[pdal] [EXTERNAL] Re: Oracle PDAL queries not scaling
Oscar Martinez Rubi
o.rubi at esciencecenter.nl
Wed Aug 12 02:53:59 PDT 2015
Hi,
When you say that statistics are auto-gathered...by who? PDAL or Oracle?
- In PDAL OCIWritter I do not see anything to do the analyze and
gather_stats. I would maybe put it just after creating the indexes, and
also optional as the indexes creation, because you only want to do that
after the loading of the last file.
- In Oracle itself I have not disabled anything (as far as I remember)
and they are indeed computed automatically after a while, the problem is
how long is "this while", to be sure, and as you recommend, it is maybe
just better to do it your own once you know the loading is over.
So, bottom line: I do the loading of all the files (with pdal) with
deactivated indexing. And then, the stuff I do after the last pdal
loading is:
- Create primary key on obj_id/blk_id. This is the one you suggest
- Insert info in USER_SDO_GEOM_METADATA of the whole extent of all the
loaded data (from different files and in different PDAL runs)
- Create the spatial index
- Analyze and gather stats
The SQL commands for that are:
ALTER TABLE AHN_BLCK ADD CONSTRAINT AHN_BLCK_PK PRIMARY KEY (OBJ_ID,
BLK_ID) USING INDEX TABLESPACE INDX;
INSERT INTO USER_SDO_GEOM_METADATA VALUES ('AHN_BLCK','BLK_EXTENT',
SDO_DIM_ARRAY(SDO_DIM_ELEMENT('X',60000.0,100000.0,0.0001),
SDO_DIM_ELEMENT('Y',425000.0,475000.0,0.0001)),28992);
CREATE INDEX AHN_BLCK_SIDX ON AHN_BLCK (BLK_EXTENT) INDEXTYPE IS
MDSYS.SPATIAL_INDEX PARAMETERS ('TABLESPACE=INDX WORK_TABLESPACE=PCWORK
LAYER_GTYPE=POLYGON SDO_INDX_DIMS=2 SDO_RTR_PCTFREE=0') PARALLEL 16 ;
ANALYZE TABLE AHN_BLCK COMPUTE SYSTEM STATISTICS FOR TABLE;
BEGIN
DBMS_STATS.GATHER_TABLE_STATS('PDAL23090M','AHN_BLCK',NULL,NULL,FALSE,'FOR
ALL COLUMNS SIZE AUTO',8,'ALL');
END;
After the doing all these steps the query times are as expected so I am
going to assume those are the exact proper steps. The times are now
scalable and quite nice (right now still busy with the 23 billion
dataset but I guess it is safe to assume they will also be fine ;) )!
Time[s] pdal20M pdal210M pdal2201M pdal23090M
--------- --------- ---------- ----------- ------------
01_0 0.63 0.37 0.41 -
01_1 0.18 0.2 0.22 -
02_0 1.18 1.51 1.54 -
02_1 0.96 0.96 0.93 -
03_0 0.24 0.25 0.25 -
03_1 0.18 0.18 0.18 -
04_0 1.49 1.53 1.44 -
04_1 1.05 1.07 1.06 -
05_0 0.66 0.78 0.76 -
05_1 0.49 0.51 0.49 -
06_0 1.42 1.61 1.64 -
06_1 1.17 1.2 1.21 -
07_0 1.6 2.12 2.15 -
07_1 1.62 1.35 1.43 -
Thanks for your help and suggestions!
Regards,
O.
On 12-08-15 00:30, Smith, Michael ERDC-RDE-CRREL-NH wrote:
> The statistics should actually auto gather (unless you've disabled
> that part). Its done as part of the DBMS Auto tasks and should gather
> when the tables are stale. Although this is more for a production type
> operation. If you are doing testing, you absolutely should make sure
> your statistics are up to date otherwise you will get bad access plans.
>
> Its also recommended to set a unique index on your Block table on the
> Obj_ID/Blk_ID (although this is primarily used to individually select
> pointclouds). The more info you can give the optimizer, the better
> your query will perform.
>
> You can run (and should) explain plan's on your data access queries
> and see what estimates the optimizer returns. If they don't match what
> you expect, then you're probably feeding bad information to the optimizer.
>
> Mike
>
> ----
> Michael Smith
> US Army Corps
> Remote Sensing GIS/Center
> michael.smith at usace.army.mil
>
>
> From: <pdal-bounces at lists.osgeo.org
> <mailto:pdal-bounces at lists.osgeo.org>> on behalf of Oscar Martinez
> Rubi <o.rubi at esciencecenter.nl <mailto:o.rubi at esciencecenter.nl>>
> Date: Tuesday, August 11, 2015 at 11:04 AM
> To: Peter van Oosterom <P.J.M.vanOosterom at tudelft.nl
> <mailto:P.J.M.vanOosterom at tudelft.nl>>, Albert Godfrind
> <albert.godfrind at oracle.com <mailto:albert.godfrind at oracle.com>>,
> "pdal at lists.osgeo.org <mailto:pdal at lists.osgeo.org>"
> <pdal at lists.osgeo.org <mailto:pdal at lists.osgeo.org>>
> Cc: Theo Tijssen <T.P.M.Tijssen at tudelft.nl
> <mailto:T.P.M.Tijssen at tudelft.nl>>, "mike.horhammer at oracle.com
> <mailto:mike.horhammer at oracle.com>" <mike.horhammer at oracle.com
> <mailto:mike.horhammer at oracle.com>>
> Subject: [EXTERNAL] Re: [pdal] Oracle PDAL queries not scaling
> Resent-From: Michael Smith <michael.smith at usace.army.mil
> <mailto:michael.smith at usace.army.mil>>
>
> Hi,
>
> What I did now is to force statistics gathering, so:
>
> ANALYZE TABLE AHN_BLCK compute system statistics for table;
> BEGIN
> dbms_stats.gather_table_stats('PDAL20M','AHN_BLCK',NULL,NULL,FALSE,'FOR
> ALL COLUMNS SIZE AUTO',8,'ALL');
> END;
>
> And after doing this the queries are scalable, so in this way I do
> not need to wait for the DB to learn...
>
> Regards,
>
> O.
>
>
> On 11-08-15 16:51, Peter van Oosterom wrote:
>> Hi Oscar,
>>
>> It feels like when you fetch the data, this is based on a query
>> execution plan that does a full table scan to get the blocks.
>> Even if there is an index, the database may not use this.
>> However, the database may notice that the actual query execution
>> was disappointing (collecting statistics), and that after
>> repeating the same tests, the database behaviour changed its
>> behaviour and does scale well.
>>
>> [others: this was not in email of Oscar, but after repeating the
>> test the data was fetched in about 0.02 seconds for all sizes
>> 20M, 210M and 2201M. So, also the fetching in case of small
>> dataset becomes significantly faster form 0.5 vs. 0.02 seconds.]
>>
>> Would be good to see the actual query execution plain or force
>> the database to use the index (with an hint). My hand-on
>> practical Oracle syntax knowledge is too low to give exact hits
>> how to do this, but perhaps others can help here.
>>
>> Kind regards, Peter.
>>
>>
>> On 11-8-2015 16:26, Oscar Martinez Rubi wrote:
>>> Hi,
>>>
>>> I have investigated a bit more this issue.
>>>
>>> I wanted to see what data does the OCI reader actually reads, so
>>> I executed the pre-selection query out of PDAL, in python. So I
>>> run the attached script (freshly after loading the data).
>>>
>>> The script runs the same exact query as done in PDAL twice and
>>> prints for each run the number of returned blocks, time spent in
>>> the query and time spent to fetch the results.
>>>
>>> the exact query is:
>>>
>>> SELECT
>>> l."OBJ_ID", l."BLK_ID", l."BLK_EXTENT", l."BLK_DOMAIN",
>>> l."PCBLK_MIN_RES", l."PCBLK_MAX_RES", l."NUM_POINTS",
>>> l."NUM_UNSORTED_POINTS", l."PT_SORT_DIM", l."POINTS", b.pc
>>> FROM
>>> AHN_BLCK l, AHN_BASE b, QUERY_POLYGONS g
>>> WHERE
>>> l.obj_id = b.id
>>> AND
>>> SDO_FILTER(l.blk_extent,g.geom) = 'TRUE' AND g.id = 1;
>>>
>>> The results I get are:
>>>
>>> 20M run 1:
>>> #blocks: 12
>>> query time[s]: 0.113833904266
>>> fetch time[s]: *0.571593046188*
>>> 20M run 2:
>>> #blocks: 12
>>> query time[s]: 0.000102996826172
>>> fetch time[s]: *0.500910997391*
>>> 210M run 1:
>>> #blocks: 13
>>> query time[s]: 0.0586049556732
>>> fetch time[s]: *5.09832000732*
>>> 210M run 2:
>>> #blocks: 13
>>> query time[s]: 0.000245094299316
>>> fetch time[s]: *5.05038785934*
>>> 2201M run 1:
>>> #blocks: 13
>>> query time[s]: 0.070690870285
>>> fetch time[s]: *52.4960811138*
>>> 2201M run 2:
>>> #blocks: 13
>>> query time[s]: 0.000225067138672
>>> fetch time[s]: *53.1006689072*
>>>
>>> So, even though the query times and the number of returned
>>> blocks are similar the fetch times are the not. We can see the
>>> scaling issue there. Somehow the fetching is much more expensive
>>> (10x) when points are 10x.
>>>
>>> I also noticed that after a while doing queries the times get
>>> much better and scalable even when I do new queries with other
>>> polygons. So, the first queries suffer of scaling issues but
>>> later it gets better.
>>>
>>> Any idea why?
>>>
>>> Regards,
>>>
>>> O.
>>>
>>>
>>>
>>>
>>> On 10-08-15 18:40, Albert Godfrind wrote:
>>>> Like many tools that access an Oracle database, we lack the
>>>> ability to see what actually happens in the database at a
>>>> detailed level, i.e. which actual queries are sent, and how the
>>>> database executes them in terms of CPU use, logical and
>>>> physical I/Os, network throughput and latency.
>>>>
>>>> So I think it is important to add some debugging / tracing
>>>> facility to let me see what happens:
>>>>
>>>> 1) An option to make PDAL (actually the OCI driver here) log
>>>> each SQL statement it executes, together with the elapsed time
>>>> and the number of rows (blocks) fetched. Obviously we have that
>>>> statement in the input XML file, but a trace would put
>>>> everything in a single log and include proper measurements.
>>>>
>>>> 2) More important: an option to make the OCI driver enable SQL
>>>> tracing at the database side. This is simple to do by just
>>>> issuing an “ALTER SESSION …” statement before running the
>>>> queries. The resulting trace will show all details about
>>>> execution times as well as resource consumption (CPU and IO)
>>>> and wait times. That could be added as an option in the XML
>>>> file. Or maybe extend the XML file with the option to specify a
>>>> SQ statement to be performed before each query (we could then
>>>> use that to manually add the ALTER SESSION statement.
>>>>
>>>> The resulting trace can help isolate the bottleneck as one of:
>>>>
>>>> 1) the I/Os in the database, to fetch the blocks from disk
>>>> (mostly I/O)
>>>> 2) the network time to pass the blocks to the PDAL client
>>>> (network throughput and latency)
>>>> 3) the time to process the blocks in the PDAL client (mostly CPU)
>>>>
>>>> Albert
>>>>
>>>>> On 5-Aug-2015, at 12:26, Oscar Martinez Rubi
>>>>> <o.rubi at esciencecenter.nl <mailto:o.rubi at esciencecenter.nl>>
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I did a test to see how good Oracle with PDAL scale with
>>>>> bigger data sets. I had 3 datasets that are self-contained
>>>>> with 20M, 210M and 2201M points. I loaded them in different
>>>>> Oracle DBs with PDAL and laz-perf. And, for each of them I ran
>>>>> 7 queries (via a pdal pipeline that preselects blocks, applies
>>>>> a crop and then write to a LAS file)
>>>>>
>>>>> The results are in the attached file.
>>>>>
>>>>> Regarding the loading, for the 20M I only used one core (it is
>>>>> only one file) while for the others I used 16 cores, i.e. 16
>>>>> simult. PDAL instances loading data to Oracle. I opened an
>>>>> issue in GitHub because I noticed that in some of the runs the
>>>>> size that I got was too large, and I do not know what caused
>>>>> that. The attached numbers are when everything seemed to work
>>>>> and the sizes were as expected.
>>>>>
>>>>> This message, though, is about the queries. Each query is run
>>>>> twice in each DB. As you can see in the results file, for 10x
>>>>> more points in the data set the queries are 10x slower, at
>>>>> least for the first run (with the 2201M the second run is much
>>>>> faster but this does not happen with the 210M).
>>>>>
>>>>> Find also attached one of the XML that i used for the queries
>>>>> (example is for query1). Note that the geometry is previously
>>>>> inserted in oracle so I can use to pre-filter blocks with the
>>>>> query option in oci reader
>>>>>
>>>>> First I though that maybe the query option in the oci reader
>>>>> in the XML was ignored and that all the blocks of the dataset
>>>>> were being processed by PDAL (that would explain 10x more
>>>>> points 10x slower queries) but I ran a pdal pipeline for
>>>>> query1 with verbose and I saw that the crop filter "only"
>>>>> processed 120000 points which makes sense taking into account
>>>>> that region of query 1 only has 74818 points. Or maybe the
>>>>> crop still process all the blocks extents but only opens and
>>>>> decompress the points of the overlapping ones?
>>>>>
>>>>> Any idea what is happening?
>>>>>
>>>>> Regards,
>>>>>
>>>>> O.
>>>>> <results.txt><query1.xml>
>>>>
>>>> --
>>>> ORACLE <BLOCKEDoracle.comBLOCKED>
>>>> Albert Godfrind | Geospatial technologies | Tel: +33 4 93 00 80
>>>> 67| Mobile: +33 6 09 97 27 23| Skype:albert-godfrind
>>>> <skype:albert-godfrind>
>>>> OracleServer Technologies
>>>> 400 Av. Roumanille,BP 309 |06906 Sophia Antipolis cedex|France
>>>> Everything you ever wanted to know about Oracle Spatial
>>>> <BLOCKEDapress.com/9781590598993BLOCKED>
>>>>
>>>> <BLOCKEDlocationintelligence.net/dc/BLOCKED>
>>>>
>>>>
>>>>
>>>
>>
>>
>> --
>> Peter van OosteromP.J.M.vanOosterom at tudelft.nl
>> Section GIS technology (room 00-west-520) Department OTB
>> Faculty of Architecture and the Built Environment, TU Delft
>> tel (+31) 15 2786950 Julianalaan 134, 2628 BL Delft, NL
>> fax (+31) 15 2784422 P.O. Box 5043, 2600 GA Delft, NL
>> BLOCKEDgeomatics.tudelft.nlBLOCKED MSc Geomatics
>> BLOCKEDmsc-gima.nlBLOCKED MSc GIMA (Geo-Info Management&Appl)
>> BLOCKEDgdmc.nlBLOCKED
>>
>
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