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  1. Kafka
  2. KAFKA-4614

Long GC pause harming broker performance which is caused by mmap objects created for OffsetIndex

    Details

    • Type: Improvement
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 0.10.0.1
    • Fix Version/s: 0.10.2.0
    • Component/s: core

      Description

      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

      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.

      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()
        }
      }
      

      As the result, we could observe many logs like below:

      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
      

      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)):

      $ grep 0x1ecab /tmp/jstack.dump
      "Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007ff278d0c800 nid=0x1ecab in Object.wait() [0x00007ff17da11000]
      

      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.

      $ 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
      

      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.

      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.

      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;
              }
          }
      }
      

      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:

      $ 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]
      

      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:

      $ 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
      

      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.

      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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              • Assignee:
                kawamuray Yuto Kawamura
                Reporter:
                kawamuray Yuto Kawamura
                Reviewer:
                Jun Rao
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                Dates

                • Created:
                  Updated:
                  Resolved: