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From Anishek Agarwal <anis...@gmail.com>
Subject Re: Lot of GC on two nodes out of 7
Date Fri, 04 Mar 2016 04:55:45 GMT
Hello,

Bryan, most of the partition sizes are under 45 KB

I have tried with concurrent_compactors : 8 for one of the nodes still no
improvement,
I have tried max_heap_Size : 8G, no improvement.

I will try the newHeapsize of 2G though i am sure CMS will be a longer then.

Also doesn't look like i mentioned what type of GC was causing the
problems. On both the nodes its the ParNewGC thats taking long for each run
and too many runs are happening in succession.

anishek


On Fri, Mar 4, 2016 at 5:36 AM, Bryan Cheng <bryan@blockcypher.com> wrote:

> Hi Anishek,
>
> In addition to the good advice others have given, do you notice any
> abnormally large partitions? What does cfhistograms report for 99%
> partition size? A few huge partitions will cause very disproportionate load
> on your cluster, including high GC.
>
> --Bryan
>
> On Wed, Mar 2, 2016 at 9:28 AM, Amit Singh F <amit.f.singh@ericsson.com>
> wrote:
>
>> Hi Anishek,
>>
>>
>>
>> We too faced similar problem in 2.0.14 and after doing some research we
>> config few parameters in Cassandra.yaml and was able to overcome GC pauses
>> . Those are :
>>
>>
>>
>> ·         memtable_flush_writers : increased from 1 to 3 as from tpstats
>> output  we can see mutations dropped so it means writes are getting
>> blocked, so increasing number will have those catered.
>>
>> ·         memtable_total_space_in_mb : Default (1/4 of heap size), can
>> lowered because larger long lived objects will create pressure on HEAP, so
>> its better to reduce some amount of size.
>>
>> ·         Concurrent_compactors : Alain righlty pointed out this i.e
>> reduce it to 8. You need to try this.
>>
>>
>>
>> Also please check whether you have mutations drop in other nodes or not.
>>
>>
>>
>> Hope this helps in your cluster too.
>>
>>
>>
>> Regards
>>
>> Amit Singh
>>
>> *From:* Jonathan Haddad [mailto:jon@jonhaddad.com]
>> *Sent:* Wednesday, March 02, 2016 9:33 PM
>> *To:* user@cassandra.apache.org
>> *Subject:* Re: Lot of GC on two nodes out of 7
>>
>>
>>
>> Can you post a gist of the output of jstat -gccause (60 seconds worth)?
>> I think it's cool you're willing to experiment with alternative JVM
>> settings but I've never seen anyone use max tenuring threshold of 50 either
>> and I can't imagine it's helpful.  Keep in mind if your objects are
>> actually reaching that threshold it means they've been copied 50x (really
>> really slow) and also you're going to end up spilling your eden objects
>> directly into your old gen if your survivor is full.  Considering the small
>> amount of memory you're using for heap I'm really not surprised you're
>> running into problems.
>>
>>
>>
>> I recommend G1GC + 12GB heap and just let it optimize itself for almost
>> all cases with the latest JVM versions.
>>
>>
>>
>> On Wed, Mar 2, 2016 at 6:08 AM Alain RODRIGUEZ <arodrime@gmail.com>
>> wrote:
>>
>> It looks like you are doing a good work with this cluster and know a lot
>> about JVM, that's good :-).
>>
>>
>>
>> our machine configurations are : 2 X 800 GB SSD , 48 cores, 64 GB RAM
>>
>>
>>
>> That's good hardware too.
>>
>>
>>
>> With 64 GB of ram I would probably directly give a try to
>> `MAX_HEAP_SIZE=8G` on one of the 2 bad nodes probably.
>>
>>
>>
>> Also I would also probably try lowering `HEAP_NEWSIZE=2G.` and using
>> `-XX:MaxTenuringThreshold=15`, still on the canary node to observe the
>> effects. But that's just an idea of something I would try to see the
>> impacts, I don't think it will solve your current issues or even make it
>> worse for this node.
>>
>>
>>
>> Using G1GC would allow you to use a bigger Heap size. Using C*2.1 would
>> allow you to store the memtables off-heap. Those are 2 improvements
>> reducing the heap pressure that you might be interested in.
>>
>>
>>
>> I have spent time reading about all other options before including them
>> and a similar configuration on our other prod cluster is showing good GC
>> graphs via gcviewer.
>>
>>
>>
>> So, let's look for an other reason.
>>
>>
>>
>> there are MUTATION and READ messages dropped in high number on nodes in
>> question and on other 5 nodes it varies between 1-3.
>>
>>
>>
>> - Is Memory, CPU or disk a bottleneck? Is one of those running at the
>> limits?
>>
>>
>>
>> concurrent_compactors: 48
>>
>>
>>
>> Reducing this to 8 would free some space for transactions (R&W requests).
>> It is probably worth a try, even more when compaction is not keeping up and
>> compaction throughput is not throttled.
>>
>>
>>
>> Just found an issue about that:
>> https://issues.apache.org/jira/browse/CASSANDRA-7139
>>
>>
>>
>> Looks like `concurrent_compactors: 8` is the new default.
>>
>>
>>
>> C*heers,
>>
>> -----------------------
>>
>> Alain Rodriguez - alain@thelastpickle.com
>>
>> France
>>
>>
>>
>> The Last Pickle - Apache Cassandra Consulting
>>
>> http://www.thelastpickle.com
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 2016-03-02 12:27 GMT+01:00 Anishek Agarwal <anishek@gmail.com>:
>>
>> Thanks a lot Alian for the details.
>>
>> `HEAP_NEWSIZE=4G.` is probably far too high (try 1200M <-> 2G)
>> `MAX_HEAP_SIZE=6G` might be too low, how much memory is available (You
>> might want to keep this as it or even reduce it if you have less than 16 GB
>> of native memory. Go with 8 GB if you have a lot of memory.
>> `-XX:MaxTenuringThreshold=50` is the highest value I have seen in use so
>> far. I had luck with values between 4 <--> 16 in the past. I would give  a
>> try with 15.
>> `-XX:CMSInitiatingOccupancyFraction=70`--> Why not using default - 75 ?
>> Using default and then tune from there to improve things is generally a
>> good idea.
>>
>>
>>
>>
>>
>> we have a lot of reads and writes onto the system so keeping the high new
>> size to make sure enough is held in memory including caches / memtables etc
>> --number of flush_writers : 4 for us. similarly keeping less in old
>> generation to make sure we spend less time with CMS GC most of the data is
>> transient in memory for us. Keeping high TenuringThreshold because we don't
>> want objects going to old generation and just die in young generation given
>> we have configured large survivor spaces.
>>
>> using occupancyFraction as 70 since
>>
>> given heap is 4G
>>
>> survivor space is : 400 mb -- 2 survivor spaces
>>
>> 70 % of 2G (old generation) = 1.4G
>>
>>
>>
>> so once we are just below 1.4G and we have to move the full survivor +
>> some extra during a par new gc due to promotion failure, everything will
>> fit in old generation, and will trigger CMS.
>>
>>
>>
>> I have spent time reading about all other options before including them
>> and a similar configuration on our other prod cluster is showing good GC
>> graphs via gcviewer.
>>
>>
>>
>> tp stats on all machines show flush writer blocked at : 0.3% of total
>>
>>
>>
>> the two nodes in question have stats almost as below
>>
>>    - specifically there are pending was in readStage, MutationStage and
>>    RequestResponseStage
>>
>> Pool Name                    Active   Pending      Completed   Blocked
>> All time blocked
>>
>> ReadStage                        21        19     2141798645         0
>>               0
>>
>> RequestResponseStage              0         1      803242391         0
>>               0
>>
>> MutationStage                     0         0      291813703         0
>>               0
>>
>> ReadRepairStage                   0         0      200544344         0
>>               0
>>
>> ReplicateOnWriteStage             0         0              0         0
>>               0
>>
>> GossipStage                       0         0         292477         0
>>               0
>>
>> CacheCleanupExecutor              0         0              0         0
>>               0
>>
>> MigrationStage                    0         0              0         0
>>               0
>>
>> MemoryMeter                       0         0           2172         0
>>               0
>>
>> FlushWriter                       0         0           2756         0
>>               6
>>
>> ValidationExecutor                0         0            101         0
>>               0
>>
>> InternalResponseStage             0         0              0         0
>>               0
>>
>> AntiEntropyStage                  0         0            202         0
>>               0
>>
>> MemtablePostFlusher               0         0           4395         0
>>               0
>>
>> MiscStage                         0         0              0         0
>>               0
>>
>> PendingRangeCalculator            0         0             20         0
>>               0
>>
>> CompactionExecutor                4         4          49323         0
>>               0
>>
>> commitlog_archiver                0         0              0         0
>>               0
>>
>> HintedHandoff                     0         0            116         0
>>               0
>>
>>
>>
>> Message type           Dropped
>>
>> RANGE_SLICE                  0
>>
>> READ_REPAIR                 36
>>
>> PAGED_RANGE                  0
>>
>> BINARY                       0
>>
>> READ                     11471
>>
>> MUTATION                   898
>>
>> _TRACE                       0
>>
>> REQUEST_RESPONSE             0
>>
>> COUNTER_MUTATION             0
>>
>>
>>
>> all the other 5 nodes show no pending numbers.
>>
>>
>>
>>
>>
>> our machine configurations are : 2 X 800 GB SSD , 48 cores, 64 GB RAM
>>
>> compaction throughput is 0 MB/s
>>
>> concurrent_compactors: 48
>>
>> flush_writers: 4
>>
>>
>>
>>
>> I think Jeff is trying to spot a wide row messing with your system, so
>> looking at the max row size on those nodes compared to other is more
>> relevant than average size for this check.
>>
>>
>>
>> i think is what you are looking for, please correct me if i am wrong
>>
>> Compacted partition maximum bytes: 1629722
>>
>> similar value on all 7 nodes.
>>
>>
>>
>> grep -i "ERROR" /var/log/cassandra/system.log
>>
>>
>>
>> there are MUTATION and READ messages dropped in high number on nodes in
>> question and on other 5 nodes it varies between 1-3.
>>
>>
>>
>> On Wed, Mar 2, 2016 at 4:15 PM, Alain RODRIGUEZ <arodrime@gmail.com>
>> wrote:
>>
>> Hi Anishek,
>>
>>
>>
>> Even if it highly depends on your workload, here are my thoughts:
>>
>>
>>
>> `HEAP_NEWSIZE=4G.` is probably far too high (try 1200M <-> 2G)
>>
>> `MAX_HEAP_SIZE=6G` might be too low, how much memory is available (You
>> might want to keep this as it or even reduce it if you have less than 16 GB
>> of native memory. Go with 8 GB if you have a lot of memory.
>>
>> `-XX:MaxTenuringThreshold=50` is the highest value I have seen in use so
>> far. I had luck with values between 4 <--> 16 in the past. I would give  a
>> try with 15.
>>
>> `-XX:CMSInitiatingOccupancyFraction=70`--> Why not using default - 75 ?
>> Using default and then tune from there to improve things is generally a
>> good idea.
>>
>>
>>
>> You also use a bunch of option I don't know about, if you are uncertain
>> about them, you could try a default conf without the options you added and
>> just the using the changes above from default
>> https://github.com/apache/cassandra/blob/cassandra-2.0/conf/cassandra-env.sh.
>> Or you might find more useful information on a nice reference about this
>> topic which is Al Tobey's blog post about tuning 2.1. Go to the 'Java
>> Virtual Machine' part:
>> https://tobert.github.io/pages/als-cassandra-21-tuning-guide.html
>>
>>
>>
>> FWIW, I also saw improvement in the past by upgrading to 2.1, Java 8 and
>> G1GC. G1GC is supposed to be easier to configure too.
>>
>>
>>
>> the average row size for compacted partitions is about 1640 bytes on all
>> nodes. We have replication factor 3 but the problem is only on two nodes.
>>
>>
>>
>> I think Jeff is trying to spot a wide row messing with your system, so
>> looking at the max row size on those nodes compared to other is more
>> relevant than average size for this check.
>>
>>
>>
>> the only other thing that stands out in cfstats is the read time and
>> write time on the nodes with high GC is 5-7 times higher than other 5
>> nodes, but i think thats expected.
>>
>>
>>
>> I would probably look at this the reverse way: I imagine that extra GC
>>  is a consequence of something going wrong on those nodes as JVM / GC are
>> configured the same way cluster-wide. GC / JVM issues are often due to
>> Cassandra / system / hardware issues, inducing extra pressure on the JVM. I
>> would try to tune JVM / GC only once the system is healthy. So I often saw
>> high GC being a consequence rather than the root cause of an issue.
>>
>>
>>
>> To explore this possibility:
>>
>>
>>
>> Does this command show some dropped or blocked tasks? This would add
>> pressure to heap.
>>
>> nodetool tpstats
>>
>>
>>
>> Do you have errors in logs? Always good to know when facing an issue.
>>
>> grep -i "ERROR" /var/log/cassandra/system.log
>>
>>
>>
>> How are compactions tuned (throughput + concurrent compactors)? This
>> tuning might explain compactions not keeping up or a high GC pressure.
>>
>>
>>
>> What are your disks / CPU? To help us giving you good arbitrary values to
>> try.
>>
>>
>>
>> Is there some iowait ? Could point to a bottleneck or bad hardware.
>>
>> iostats -mx 5 100
>>
>>
>>
>> ...
>>
>>
>>
>> Hope one of those will point you to an issue, but there are many more
>> thing you could check.
>>
>>
>>
>> Let us know how it goes,
>>
>>
>>
>> C*heers,
>>
>> -----------------------
>>
>> Alain Rodriguez - alain@thelastpickle.com
>>
>> France
>>
>>
>>
>> The Last Pickle - Apache Cassandra Consulting
>>
>> http://www.thelastpickle.com
>>
>>
>>
>>
>>
>>
>>
>> 2016-03-02 10:33 GMT+01:00 Anishek Agarwal <anishek@gmail.com>:
>>
>> also MAX_HEAP_SIZE=6G and HEAP_NEWSIZE=4G.
>>
>>
>>
>> On Wed, Mar 2, 2016 at 1:40 PM, Anishek Agarwal <anishek@gmail.com>
>> wrote:
>>
>> Hey Jeff,
>>
>>
>>
>> one of the nodes with high GC has 1400 SST tables, all other nodes have
>> about 500-900 SST tables. the other node with high GC has 636 SST tables.
>>
>>
>>
>> the average row size for compacted partitions is about 1640 bytes on all
>> nodes. We have replication factor 3 but the problem is only on two nodes.
>>
>> the only other thing that stands out in cfstats is the read time and
>> write time on the nodes with high GC is 5-7 times higher than other 5
>> nodes, but i think thats expected.
>>
>>
>>
>> thanks
>>
>> anishek
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Mar 2, 2016 at 1:09 PM, Jeff Jirsa <jeff.jirsa@crowdstrike.com>
>> wrote:
>>
>> Compaction falling behind will likely cause additional work on reads
>> (more sstables to merge), but I’d be surprised if it manifested in super
>> long GC. When you say twice as many sstables, how many is that?.
>>
>>
>>
>> In cfstats, does anything stand out? Is max row size on those nodes
>> larger than on other nodes?
>>
>>
>>
>> What you don’t show in your JVM options is the new gen size – if you do
>> have unusually large partitions on those two nodes (especially likely if
>> you have rf=2 – if you have rf=3, then there’s probably a third node
>> misbehaving you haven’t found yet), then raising new gen size can help
>> handle the garbage created by reading large partitions without having to
>> tolerate the promotion. Estimates for the amount of garbage vary, but it
>> could be “gigabytes” of garbage on a very wide partition (see
>> https://issues.apache.org/jira/browse/CASSANDRA-9754 for work in
>> progress to help mitigate that type of pain).
>>
>>
>>
>> - Jeff
>>
>>
>>
>> *From: *Anishek Agarwal
>> *Reply-To: *"user@cassandra.apache.org"
>> *Date: *Tuesday, March 1, 2016 at 11:12 PM
>> *To: *"user@cassandra.apache.org"
>> *Subject: *Lot of GC on two nodes out of 7
>>
>>
>>
>> Hello,
>>
>>
>>
>> we have a cassandra cluster of 7 nodes, all of them have the same JVM GC
>> configurations, all our writes /  reads use the TokenAware Policy wrapping
>> a DCAware policy. All nodes are part of same Datacenter.
>>
>>
>>
>> We are seeing that two nodes are having high GC collection times. Then
>> mostly seem to spend time in GC like about 300-600 ms. This also seems to
>> result in higher CPU utilisation on these machines. Other  5 nodes don't
>> have this problem.
>>
>>
>>
>> There is no additional repair activity going on the cluster, we are not
>> sure why this is happening.
>>
>> we checked cfhistograms on the two CF we have in the cluster and number
>> of reads seems to be almost same.
>>
>>
>>
>> we also used cfstats to see the number of ssttables on each node and one
>> of the nodes with the above problem has twice the number of ssttables than
>> other nodes. This still doesnot explain why two nodes have high GC
>> Overheads. our GC config is as below:
>>
>> JVM_OPTS="$JVM_OPTS -XX:+UseParNewGC"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+UseConcMarkSweepGC"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+CMSParallelRemarkEnabled"
>>
>> JVM_OPTS="$JVM_OPTS -XX:SurvivorRatio=8"
>>
>> JVM_OPTS="$JVM_OPTS -XX:MaxTenuringThreshold=50"
>>
>> JVM_OPTS="$JVM_OPTS -XX:CMSInitiatingOccupancyFraction=70"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+UseCMSInitiatingOccupancyOnly"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+UseTLAB"
>>
>> JVM_OPTS="$JVM_OPTS -XX:MaxPermSize=256m"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+AggressiveOpts"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+UseCompressedOops"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+CMSScavengeBeforeRemark"
>>
>> JVM_OPTS="$JVM_OPTS -XX:ConcGCThreads=48"
>>
>> JVM_OPTS="$JVM_OPTS -XX:ParallelGCThreads=48"
>>
>> JVM_OPTS="$JVM_OPTS -XX:-ExplicitGCInvokesConcurrent"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+UnlockDiagnosticVMOptions"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+UseGCTaskAffinity"
>>
>> JVM_OPTS="$JVM_OPTS -XX:+BindGCTaskThreadsToCPUs"
>>
>> # earlier value 131072 = 32768 * 4
>>
>> JVM_OPTS="$JVM_OPTS -XX:ParGCCardsPerStrideChunk=131072"
>>
>> JVM_OPTS="$JVM_OPTS -XX:CMSScheduleRemarkEdenSizeThreshold=104857600"
>>
>> JVM_OPTS="$JVM_OPTS -XX:CMSRescanMultiple=32768"
>>
>> JVM_OPTS="$JVM_OPTS -XX:CMSConcMarkMultiple=32768"
>>
>> #new
>>
>> JVM_OPTS="$JVM_OPTS -XX:+CMSConcurrentMTEnabled"
>>
>>
>>
>> We are using cassandra 2.0.17. If anyone has any suggestion as to how
>> what else we can look for to understand why this is happening please do
>> reply.
>>
>>
>>
>>
>>
>>
>>
>> Thanks
>>
>> anishek
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>

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