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https://issues.apache.org/jira/browse/DRILL-4723?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15330729#comment-15330729
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Jacques Nadeau commented on DRILL-4723:
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I'm pretty sure that a decent chunk of Parquet writing is done on Heap. That
memory consumption would go up as you increase block size since an entire block
for each thread must be held in memory (~1gb x # of threads + any overhead
structures). GC death is very hard to manage gracefully. Especially in a
distributed system (since the GC pauses cause loss of cluster cohesion). There
are ways to combat by increasing Zookeeper timeouts, but it is under the "gc
tuning" concept. This is why most of Drill doesn't use Java heap for data. I'd
guess that the best way to fix this would be to go through the rest of the
write pipeline in Parquet and support using off-heap data structures,
especially in slab allocation. Our initial of this nature was mostly focused on
updating the Parquet readers to use off-heap structures. Then Drill can
gracefully manage out-of-memory.
In terms of workarounds: you'll either need to reduce parallelization or
increase heap to support writing as many concurrent 1gb Parquet files as you
are attempting to write.
> GC Memory Allocation Issues
> ---------------------------
>
> Key: DRILL-4723
> URL: https://issues.apache.org/jira/browse/DRILL-4723
> Project: Apache Drill
> Issue Type: Bug
> Components: Server
> Affects Versions: 1.6.0
> Environment: 5 Drill bits, MapR 1.6 release. 84GB of Direct Memory,
> 24GB of Heap
> Reporter: John Omernik
> Labels: memory, stability
> Fix For: Future
>
> Attachments: node3.log
>
>
> This issue is reposted from the Drill User List. More logs available on
> request in comments (please specify which logs you may want)
> High level: Drill Cluster gets into a bad state when this occurs.
> This is what I have thus far... I can provide more complete logs on a one on
> one basis.
> The cluster was completely mine, with fresh logs. I ran a CTAS query on a
> large table that over 100 fields. This query works well in other cases,
> however I was working with the Block size, both in MapR FS and Drill Parquet.
> I had successfully tested 512m on each, this case was different. Here are the
> facts in this setup:
> - No Compression in MapRFS - Using Standard Parquet Snappy Compression
> - MapR Block Size 1024m
> - Parquet Block size 1024m
> - Query ends up disappearing in the profiles
> - The UI page listing bits only show 4 bits however 5 are running (node 03
> process is running, but no longer in the bit)
> - Error (copied below) from rest API
> - No output in STD out or STD error on node3. Only two nodes actually had
> "Parquet Writing" logs. The other three on Stdout, did not have any
> issues/errors/
> - I have standard log files, gclogs, the profile.json (before it
> disappeared), and the physical plan. Only some components that looked
> possibly at issue included here
> - The Node 3 GC log shows a bunch of "Full GC Allocation Failures" that take
> 4 seconds or more (When I've seen this in other cases, this time can balloon
> to 8 secs or more)
> - The node 3 output log show some issues with really long RPC issues. Perhaps
> the GCs prevent RPC communication and create a snowball loop effect?
> Other logs if people are interested can be provided upon request. I just
> didn't want to flood the whole list with all the logs.
> Thanks!
> John
> Rest Error:
> ./load_day.py 2016-05-09
> Drill Rest Endpoint: https://drillprod.marathonprod.zeta:20000
> Day: 2016-05-09
> /usr/lib/python2.7/site-packages/urllib3/connectionpool.py:769:
> InsecureRequestWarning: Unverified HTTPS request is being made. Adding
> certificate verification is strongly advised. See:
> https://urllib3.readthedocs.org/en/latest/security.html
> InsecureRequestWarning)
> Authentication successful
> Error encountered: 500
> {
> "errorMessage" : "SYSTEM ERROR: ForemanException: One more more nodes lost
> connectivity during query. Identified nodes were
> [atl1ctuzeta03:20001].\n\n\n[Error Id: d7dd0120-f7c0-44ef-ac54-29c746b26354
> on atl1ctuzeta01:20001"
> }
> Possible issue in Node3 Log:
> 2016-06-14 17:25:27,860 [289fc208-7266-6a81-73a1-709efff6c412:frag:1:90] INFO
> o.a.d.e.w.f.FragmentStatusReporter -
> 289fc208-7266-6a81-73a1-709efff6c412:1:90: State to report: RUNNING
> 2016-06-14 17:25:27,871 [289fc208-7266-6a81-73a1-709efff6c412:frag:1:70] INFO
> o.a.d.e.w.fragment.FragmentExecutor -
> 289fc208-7266-6a81-73a1-709efff6c412:1:70: State change requested
> AWAITING_ALLOCATION --> RUNNING
> 2016-06-14 17:25:27,871 [289fc208-7266-6a81-73a1-709efff6c412:frag:1:70] INFO
> o.a.d.e.w.f.FragmentStatusReporter -
> 289fc208-7266-6a81-73a1-709efff6c412:1:70: State to report: RUNNING
> 2016-06-14 17:43:41,869 [BitServer-4] WARN
> o.a.d.exec.rpc.control.ControlClient - Message of mode RESPONSE of rpc type 1
> took longer than 500ms. Actual duration was 4192ms.
> 2016-06-14 17:45:36,720 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.fragment.FragmentExecutor -
> 289fc208-7266-6a81-73a1-709efff6c412:1:0: State change requested RUNNING -->
> CANCELLATION_REQUESTED
> 2016-06-14 17:45:45,740 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.f.FragmentStatusReporter -
> 289fc208-7266-6a81-73a1-709efff6c412:1:0: State to report:
> CANCELLATION_REQUESTED
> 2016-06-14 17:46:15,318 [BitServer-3] WARN
> o.a.d.exec.rpc.control.ControlServer - Message of mode REQUEST of rpc type 6
> took longer than 500ms. Actual duration was 55328ms.
> 2016-06-14 17:46:36,057 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.fragment.FragmentExecutor -
> 289fc208-7266-6a81-73a1-709efff6c412:1:5: State change requested RUNNING -->
> CANCELLATION_REQUESTED
> 2016-06-14 17:46:44,620 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.f.FragmentStatusReporter -
> 289fc208-7266-6a81-73a1-709efff6c412:1:5: State to report:
> CANCELLATION_REQUESTED
> 2016-06-14 17:47:01,393 [BitServer-3] WARN
> o.a.d.exec.rpc.control.ControlServer - Message of mode REQUEST of rpc type 6
> took longer than 500ms. Actual duration was 29781ms.
> 2016-06-14 17:47:09,463 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.fragment.FragmentExecutor -
> 289fc208-7266-6a81-73a1-709efff6c412:1:10: State change requested RUNNING -->
> CANCELLATION_REQUESTED
> 2016-06-14 17:47:26,967 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.f.FragmentStatusReporter -
> 289fc208-7266-6a81-73a1-709efff6c412:1:10: State to report:
> CANCELLATION_REQUESTED
> 2016-06-14 17:47:55,593 [BitServer-3] WARN
> o.a.d.exec.rpc.control.ControlServer - Message of mode REQUEST of rpc type 6
> took longer than 500ms. Actual duration was 46130ms.
> 2016-06-14 17:48:04,497 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.fragment.FragmentExecutor -
> 289fc208-7266-6a81-73a1-709efff6c412:1:15: State change requested RUNNING -->
> CANCELLATION_REQUESTED
> 2016-06-14 17:48:12,742 [BitServer-4] WARN
> o.a.d.exec.rpc.control.ControlClient - Message of mode RESPONSE of rpc type 1
> took longer than 500ms. Actual duration was 4236ms.
> 2016-06-14 17:48:42,328 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.f.FragmentStatusReporter -
> 289fc208-7266-6a81-73a1-709efff6c412:1:15: State to report:
> CANCELLATION_REQUESTED
> 2016-06-14 17:49:36,351 [BitServer-4] WARN
> o.a.d.exec.rpc.control.ControlClient - Message of mode RESPONSE of rpc type 1
> took longer than 500ms. Actual duration was 4260ms.
> 2016-06-14 17:49:36,351 [BitServer-3] WARN
> o.a.d.exec.rpc.control.ControlServer - Message of mode REQUEST of rpc type 6
> took longer than 500ms. Actual duration was 91854ms.
> 2016-06-14 17:50:35,273 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.fragment.FragmentExecutor -
> 289fc208-7266-6a81-73a1-709efff6c412:1:20: State change requested RUNNING -->
> CANCELLATION_REQUESTED
> 2016-06-14 17:50:39,322 [289fc208-7266-6a81-73a1-709efff6c412:frag:1:15] INFO
> o.a.d.e.w.fragment.FragmentExecutor -
> 289fc208-7266-6a81-73a1-709efff6c412:1:15: State change requested
> CANCELLATION_REQUESTED --> FAILED
> 2016-06-14 17:50:51,546 [CONTROL-rpc-event-queue] INFO
> o.a.d.e.w.f.FragmentStatusReporter -
> 289fc208-7266-6a81-73a1-709efff6c412:1:20: State to report:
> CANCELLATION_REQUESTED
> 2016-06-14 17:51:36,905 [BitServer-4] WARN
> o.a.d.exec.rpc.control.ControlClient - Message of mode RESPONSE of rpc type 1
> took longer than 500ms. Actual duration was 4426ms.
> 2016-06-14 17:52:30,805 [BitServer-3] WARN
> o.a.d.exec.rpc.control.ControlServer - Message of mode REQUEST of rpc type 6
> took longer than 500ms. Actual duration was 98767ms.
> 2016-06-14 17:52:47,042 [BitServer-4] WARN
> o.a.d.exec.rpc.control.ControlClient - Message of mode RESPONSE of rpc type 1
> took longer than 500ms. Actual duration was 12041ms.
> Possible issues in Node3 gclog:
> 1819.137: [Full GC (Allocation Failure) 23G->23G(24G), 4.0657064 secs]
> 1823.205: [GC concurrent-mark-abort]
> 1823.221: [GC pause (G1 Evacuation Pause) (young)-- 23G->23G(24G), 0.0382934
> secs]
> 1823.271: [GC pause (G1 Evacuation Pause) (young) (initial-mark)
> 23G->23G(24G), 0.0250215 secs]
> 1823.296: [GC concurrent-root-region-scan-start]
> 1823.296: [GC concurrent-root-region-scan-end, 0.0000105 secs]
> 1823.296: [GC concurrent-mark-start]
> 1823.308: [Full GC (Allocation Failure) 23G->23G(24G), 4.3719713 secs]
> 1827.694: [GC pause (G1 Evacuation Pause) (young)-- 23G->23G(24G), 0.0312666
> secs]
> 1827.727: [GC concurrent-mark-abort]
> 1827.735: [GC pause (G1 Evacuation Pause) (young) 23G->23G(24G), 0.0212359
> secs]
> 1827.766: [Full GC (Allocation Failure) 23G->23G(24G), 3.9308980 secs]
> 1831.710: [GC pause (G1 Evacuation Pause) (young)-- 23G->23G(24G), 0.0298229
> secs]
> 1831.750: [GC pause (G1 Evacuation Pause) (young) (initial-mark)
> 23G->23G(24G), 0.0268410 secs]
> 1831.777: [GC concurrent-root-region-scan-start]
> 1831.777: [GC concurrent-root-region-scan-end, 0.0000212 secs]
> 1831.777: [GC concurrent-mark-start]
> 1831.789: [Full GC (Allocation Failure) 23G->23G(24G), 3.9250410 secs]
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