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From Philip Ó Condúin <philipocond...@gmail.com>
Subject Re: Datafile Corruption
Date Thu, 08 Aug 2019 11:20:16 GMT
Hi All,

Thank you so much for the replies.

Currently, I have the following list that can potentially cause some sort
of corruption in a Cassandra cluster.


   - Sudden Power cut  -  *We have had no power cuts in the datacenters*
   - Network Issues - *no network issues from what I can tell*
   - Disk full - *I don't think this is an issue for us, see disks below.*
   - An issue in Casandra version like Cassandra-13752 -* couldn't find any
   Jira issues similar to ours.*
   - Bit Flips -* we have compression enabled so I don't think this should
   be an issue.*
   - Repair during upgrade has caused corruption too -* we have not
   upgraded*
   - Dropping and adding columns with the same name but a different type - *I
   will need to ask the apps team how they are using the database.*



Ok, let me try and explain the issue we are having, I am under a lot of
pressure from above to get this fixed and I can't figure it out.

This is a PRE-PROD environment.

   - 2 datacenters.
   - 9 physical servers in each datacenter
   - 4 Cassandra instances on each server
   - 72 Cassandra instances across the 2 data centres, 36 in site A, 36 in
   site B.


We also have 2 Reaper Nodes we use for repair.  One reaper node in each
datacenter each running with its own Cassandra back end in a cluster
together.

OS Details [Red Hat Linux]
cass_a@x 0 10:53:01 ~ $ uname -a
Linux x 3.10.0-957.5.1.el7.x86_64 #1 SMP Wed Dec 19 10:46:58 EST 2018
x86_64 x86_64 x86_64 GNU/Linux

cass_a@x 0 10:57:31 ~ $ cat /etc/*release
NAME="Red Hat Enterprise Linux Server"
VERSION="7.6 (Maipo)"
ID="rhel"

Storage Layout
cass_a@xx 0 10:46:28 ~ $ df -h
Filesystem                         Size  Used Avail Use% Mounted on
/dev/mapper/vg01-lv_root            20G  2.2G   18G  11% /
devtmpfs                            63G     0   63G   0% /dev
tmpfs                               63G     0   63G   0% /dev/shm
tmpfs                               63G  4.1G   59G   7% /run
tmpfs                               63G     0   63G   0% /sys/fs/cgroup
>> 4 cassandra instances
/dev/sdd                           1.5T  802G  688G  54% /data/ssd4
/dev/sda                           1.5T  798G  692G  54% /data/ssd1
/dev/sdb                           1.5T  681G  810G  46% /data/ssd2
/dev/sdc                           1.5T  558G  932G  38% /data/ssd3

Cassandra load is about 200GB and the rest of the space is snapshots

CPU
cass_a@x 127 10:58:47 ~ $ lscpu | grep -E '^Thread|^Core|^Socket|^CPU\('
CPU(s):                64
Thread(s) per core:    2
Core(s) per socket:    16
Socket(s):             2

*Description of problem:*
During repair of the cluster, we are seeing multiple corruptions in the log
files on a lot of instances.  There seems to be no pattern to the
corruption.  It seems that the repair job is finding all the corrupted
files for us.  The repair will hang on the node where the corrupted file is
found.  To fix this we remove/rename the datafile and bounce the Cassandra
instance.  Our hardware/OS team have stated there is no problem on their
side.  I do not believe it the repair causing the corruption.

We have maintenance scripts that run every night running compactions and
creating snapshots, I decided to turn these off, fix any corruptions we
currently had and ran major compaction on all nodes, once this was done we
had a "clean" cluster and we left the cluster for a few days.  After the
process we noticed one corruption in the cluster, this datafile was created
after I turned off the maintenance scripts so my theory of the scripts
causing the issue was wrong.  We then kicked off another repair and started
to find more corrupt files created after the maintenance script was turned
off.


So let me give you an example of a corrupted file and maybe someone might
be able to work through it with me?

When this corrupted file was reported in the log it looks like it was the
repair that found it.

$ journalctl -u cassmeta-cass_b.service --since "2019-08-07 22:25:00"
--until "2019-08-07 22:45:00"

Aug 07 22:30:33 cassandra[34611]: INFO  21:30:33 Writing
Memtable-compactions_in_progress@830377457(0.008KiB serialized bytes, 1
ops, 0%/0% of on/off-heap limit)
Aug 07 22:30:33 cassandra[34611]: ERROR 21:30:33 Failed creating a merkle
tree for [repair #9587a200-b95a-11e9-8920-9f72868b8375 on
KeyspaceMetadata/x, (-1476350953672479093,-1474461
Aug 07 22:30:33 cassandra[34611]: ERROR 21:30:33 Exception in thread
Thread[ValidationExecutor:825,1,main]
Aug 07 22:30:33 cassandra[34611]: org.apache.cassandra.io.FSReadError:
org.apache.cassandra.io.sstable.CorruptSSTableException: Corrupted:
/x/ssd2/data/KeyspaceMetadata/x-1e453cb0
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.io.util.RandomAccessReader.readBytes(RandomAccessReader.java:365)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.utils.ByteBufferUtil.read(ByteBufferUtil.java:361)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.utils.ByteBufferUtil.readWithShortLength(ByteBufferUtil.java:340)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.composites.AbstractCType$Serializer.deserialize(AbstractCType.java:382)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.composites.AbstractCType$Serializer.deserialize(AbstractCType.java:366)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.OnDiskAtom$Serializer.deserializeFromSSTable(OnDiskAtom.java:81)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.AbstractCell$1.computeNext(AbstractCell.java:52)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.AbstractCell$1.computeNext(AbstractCell.java:46)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
~[guava-16.0.jar:na]
Aug 07 22:30:33 cassandra[34611]: at
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
~[guava-16.0.jar:na]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.io.sstable.SSTableIdentityIterator.hasNext(SSTableIdentityIterator.java:169)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.utils.MergeIterator$OneToOne.computeNext(MergeIterator.java:202)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
~[guava-16.0.jar:na]
Aug 07 22:30:33 cassandra[34611]: at
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
~[guava-16.0.jar:na]
Aug 07 22:30:33 cassandra[34611]: at
com.google.common.collect.Iterators$7.computeNext(Iterators.java:645)
~[guava-16.0.jar:na]
Aug 07 22:30:33 cassandra[34611]: at
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
~[guava-16.0.jar:na]
Aug 07 22:30:33 cassandra[34611]: at
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
~[guava-16.0.jar:na]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.ColumnIndex$Builder.buildForCompaction(ColumnIndex.java:174)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.compaction.LazilyCompactedRow.update(LazilyCompactedRow.java:187)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.repair.Validator.rowHash(Validator.java:201)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.repair.Validator.add(Validator.java:150)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.compaction.CompactionManager.doValidationCompaction(CompactionManager.java:1166)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.compaction.CompactionManager.access$600(CompactionManager.java:76)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.db.compaction.CompactionManager$10.call(CompactionManager.java:736)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_172]
Aug 07 22:30:33 cassandra[34611]: at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
~[na:1.8.0_172]
Aug 07 22:30:33 cassandra[34611]: at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
[na:1.8.0_172]
Aug 07 22:30:33 cassandra[34611]: at java.lang.Thread.run(Thread.java:748)
[na:1.8.0_172]
Aug 07 22:30:33 cassandra[34611]: Caused by:
org.apache.cassandra.io.sstable.CorruptSSTableException: Corrupted:
/data/ssd2/data/KeyspaceMetadata/x-x/l
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.io.compress.CompressedRandomAccessReader.reBufferMmap(CompressedRandomAccessReader.java:216)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.io.compress.CompressedRandomAccessReader.reBuffer(CompressedRandomAccessReader.java:226)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.io.compress.CompressedThrottledReader.reBuffer(CompressedThrottledReader.java:42)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.io.util.RandomAccessReader.readBytes(RandomAccessReader.java:352)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: ... 27 common frames omitted
Aug 07 22:30:33 cassandra[34611]: Caused by:
org.apache.cassandra.io.compress.CorruptBlockException:
(/data/ssd2/data/KeyspaceMetadata/x-x/lb-26203-big
Aug 07 22:30:33 cassandra[34611]: at
org.apache.cassandra.io.compress.CompressedRandomAccessReader.reBufferMmap(CompressedRandomAccessReader.java:185)
~[apache-cassandra-2.2.13.jar:2.2.13]
Aug 07 22:30:33 cassandra[34611]: ... 30 common frames omitted
Aug 07 22:30:33 cassandra[34611]: INFO  21:30:33 Not a global repair, will
not do anticompaction
Aug 07 22:30:33 cassandra[34611]: ERROR 21:30:33 Stopping gossiper
Aug 07 22:30:33 cassandra[34611]: WARN  21:30:33 Stopping gossip by
operator request
Aug 07 22:30:33 cassandra[34611]: INFO  21:30:33 Announcing shutdown
Aug 07 22:30:33 cassandra[34611]: INFO  21:30:33 Node /10.2.57.37 state
jump to shutdown


So I went to the file system to see when this corrupt file was created and
it was created on July 30th at 15.55

root@x 0 01:14:03 ~ # ls -l
/data/ssd2/data/KeyspaceMetadata/x-x/lb-26203-big-Data.db
-rw-r--r-- 1 cass_b cass_b 3182243670 Jul 30 15:55
/data/ssd2/data/KeyspaceMetadata/x-x/lb-26203-big-Data.db



So I checked /var/log/messages for errors around that time
The only thing that stands out to me is the message "Cannot perform a full
major compaction as repaired and unrepaired sstables cannot be compacted
together", I'm not sure if this would be an issue though and cause
corruption.

Jul 30 15:55:06 x systemd: Created slice User Slice of root.
Jul 30 15:55:06 x systemd: Started Session c165280 of user root.
Jul 30 15:55:06 x audispd: node=x. type=USER_START
msg=audit(1564498506.021:457933): pid=17533 uid=0 auid=4294967295
ses=4294967295 msg='op=PAM:session_open
grantors=pam_keyinit,pam_limits,pam_keyinit,pam_limits,pam_tty_audit,pam_systemd,pam_unix
acct="root" exe="/usr/bin/sudo" hostname=? addr=? terminal=? res=success'
Jul 30 15:55:06 x systemd: Removed slice User Slice of root.
Jul 30 15:55:14 x tag_audit_log: type=USER_CMD
msg=audit(1564498506.013:457932): pid=17533 uid=509 auid=4294967295
ses=4294967295 msg='cwd="/"
cmd=2F7573722F7362696E2F69706D692D73656E736F7273202D2D71756965742D6361636865202D2D7364722D63616368652D7265637265617465202D2D696E746572707265742D6F656D2D64617461202D2D6F75747075742D73656E736F722D7374617465202D2D69676E6F72652D6E6F742D617661696C61626C652D73656E736F7273202D2D6F75747075742D73656E736F722D7468726573686F6C6473
terminal=? res=success'
Jul 30 15:55:14 x tag_audit_log: type=USER_START
msg=audit(1564498506.021:457933): pid=17533 uid=0 auid=4294967295
ses=4294967295 msg='op=PAM:session_open
grantors=pam_keyinit,pam_limits,pam_keyinit,pam_limits,pam_tty_audit,pam_systemd,pam_unix
acct="root" exe="/usr/bin/sudo" hostname=? addr=? terminal=? res=success'
Jul 30 15:55:19 x cassandra: INFO  14:55:19 Writing
Memtable-compactions_in_progress@1462227999(0.008KiB serialized bytes, 1
ops, 0%/0% of on/off-heap limit)
Jul 30 15:55:19 x cassandra: INFO  14:55:19 Cannot perform a full major
compaction as repaired and unrepaired sstables cannot be compacted
together. These two set of sstables will be compacted separately.
Jul 30 15:55:19 x cassandra: INFO  14:55:19 Writing
Memtable-compactions_in_progress@1198535528(1.002KiB serialized bytes, 57
ops, 0%/0% of on/off-heap limit)
Jul 30 15:55:20 x cassandra: INFO  14:55:20 Writing
Memtable-compactions_in_progress@2039409834(0.008KiB serialized bytes, 1
ops, 0%/0% of on/off-heap limit)
Jul 30 15:55:24 x audispd: node=x. type=USER_LOGOUT
msg=audit(1564498524.409:457934): pid=46620 uid=0 auid=464400029 ses=2747
msg='op=login id=464400029 exe="/usr/sbin/sshd" hostname=? addr=?
terminal=/dev/pts/0 res=success'
Jul 30 15:55:24 x audispd: node=x. type=USER_LOGOUT
msg=audit(1564498524.409:457935): pid=4878 uid=0 auid=464400029 ses=2749
msg='op=login id=464400029 exe="/usr/sbin/sshd" hostname=? addr=?
terminal=/dev/pts/1 res=success'

Jul 30 15:55:57 x systemd: Created slice User Slice of root.
Jul 30 15:55:57 x systemd: Started Session c165288 of user root.
Jul 30 15:55:57 x audispd: node=x. type=USER_START
msg=audit(1564498557.294:457958): pid=19687 uid=0 auid=4294967295
ses=4294967295 msg='op=PAM:session_open
grantors=pam_keyinit,pam_limits,pam_keyinit,pam_limits,pam_tty_audit,pam_systemd,pam_unix
acct="root" exe="/usr/bin/sudo" hostname=? addr=? terminal=? res=success'
Jul 30 15:55:57 x audispd: node=x. type=USER_START
msg=audit(1564498557.298:457959): pid=19690 uid=0 auid=4294967295
ses=4294967295 msg='op=PAM:session_open
grantors=pam_keyinit,pam_systemd,pam_keyinit,pam_limits,pam_unix
acct="cass_b" exe="/usr/sbin/runuser" hostname=? addr=? terminal=?
res=success'
Jul 30 15:55:58 x systemd: Removed slice User Slice of root.
Jul 30 15:56:02 x cassandra: INFO  14:56:02 Writing
Memtable-compactions_in_progress@1532791194(0.008KiB serialized bytes, 1
ops, 0%/0% of on/off-heap limit)
Jul 30 15:56:02 x cassandra: INFO  14:56:02 Cannot perform a full major
compaction as repaired and unrepaired sstables cannot be compacted
together. These two set of sstables will be compacted separately.
Jul 30 15:56:02 x cassandra: INFO  14:56:02 Writing
Memtable-compactions_in_progress@1455399453(0.281KiB serialized bytes, 16
ops, 0%/0% of on/off-heap limit)
Jul 30 15:56:04 x tag_audit_log: type=USER_CMD
msg=audit(1564498555.190:457951): pid=19294 uid=509 auid=4294967295
ses=4294967295 msg='cwd="/"
cmd=72756E75736572202D73202F62696E2F62617368202D6C20636173735F62202D632063617373616E6472612D6D6574612F63617373616E6472612F62696E2F6E6F6465746F6F6C2074707374617473
terminal=? res=success'



We have checked a number of other things like NTP setting etc but nothing
is telling us what could cause so many corruptions across the entire
cluster.
Things were healthy with this cluster for months, the only thing I can
think is that we started loading data from a load of 20GB per instance up
to 200GB where it sits now, maybe this just highlighted the issue.



Compaction and Compression on Keyspace CL's [mixture]
All CF's are using compression.

AND compaction = {'min_threshold': '4', 'class':
'org.apache.cassandra.db.compaction.*SizeTieredCompactionStrategy*',
'max_threshold': '32'}
AND compression = {'sstable_compression': 'org.apache.cassandra.io.compress.
*SnappyCompressor*'}

AND compaction = {'min_threshold': '4', 'class':
'org.apache.cassandra.db.compaction.*SizeTieredCompactionStrategy*',
'max_threshold': '32'}
AND compression = {'sstable_compression': 'org.apache.cassandra.io.compress.
*LZ4Compressor*'}

AND compaction = {'class': 'org.apache.cassandra.db.compaction.
*LeveledCompactionStrategy*'}
AND compression = {'sstable_compression': 'org.apache.cassandra.io.compress.
*SnappyCompressor*'}

--We are also using internode network compression:
internode_compression: all



Does anyone have any idea what I should check next?
Our next theory is that there may be an issue with Checksum, but I'm not
sure where to go with this.

Any help would be very much appreciated before I lose the last bit of hair
I have on my head.

Kind Regards,
Phil

On Wed, 7 Aug 2019 at 20:51, Nitan Kainth <nitankainth@gmail.com> wrote:

> Repair during upgrade have caused corruption too.
>
> Also, dropping and adding columns with same name but different type
>
>
> Regards,
>
> Nitan
>
> Cell: 510 449 9629
>
> On Aug 7, 2019, at 2:42 PM, Jeff Jirsa <jjirsa@gmail.com> wrote:
>
> Is compression enabled?
>
> If not, bit flips on disk can corrupt data files and reads + repair may
> send that corruption to other hosts in the cluster
>
>
> On Aug 7, 2019, at 3:46 AM, Philip Ó Condúin <philipoconduin@gmail.com>
> wrote:
>
> Hi All,
>
> I am currently experiencing multiple datafile corruptions across most
> nodes in my cluster, there seems to be no pattern to the corruption.  I'm
> starting to think it might be a bug, we're using Cassandra 2.2.13.
>
> Without going into detail about the issue I just want to confirm something.
>
> Can someone share with me a list of scenarios that would cause corruption?
>
> 1. OS failure
> 2. Cassandra disturbed during the writing
>
> etc etc.
>
> I need to investigate each scenario and don't want to leave any out.
>
> --
> Regards,
> Phil
>
>

-- 
Regards,
Phil

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