>>>>>>>>>> Wail Alkowaileet
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> --
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> *Regards,*
> >>>>>>>>>>>>>> Wail Alkowaileet
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> --
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> *Regards,*
> >>>>>>>>>>>>> Wail Alkowaileet
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> --
> >>>>>>>>>>>>>
> >>>>>>>>>>>> *Regards,*
> >>>>>>>>>> Wail Alkowaileet
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> Best,
> >>>>>>>>>
> >>>>>>>>> Jianfeng Jia
> >>>>>>>>> PhD Candidate of Computer Science
> >>>>>>>>> University of California, Irvine
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>> --
> >>>>
> >>>> *Regards,*
> >>>> Wail Alkowaileet
> >>>>
> >>>>
> >
>
>
> --
>
> *Regards,*
> Wail Alkowaileet
>

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