Tuesday, 28 February 2012

Performance Evaluation of HBase

Update: See also followup posts: part 2 and part 3.

In the last post Lars talked about setting up Ganglia for monitoring our Hadoop and HBase installations.  That was in preparation for giving HBase a solid testing run to assess its suitability for hosting our index of occurrence records.  One of the important features in our new Data Portal will be the "Download" function that lets people download occurrences matching some search criteria and currently that process is a very manual and labour intensive one, so automating it will be a big help to us.  Using HBase it would be implemented as a full table scan, and that's why I've spent some time testing our scan performance. Anyone who has been down this road will probably have encountered the myriad opinions on what will improve performance (some of them conflicting) along with the seemingly endless parameters that can be tuned in a given cluster.  The overall result of that kind of research is: "You gotta do it yourself".  So here we go.

Because we hope to get some feedback from the HBase community on our results (ideally comparisons to other running clusters) we decided to use the PerformanceEvaluation class that ships with HBase.  Unfortunately it's not completely bug free so I've had to patch it to work in the way we would like.  From a stock cdh3u3 HBase I patched HBASE-5401 and HBASE-4688, and had a good, hard think about HBASE-5402.  There are a bunch of things I learned about the PerformanceEvaluation (PE) class in the last few weeks, and the implications of 5402 are some of them.  If anyone's interested I'll blog about those another time, but for now suffice it to say that in my final suite of tests I went with writing tables using "sequentialWrite" (which obviates the difficulties in 5402) and doing scans with the "scan" test.

There are many variables that can be changed in an HBase/Hadoop cluster setup but you have to start somewhere so here's our basic config that remained unchanged throughout the test (you can see more at its ganglia page):

Master (c1n2): HDFS NameNode, Hadoop JobTracker, HBase Master, and Zookeeper
Slaves (c2n1, c2n2, c2n3): HDFS DataNode, Hadoop TaskTracker, HBase RegionServer (6 GB heap)

c1n2: 1x Intel(R) Xeon(R) X3363 @ 2.83GHz (quad), 8GB RAM, 2x500G SATA 5.4K
c2n*: 2x Intel(R) Xeon(R) E5630 @ 2.53GHz (quad), 24GB RAM, 6x250G SATA 7.2K

The parameters I varied are:
  • number of rows in the test table (50M, 100M, 200M)
  • number of mappers per server (8, 10, 12, 14, 20 - more than 20 and we ran out of RAM)
  • snappy compression (on/off)
  • scanner caching (size)
  • block caching (on/off)
Test Methodology

The test methodology was to start with an empty HDFS (replication factor of 2), an empty HBase and no other tasks running on the machines.  Then build a table using a command line like 

hbase org.apache.hadoop.hbase.PerformanceEvaluation sequentialWrite 100

and then wait for the split/compaction cycle to complete, and then run a major compaction to encourage data locality.  In tests using compression I would construct an empty table by hand, specifying compression=>'SNAPPY' for the info column family before running the sequentialWrite. I'd also wait for the region balancer to run, ensuring that all regionservers had an equal number of regions (+/- 1). Once that was complete I would run a scan test with a command like:

hbase org.apache.hadoop.hbase.PerformanceEvaluation scan 100

and note the real time taken as reported by the JobTracker as well as the total time spent in mappers as reported by PE itself.  I ran each scan test 3 times unless the first 2 tests were very close, in which case I sometimes skipped the 3rd run. Note also that PE uses 10 byte keys and 1000 kilobyte values by default. 

Two things were immediately obvious in my caching tests, which I'll talk about briefly before getting into the results proper.

Scanner Caching

The HBase API Scan class takes a setting called setCaching(int caching) which tells the scanner how many rows to fetch at a time from the server.  This defaults to 1, which is optimal for single gets, but is decidedly suboptimal for big scans like ours. Unfortunately PE doesn't allow for explicitly setting this value on the command line and so I took the advice of the API Javadoc and passed in a value of 1000 for the property hbase.client.scanner.caching in the hbase-site.xml file that forms the configuration for the MapReduce job that is PE.  It would seem, though, that this property is not being honoured by HBase and so my initial tests all ran with a cache size of 1, producing poor results.  I subsequently hard-coded the setCaching(1000) on the scans themselves in the PE and saw significant improvements. Those differences are visible in the results, below.

Block Caching

When I say block caching I mean HBase blocks - not HDFS blocks.  See the HBase guide or Lars George's excellent HBase: The Definitive Guide for many more details. You'll see many recommendations from different sources to turn block caching off during scans but it's not immediately obvious why that should be.  It turns out that it has no performance implications for the scan itself, but will significantly impact any random reads (gets) that may be relying on recently loaded blocks.  If the scan is using the block cache then it will load the cache with a block, read the block, and then load the next one, ignoring the first one for the rest of the scan.  The earlier loaded blocks will be evicted quickly (as new blocks are loaded) leading to "cache churn".  So I tested the block cache on and off and concluded that there was no difference in a dedicated scan test (no other activity in the cluster) and so for the rest of my tests I left the block cache on.  In order to test this behaviour I again had to hard-code PE with setCacheBlocks(false) (it defaults to true).

The Results

The full spreadsheet is available for download from our google code site.  I've just included the summary chart here, because it pretty much tells the story.  Of note: the y-axis is Records / second which I calculate as the total records scanned divided by the total time for the job as reported by the JobTracker.  This doesn't, therefore, take any of the PE generated per-mapper counts/times into account (which are still somewhat mysterious to me).

Conclusions (within our obviously limited test environment):

  • with bigger datasets, more mappers are better; with smaller datasets, somewhat fewer are better
  • compression slows things down.  This is probably the most surprising (and contentious) finding.  We would expect performance to improve with compression (at worst staying the same) because there is much less data to transfer when the files are compressed, and I/O is typically the limiting factor in HBase performance.  I kept an eye on the cpus with ganglia during the uncompressed tests and sure enough, they spent approximately double the amount of time in io_wait as in the compressed tests.
  • ganglia revealed no obvious bottlenecks during the scan.  You can look at our ganglia charts from the past few weeks and apart from a few purposefully degenerate tests there was no obvious component that was limiting things - cpus never went above 60% (io_wait never above 30%), and RAM and disks "looked ok".  If anyone has insight here we'd really appreciate it.
  • total variability across all these tests was only about 20%.  Either all tests are hitting the same, as yet unseen, hardware or configuration limit, or there really is no silver bullet to performance increases - tuning is an incremental thing.
  • there are still strange things going on :)  I can't explain the fact that in the compressed test performance increases from 50 to 100M records, and then decreases dramatically with 200M records.
We'd love feedback on these results, both in terms of how we can improve our testing and in interpreting the results, as well as any numbers you may have from your clusters when running PE.  Is 300k records per second even in the ballpark?  It's crazy that these data don't exist out there already, so hopefully this post helps alleviate that somewhat.  

The good news is that we'll be getting new cluster hardware soon, and then I think the next step is to load our real occurrences data into a table and run similar scanning tests against it to optimize those scans.  Of course then we'll start writing new records at the same time, and then things will get.... interesting.  Should be fun :)

Wednesday, 8 February 2012

Monitoring Hadoop and HBase

We're getting serious in our Hadoop adoption. The first process (our so called "rollover") is now in production and it uses Hadoop, Hive, Oozie and various other parts of the Hadoop ecosystem.

Our next step is evaluating HBase and its performance on our (small and aging) cluster. To do that properly and to fix a rather embarrassing situation we first had to get proper monitoring up and running for our cluster. So far we've only had Cacti stats for OS level things (CPU, I/O, etc.) but we were missing actual Hadoop statistics.

So we've now set up Ganglia at GBIF and the best news is it's public and using the very latest Ganglia 3.3 which was released only a few days ago in February 2012. The setup was relatively painless. Ganglia was just nice to work with. To get monitoring of HBase working we had to apply HBASE-4854 because it's not included in our Hadoop distribution (CDH3u2). Thanks to Lars George for the hint.

So we can happily report that Ganglia 3.3 works perfect with the GangliaContext31 from Hadoop.

Now all that's left is learning what most of these stats mean and then trying to extract useful information from them. Any hints are more than welcome and the HBase community already offered to help. Thank you very much!

For anyone interested in a few notes and details about how we set Ganglia up keep on reading.