@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 <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote: > >> > >> ☺! > >>> > >>> On Sep 14, 2016 1:11 AM, "Wail Alkowaileet" <[email protected]> > 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 <[email protected]> > 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 <[email protected]> > >>>>>> > >>>>> 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 < > >>>>>>>> > >>>>>>> [email protected] > >>> > >>>> 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 < > [email protected] > >>>>>>>>> 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 < > >>>>>>>>> > >>>>>>>>>> [email protected]> > >>>>>>>>>> > >>>>>>>>> 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 <[email protected]> > >>>>>>>>>>> > >>>>>>>>>> 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 < > >>>>>>>>>>> > >>>>>>>>>>>> [email protected] > >>>>>>>>>>>> wrote: > >>>>>>>>>>>> > >>>>>>>>>>>> I was monitoring Inodes ... it didn't go beyond 1%. > >>>>>>>>>>>> > >>>>>>>>>>>> On Tue, Aug 23, 2016 at 7:58 PM, Wail Alkowaileet < > >>>>>>>>>>>>> [email protected] > >>>>>>>>>>>>> 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 < > >>>>>>>>>>>>>> > >>>>>>>>>>>>> [email protected]> > >>> > >>>> 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 < > >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> [email protected]> > >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> 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 < > >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> [email protected] > >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> 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 >
