| Re: [geomesa-users] Geomesa is not returning Entire WW data. |
Hi Amit,
Have you been able to figure anything out? I haven't found anything on my end, but it does seem like something that needs to be addressed.
Thanks,
Emilio
On 1/23/20 4:40 PM, Emilio Lahr-Vivaz wrote:
I haven't been able to find anything. I ingested ~700k osm way points from the D.C. area[1] in a local psuedo-distributed 1 node cluster, and ran some bbox queries against them. I'm not going to have time to look into it further until next week, but if you want to do your own investigation I created a 2.3.3-SNAPSHOT branch with rather verbose logging here: https://github.com/elahrvivaz/geomesa/tree/fcr_filter_debug_2.3
You would have to build that branch and deploy the geomesa-hbase-distributed-runtime jar to your region servers, then enable the logging by setting `org.locationtech.geomesa` to DEBUG level in your region server log4j configuration. If you also update your client, you can toggle between using the old java filter implementation by setting the system property `-Dgeomesa.hbase.java=true` on your client (e.g. geoserver), though I didn't see any difference between the two.
The region servers will log any filter serialization/deserialization, and how long it takes to filter/transform each row. In my testing the deserialization was usually < 10ms and the filtering was almost always 0ms and occasionally 1 or 2 ms.
Just as a guess, it may be something with the large number of scans your query is generating, or maybe the selectivity of your filter compared to the data set, or possibly memory constraints in the region servers.
Thanks,
Emilio
[1]: https://download.bbbike.org/osm/bbbike/WashingtonDC/
On 1/23/20 9:16 AM, Emilio Lahr-Vivaz wrote:
Interesting. I will add some debug logging and see if I can replicate the issue and see where the remote filter slowdown is coming from.
Thanks,
Emilio
On 1/22/20 5:33 PM, Amit Srivastava wrote:
Hi Emilio,
We played with hbase.client.operation.timeout value which reduced the number of missing feature to 7K, but when we disabled the remote filtering, we start getting full data and scan time also reduced to 6K from 120K. I think we should investigate more on what is happening with remote filtering?
On Fri, Jan 17, 2020 at 8:10 AM Amit Srivastava <amit.bit96@xxxxxxxxx> wrote:
We are using 1800,000 as a timeout. Below are the Ganglia metrics for scan Max Time. It is showing the maximum time taken is around 120,000 ms that is the default value of hbase.client.operation.timeout. Increasing hbase.client.operation.timeout and see if it is blocking it to reach 30 mins.
On Fri, Jan 17, 2020 at 7:59 AM Emilio Lahr-Vivaz <elahrvivaz@xxxxxxxx> wrote:
Is the query taking over 30 minutes to run? I believe the timeout is specified in milliseconds, so if you are setting it as 30 that might be the problem.
Thanks,
Emilio
On 1/17/20 10:57 AM, Amit Srivastava wrote:
Thanks, currently we are using 30mins as scanner timeout. I will increase the value to see, if we get whole result with this. It will help us to scope down the problem. I am increasing timeout temroraly to 1 hour and see the difference. I will get back to you based on the result.
On Fri, Jan 17, 2020 at 6:45 AM Austin Heyne <aheyne@xxxxxxxx> wrote:
We use hbase.client.scanner.timeout.period = 300000 in addition to >60 other custom configurations on our production EMR clusters. I can't promise that would fix the problem in your case but we haven't experienced this symptom. Tuning HBase to work well on S3 can be considerably complicated.
-Austin
On 1/17/20 8:56 AM, Emilio Lahr-Vivaz wrote:
Hello,
That's interesting. Were you able to return all the data by increasing the scanner timeout?
We don't currently renew leases. Did the expert suggest how to know when to renew a lease? I can't find much/any documentation on that method. The associated JIRA ticket [1] seems to indicate that you would only have to renew the lease if you are not advancing the scanner. Possibly the results are not being processed quickly enough in geoserver to where the scanners are sitting idle and timing out. Similarly, there is another ticket about timeouts from pruning results in server-side filters[2] which seems relevant, but that also seems to have been fixed.
In general, I've found that changing timeouts in hbase can have unexpected consequences, as the various timeout flags seem to be used in more places than you might expect. I don't fully understand which timeouts would even need to be increased where to help with long-running scans, but not affect other parts of the system.
Thanks,
Emilio
[1]: https://issues.apache.org/jira/browse/HBASE-13333
[2]: https://issues.apache.org/jira/browse/HBASE-13090
On 1/17/20 1:53 AM, Amit Srivastava wrote:
Hi Emilio,
I did further deep dive into this issue. We see below exception [1] in the impacted region server. When I spoke about this with the AWS EMR HBase expert, then they told me this exception might cause data loss for the scan query. If the time limit exceeds (set via hbase.client.scanner.timeout.period), then the server returns the results that got accumulated up to that point. Due to this, we might be seeing the data loss.
There suggested two solutions for it:
- Renew lease programmatically [2]
- Increase the hbase.client.scanner.timeout.period, but it will be just a temporary solution. Since currently, we are using hbase.client.scanner.timeout.period as 30. Do you have any recommendations? I think solution 1 is the right long term approach. Do you guys renew the scanner lease programmatically? If not, can you help in fixing it?
Do you think it is the issue? If yes, do you have any alternate solution?
[1] 2020-01-17 05:04:58,527 INFO [regionserver/ip-10-0-21-111.ec2.internal/10.0.21.111:16020.leaseChecker]regionserver.RSRpcServices: Scanner -3738486765916797690 lease expired on region atlas_OSMWays_xz3_geometry_ingestionTimestamp_v2,9,1579207349986.38c67f9825538ce5326181f4cc15b913.
[2] https://hbase.apache.org/devapidocs/org/apache/hadoop/hbase/client/ResultScanner.html#renewLease--
On Thu, Jan 16, 2020 at 10:38 PM Amit Srivastava <amit.bit96@xxxxxxxxx> wrote:
Hi Emilio,
I did further deep dive on this issue, we are seeing below exception [1] in the region server. When I spoke about this with AWS EMR HBase experts then they told me this exception may cause loss of data during scan query. When the time limit is reached (set via hbase.client.scanner.timeout.period), the server returns the results it has accumulated up to that point. Due to this, you might be seeing loss of data.
There suggested 2 solution for it:
1. Renew lease programmatically [2]2. Increase the hbase.client.scanner.timeout.period, but it will be just a temporary solution. Since currently we are using hbase.client.scanner.timeout.period as 30. Do you have any recommendations? I think 1 solution is the right long term solution. Do you guys renew the scanner lease programmatically? If not, can you help in fixing it?
- [1] 2020-01-17 05:04:58,527 INFO [regionserver/ip-10-0-21-111.ec2.internal/10.0.21.111:16020.leaseChecker] regionserver.RSRpcServices: Scanner -3738486765916797690 lease expired on region atlas_OSMWays_xz3_geometry_ingestionTimestamp_v2,9,1579207349986.38c67f9825538ce5326181f4cc15b913.
On Thu, Jan 16, 2020 at 8:34 AM Emilio Lahr-Vivaz <elahrvivaz@xxxxxxxx> wrote:
Interesting - it appears that bug was fixed a while ago though. I don't have a suggestion on an appropriate value to set, but it would be interesting to see if changing the various scan flags had any impact on the results.
Thanks,
Emilio
On 1/16/20 11:26 AM, Amit Srivastava wrote:
Thanks Emilio, We are trying and get back to you if it worked or not. I was going through geomesa doc [1], where I found geomesa allow client to use hbase scanner cache size. I found similar error in HBase (https://issues.apache.org/jira/browse/HBASE-13262) where client reported same bug in one of the HBase version. We are using HBase version 1.4.10 do you think that it could be a potential issue? If yes, then what value will you suggest?
On Thu, Jan 16, 2020 at 6:02 AM Emilio Lahr-Vivaz <elahrvivaz@xxxxxxxx> wrote:
Hello,
Could you try running the query with remote filtering disabled? You can do that by settings 'hbase.remote.filtering' to false in the data store params[1].
We had a user report a similar issue a while ago, and it seemed to be related to our remote cql filtering. That user was able to patch the issue by reverting to an older version of our cql filtering class written in java. We added a bunch of error handling and removed all caching in our newer scala cql filtering class in an attempt to fix the problem, but we never were able to follow up with the user to verify if it was resolved. Disabling remote filtering should bypass that class entirely, so if that works then it would indicate there are still some issues there.
Thanks,
Emilio
[1]: https://www.geomesa.org/documentation/user/hbase/usage.html#hbase-data-store-parameters
On 1/15/20 6:17 PM, Jun Cai wrote:
Sorry. This is the actual BBOX we were using:
[hadoop@ip-10-0-22-146 ~]$ geomesa-hbase explain -c atlas -f OSMWays -q "BBOX(geometry,-126.0,27.0,-117.0,36.0) AND ingestionTimestamp <= '2019-12-23 06:00:00' AND nextTimestamp > '2019-12-23 06:00:00'"
Planning 'OSMWays' (BBOX(geometry, -126.0,27.0,-117.0,36.0) AND ingestionTimestamp <= 2019-12-23T06:00:00+00:00) AND nextTimestamp > 2019-12-23T06:00:00+00:00
Original filter: (BBOX(geometry, -126.0,27.0,-117.0,36.0) AND ingestionTimestamp <= '2019-12-23 06:00:00') AND nextTimestamp > '2019-12-23 06:00:00'
Hints: bin[false] arrow[false] density[false] stats[false] sampling[none]
Sort: none
Transforms: none
Strategy selection:
Query processing took 16ms for 1 options
Filter plan: FilterPlan[XZ3Index(geometry,ingestionTimestamp)[BBOX(geometry, -126.0,27.0,-117.0,36.0) AND ingestionTimestamp <= 2019-12-23T06:00:00+00:00][nextTimestamp > 2019-12-23T06:00:00+00:00]]
Strategy selection took 1ms for 1 options
Strategy 1 of 1: XZ3Index(geometry,ingestionTimestamp)
Strategy filter: XZ3Index(geometry,ingestionTimestamp)[BBOX(geometry, -126.0,27.0,-117.0,36.0) AND ingestionTimestamp <= 2019-12-23T06:00:00+00:00][nextTimestamp > 2019-12-23T06:00:00+00:00]
Geometries: FilterValues(ArrayBuffer(POLYGON ((-126 27, -126 36, -117 36, -117 27, -126 27))),true,false)
Intervals: FilterValues(List((-∞,2019-12-23T06:00Z]),true,false)
Plan: ScanPlan
Tables: atlas_OSMWays_xz3_geometry_ingestionTimestamp_v2
Ranges (31860): [%00;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%00;%0a;/%00;%00;%00;%00;%00;%00;%00;%02;], [%01;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%01;%0a;/%00;%00;%00;%00;%00;%00;%00;%02;], [%02;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%02;%0a;/%00;%00;%00;%00;%00;%00;%00;%02;], [%03;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%03;%0a;/%00;%00;%00;%00;%00;%00;%00;%02;], [%04;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%04;%0a;/%00;%00;%00;%00;%00;%00;%00;%02;]
Scans (360): [%0d;%0a;/%00;%00;%00;%0d;%cb;I$%95;::%0d;%0a;/%00;%00;%00;%0d;%d9;%e4;%92;M], [(%0a;/%00;%00;%00;%04;%ae;%bc;%92;N::(%0a;/%00;%00;%00;%04;%b3;NI*], [%05;%0a;/%00;%00;%00;%05;%cf;%db;m%b9;::%05;%0a;/%00;%00;%00;%0d;%cb;%00;%00;%04;], [9%0a;/%00;%00;%00;%04;%b3;N%db;r::9%0a;/%00;%00;%00;%04;%d2;%bf;m%bc;], [%19;%0a;/%00;%00;%00;%04;%d2;%c0;%00;%04;::%19;%0a;/%00;%00;%00;%05;%cf;%92;I(]
Column families: d
Remote filters: MultiRowRangeFilter, CqlFilter[(BBOX(geometry, -126.0,27.0,-117.0,36.0) AND ingestionTimestamp <= 2019-12-23T06:00:00+00:00) AND nextTimestamp > 2019-12-23T06:00:00+00:00]
Plan creation took 167ms
Query planning took 454ms
On Wed, Jan 15, 2020 at 3:14 PM Jun Cai <joncai2012@xxxxxxxxx> wrote:
And here is the output from the explain query CLI:
Planning 'OSMWays' ingestionTimestamp <= 2019-12-23T06:00:00+00:00 AND nextTimestamp > 2019-12-23T06:00:00+00:00
Original filter: (BBOX(geometry, -180.0,-90.0,180.0,90.0) AND ingestionTimestamp <= '2019-12-23 06:00:00') AND nextTimestamp > '2019-12-23 06:00:00'
Hints: bin[false] arrow[false] density[false] stats[false] sampling[none]
Sort: none
Transforms: none
Strategy selection:
Query processing took 17ms for 1 options
Filter plan: FilterPlan[XZ3Index(geometry,ingestionTimestamp)[ingestionTimestamp <= 2019-12-23T06:00:00+00:00][nextTimestamp > 2019-12-23T06:00:00+00:00]]
Strategy selection took 2ms for 1 options
Strategy 1 of 1: XZ3Index(geometry,ingestionTimestamp)
Strategy filter: XZ3Index(geometry,ingestionTimestamp)[ingestionTimestamp <= 2019-12-23T06:00:00+00:00][nextTimestamp > 2019-12-23T06:00:00+00:00]
Geometries: FilterValues(List(POLYGON ((-180 -90, 180 -90, 180 90, -180 90, -180 -90))),true,false)
Intervals: FilterValues(List((-∞,2019-12-23T06:00Z]),true,false)
Plan: ScanPlan
Tables: atlas_OSMWays_xz3_geometry_ingestionTimestamp_v2
Ranges (1020): [%00;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%00;%0a;/%00;%00;%00;%09;I$%92;L], [%01;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%01;%0a;/%00;%00;%00;%09;I$%92;L], [%02;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%02;%0a;/%00;%00;%00;%09;I$%92;L], [%03;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%03;%0a;/%00;%00;%00;%09;I$%92;L], [%04;%0a;/%00;%00;%00;%00;%00;%00;%00;%01;::%04;%0a;/%00;%00;%00;%09;I$%92;L]
Scans (60): [%0b;::%0b;%0a;/%00;%00;%00;%11;%00;%00;%00;%02;], [%1d;::%1d;%0a;/%00;%00;%00;%11;%00;%00;%00;%02;], [%0d;::%0d;%0a;/%00;%00;%00;%11;%00;%00;%00;%02;], [%04;::%04;%0a;/%00;%00;%00;%11;%00;%00;%00;%02;], [%00;::%00;%0a;/%00;%00;%00;%11;%00;%00;%00;%02;]
Column families: d
Remote filters: MultiRowRangeFilter, CqlFilter[ingestionTimestamp <= 2019-12-23T06:00:00+00:00 AND nextTimestamp > 2019-12-23T06:00:00+00:00]
Plan creation took 108ms
Query planning took 329ms
On Wed, Jan 15, 2020 at 3:08 PM Jun Cai <joncai2012@xxxxxxxxx> wrote:
Hi Emilio,
This is Jun. I am working with Amit on this issue. Here is the query summary from our log:
15 Jan 2020 22:10:40,583 org.locationtech.geomesa.utils.audit.AuditLogger$: {"storeType":"hbase","typeName":"OSMWays","date":1579126240583,"user":"unknown","filter":"(BBOX(geometry, 0.0,45.0,9.0,54.0) AND ingestionTimestamp \u003c\u003d \u00272019-12-23 06:00:00\u0027) AND nextTimestamp \u003e \u00272019-12-23 06:00:00\u0027","hints":"RETURN_SFT\u003d*geometry:LineString:srid\u003d4326,ingestionTimestamp:Timestamp,nextTimestamp:Timestamp,serializerVersion:String,featurePayload:String","planTime":31,"scanTime":1139426,"hits":82089533,"deleted":false}
We are firing the query via GeoTools interface. The missing features are not consistent between runs. Later runs always tend to have more data than previous ones.
Thanks,Jun
On Wed, Jan 15, 2020 at 2:51 PM Emilio Lahr-Vivaz <elahrvivaz@xxxxxxxx> wrote:
Sorry, I pointed you to the wrong mailing list. I've included the right one now.
The bug I am thinking of was related to partitioned tables, but as you aren't using partitioning then that wouldn't affect you. Can you provide the explain plan[1] for the query? Are you querying this through geoserver? Are the missing features consistent when you run the same filter?
Thanks,
Emilio
[1]: https://www.geomesa.org/documentation/user/datastores/query_planning.html#explaining-query-plans
On 1/15/20 5:42 PM, Amit Srivastava wrote:
Hi Emilio,
Can you also point me to the bug which got fixed in 2.3.2. and 2.4.0?
On Wed, Jan 15, 2020 at 2:37 PM Amit Srivastava <amit.bit96@xxxxxxxxx> wrote:
Thanks Emilio for quick response. Below are the required details. Regarding update from 2.3.2 to 2.4.0, we can upgrade it but it will require some effort and time which I want to avoid for now.
Exact filter which I am using: BBOX(geometry,-180.0,-90.0,180.0,90.0) AND ingestionTimestamp <= '2019-12-23 06:00:00' AND nextTimestamp > '2019-12-23 06:00:00'hbase(main):002:0> scan 'atlas' ROW COLUMN+CELL OSMNodes~attributes column=m:v, timestamp=1577234629875, value=*geometry:Point:srid=4326,ingestionTimestamp:Timestamp,nextTimestamp:Timestamp,serializerVersion:String,featurePayload:String;geomesa.index.dtg='ingestionTimestamp',geomesa.z.splits='60',geomesa.indices='z3:6:3:geometry:ingestionTimestamp,id:4:3:' OSMNodes~stats-date column=m:v, timestamp=1577234629875, value=2019-12-25T00:43:49.836Z OSMNodes~table.id.v4 column=m:v, timestamp=1577234646266, value=atlas_OSMNodes_id_v4 OSMNodes~table.z3.geometry.ingestionTimestamp.v6 column=m:v, timestamp=1577234629897, value=atlas_OSMNodes_z3_geometry_ingestionTimestamp_v6 OSMRelationMembers~attributes column=m:v, timestamp=1577234747359, value=ingestionTimestamp:Timestamp,relationId:String,featureTypeId:String,serializerVersion:String,featurePayload:String;geomesa.index.dtg='ingestionTimestamp',geomesa.indices='attr:8:3:relationId:ingestionTimestamp,attr:8:3:featureTypeId:ingestionTimestamp,id:4:3:' OSMRelationMembers~stats-date column=m:v, timestamp=1577234747359, value=2019-12-25T00:45:47.320Z OSMRelationMembers~table.attr.featureTypeId.ingestionTimestamp.v8 column=m:v, timestamp=1577234751575, value=atlas_OSMRelationMembers_attr_featureTypeId_ingestionTimestamp_v8 OSMRelationMembers~table.attr.relationId.ingestionTimestamp.v8 column=m:v, timestamp=1577234747380, value=atlas_OSMRelationMembers_attr_relationId_ingestionTimestamp_v8 OSMRelationMembers~table.id.v4 column=m:v, timestamp=1577234755743, value=atlas_OSMRelationMembers_id_v4 OSMRelations~attributes column=m:v, timestamp=1577234692949, value=*geometry:MultiPolygon:srid=4326,ingestionTimestamp:Timestamp,nextTimestamp:Timestamp,serializerVersion:String,featurePayload:String;geomesa.index.dtg='ingestionTimestamp',geomesa.z.splits='60',geomesa.indices='xz3:2:3:geometry:ingestionTimestamp,id:4:3:' OSMRelations~stats-date column=m:v, timestamp=1577234692949, value=2019-12-25T00:44:52.909Z �� OSMRelations~table.id.v4 column=m:v, timestamp=1577234710295, value=atlas_OSMRelations_id_v4 OSMRelations~table.xz3.geometry.ingestionTimestamp.v2 column=m:v, timestamp=1577234692970, value=atlas_OSMRelations_xz3_geometry_ingestionTimestamp_v2 OSMTestNodes~attributes �� column=m:v, timestamp=1577143864743, value=*geometry:Point:srid=4326,ingestionTimestamp:Timestamp,nextTimestamp:Timestamp,serializerVersion:String,featurePayload:String;geomesa.index.dtg='ingestionTimestamp',geomesa.z.splits='60',geomesa.indices='z3:6:3:geometry:ingestionTimestamp,id:4:3:' OSMTestNodes~stats-date column=m:v, timestamp=1577143864743, value=2019-12-23T23:30:56.200Z OSMTestNodes~table.id.v4 column=m:v, timestamp=1577143890005, value=atlas_OSMTestNodes_id_v4 OSMTestNodes~table.z3.geometry.ingestionTimestamp.v6 column=m:v, timestamp=1577143864809, value=atlas_OSMTestNodes_z3_geometry_ingestionTimestamp_v6 OSMWayNodes~attributes column=m:v, timestamp=1577234724952, value=ingestionTimestamp:Timestamp,wayId:String,nodeId:String,serializerVersion:String,featurePayload:String;geomesa.index.dtg='ingestionTimestamp',geomesa.indices='attr:8:3:wayId:ingestionTimestamp,attr:8:3:nodeId:ingestionTimestamp,id:4:3:' OSMWayNodes~stats-date column=m:v, timestamp=1577234724952, value=2019-12-25T00:45:24.908Z OSMWayNodes~table.attr.nodeId.ingestionTimestamp.v8 column=m:v, timestamp=1577234729162, value=atlas_OSMWayNodes_attr_nodeId_ingestionTimestamp_v8 OSMWayNodes~table.attr.wayId.ingestionTimestamp.v8 column=m:v, timestamp=1577234724973, value=atlas_OSMWayNodes_attr_wayId_ingestionTimestamp_v8 OSMWayNodes~table.id.v4 column=m:v, timestamp=1577234733300, value=atlas_OSMWayNodes_id_v4 OSMWays~attributes column=m:v, timestamp=1577234660315, value=*geometry:LineString:srid=4326,ingestionTimestamp:Timestamp,nextTimestamp:Timestamp,serializerVersion:String,featurePayload:String;geomesa.index.dtg='ingestionTimestamp',geomesa.z.splits='60',geomesa.indices='xz3:2:3:geometry:ingestionTimestamp,id:4:3:' OSMWays~stats-date column=m:v, timestamp=1577234660315, value=2019-12-25T00:44:20.278Z OSMWays~table.id.v4 column=m:v, timestamp=1577234677610, value=atlas_OSMWays_id_v4 OSMWays~table.xz3.geometry.ingestionTimestamp.v2 column=m:v, timestamp=1577234660337, value=atlas_OSMWays_xz3_geometry_ingestionTimestamp_v2
On Wed, Jan 15, 2020 at 2:20 PM Emilio Lahr-Vivaz <elahrvivaz@xxxxxxxx> wrote:
Hello,
If possible, can you upgrade to 2.3.2 or 2.4.0? There is at least one bug that may cause that behavior, that has been fixed in those versions. Aside from that, it would be helpful if you could provide the exact filters you're using, and the data from your catalog table in hbase, as output by scanning it through the hbase shell.
Thanks,
Emilio
On 1/15/20 2:58 PM, Amit Srivastava wrote:
Hi All,
I am using Geomesa v2.3.0 with HBase. While running BBOX export query on Geomesa the results are inconsistent. I am seeing few features are missing in export. Can someone help in debugging this?
What investigation I have done so far?
- Compare the data ingested vs exported. Found below diff for it.
- Checked the Application logs which is calling Geomesa via GeoTools interface. I am not seeing any error in the application log.
- Checked HBase related metrics and logs. I am not seeing any error during the time when we performed the execution.
- Re-Run the query on a smaller BBOX which has missing data, the reported missing data in 2nd export got returned by Geomesa in 3rd query. Hence I can't find repreoducable steps for this issue.
Missing Features In 2nd Export Run:
Missing Features in 1st Export Run:
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