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From "stack (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (HBASE-17072) CPU usage starts to climb up to 90-100% when using G1GC
Date Wed, 23 Nov 2016 23:25:59 GMT

    [ https://issues.apache.org/jira/browse/HBASE-17072?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15691636#comment-15691636
] 

stack commented on HBASE-17072:
-------------------------------

Test fails because of the below part of the patch which tries to go to the index to find block
lengths seeking. If I instrument the test, I can see that we seek one time less w/ the below
in place. We are hitting cache one time extra which is why the test fails. The patch also
seems to change how we start up our scan. Before patch we seek twice to point zero then twice
to the trailer. With the below in place we seek to the trailer twice, to zero twice, and then
back to the trailer. Not sure why.

{code}
diff --git a/hbase-server/src/main/java/org/apache/hadoop/hbase/io/hfile/HFileReaderImpl.java
b/hbase-server/src/main/java/org/apache/hadoop/hbase/io/hfile/HFileReaderImpl.java
index 4887550..be8fc89 100644
--- a/hbase-server/src/main/java/org/apache/hadoop/hbase/io/hfile/HFileReaderImpl.java
+++ b/hbase-server/src/main/java/org/apache/hadoop/hbase/io/hfile/HFileReaderImpl.java
@@ -1087,7 +1087,6 @@ public class HFileReaderImpl implements HFile.Reader, Configurable {

     /**
      * Positions this scanner at the start of the file.
-     *
      * @return false if empty file; i.e. a call to next would return false and
      *         the current key and value are undefined.
      * @throws IOException
@@ -1104,12 +1103,14 @@ public class HFileReaderImpl implements HFile.Reader, Configurable
{
       }

       long firstDataBlockOffset = reader.getTrailer().getFirstDataBlockOffset();
-      if (curBlock != null
-          && curBlock.getOffset() == firstDataBlockOffset) {
+      if (curBlock != null && curBlock.getOffset() == firstDataBlockOffset) {
         return processFirstDataBlock();
       }
-
-      readAndUpdateNewBlock(firstDataBlockOffset);
+      Cell firstKey = this.reader.getFirstKey();
+      HFileBlockIndex.BlockIndexReader indexReader = reader.getDataBlockIndexReader();
+      BlockWithScanInfo blockWithScanInfo = indexReader.loadDataBlockWithScanInfo(firstKey,
curBlock,
+          cacheBlocks, pread, isCompaction, getEffectiveDataBlockEncoding());
+      updateCurrentBlock(blockWithScanInfo.getHFileBlock());
       return true;
     }

@@ -1119,16 +1120,6 @@ public class HFileReaderImpl implements HFile.Reader, Configurable
{
       return true;
     }

-    protected void readAndUpdateNewBlock(long firstDataBlockOffset) throws IOException,
-        CorruptHFileException {
-      HFileBlock newBlock = reader.readBlock(firstDataBlockOffset, -1, cacheBlocks, pread,
-          isCompaction, true, BlockType.DATA, getEffectiveDataBlockEncoding());
-      if (newBlock.getOffset() < 0) {
-        throw new IOException("Invalid block offset: " + newBlock.getOffset());
-      }
-      updateCurrentBlock(newBlock);
-    }
-
     protected int loadBlockAndSeekToKey(HFileBlock seekToBlock, Cell nextIndexedKey,
         boolean rewind, Cell key, boolean seekBefore) throws IOException {
       if (this.curBlock == null
{code}

> CPU usage starts to climb up to 90-100% when using G1GC
> -------------------------------------------------------
>
>                 Key: HBASE-17072
>                 URL: https://issues.apache.org/jira/browse/HBASE-17072
>             Project: HBase
>          Issue Type: Bug
>          Components: Performance, regionserver
>    Affects Versions: 1.0.0, 2.0.0, 1.2.0
>            Reporter: Eiichi Sato
>         Attachments: HBASE-17072.master.001.patch, HBASE-17072.master.002.patch, disable-block-header-cache.patch,
mat-threadlocals.png, mat-threads.png, metrics.png, slave1.svg, slave2.svg, slave3.svg, slave4.svg
>
>
> h5. Problem
> CPU usage of a region server in our CDH 5.4.5 cluster, at some point, starts to gradually
get higher up to nearly 90-100% when using G1GC.  We've also run into this problem on CDH
5.7.3 and CDH 5.8.2.
> In our production cluster, it normally takes a few weeks for this to happen after restarting
a RS.  We reproduced this on our test cluster and attached the results.  Please note that,
to make it easy to reproduce, we did some "anti-tuning" on a table when running tests.
> In metrics.png, soon after we started running some workloads against a test cluster (CDH
5.8.2) at about 7 p.m. CPU usage of the two RSs started to rise.  Flame Graphs (slave1.svg
to slave4.svg) are generated from jstack dumps of each RS process around 10:30 a.m. the next
day.
> After investigating heapdumps from another occurrence on a test cluster running CDH 5.7.3,
we found that the ThreadLocalMap contain a lot of contiguous entries of {{HFileBlock$PrefetchedHeader}}
probably due to primary clustering.  This caused more loops in {{ThreadLocalMap#expungeStaleEntries()}},
consuming a certain amount of CPU time.  What is worse is that the method is called from RPC
metrics code, which means even a small amount of per-RPC time soon adds up to a huge amount
of CPU time.
> This is very similar to the issue in HBASE-16616, but we have many {{HFileBlock$PrefetchedHeader}}
not only {{Counter$IndexHolder}} instances.  Here are some OQL counts from Eclipse Memory
Analyzer (MAT).  This shows a number of ThreadLocal instances in the ThreadLocalMap of a single
handler thread.
> {code}
> SELECT *
> FROM OBJECTS (SELECT AS RETAINED SET OBJECTS value
> 			  FROM OBJECTS 0x4ee380430) obj
> WHERE obj.@clazz.@name = "org.apache.hadoop.hbase.io.hfile.HFileBlock$PrefetchedHeader"
> #=> 10980 instances
> {code}
> {code}
> SELECT *
> FROM OBJECTS (SELECT AS RETAINED SET OBJECTS value
> 			  FROM OBJECTS 0x4ee380430) obj
> WHERE obj.@clazz.@name = "org.apache.hadoop.hbase.util.Counter$IndexHolder"
> #=> 2052 instances
> {code}
> Although as described in HBASE-16616 this somewhat seems to be an issue in G1GC side
regarding weakly-reachable objects, we should keep ThreadLocal usage minimal and avoid creating
an indefinite number (in this case, a number of HFiles) of ThreadLocal instances.
> HBASE-16146 removes ThreadLocals from the RPC metrics code.  That may solve the issue
(I just saw the patch, never tested it at all), but the {{HFileBlock$PrefetchedHeader}} are
still there in the ThreadLocalMap, which may cause issues in the future again.
> h5. Our Solution
> We simply removed the whole {{HFileBlock$PrefetchedHeader}} caching and fortunately we
didn't notice any performance degradation for our production workloads.
> Because the PrefetchedHeader caching uses ThreadLocal and because RPCs are handled randomly
in any of the handlers, small Get or small Scan RPCs do not benefit from the caching (See
HBASE-10676 and HBASE-11402 for the details).  Probably, we need to see how well reads are
saved by the caching for large Scan or Get RPCs and especially for compactions if we really
remove the caching. It's probably better if we can remove ThreadLocals without breaking the
current caching behavior.
> FWIW, I'm attaching the patch we applied. It's for CDH 5.4.5.



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