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From d..@eiler.net
Subject Re: Help with tuning for larger clusters
Date Sat, 31 Oct 2015 00:13:55 GMT
No problem Denis, it is good to make sure we are using the same  
terminology too.

All the nodes successfully join the cluster every time (i.e. I see a  
"Topology snaphot" log message with "servers=64") typically in between  
about 30 seconds and 1 minute. This is the part that was originally  
taking a long time that you helped me fix by adjusting the port range.

At that point I don't consider the cluster usable, I am still seeing  
the "Retrying preload partition exchange" messages and if I try to run  
a map reduce job like pi estimator it will hang (I see Number of  
Maps/Samples per Map messages, but never see any of the "Wrote input  
for Map".

If I don't do anything I've seen two scenarios
1) a bunch of "Retrying preload partition exchange" for several  
minutes and then all I see in the logs are the metric messages if I  
don't see a "Retrying preload partition exchange" for a minute or so  
in any of the logs then I can run pi estimator and hdfs cli commands

2) a bunch of "Retrying preload partition exchange" for 15+ minutes  
and then I see the "Closing NIO" message and nothing will run.

So yes, with larger numbers of nodes, just starting ignite.sh on the  
nodes and letting it sit idle will most often result in "Closing NIO"  
messages with nothing else being run.

After the "Closing NIO" message everything still looks like it should  
be fine, the "Retrying preload partition" messages stop and all the  
nodes are still part of the topology, but I can't run anything (it  
seems to hang at the first data write)

Did this clear things up or did I just make it worse?
Joe


Quoting Denis Magda <dmagda@gridgain.com>:

> Joe,
>
> Before moving forward and make things clearer.
>
> After applying all the suggestions (timeouts, VM settings) how stable is
> your cluster without any load (without examples execution)?
>
> In particular:
> - how often is the case when a node fails to join the topology and you see
> topology snapshot containing less than 64 nodes? In the logs you sent me I
> see that topology assembled without any issue. If this happens please share
> the such logs with us.
>
> - how long does the cluster live (without any load) before you see I/O
> related issues or some other instability?
>
> Sorry if I haven't seen the answers on these questions in your previous
> responses. For me it's still unclear whether you start seeing the
> instability when the cluster under load or not.
>
> --
> Denis
>
> On Fri, Oct 30, 2015 at 8:26 PM, <dev@eiler.net> wrote:
>
>> Adding the networkTimeouts for 15 seconds did not help, but I'm going to
>> bump up the networkTimeout to 30 seconds and try it again. (note: 30
>> seconds didn't help either)
>>
>> adding the additional GC options did not help
>>
>> Each ignite node (i.e. each ignite.sh run) is on its own dedicated
>> physical hardware (2x Intel Xeon w/ 8 cores each..so /proc/cpuinfo shows 32
>> processors, all have 64GB RAM some have 128GB, no local disk, Mellanox
>> ConnectX-3 FDR IB)
>>
>> Again just some recap of what I think I currently know:
>> 8 nodes works fine, as I increase cluster size the probability of success
>> drops.
>>
>> I have occasionally (about 5 times) gotten everything to come up with 64
>> nodes and run and I can run pi estimator fine then, I usually kill it when
>> trying to load data to do something real but that could be issues with my
>> stuff still. I've also confirmed that using hdfs cli is also affected in
>> the same way (both put and ls).
>>
>> I can predict if a job (either pi estimator or hdfs put) will fail (i.e.
>> hang). If I see any of the ignite node logs contain a "Closing NIO session
>> because unhandled exception". I add a couple printStackTrace calls and it
>> is being thrown from the sockCh.read(readBuf) in the nested
>> DirectNioClientWorker in GridNioServer.java. Since I have been paying
>> attention, the exception comes just under 15 minutes after starting the
>> ignite nodes. (and I am still seeing the "Retrying preload partition
>> exchange due to timeout" on some nodes when that happens)
>>
>> In the cases when stuff comes up and works, it seems to only take a few
>> minutes (but I've been to excited to remember to check the logs for actual
>> times and I keep forgetting to save away a "working" set of logs).
>>
>>
>> Other ideas bouncing around in my head (in addition to any suggestions
>> provided):
>> Enable tracing.
>> My ignite framework and my log files all go to a shared filesystem across
>> the nodes, I'm going to try to push the log files down to a local tmpfs
>> area in case that is contributing somehow
>> I might try wrapping the sockCh.read() call in some debug, and maybe even
>> a retry loop just to see if I can learn anything about the health of the
>> channel.
>> I want to take a look at the system logs (/var/log/messages, etc.) and see
>> if anything is showing up there but I currently don't have read access
>> Start making thread dumps of processes.
>> I might try to flip all my caches mode to something else (local probably)
>> Take a look at rebalancing (can I increase threads, transfer sizes,etc.)
>> Do slow ramp up of nodes (start 8, wait until they are up, add a couple
>> more at a time)
>>
>>
>> Thanks again for the suggestions (and any future ones),
>>
>> Joe
>>
>>
>>
>>
>> Quoting Denis Magda <dmagda@gridgain.com>:
>>
>> Joe,
>>>
>>> After taking a look at the logs I should say that the topology and the
>>> whole cluster is stable, no any node left the topology.  So
>>> 'failureDetectionTimeout' did what it had been created for. You can keep
>>> using its current value.
>>>
>>> Preloading timeout happens from time to time on some nodes but finally it
>>> finishes. I'm quite confident that if you increase
>>> IgniteConfiguration.networkTimeout and TcpDiscoverySpi.networkTimeout
>>> values then this message will disappear at all.
>>> Let's try to set it to 15 secs. The example is below. In general, I think
>>> that we will simplify network timeouts configuration in the nearest
>>> releases.
>>>
>>> <bean id="ignite.cfg"
>>> class="org.apache.ignite.configuration.IgniteConfiguration">
>>>
>>>     <property name="networkTimeout" value="15000"/>
>>>
>>>     ......
>>>         <property name="discoverySpi">
>>>         <bean class="org.apache.ignite.spi.discovery.tcp.TcpDiscoverySpi">
>>>             <property name="networkTimeout" value="15000"/>
>>>                     .............
>>>         </bean>
>>>     </property>
>>> </bean>
>>>
>>>
>>> Next. Since you have quite a big cluster I would suggest you tuning VM
>>> settings a bit.
>>>
>>> - server
>>> -XX:+UseParNewGC
>>> -XX:+UseConcMarkSweepGC
>>> -XX:+UseTLAB
>>> -XX:+UseCMSInitiatingOccupancyOnly
>>> -XX:CMSInitiatingOccupancyFraction=70
>>> -XX:+ScavengeBeforeFullGC
>>> -XX:+CMSScavengeBeforeRemark
>>>
>>> Finally, the only clue I see that may help us to realize why pi estimator
>>> example hangs is the following line in the logs of some nodes
>>>
>>> [07:33:41,704][WARN ][main][IgfsServerManager] Failed to start IGFS
>>> endpoint (will retry every 3s). Failed to bind to port (is port already in
>>> use?): 10500
>>>
>>> This can probably lead to the hangs.
>>>
>>> Is every node started on its own physical machine?
>>> I guess that you start several nodes per one single machine. If my
>>> understanding is correct then please make sure that every node that is
>>> running on a single machine has unique IGFS endpoint port number.
>>>
>>> Joe, if fixing of IGFS endpoints port numbers doesn't help then please
>>> send us thread dumps from the nodes that are hanging during examples
>>> execution.
>>>
>>> Regards,
>>> Denis
>>>
>>> On 10/29/2015 4:37 PM, dev@eiler.net wrote:
>>>
>>>> Nope, not trying to load any data yet. Just starting up all the nodes
>>>> and trying to run the hadoop mapreduce pi estimator example.
>>>>
>>>> I made all the changes below and started all the nodes (I have a script
>>>> the does a pssh so all the nodes start at about the same time.) I then
>>>> waited quite a while until all the node logs stopped showing the "Retrying
>>>> preload" messages. At this point one of the nodes already had the NIO
>>>> exception.
>>>>
>>>> But I then attempted to run the pi estimator example anyways.
>>>> It prints out the Number of Maps / Samples per Map messages but it just
>>>> hangs and I never see the "Wrote input for Map" messages (there have been
>>>> times were I'll see a few and then it will hang. That is what  
>>>> made me think
>>>> it was the writes using the "hdfs api" that were hanging.
>>>>
>>>> Denis, I'll send a tar file with the logs directly to you shortly so as
>>>> not to clog peoples inboxes.
>>>>
>>>> Joe
>>>>
>>>>
>>>> Quoting Denis Magda <dmagda@gridgain.com>:
>>>>
>>>> Hi Joe,
>>>>>
>>>>> No problems, I'll guide you until we get to the bottom.
>>>>>
>>>>> Do you start pre-loading the caches with data right after the cluster
>>>>> is ready? If so let's postpone doing this until you have a stable cluster
>>>>> with caches rebalanced and ready to be used.
>>>>>
>>>>> Please, do the following as the next steps:
>>>>>
>>>>> 1) Set 'failureDetectionTimeout' to a bigger value (~ 15 secs);
>>>>>
>>>>> 2) Set CacheConfiguration.setRebalanceTimeout to a value that is
>>>>> approximately equal to the time when all the nodes are joined  
>>>>> the topology
>>>>> (~ 1 minute or so).
>>>>>
>>>>> 3) Enable verbose logging for every node by passing
>>>>> -DIGNITE_QUEIT=false parameter to virtual machine arguments list. If you
>>>>> use ignite.sh script then just pass '-v' flag.
>>>>>
>>>>> 4) Enable garbage collection logs for every node by passing this string
>>>>> to virtual machine arguments list -Xloggc:./gc.log -XX:+PrintGCDetails
>>>>> -verbose:gc
>>>>>
>>>>> When you did a test run taking into account all the points above please
>>>>> gather all the logs (including garbage collection logs) and send us for
>>>>> further investigation.
>>>>>
>>>>> Regards,
>>>>> Denis
>>>>>
>>>>> On 10/28/2015 1:40 PM, dev@eiler.net wrote:
>>>>>
>>>>>> Thanks for the info Denis.
>>>>>>
>>>>>> Removing the failureDetectionTimeout and using the networkTimeout
>>>>>> seems to allow the nodes to join the topology in about the same  
>>>>>> amount of
>>>>>> time. I'm still only having occasional success running anything  
>>>>>> (even just
>>>>>> the pi estimator)
>>>>>>
>>>>>> I seem to always see a bunch of warnings...a summary is dumped below
>>>>>> along with my config at the end, any guidance you can provide is
>>>>>> appreciated.
>>>>>>
>>>>>> Thanks,
>>>>>> Joe
>>>>>>
>>>>>> Every node seems to see a bunch of "Retrying preload partition", with
>>>>>> the lowest locNodeOrder having fewer nodes in the remaining
>>>>>>
>>>>>> [14:52:38,979][WARN
>>>>>> ][ignite-#104%sys-null%][GridDhtPartitionsExchangeFuture]  
>>>>>> Retrying preload
>>>>>> partition exchange due to timeout [done=false, dummy=false,
>>>>>> exchId=GridDhtPartitionExchangeId [topVer=AffinityTopologyVersion
>>>>>> [topVer=62, minorTopVer=0], nodeId=fd9620f5, evt=NODE_JOINED],  
>>>>>> rcvdIds=[],
>>>>>> rmtIds=[0ab29a08, 5216f6ba, f882885f, 0d232f1a, b74f5ebb, 5790761a,
>>>>>> 55d2082e, b1bf93b3, 2fd79f9f, a899ccce, 3dd74aba, 320d05fd, 0d44a4b3,
>>>>>> 9a00f235, 4426467e, 7837fdfc, e8778da0, 4a988e3e, f8cabdbb, 494ad6fd,
>>>>>> 7c05abfb, 5902c851, c406028e, a0b57685, e213b903, c85a0b46, df981c08,
>>>>>> 187cd54f, f0b7b298, 94ec7576, 041975f5, aecba5d0, 5549256d, f9b5a77a,
>>>>>> 596d0df7, 26266d8c, 0e664e25, 97d112b2, aac08043, 6b81a2b1, 5a2a1012,
>>>>>> 534ac94b, b34cb942, 837785eb, 966d70b2, 3aab732e, 4e34ad89, 6df0ffff,
>>>>>> 4c7c3c47, 85eea5fe, 1c5e2f6b, 3f426f4e, 27a9bef9, cd874e96, dc3256a7,
>>>>>> 4da50521, 1d370c9e, 19c334eb, 24be15dd, 6c922af3, 01ea2812],
>>>>>> remaining=[0ab29a08, 5216f6ba, f882885f, 0d232f1a, b74f5ebb, 5790761a,
>>>>>> 55d2082e, b1bf93b3, 2fd79f9f, a899ccce, 3dd74aba, 320d05fd, 0d44a4b3,
>>>>>> 9a00f235, 4426467e, 7837fdfc, e8778da0, 4a988e3e, f8cabdbb, 494ad6fd,
>>>>>> 7c05abfb, 5902c851, c406028e, a0b57685, e213b903, c85a0b46, df981c08,
>>>>>> 187cd54f, f0b7b298, 94ec7576, 041975f5, aecba5d0, 5549256d, f9b5a77a,
>>>>>> 596d0df7, 26266d8c, 0e664e25, 97d112b2, aac08043, 6b81a2b1, 5a2a1012,
>>>>>> 534ac94b, b34cb942, 837785eb, 966d70b2, 3aab732e, 4e34ad89, 6df0ffff,
>>>>>> 4c7c3c47, 85eea5fe, 1c5e2f6b, 3f426f4e, 27a9bef9, cd874e96, dc3256a7,
>>>>>> 4da50521, 1d370c9e, 19c334eb, 24be15dd, 6c922af3, 01ea2812], init=true,
>>>>>> initFut=true, ready=true, replied=false, added=true, oldest=0d44a4b3,
>>>>>> oldestOrder=1, evtLatch=0, locNodeOrder=62,
>>>>>> locNodeId=fd9620f5-3ebb-4a71-a482-73d6a81b1688]
>>>>>>
>>>>>>
>>>>>> [14:38:41,893][WARN
>>>>>> ][ignite-#95%sys-null%][GridDhtPartitionsExchangeFuture]  
>>>>>> Retrying preload
>>>>>> partition exchange due to timeout [done=false, dummy=false,
>>>>>> exchId=GridDhtPartitionExchangeId [topVer=AffinityTopologyVersion
>>>>>> [topVer=25, minorTopVer=0], nodeId=df981c08, evt=NODE_JOINED],
>>>>>> rcvdIds=[7c05abfb, b34cb942, e213b903, 320d05fd, 5902c851, f0b7b298,
>>>>>> 1d370c9e, 0d232f1a, 494ad6fd, 5a2a1012, b1bf93b3, 55d2082e, 7837fdfc,
>>>>>> 85eea5fe, 4e34ad89, 5790761a, 3f426f4e, aac08043, 187cd54f, 01ea2812,
>>>>>> c406028e, 24be15dd, 966d70b2], rmtIds=[0d232f1a, 5790761a, 55d2082e,
>>>>>> b1bf93b3, aac08043, 5a2a1012, b34cb942, 320d05fd, 966d70b2, 4e34ad89,
>>>>>> 85eea5fe, 7837fdfc, 3f426f4e, 1d370c9e, 494ad6fd, 7c05abfb, 5902c851,
>>>>>> c406028e, 24be15dd, e213b903, df981c08, 187cd54f, f0b7b298, 01ea2812],
>>>>>> remaining=[df981c08], init=true, initFut=true, ready=true,  
>>>>>> replied=false,
>>>>>> added=true, oldest=0d44a4b3, oldestOrder=1, evtLatch=0, locNodeOrder=1,
>>>>>> locNodeId=0d44a4b3-4d10-4f67-b8bd-005be226b1df]
>>>>>>
>>>>>>
>>>>>> I also see a little over half the nodes getting "Still waiting for
>>>>>> initial partition map exchange" warnings like this
>>>>>>
>>>>>>
>>>>>> [14:39:37,848][WARN ][main][GridCachePartitionExchangeManager] Still
>>>>>> waiting for initial partition map exchange
>>>>>> [fut=GridDhtPartitionsExchangeFuture [dummy=false, forcePreload=false,
>>>>>> reassign=false, discoEvt=DiscoveryEvent [evtNode=TcpDiscoveryNode
>>>>>> [id=27a9bef9-de04-486d-aac0-bfa749e9007d, addrs=[0:0:0:0:0:0:0:1%1,
>>>>>> 10.148.0.87, 10.159.1.182, 127.0.0.1], sockAddrs=[
>>>>>> r1i4n10.redacted.com/10.148.0.87:47500, /0:0:0:0:0:0:0:1%1:47500, /
>>>>>> 10.159.1.182:47500, /10.148.0.87:47500, /10.159.1.182:47500, /
>>>>>> 127.0.0.1:47500], discPort=47500, order=48, intOrder=48,
>>>>>> lastExchangeTime=1445974777828, loc=true,  
>>>>>> ver=1.4.0#19691231-sha1:00000000,
>>>>>> isClient=false], topVer=48, nodeId8=27a9bef9, msg=null,  
>>>>>> type=NODE_JOINED,
>>>>>> tstamp=1445974647187], rcvdIds=GridConcurrentHashSet [elements=[]],
>>>>>> rmtIds=[0ab29a08-9c95-4054-8035-225f5828b3d4,
>>>>>> 0d232f1a-0f46-4798-a39a-63a17dc4dc7f,  
>>>>>> f9b5a77a-a4c1-46aa-872e-aeaca9b76ee3,
>>>>>> 596d0df7-3edf-4078-8f4a-ffa3d96296c6,  
>>>>>> 5790761a-aeeb-44d1-9fce-3fee31ef39b7,
>>>>>> 55d2082e-3517-4828-8d47-57b4ed5a41bc,  
>>>>>> 26266d8c-cc87-4472-9fa4-c526d6da2233,
>>>>>> 0e664e25-8dde-4df8-966b-53b60f9a1087,  
>>>>>> b1bf93b3-24bb-4520-ade0-31d05a93558d,
>>>>>> aac08043-875a-485a-ab2c-cd7e66d68f8f,  
>>>>>> 2fd79f9f-9590-41d2-962e-004a3d7690b5,
>>>>>> 5a2a1012-0766-448c-9583-25873c305de9,  
>>>>>> 534ac94b-8dd1-4fa8-a481-539fa4f4ce55,
>>>>>> b34cb942-e960-4a00-b4fb-10add6466a93,  
>>>>>> 320d05fd-e021-40ac-83bc-62f54756771b,
>>>>>> 0d44a4b3-4d10-4f67-b8bd-005be226b1df,  
>>>>>> 837785eb-24e0-496a-a0cc-f795b64b5929,
>>>>>> 9a00f235-3b6a-4be5-b0e3-93cd1beacaf4,  
>>>>>> 966d70b2-e1dc-4e20-9876-b63736545abd,
>>>>>> 3aab732e-a075-4b19-9525-e97a1260a4fe,  
>>>>>> 4e34ad89-fa46-4503-a599-b8c937ca1f47,
>>>>>> 4c7c3c47-6e5c-4c15-80a9-408192596bc2,  
>>>>>> 85eea5fe-9aff-4821-970c-4ce006ee853a,
>>>>>> 7837fdfc-6255-4784-8088-09d4e6e37bb9,  
>>>>>> 3f426f4e-2d0c-402a-a4af-9d7656f46484,
>>>>>> e8778da0-a764-4ad9-afba-8a748564e12a,  
>>>>>> 4a988e3e-3434-4271-acd6-af2a1e30524c,
>>>>>> cd874e96-63cf-41c9-8e8a-75f3223bfe9d,  
>>>>>> f8cabdbb-875a-480b-8b5e-4b5313c5fcbd,
>>>>>> dc3256a7-ae23-4c2e-b375-55e2884e045d,  
>>>>>> 4da50521-aad0-48a4-9f79-858bbc2e6b89,
>>>>>> 1d370c9e-250f-4733-8b8a-7b6f5c6e1b2b,  
>>>>>> 494ad6fd-1637-44b8-8d3a-1fa19681ba64,
>>>>>> 7c05abfb-dba1-43c3-a8b1-af504762ec60,  
>>>>>> 5902c851-5275-41fd-89c4-cd6390c88670,
>>>>>> 19c334eb-5661-4697-879d-1082571dfef8,  
>>>>>> c406028e-768e-404e-8417-40d2960c4ba3,
>>>>>> a0b57685-e5dc-498c-99a4-33b1aef32632,  
>>>>>> 24be15dd-45f7-4980-b4f8-3176ab67e8f6,
>>>>>> e213b903-107b-4465-8fe1-78b7b393d631,  
>>>>>> df981c08-148d-4266-9ea7-163168012968,
>>>>>> 187cd54f-396b-4c3c-9bfc-9883ac37f556,  
>>>>>> f0b7b298-6432-477a-85a0-83e29e8c5380,
>>>>>> 94ec7576-7a02-4c08-8739-4e0fc52a3d3a,  
>>>>>> 041975f5-990a-4792-b384-eded32966783,
>>>>>> 01ea2812-5005-4152-af2e-2586bf65b4c6,
>>>>>> aecba5d0-9d9b-4ab6-9018-62f5abb7b809], exchId=GridDhtPartitionExchangeId
>>>>>> [topVer=AffinityTopologyVersion [topVer=48, minorTopVer=0],
>>>>>> nodeId=27a9bef9, evt=NODE_JOINED], init=true, ready=true, replied=false,
>>>>>> added=true, initFut=GridFutureAdapter [resFlag=2, res=true,
>>>>>> startTime=1445974657836, endTime=1445974658400, ignoreInterrupts=false,
>>>>>> lsnr=null, state=DONE], topSnapshot=null, lastVer=null,
>>>>>> partReleaseFut=GridCompoundFuture [lsnrCalls=3, finished=true, rdc=null,
>>>>>> init=true,  
>>>>>> res=java.util.concurrent.atomic.AtomicMarkableReference@6b58be0e,
>>>>>> err=null, done=true, cancelled=false, err=null, futs=[true,  
>>>>>> true, true]],
>>>>>> skipPreload=false, clientOnlyExchange=false,
>>>>>> oldest=0d44a4b3-4d10-4f67-b8bd-005be226b1df, oldestOrder=1, evtLatch=0,
>>>>>> remaining=[0ab29a08-9c95-4054-8035-225f5828b3d4,
>>>>>> 0d232f1a-0f46-4798-a39a-63a17dc4dc7f,  
>>>>>> f9b5a77a-a4c1-46aa-872e-aeaca9b76ee3,
>>>>>> 596d0df7-3edf-4078-8f4a-ffa3d96296c6,  
>>>>>> 5790761a-aeeb-44d1-9fce-3fee31ef39b7,
>>>>>> 55d2082e-3517-4828-8d47-57b4ed5a41bc,  
>>>>>> 26266d8c-cc87-4472-9fa4-c526d6da2233,
>>>>>> 0e664e25-8dde-4df8-966b-53b60f9a1087,  
>>>>>> b1bf93b3-24bb-4520-ade0-31d05a93558d,
>>>>>> aac08043-875a-485a-ab2c-cd7e66d68f8f,  
>>>>>> 2fd79f9f-9590-41d2-962e-004a3d7690b5,
>>>>>> 5a2a1012-0766-448c-9583-25873c305de9,  
>>>>>> 534ac94b-8dd1-4fa8-a481-539fa4f4ce55,
>>>>>> b34cb942-e960-4a00-b4fb-10add6466a93,  
>>>>>> 320d05fd-e021-40ac-83bc-62f54756771b,
>>>>>> 0d44a4b3-4d10-4f67-b8bd-005be226b1df,  
>>>>>> 837785eb-24e0-496a-a0cc-f795b64b5929,
>>>>>> 9a00f235-3b6a-4be5-b0e3-93cd1beacaf4,  
>>>>>> 966d70b2-e1dc-4e20-9876-b63736545abd,
>>>>>> 3aab732e-a075-4b19-9525-e97a1260a4fe,  
>>>>>> 4e34ad89-fa46-4503-a599-b8c937ca1f47,
>>>>>> 4c7c3c47-6e5c-4c15-80a9-408192596bc2,  
>>>>>> 85eea5fe-9aff-4821-970c-4ce006ee853a,
>>>>>> 7837fdfc-6255-4784-8088-09d4e6e37bb9,  
>>>>>> 3f426f4e-2d0c-402a-a4af-9d7656f46484,
>>>>>> e8778da0-a764-4ad9-afba-8a748564e12a,  
>>>>>> 4a988e3e-3434-4271-acd6-af2a1e30524c,
>>>>>> cd874e96-63cf-41c9-8e8a-75f3223bfe9d,  
>>>>>> f8cabdbb-875a-480b-8b5e-4b5313c5fcbd,
>>>>>> dc3256a7-ae23-4c2e-b375-55e2884e045d,  
>>>>>> 4da50521-aad0-48a4-9f79-858bbc2e6b89,
>>>>>> 1d370c9e-250f-4733-8b8a-7b6f5c6e1b2b,  
>>>>>> 494ad6fd-1637-44b8-8d3a-1fa19681ba64,
>>>>>> 7c05abfb-dba1-43c3-a8b1-af504762ec60,  
>>>>>> 5902c851-5275-41fd-89c4-cd6390c88670,
>>>>>> 19c334eb-5661-4697-879d-1082571dfef8,  
>>>>>> c406028e-768e-404e-8417-40d2960c4ba3,
>>>>>> a0b57685-e5dc-498c-99a4-33b1aef32632,  
>>>>>> 24be15dd-45f7-4980-b4f8-3176ab67e8f6,
>>>>>> e213b903-107b-4465-8fe1-78b7b393d631,  
>>>>>> df981c08-148d-4266-9ea7-163168012968,
>>>>>> 187cd54f-396b-4c3c-9bfc-9883ac37f556,  
>>>>>> f0b7b298-6432-477a-85a0-83e29e8c5380,
>>>>>> 94ec7576-7a02-4c08-8739-4e0fc52a3d3a,  
>>>>>> 041975f5-990a-4792-b384-eded32966783,
>>>>>> 01ea2812-5005-4152-af2e-2586bf65b4c6,
>>>>>> aecba5d0-9d9b-4ab6-9018-62f5abb7b809], super=GridFutureAdapter  
>>>>>> [resFlag=0,
>>>>>> res=null, startTime=1445974657836, endTime=0, ignoreInterrupts=false,
>>>>>> lsnr=null, state=INIT]]]
>>>>>>
>>>>>>
>>>>>>
>>>>>> Then on the occasions when mapreduce jobs fail I will see one node
>>>>>> with (it isn't always the same node)
>>>>>>
>>>>>>
>>>>>> [14:52:57,080][WARN
>>>>>> ][grid-nio-worker-3-#135%null%][TcpCommunicationSpi] Closing NIO session
>>>>>> because of unhandled exception [cls=class
>>>>>> o.a.i.i.util.nio.GridNioException, msg=Connection timed out]
>>>>>> [14:52:59,123][WARN
>>>>>> ][grid-nio-worker-3-#135%null%][TcpCommunicationSpi] Failed to process
>>>>>> selector key (will close): GridSelectorNioSessionImpl [selectorIdx=3,
>>>>>> queueSize=0, writeBuf=java.nio.DirectByteBuffer[pos=0 lim=32768  
>>>>>> cap=32768],
>>>>>> readBuf=java.nio.DirectByteBuffer[pos=0 lim=32768 cap=32768],
>>>>>> recovery=GridNioRecoveryDescriptor [acked=3, resendCnt=0, rcvCnt=0,
>>>>>> reserved=true, lastAck=0, nodeLeft=false, node=TcpDiscoveryNode
>>>>>> [id=837785eb-24e0-496a-a0cc-f795b64b5929, addrs=[0:0:0:0:0:0:0:1%1,
>>>>>> 10.148.0.81, 10.159.1.176, 127.0.0.1], sockAddrs=[/10.159.1.176:47500,
>>>>>> /0:0:0:0:0:0:0:1%1:47500, r1i4n4.redacted.com/10.148.0.81:47500, /
>>>>>> 10.148.0.81:47500, /10.159.1.176:47500, /127.0.0.1:47500],
>>>>>> discPort=47500, order=45, intOrder=45, lastExchangeTime=1445974625750,
>>>>>> loc=false, ver=1.4.0#19691231-sha1:00000000, isClient=false],
>>>>>> connected=true, connectCnt=1, queueLimit=5120], super=GridNioSessionImpl
>>>>>> [locAddr=/10.159.1.112:46222, rmtAddr=/10.159.1.176:47100,
>>>>>> createTime=1445974646591, closeTime=0, bytesSent=30217, bytesRcvd=9,
>>>>>> sndSchedTime=1445975577912, lastSndTime=1445975577912,
>>>>>> lastRcvTime=1445974655114, readsPaused=false,
>>>>>> filterChain=FilterChain[filters=[GridNioCodecFilter
>>>>>> [parser=o.a.i.i.util.nio.GridDirectParser@44de55ba, directMode=true],
>>>>>> GridConnectionBytesVerifyFilter], accepted=false]]
>>>>>> [14:52:59,124][WARN
>>>>>> ][grid-nio-worker-3-#135%null%][TcpCommunicationSpi] Closing NIO session
>>>>>> because of unhandled exception [cls=class
>>>>>> o.a.i.i.util.nio.GridNioException, msg=Connection timed out]
>>>>>> [14:53:00,105][WARN
>>>>>> ][grid-nio-worker-3-#135%null%][TcpCommunicationSpi] Failed to process
>>>>>> selector key (will close): GridSelectorNioSessionImpl [selectorIdx=3,
>>>>>> queueSize=0, writeBuf=java.nio.DirectByteBuffer[pos=0 lim=32768  
>>>>>> cap=32768],
>>>>>> readBuf=java.nio.DirectByteBuffer[pos=0 lim=32768 cap=32768],
>>>>>> recovery=GridNioRecoveryDescriptor [acked=0, resendCnt=0, rcvCnt=0,
>>>>>> reserved=true, lastAck=0, nodeLeft=false, node=TcpDiscoveryNode
>>>>>> [id=4426467e-b4b4-4912-baa1-d7cc839d9188, addrs=[0:0:0:0:0:0:0:1%1,
>>>>>> 10.148.0.106, 10.159.1.201, 127.0.0.1], sockAddrs=[/10.159.1.201:47500,
>>>>>> /0:0:0:0:0:0:0:1%1:47500, r1i5n11.redacted.com/10.148.0.106:47500, /
>>>>>> 10.148.0.106:47500, /10.159.1.201:47500, /127.0.0.1:47500],
>>>>>> discPort=47500, order=57, intOrder=57, lastExchangeTime=1445974625790,
>>>>>> loc=false, ver=1.4.0#19691231-sha1:00000000, isClient=false],
>>>>>> connected=true, connectCnt=1, queueLimit=5120], super=GridNioSessionImpl
>>>>>> [locAddr=/10.159.1.112:60869, rmtAddr=/10.159.1.201:47100,
>>>>>> createTime=1445974654478, closeTime=0, bytesSent=22979, bytesRcvd=0,
>>>>>> sndSchedTime=1445975577912, lastSndTime=1445975577912,
>>>>>> lastRcvTime=1445974654478, readsPaused=false,
>>>>>> filterChain=FilterChain[filters=[GridNioCodecFilter
>>>>>> [parser=o.a.i.i.util.nio.GridDirectParser@44de55ba, directMode=true],
>>>>>> GridConnectionBytesVerifyFilter], accepted=false]]
>>>>>> [14:53:00,105][WARN
>>>>>> ][grid-nio-worker-3-#135%null%][TcpCommunicationSpi] Closing NIO session
>>>>>> because of unhandled exception [cls=class
>>>>>> o.a.i.i.util.nio.GridNioException, msg=Connection timed out]
>>>>>>
>>>>>>
>>>>>> I've tried adjusting the timeout settings further but haven't had much
>>>>>> success.
>>>>>>
>>>>>> Here is what my config looks like, it is obviously heavily based off
>>>>>> the hadoop example config.
>>>>>>
>>>>>>
>>>>>> <?xml version="1.0" encoding="UTF-8"?>
>>>>>> <beans ns1:schemaLocation="http://www.springframework.org/schema/beans
>>>>>> http://www.springframework.org/schema/beans/spring-beans.xsd
>>>>>> http://www.springframework.org/schema/util
>>>>>> http://www.springframework.org/schema/util/spring-util.xsd" xmlns="
>>>>>> http://www.springframework.org/schema/beans" xmlns:ns1="
>>>>>> http://www.w3.org/2001/XMLSchema-instance">
>>>>>> <description>
>>>>>>       Spring file for Ignite node configuration with IGFS and Apache
>>>>>> Hadoop map-reduce support enabled.
>>>>>>       Ignite node will start with this configuration by default.
>>>>>>   </description>
>>>>>> <bean
>>>>>> class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer"
>>>>>> id="propertyConfigurer">
>>>>>>   <property name="systemPropertiesModeName"
>>>>>> value="SYSTEM_PROPERTIES_MODE_FALLBACK" />
>>>>>>   <property name="searchSystemEnvironment" value="true" />
>>>>>> </bean>
>>>>>> <bean abstract="true"
>>>>>> class="org.apache.ignite.configuration.FileSystemConfiguration"
>>>>>> id="igfsCfgBase">
>>>>>>   <property name="blockSize" value="#{128 * 1024}" />
>>>>>>   <property name="perNodeBatchSize" value="512" />
>>>>>>   <property name="perNodeParallelBatchCount" value="16" />
>>>>>>   <property name="prefetchBlocks" value="32" />
>>>>>> </bean>
>>>>>> <bean abstract="true"
>>>>>> class="org.apache.ignite.configuration.CacheConfiguration"
>>>>>> id="dataCacheCfgBase">
>>>>>>   <property name="cacheMode" value="PARTITIONED" />
>>>>>>   <property name="atomicityMode" value="TRANSACTIONAL" />
>>>>>>   <property name="writeSynchronizationMode" value="FULL_SYNC" />
>>>>>>   <property name="backups" value="0" />
>>>>>>   <property name="affinityMapper">
>>>>>>     <bean class="org.apache.ignite.igfs.IgfsGroupDataBlocksKeyMapper">
>>>>>>       <constructor-arg value="512" />
>>>>>>     </bean>
>>>>>>   </property>
>>>>>>   <property name="startSize" value="#{100*1024*1024}" />
>>>>>>   <property name="offHeapMaxMemory" value="0" />
>>>>>> </bean>
>>>>>> <bean abstract="true"
>>>>>> class="org.apache.ignite.configuration.CacheConfiguration"
>>>>>> id="metaCacheCfgBase">
>>>>>>   <property name="cacheMode" value="REPLICATED" />
>>>>>>   <property name="atomicityMode" value="TRANSACTIONAL" />
>>>>>>   <property name="writeSynchronizationMode" value="FULL_SYNC" />
>>>>>> </bean>
>>>>>> <bean class="org.apache.ignite.configuration.IgniteConfiguration"
>>>>>> id="grid.cfg">
>>>>>>   <property name="failureDetectionTimeout" value="3000" />
>>>>>>   <property name="hadoopConfiguration">
>>>>>>     <bean class="org.apache.ignite.configuration.HadoopConfiguration">
>>>>>>       <property name="finishedJobInfoTtl" value="30000" />
>>>>>>     </bean>
>>>>>>   </property>
>>>>>>   <property name="connectorConfiguration">
>>>>>>     <bean
>>>>>> class="org.apache.ignite.configuration.ConnectorConfiguration">
>>>>>>       <property name="port" value="11211" />
>>>>>>     </bean>
>>>>>>   </property>
>>>>>>   <property name="fileSystemConfiguration">
>>>>>>     <list>
>>>>>>       <bean
>>>>>> class="org.apache.ignite.configuration.FileSystemConfiguration"
>>>>>> parent="igfsCfgBase">
>>>>>>         <property name="name" value="igfs" />
>>>>>>         <property name="metaCacheName" value="igfs-meta" />
>>>>>>         <property name="dataCacheName" value="igfs-data" />
>>>>>>         <property name="ipcEndpointConfiguration">
>>>>>>           <bean
>>>>>> class="org.apache.ignite.igfs.IgfsIpcEndpointConfiguration">
>>>>>>             <property name="type" value="TCP" />
>>>>>>             <property name="host" value="r1i0n12" />
>>>>>>             <property name="port" value="10500" />
>>>>>>           </bean>
>>>>>>         </property>
>>>>>>       </bean>
>>>>>>     </list>
>>>>>>   </property>
>>>>>>   <property name="cacheConfiguration">
>>>>>>     <list>
>>>>>>       <bean class="org.apache.ignite.configuration.CacheConfiguration"
>>>>>> parent="metaCacheCfgBase">
>>>>>>         <property name="name" value="igfs-meta" />
>>>>>>       </bean>
>>>>>>       <bean class="org.apache.ignite.configuration.CacheConfiguration"
>>>>>> parent="dataCacheCfgBase">
>>>>>>         <property name="name" value="igfs-data" />
>>>>>>       </bean>
>>>>>>     </list>
>>>>>>   </property>
>>>>>>   <property name="includeEventTypes">
>>>>>>     <list>
>>>>>>       <ns2:constant
>>>>>> static-field="org.apache.ignite.events.EventType.EVT_TASK_FAILED"
>>>>>> xmlns:ns2="http://www.springframework.org/schema/util" />
>>>>>>       <ns2:constant
>>>>>> static-field="org.apache.ignite.events.EventType.EVT_TASK_FINISHED"
>>>>>> xmlns:ns2="http://www.springframework.org/schema/util" />
>>>>>>       <ns2:constant
>>>>>> static-field="org.apache.ignite.events.EventType.EVT_JOB_MAPPED"  
>>>>>> xmlns:ns2="
>>>>>> http://www.springframework.org/schema/util" />
>>>>>>     </list>
>>>>>>   </property>
>>>>>>   <property name="discoverySpi">
>>>>>>     <bean class="org.apache.ignite.spi.discovery.tcp.TcpDiscoverySpi">
>>>>>>       <property name="ipFinder">
>>>>>>         <bean
>>>>>> class="org.apache.ignite.spi.discovery.tcp.ipfinder.vm.TcpDiscoveryVmIpFinder">
>>>>>>           <property name="addresses">
>>>>>>             <list>
>>>>>>               <value>r1i0n12:47500</value>
>>>>>>             </list>
>>>>>>           </property>
>>>>>>         </bean>
>>>>>>       </property>
>>>>>>     </bean>
>>>>>>   </property>
>>>>>> </bean>
>>>>>> </beans>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Quoting Denis Magda <dmagda@gridgain.com>:
>>>>>>
>>>>>> Hi Joe,
>>>>>>>
>>>>>>> Great!
>>>>>>>
>>>>>>> Please see below
>>>>>>>
>>>>>>> On 10/27/2015 9:37 AM, dev@eiler.net wrote:
>>>>>>>
>>>>>>>> Reducing the port range (to a single port) and lowering the
>>>>>>>> IgniteConfiguration.setFailureDetectionTimeout to 1000 helped speed up
>>>>>>>> everybody joining the topology and I was able to get a pi  
>>>>>>>> estimator run on
>>>>>>>> 64 nodes.
>>>>>>>>
>>>>>>>>
>>>>>>> I suspect that the reason was in the number of ports specified in the
>>>>>>> range.  By some reason it takes significant time to get a response from
>>>>>>> TCP/IP stack that a connection can't be established on a  
>>>>>>> particular port
>>>>>>> number.
>>>>>>> Please try to reduce the port range, lower
>>>>>>> TcpDiscoverySpi.setNetworkTimeout, keep
>>>>>>> IgniteConfiguration.setFailureDetectionTimeout's default value  
>>>>>>> and share
>>>>>>> results with us.
>>>>>>>
>>>>>>> Thanks again for the help, I'm over the current hurdle.
>>>>>>>> Joe
>>>>>>>>
>>>>>>>>
>>>>>>>> Quoting dev@eiler.net:
>>>>>>>>
>>>>>>>> Thanks for the quick response Denis.
>>>>>>>>>
>>>>>>>>> I did a port range of 10 ports. I'll take a look at the
>>>>>>>>> failureDetectionTimeout and networkTimeout.
>>>>>>>>>
>>>>>>>>> Side question: Is there an easy way to map between the programmatic
>>>>>>>>> API and the spring XML properties? For instance I was trying  
>>>>>>>>> to find the
>>>>>>>>> correct xml incantation for  
>>>>>>>>> TcpDiscoverySpi.setMaxMissedHeartbeats(int) and
>>>>>>>>> I might have a similar issue finding
>>>>>>>>> IgniteConfiguration.setFailureDetectionTimeout(long). It  
>>>>>>>>> seems like I can
>>>>>>>>> usually drop the set and adjust capitalization (setFooBar()  
>>>>>>>>> == <property
>>>>>>>>> name="fooBar")
>>>>>>>>>
>>>>>>>>> Yes, your understanding is correct.
>>>>>>>
>>>>>>>> Please pardon my ignorance on terminology:
>>>>>>>>> Are the nodes I run ignite.sh on considered server nodes or cluster
>>>>>>>>> nodes (I would have thought they are the same)
>>>>>>>>>
>>>>>>>>> Actually we have a notion of server and client nodes. This page
>>>>>>> contains extensive information on the type of nodes:
>>>>>>> https://apacheignite.readme.io/docs/clients-vs-servers
>>>>>>>
>>>>>>> A cluster node is just a server or client node.
>>>>>>>
>>>>>>> Regards,
>>>>>>> Denis
>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>> Joe
>>>>>>>>>
>>>>>>>>> Quoting Denis Magda <dmagda@gridgain.com>:
>>>>>>>>>
>>>>>>>>> Hi Joe,
>>>>>>>>>>
>>>>>>>>>> How big is a port range, that you specified in your discovery
>>>>>>>>>> configuration, for a every single node?
>>>>>>>>>> Please take into account that the discovery may iterate over every
>>>>>>>>>> port from the range before one node connects to the other  
>>>>>>>>>> and depending on
>>>>>>>>>> the TCP related settings of your network it may take  
>>>>>>>>>> significant time
>>>>>>>>>> before the cluster is assembled.
>>>>>>>>>>
>>>>>>>>>> Here I would recommend you to reduce the port range as much as
>>>>>>>>>> possible and to play with the following network related parameters:
>>>>>>>>>> - Try to use the failure detection timeout instead of setting
>>>>>>>>>> socket, ack and many other timeouts explicitly (
>>>>>>>>>> https://apacheignite.readme.io/docs/cluster-config#failure-detection-timeout);
>>>>>>>>>> - Try to play with TcpDiscoverySpi.networkTimeout because  
>>>>>>>>>> this timeout is
>>>>>>>>>> considered during the time when a cluster node tries to  
>>>>>>>>>> join a cluster.
>>>>>>>>>>
>>>>>>>>>> In order to help you with the hanging compute tasks and to give
>>>>>>>>>> you more specific recommendations regarding the slow join  
>>>>>>>>>> process please
>>>>>>>>>> provide us with the following:
>>>>>>>>>> - config files for server and cluster nodes;
>>>>>>>>>> - log files from all the nodes. Please start the nodes with
>>>>>>>>>> -DIGNITE_QUIET=false virtual machine property. If you start  
>>>>>>>>>> the nodes using
>>>>>>>>>> ignite.sh/bat then just pass '-v' as an argument to the script.
>>>>>>>>>> - thread dumps for the nodes that are hanging waiting for the
>>>>>>>>>> compute tasks to be completed.
>>>>>>>>>>
>>>>>>>>>> Regards,
>>>>>>>>>> Denis
>>>>>>>>>>
>>>>>>>>>> On 10/26/2015 6:56 AM, dev@eiler.net wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi all,
>>>>>>>>>>>
>>>>>>>>>>> I have been experimenting with ignite and have run into a problem
>>>>>>>>>>> scaling up to larger clusters.
>>>>>>>>>>>
>>>>>>>>>>> I am playing with only two different use cases, 1) a Hadoop
>>>>>>>>>>> MapReduce accelerator 2) an in memory data grid (no  
>>>>>>>>>>> secondary file system)
>>>>>>>>>>> being accessed by frameworks using the HDFS
>>>>>>>>>>>
>>>>>>>>>>> Everything works fine with a smaller cluster (8 nodes) but with a
>>>>>>>>>>> larger cluster (64 nodes) it takes a couple of minutes for  
>>>>>>>>>>> all the nodes to
>>>>>>>>>>> register with the cluster(which would be ok) and mapreduce  
>>>>>>>>>>> jobs just hang
>>>>>>>>>>> and never return.
>>>>>>>>>>>
>>>>>>>>>>> I've compiled the latest Ignite 1.4 (with ignite.edition=hadoop)
>>>>>>>>>>> from source, and am using it with Hadoop 2.7.1 just trying  
>>>>>>>>>>> to run things
>>>>>>>>>>> like the pi estimator and wordcount examples.
>>>>>>>>>>>
>>>>>>>>>>> I started with the config/hadoop/default-config.xml
>>>>>>>>>>>
>>>>>>>>>>> I can't use multicast so I've configured it to use static IP
>>>>>>>>>>> based discovery with just a single node/port range.
>>>>>>>>>>>
>>>>>>>>>>> I've increased the heartbeat frequency to 10000 and that seemed
>>>>>>>>>>> to help make things more stable once all the nodes do join  
>>>>>>>>>>> the cluster.
>>>>>>>>>>> I've also played with increasing both the socket timeout  
>>>>>>>>>>> and the ack
>>>>>>>>>>> timeout but that seemed to just make it take longer for  
>>>>>>>>>>> nodes to attempt to
>>>>>>>>>>> join the cluster after a failed attempt.
>>>>>>>>>>>
>>>>>>>>>>> I have access to a couple of different clusters, we allocate
>>>>>>>>>>> resources with slurm so I get a piece of a cluster to play  
>>>>>>>>>>> with (hence the
>>>>>>>>>>> no-multicast restriction). The nodes all have fast networks (FDR
>>>>>>>>>>> InfiniBand) and a decent amount of memory (64GB-128GB) but  
>>>>>>>>>>> no local storage
>>>>>>>>>>> (or swap space).
>>>>>>>>>>>
>>>>>>>>>>> As mentioned earlier, I disable the secondaryFilesystem.
>>>>>>>>>>>
>>>>>>>>>>> Any advice/hints/example xml configs would be extremely welcome.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> I also haven't been seeing the expected performance using the
>>>>>>>>>>> hdfs api to access ignite. I've tried both using the hdfs  
>>>>>>>>>>> cli to do some
>>>>>>>>>>> simple timings of put/get and a little java program that  
>>>>>>>>>>> writes then reads
>>>>>>>>>>> a file.  Even with small files (500MB) that should be kept  
>>>>>>>>>>> completely in a
>>>>>>>>>>> single node, I only see about 250MB/s for writes and reads  
>>>>>>>>>>> are much slower
>>>>>>>>>>> than that (4x to 10x).  The writes are better than hdfs  
>>>>>>>>>>> (our hdfs is backed
>>>>>>>>>>> with pretty poor storage) but reads are much slower. Now I  
>>>>>>>>>>> haven't tried
>>>>>>>>>>> scaling this at all but with an 8 node ignite cluster and  
>>>>>>>>>>> a single "client"
>>>>>>>>>>> access a single file I would hope for something closer to  
>>>>>>>>>>> memory speeds.
>>>>>>>>>>> (if you would like me to split this into another message  
>>>>>>>>>>> to the list just
>>>>>>>>>>> let me know, I'm assuming the cause it the same---I missed  
>>>>>>>>>>> a required
>>>>>>>>>>> config setting ;-) )
>>>>>>>>>>>
>>>>>>>>>>> Thanks in advance for any help,
>>>>>>>>>>> Joe
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>>>
>>
>>
>>





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