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https://issues.apache.org/jira/browse/KAFKA-4614?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15820924#comment-15820924
]
ASF GitHub Bot commented on KAFKA-4614:
---------------------------------------
GitHub user kawamuray opened a pull request:
https://github.com/apache/kafka/pull/2352
KAFKA-4614 Forcefully unmap mmap of OffsetIndex to prevent long GC pause
Issue: https://issues.apache.org/jira/browse/KAFKA-4614
Fixes the problem that the broker threads suffered by long GC pause.
When GC thread collects mmap objects which were created for index files, it
unmaps memory mapping so kernel turns to delete a file physically. This work
may transparently read file's metadata from physical disk if it's not available
on cache.
This seems to happen typically when we're using G1GC, due to it's strategy
to left a garbage for a long time if other objects in the same region are still
alive.
See the link for the details.
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/kawamuray/kafka
KAFKA-4614-force-munmap-for-index
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/kafka/pull/2352.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #2352
----
commit 8c3a4c9f5a6188c641a45cb3e111094f545f7e66
Author: Yuto Kawamura <kawamuray.dad...@gmail.com>
Date: 2017-01-11T08:10:05Z
KAFKA-4614 Forcefully unmap mmap of OffsetIndex to prevent long GC pause
----
> Long GC pause harming broker performance which is caused by mmap objects
> created for OffsetIndex
> ------------------------------------------------------------------------------------------------
>
> Key: KAFKA-4614
> URL: https://issues.apache.org/jira/browse/KAFKA-4614
> Project: Kafka
> Issue Type: Improvement
> Components: core
> Affects Versions: 0.10.0.1
> Reporter: Yuto Kawamura
> Assignee: Yuto Kawamura
> Labels: latency, performance
>
> First let me clarify our system environment information as I think it's
> important to understand this issue:
> OS: CentOS6
> Kernel version: 2.6.32-XX
> Filesystem used for data volume: XFS
> Java version: 1.8.0_66
> GC option: Kafka default(G1GC)
> Kafka version: 0.10.0.1
> h2. Phenomenon
> In our Kafka cluster, an usual response time for Produce request is about 1ms
> for 50th percentile to 10ms for 99th percentile. All topics are configured to
> have 3 replicas and all producers are configured {{acks=all}} so this time
> includes replication latency.
> Sometimes we observe 99th percentile latency get increased to 100ms ~ 500ms
> but for the most cases the time consuming part is "Remote" which means it is
> caused by slow replication which is known to happen by various reasons(which
> is also an issue that we're trying to improve, but out of interest within
> this issue).
> However, we found that there are some different patterns which happens rarely
> but stationary 3 ~ 5 times a day for each servers. The interesting part is
> that "RequestQueue" also got increased as well as "Total" and "Remote".
> At the same time, we observed that the disk read metrics(in terms of both
> read bytes and read time) spikes exactly for the same moment. Currently we
> have only caught up consumers so this metric sticks to zero while all
> requests are served by page cache.
> In order to investigate what Kafka is "read"ing, I employed SystemTap and
> wrote the following script. It traces all disk reads(only actual read by
> physical device) made for the data volume by broker process.
> {code}
> global target_pid = KAFKA_PID
> global target_dev = DATA_VOLUME
> probe ioblock.request {
> if (rw == BIO_READ && pid() == target_pid && devname == target_dev) {
> t_ms = gettimeofday_ms() + 9 * 3600 * 1000 // timezone adjustment
> printf("%s,%03d: tid = %d, device = %s, inode = %d, size = %d\n",
> ctime(t_ms / 1000), t_ms % 1000, tid(), devname, ino, size)
> print_backtrace()
> print_ubacktrace()
> }
> }
> {code}
> As the result, we could observe many logs like below:
> {code}
> Thu Dec 22 17:21:39 2016,209: tid = 126123, device = sdb1, inode = -1, size
> = 4096
> 0xffffffff81275050 : generic_make_request+0x0/0x5a0 [kernel]
> 0xffffffff81275660 : submit_bio+0x70/0x120 [kernel]
> 0xffffffffa036bcaa : _xfs_buf_ioapply+0x16a/0x200 [xfs]
> 0xffffffffa036d95f : xfs_buf_iorequest+0x4f/0xe0 [xfs]
> 0xffffffffa036db46 : _xfs_buf_read+0x36/0x60 [xfs]
> 0xffffffffa036dc1b : xfs_buf_read+0xab/0x100 [xfs]
> 0xffffffffa0363477 : xfs_trans_read_buf+0x1f7/0x410 [xfs]
> 0xffffffffa033014e : xfs_btree_read_buf_block+0x5e/0xd0 [xfs]
> 0xffffffffa0330854 : xfs_btree_lookup_get_block+0x84/0xf0 [xfs]
> 0xffffffffa0330edf : xfs_btree_lookup+0xbf/0x470 [xfs]
> 0xffffffffa032456f : xfs_bmbt_lookup_eq+0x1f/0x30 [xfs]
> 0xffffffffa032628b : xfs_bmap_del_extent+0x12b/0xac0 [xfs]
> 0xffffffffa0326f34 : xfs_bunmapi+0x314/0x850 [xfs]
> 0xffffffffa034ad79 : xfs_itruncate_extents+0xe9/0x280 [xfs]
> 0xffffffffa0366de5 : xfs_inactive+0x2f5/0x450 [xfs]
> 0xffffffffa0374620 : xfs_fs_clear_inode+0xa0/0xd0 [xfs]
> 0xffffffff811affbc : clear_inode+0xac/0x140 [kernel]
> 0xffffffff811b0776 : generic_delete_inode+0x196/0x1d0 [kernel]
> 0xffffffff811b0815 : generic_drop_inode+0x65/0x80 [kernel]
> 0xffffffff811af662 : iput+0x62/0x70 [kernel]
> 0x37ff2e5347 : munmap+0x7/0x30 [/lib64/libc-2.12.so]
> 0x7ff169ba5d47 : Java_sun_nio_ch_FileChannelImpl_unmap0+0x17/0x50
> [/usr/jdk1.8.0_66/jre/lib/amd64/libnio.so]
> 0x7ff269a1307e
> {code}
> We took a jstack dump of the broker process and found that tid = 126123
> corresponds to the thread which is for GC(hex(tid) == nid(Native Thread ID)):
> {code}
> $ grep 0x1ecab /tmp/jstack.dump
> "Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007ff278d0c800
> nid=0x1ecab in Object.wait() [0x00007ff17da11000]
> {code}
> In order to confirm, we enabled {{PrintGCApplicationStoppedTime}} switch and
> confirmed that in total the time the broker paused is longer than usual, when
> a broker experiencing the issue.
> {code}
> $ grep --text 'Total time for which application threads were stopped'
> kafkaServer-gc.log | grep --text '11T01:4' | perl -ne
> '/^(.*T\d{2}:\d{2}).*stopped: ([0-9\.]+)/; $h{$1} += $2 * 1000; END { print
> "$_ = $h{$_}\n" for sort keys %h }'
> 2017-01-11T01:40 = 332.0601
> 2017-01-11T01:41 = 315.1805
> 2017-01-11T01:42 = 318.4317
> 2017-01-11T01:43 = 317.8821
> 2017-01-11T01:44 = 302.1132
> 2017-01-11T01:45 = 950.5807 # << here
> 2017-01-11T01:46 = 344.9449
> 2017-01-11T01:47 = 328.936
> 2017-01-11T01:48 = 296.3204
> 2017-01-11T01:49 = 299.2834
> $ grep --text 'Total time for which application threads were stopped'
> kafkaServer-gc.log | grep --text '11T01:45' | perl -ne
> '/^(.*T\d{2}:\d{2}:\d{2}).*stopped: ([0-9\.]+)/; $h{$1} += $2 * 1000; END {
> print "$_ = $h{$_}\n" for sort keys %h }' | head -20
> 2017-01-11T01:45:00 = 31.1591
> 2017-01-11T01:45:01 = 28.7814
> 2017-01-11T01:45:02 = 30.0265
> 2017-01-11T01:45:03 = 66.7318
> 2017-01-11T01:45:04 = 20.6993
> 2017-01-11T01:45:05 = 52.8268
> 2017-01-11T01:45:06 = 29.6571
> 2017-01-11T01:45:07 = 25.6357
> 2017-01-11T01:45:08 = 58.6863
> 2017-01-11T01:45:09 = 33.022
> 2017-01-11T01:45:10 = 3.2497
> 2017-01-11T01:45:11 = 9.916
> 2017-01-11T01:45:12 = 19.7215
> 2017-01-11T01:45:13 = 61.652
> 2017-01-11T01:45:15 = 8.9058
> 2017-01-11T01:45:16 = 16.7779
> 2017-01-11T01:45:17 = 11.3215
> 2017-01-11T01:45:18 = 82.2986
> 2017-01-11T01:45:19 = 32.2718
> 2017-01-11T01:45:20 = 1.1403
> {code}
> h2. Hypothesis
> In case of Kafka broker running on Linux, an mmap object of offset index are
> cleaned up like below:
> - OffsetIndex.delete() called and the corresponding file marked as deleted on
> VFS level(still not physically deleted at this moment, because there's an
> mmap object which holds opened reference to the same file)
> - OffsetIndex object also cut off from any reference and becomes a
> collectable garbage
> - While after, GC collects mmap object(MappedByteBuffer) and run the cleanup
> routine so it munmaps the mapping
> Hence, munmap being called from GC thread itself sounds normal.
> So the question should be why releasing mmap inside the GC thread likely
> causes such a long STW moment.
> After a tough investigation, we found that the following scenario can explain
> it:
> 1. Since OffsetIndex object kept living for a long moment(depending
> retention.ms?) it should have already promoted to old gen.
> 2. OffsetIndex.delete() called so the file marked as deleted. At the same
> time, the operation should warmed up inode cache.
> 3. However, since G1GC collects a region which contains a lot of garbages
> preferentially, if a region that an mmap object contained still has many
> living objects, it might be left and not being collected for a long moment.
> 4. During this moment, inode cache for the index file evicted from XFS layer
> cache.
> 5. Eventually the mmap object collected and munmap called, which triggers
> kernel to perform physical deletion of the inode associated to the file, but
> at this moment, metadata cache for the index file already evicted from cache
> so XFS driver have to read it from disk. Since data volume disks of Kafka
> logs are very busy for write workload, reading disk is very time-consuming
> operation. During the moment, application threads are blocked and after
> resumed, all pending requests marks slow response time.
> h2. Experiment
> In order to confirm this scenario, I tried to reproduce STW caused by GC
> freeing mmap which corresponds to a file that it's metadata out of the cache.
> I wrote below Java code and ran several times with observations.
> {code}
> import java.io.File;
> import java.io.FileInputStream;
> import java.io.FileOutputStream;
> import java.io.IOException;
> import java.io.RandomAccessFile;
> import java.nio.MappedByteBuffer;
> import java.nio.channels.FileChannel.MapMode;
> import java.text.SimpleDateFormat;
> import java.util.Date;
> import java.util.concurrent.TimeUnit;
> import sun.nio.ch.DirectBuffer;
> /**
> * Test scenario:
> *
> * - Create N(given as an argument) number of files under the directory and
> corresponding N mmaps.
> * - Remove all files created.
> * - Sleep for a while, with expect to periodic XFS cache cleaner routine
> executed.
> * - Drop VFS dentry cache
> * - Cut references to mmaps
> * - Keep creating objects to pressure heap and lead GC to collect mmap
> garbages.
> */
> public final class MmapGcTest {
> private static String filename(int num) {
> return "/path/to/data_volume/mmaps/mmap-" + num;
> }
> public static void main(String[] args) throws IOException,
> InterruptedException {
> int numFiles = Integer.parseInt(args[0]);
> boolean cleanMmapsExplicitly = Boolean.parseBoolean(args[1]);
> Thread.sleep(20000);
> MappedByteBuffer[] mmaps = new MappedByteBuffer[numFiles];
> for (int i = 0; i < numFiles; i++) {
> RandomAccessFile file = new RandomAccessFile(filename(i), "rw");
> file.setLength(128);
> MappedByteBuffer mmap = file.getChannel().map(MapMode.READ_WRITE,
> 0, file.length());
> file.close();
> mmaps[i] = mmap;
> }
> System.err.println("removing files");
> for (int i = 0; i < numFiles; i++) {
> boolean deleted = new File(filename(i)).delete();
> if (!deleted) {
> throw new RuntimeException("failed to delete file");
> }
> }
> // Wait until XFS expires inode buffer cache
> final long timeToSleep;
> try (FileInputStream fin = new
> FileInputStream("/proc/sys/fs/xfs/xfssyncd_centisecs")) {
> byte[] buf = new byte[256];
> fin.read(buf);
> timeToSleep = Long.parseLong(new String(buf).trim()) * 10 /*
> centisecs to millisecs */ + 1000 /* and little bit more */;
> }
> System.err.println("Sleeping " + timeToSleep + " ms for waiting XFS
> inode buffer expiration");
> Thread.sleep(timeToSleep);
> System.err.println("drop caches");
> try (FileOutputStream out = new
> FileOutputStream("/proc/sys/vm/drop_caches")) {
> out.write("2\n".getBytes());
> }
> // Cut references to mmaps and let GC to collect them
> if (cleanMmapsExplicitly) {
> for (MappedByteBuffer mmap : mmaps) {
> ((DirectBuffer) mmap).cleaner().clean();
> }
> System.err.println("mmaps cleaned up");
> }
> mmaps = null;
> System.err.println("cut reference to mmaps");
> SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd
> HH:mm:ss.SSS");
> // Keep creating relatively large objects and see if there's a
> significantly large interval which
> // seemingly caused by GC pause.
> byte[][] chunks = new byte[32768][];
> for (int i = 0; i < Integer.MAX_VALUE; i++) {
> long t0 = System.nanoTime();
> byte[] chunk = new byte[4096];
> long elapsedMillis =
> TimeUnit.NANOSECONDS.toMillis(System.nanoTime() - t0);
> if (elapsedMillis > 100) {
> System.err.printf("%s likely long GC pause: %d ms\n",
> sdf.format(new Date()), elapsedMillis);
> }
> chunks[i % chunks.length] = chunk;
> }
> }
> }
> {code}
> At the same time the above program executed, I ran below two commands in
> different session:
> - The SystemTap script that I pasted above: to confirm same disk access
> pattern(code path)
> - {{dd if=/dev/zero of=$DATA_VOLUME/huge-zero.out bs=1024 count=$((100 * 1024
> * 1024))}}: to simulate disk device pressure of broker servers.
> Here's the logs of execution:
> {code}
> $ sudo java -Xmx1024m -server -XX:+UseG1GC -XX:MaxGCPauseMillis=20
> -XX:InitiatingHeapOccupancyPercent=35 -XX:+DisableExplicitGC -Xloggc:gc.log
> -verbose:gc -XX:+PrintGCDetails -XX:+PrintGCDateStamps -XX:+PrintGCTimeStamps
> -XX:+PrintReferenceGC -XX:+PrintGCApplicationStoppedTime MmapGcTest 10000
> false
> removing files
> Sleeping 31000 ms for waiting XFS inode buffer expiration
> drop caches
> cut reference to mmaps
> 2017-01-06 20:52:58.195 likely long GC pause: 3372 ms
> 2017-01-06 20:53:02.802 likely long GC pause: 2311 ms
> 2017-01-06 20:53:04.275 likely long GC pause: 1467 ms
> 2017-01-06 20:53:06.572 likely long GC pause: 2268 ms
> ...
> $ grep -A 30 20:53:02 stap.log | head -30
> Fri Jan 6 20:53:02 2017,024: tid = 95825, device = XXX, inode = -1, size =
> 8192
> 0xffffffff812746d0 : generic_make_request+0x0/0x5a0 [kernel]
> 0xffffffff81274ce0 : submit_bio+0x70/0x120 [kernel]
> 0xffffffffa042acba : _xfs_buf_ioapply+0x16a/0x200 [xfs]
> 0xffffffffa042c96f : xfs_buf_iorequest+0x4f/0xe0 [xfs]
> 0xffffffffa042cb56 : _xfs_buf_read+0x36/0x60 [xfs]
> 0xffffffffa042cc2b : xfs_buf_read+0xab/0x100 [xfs]
> 0xffffffffa0422487 : xfs_trans_read_buf+0x1f7/0x410 [xfs]
> 0xffffffffa040a654 : xfs_imap_to_bp+0x54/0x130 [xfs]
> 0xffffffffa040abdc : xfs_inotobp+0x8c/0xc0 [xfs]
> 0xffffffffa040acf1 : xfs_iunlink_remove+0xe1/0x320 [xfs]
> 0xffffffffa040af57 : xfs_ifree+0x27/0x110 [xfs]
> 0xffffffffa0425c98 : xfs_inactive+0x198/0x450 [xfs]
> 0xffffffffa0433630 : xfs_fs_clear_inode+0xa0/0xd0 [xfs]
> 0xffffffff811af6fc : clear_inode+0xac/0x140 [kernel]
> 0xffffffff811afeb6 : generic_delete_inode+0x196/0x1d0 [kernel]
> 0xffffffff811aff55 : generic_drop_inode+0x65/0x80 [kernel]
> 0xffffffff811aeda2 : iput+0x62/0x70 [kernel]
> 0xffffffff811ab7a0 : dentry_iput+0x90/0x100 [kernel]
> 0xffffffff811ab901 : d_kill+0x31/0x60 [kernel]
> 0xffffffff811ad53d : dput+0xcd/0x160 [kernel]
> 0x391d6e5347 : munmap+0x7/0x30 [/lib64/libc-2.12.so]
> 0x7ff8d873dd47 : Java_sun_nio_ch_FileChannelImpl_unmap0+0x17/0x50
> [/usr/jdk1.8.0_92/jre/lib/amd64/libnio.so]
> 0x7ff9893376fe
> ...
> $ grep 20:53:02 gc.log | grep -E 'Total time for which application threads
> were stopped: [^0]\.'
> 2017-01-06T20:53:02.802+0900: 60.898: Total time for which application
> threads were stopped: 2.3118335 seconds, Stopping threads took: 2.3054883
> seconds
> $ grep 0x17651 jstack-case1
> "Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007ff9982b6000
> nid=0x17651 in Object.wait() [0x00007ff8da12f000]
> {code}
> As you can see, GC is obviously blocking the application unusually long, and
> at the same time there is a same code path that the XFS is reading metadata
> from physical disk.
> So next I switched the second argument of the program to {{true}} and
> enforeced mmap cleanup within the main thread:
> {code}
> $ sudo java -Xmx1024m -server -XX:+UseG1GC -XX:MaxGCPauseMillis=20
> -XX:InitiatingHeapOccupancyPercent=35 -XX:+DisableExplicitGC -Xloggc:gc.log
> -verbose:gc -XX:+PrintGCDetails -XX:+PrintGCDateStamps -XX:+PrintGCTimeStamps
> -XX:+PrintReferenceGC -XX:+PrintGCApplicationStoppedTime MmapGcTest 10000 true
> removing files
> Sleeping 31000 ms for waiting XFS inode buffer expiration
> drop caches
> mmaps cleaned up
> cut reference to mmaps
> $ tail -24 stap.log
> Fri Jan 6 21:06:53 2017,166: tid = 118226, device = XXX, inode = -1, size =
> 4096
> 0xffffffff812746d0 : generic_make_request+0x0/0x5a0 [kernel]
> 0xffffffff81274ce0 : submit_bio+0x70/0x120 [kernel]
> 0xffffffffa042acba : _xfs_buf_ioapply+0x16a/0x200 [xfs]
> 0xffffffffa042c96f : xfs_buf_iorequest+0x4f/0xe0 [xfs]
> 0xffffffffa042cb56 : _xfs_buf_read+0x36/0x60 [xfs]
> 0xffffffffa042cc2b : xfs_buf_read+0xab/0x100 [xfs]
> 0xffffffffa0422487 : xfs_trans_read_buf+0x1f7/0x410 [xfs]
> 0xffffffffa03ef15e : xfs_btree_read_buf_block+0x5e/0xd0 [xfs]
> 0xffffffffa03ef864 : xfs_btree_lookup_get_block+0x84/0xf0 [xfs]
> 0xffffffffa03efeef : xfs_btree_lookup+0xbf/0x470 [xfs]
> 0xffffffffa03d6fd9 : xfs_alloc_lookup_eq+0x19/0x20 [xfs]
> 0xffffffffa03d7dd4 : xfs_free_ag_extent+0x1c4/0x750 [xfs]
> 0xffffffffa03da111 : xfs_free_extent+0x101/0x130 [xfs]
> 0xffffffffa03e3fcd : xfs_bmap_finish+0x15d/0x1a0 [xfs]
> 0xffffffffa0425e97 : xfs_inactive+0x397/0x450 [xfs]
> 0xffffffffa0433630 : xfs_fs_clear_inode+0xa0/0xd0 [xfs]
> 0xffffffff811af6fc : clear_inode+0xac/0x140 [kernel]
> 0xffffffff811afeb6 : generic_delete_inode+0x196/0x1d0 [kernel]
> 0xffffffff811aff55 : generic_drop_inode+0x65/0x80 [kernel]
> 0xffffffff811aeda2 : iput+0x62/0x70 [kernel]
> 0x391d6e5347 : munmap+0x7/0x30 [/lib64/libc-2.12.so]
> 0x7fc11ca7ad47 : Java_sun_nio_ch_FileChannelImpl_unmap0+0x17/0x50
> [/usr/jdk1.8.0_92/jre/lib/amd64/libnio.so]
> 0x7fc1e90174f4
> $ grep 0x1cdd2 jstack-case2
> "main" #1 prio=5 os_prio=0 tid=0x00007fc1f8008800 nid=0x1cdd2 runnable
> [0x00007fc1fe8dd000]
> $ grep -E 'Total time for which application threads were stopped: [^0]\.'
> gc.log | wc -l
> 0
> {code}
> Of course there were same code path that XFS is reading from physical disk,
> but this time it's comming from main thread.
> This time, none of GC occurrence blocked application thread more than 100ms,
> which can be confirmed by both of program's log and gc log.
> h2. Suggestion
> In order to solve this problem, we can call
> {{DirectBuffer.cleaner().clean()}} explicitly within log cleaner thread so no
> more GC time affected by transparent disk reads for metadata.
> The only downside that I can imagine is that it uses hidden API which is not
> recommended to use directly, but we're already importing it in order to
> support Windows so it's out of consideration.
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