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    <title>MongoDB Jira</title>
    <link>https://jira.mongodb.org</link>
    <description>This file is an XML representation of an issue</description>
    <language>en-us</language>    <build-info>
        <version>9.7.1</version>
        <build-number>970001</build-number>
        <build-date>13-04-2023</build-date>
    </build-info>


<item>
            <title>[SERVER-3751] mongodb crashing on repairDatabase</title>
                <link>https://jira.mongodb.org/browse/SERVER-3751</link>
                <project id="10000" key="SERVER">Core Server</project>
                    <description>&lt;p&gt;we have a replica set of 3.&lt;br/&gt;
we can run repairdatabase on master 1 and it works fine&lt;br/&gt;
we stepdown 1&lt;br/&gt;
2 becomes master&lt;br/&gt;
when we attempt to repairdatabase on 2&lt;br/&gt;
it restarts&lt;/p&gt;

&lt;p&gt;PRIMARY&amp;gt; db.repairDatabase();&lt;br/&gt;
{&lt;br/&gt;
        &quot;errmsg&quot; : &quot;exception: nextSafe(): &lt;/p&gt;
{ $err: \&quot;not master and slaveok=false\&quot;, code: 13435 }
&lt;p&gt;&quot;,&lt;br/&gt;
        &quot;code&quot; : 13106,&lt;br/&gt;
        &quot;ok&quot; : 0&lt;br/&gt;
}&lt;br/&gt;
SECONDARY&amp;gt;&lt;/p&gt;

&lt;p&gt;so it looks like it crashed and failed over to 1 again&lt;/p&gt;

&lt;p&gt;looked at the logs and we see&lt;/p&gt;

&lt;p&gt;Fri Sep 02 12:55:45 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; warning: ClientCursor::yield can&apos;t unlock b/c of recursive lock ns: pr_blue_spruce.sessions top: { opid: 63, active: true, lockType: &quot;write&quot;, waitingForLock: false, secs_running: 68, op: &quot;query&quot;, ns: &quot;pr_blue_spruce&quot;, query: &lt;/p&gt;
{ repairDatabase: 1.0 }
&lt;p&gt;, client: &quot;127.0.0.1:53667&quot;, desc: &quot;conn&quot;, msg: &quot;index: (3/3) btree-middle&quot;, numYields: 0 }&lt;br/&gt;
Fri Sep 02 12:55:45 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; warning: ClientCursor::yield can&apos;t unlock b/c of recursive lock ns: pr_blue_spruce.sessions top: { opid: 63, active: true, lockType: &quot;write&quot;, waitingForLock: false, secs_running: 68, op: &quot;query&quot;, ns: &quot;pr_blue_spruce&quot;, query: &lt;/p&gt;
{ repairDatabase: 1.0 }
&lt;p&gt;, client: &quot;127.0.0.1:53667&quot;, desc: &quot;conn&quot;, msg: &quot;index: (3/3) btree-middle&quot;, numYields: 0 }&lt;br/&gt;
Fri Sep 02 12:55:45 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; warning: ClientCursor::yield can&apos;t unlock b/c of recursive lock ns: pr_blue_spruce.sessions top: { opid: 63, active: true, lockType: &quot;write&quot;, waitingForLock: false, secs_running: 68, op: &quot;query&quot;, ns: &quot;pr_blue_spruce&quot;, query: &lt;/p&gt;
{ repairDatabase: 1.0 }
&lt;p&gt;, client: &quot;127.0.0.1:53667&quot;, desc: &quot;conn&quot;, msg: &quot;index: (3/3) btree-middle&quot;, numYields: 0 }&lt;/p&gt;

&lt;p&gt;then it keeps failing on startup and we see this exception&lt;/p&gt;

&lt;p&gt;Fri Sep 02 12:55:57 &lt;span class=&quot;error&quot;&gt;&amp;#91;websvr&amp;#93;&lt;/span&gt; User Assertion: 13142:timeout getting readlock&lt;br/&gt;
Fri Sep 02 12:55:57 &lt;span class=&quot;error&quot;&gt;&amp;#91;websvr&amp;#93;&lt;/span&gt; Socket http response send() errno:0 The operation completed successfully. 192.168.16.35:36451&lt;br/&gt;
Fri Sep 02 12:55:57 unhandled windows exception&lt;br/&gt;
Fri Sep 02 12:55:57 ec=0xe06d7363&lt;br/&gt;
Fri Sep 02 12:55:57 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt;   external sort used : 4 files  in 11 secs&lt;br/&gt;
Fri Sep 02 12:55:57 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; New namespace: pr_blue_spruce.sessions.$&lt;em&gt;id&lt;/em&gt;&lt;br/&gt;
Fri Sep 02 12:55:57 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; allocating new extent for pr_blue_spruce.sessions.$&lt;em&gt;id&lt;/em&gt; padding:1 lenWHdr: 8192&lt;br/&gt;
Fri Sep 02 12:55:57 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; allocating new extent for pr_blue_spruce.sessions.$&lt;em&gt;id&lt;/em&gt; padding:1 lenWHdr: 8192&lt;br/&gt;
Fri Sep 02 12:55:57 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; allocating new extent for pr_blue_spruce.sessions.$&lt;em&gt;id&lt;/em&gt; padding:1 lenWHdr: 8192&lt;br/&gt;
Fri Sep 02 12:55:57 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; allocating new extent for pr_blue_spruce.sessions.$&lt;em&gt;id&lt;/em&gt; padding:1 lenWHdr: 8192&lt;br/&gt;
Fri Sep 02 12:55:57 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; allocating new extent for pr_blue_spruce.sessions.$&lt;em&gt;id&lt;/em&gt; padding:1 lenWHdr: 8192&lt;br/&gt;
Fri Sep 02 12:55:58 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; allocating new extent for pr_blue_spruce.sessions.$&lt;em&gt;id&lt;/em&gt; padding:1 lenWHdr: 8192&lt;br/&gt;
Fri Sep 02 12:55:58 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn16&amp;#93;&lt;/span&gt; run command admin.$cmd &lt;/p&gt;
{ replSetHeartbeat: &quot;prod_rudy&quot;, v: 4, pv: 1, checkEmpty: false, from: &quot;monru02.colo.rrgroup.com:27017&quot; }
&lt;p&gt;Fri Sep 02 12:55:58 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn16&amp;#93;&lt;/span&gt; command admin.$cmd command: &lt;/p&gt;
{ replSetHeartbeat: &quot;prod_rudy&quot;, v: 4, pv: 1, checkEmpty: false, from: &quot;monru02.colo.rrgroup.com:27017&quot; }
&lt;p&gt; ntoreturn:1 reslen:125 0ms&lt;br/&gt;
Fri Sep 02 12:55:58 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn14&amp;#93;&lt;/span&gt; allocating new extent for pr_blue_spruce.sessions.$&lt;em&gt;id&lt;/em&gt; padding:1 lenWHdr: 8192&lt;/p&gt;


&lt;p&gt;we have tried wiping the db folder for 2 and having it resync a few times but the error doesn&apos;t go away.&lt;/p&gt;








</description>
                <environment>windows 64bit 24cpu 48gb ram   san drive</environment>
        <key id="21833">SERVER-3751</key>
            <summary>mongodb crashing on repairDatabase</summary>
                <type id="1" iconUrl="https://jira.mongodb.org/secure/viewavatar?size=xsmall&amp;avatarId=14703&amp;avatarType=issuetype">Bug</type>
                                            <priority id="1" iconUrl="https://jira.mongodb.org/images/icons/priorities/blocker.svg">Blocker - P1</priority>
                        <status id="6" iconUrl="https://jira.mongodb.org/images/icons/statuses/closed.png" description="The issue is considered finished, the resolution is correct. Issues which are closed can be reopened.">Closed</status>
                    <statusCategory id="3" key="done" colorName="success"/>
                                    <resolution id="5">Cannot Reproduce</resolution>
                                        <assignee username="mathias@mongodb.com">Mathias Stearn</assignee>
                                    <reporter username="pbrumm">Pete Brumm</reporter>
                        <labels>
                            <label>crash</label>
                            <label>repair</label>
                            <label>replication</label>
                    </labels>
                <created>Fri, 2 Sep 2011 18:30:59 +0000</created>
                <updated>Wed, 29 Feb 2012 03:53:46 +0000</updated>
                            <resolved>Tue, 31 Jan 2012 18:17:00 +0000</resolved>
                                    <version>2.0.0-rc1</version>
                                                    <component>Replication</component>
                                        <votes>0</votes>
                                    <watches>3</watches>
                                                                                                                <comments>
                            <comment id="83472" author="pbrumm" created="Mon, 30 Jan 2012 21:27:20 +0000"  >&lt;p&gt;I no longer have an environment to test/replicate this in.&lt;/p&gt;</comment>
                            <comment id="83442" author="redbeard0531" created="Mon, 30 Jan 2012 20:23:48 +0000"  >&lt;p&gt;Have you been able to replicate this with 2.0-final or one of the dot releases?&lt;/p&gt;</comment>
                            <comment id="54834" author="pbrumm" created="Fri, 16 Sep 2011 19:37:41 +0000"  >&lt;p&gt;also in the log.  is a crash in replication that I created another ticket for.&lt;/p&gt;

&lt;p&gt;&lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-3891&quot; title=&quot;crash on slave replication&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-3891&quot;&gt;&lt;del&gt;SERVER-3891&lt;/del&gt;&lt;/a&gt;&lt;/p&gt;</comment>
                            <comment id="54829" author="pbrumm" created="Fri, 16 Sep 2011 19:28:26 +0000"  >&lt;p&gt;we made 2 master and sent repairDatabase command&lt;/p&gt;

&lt;p&gt;It took 7 seconds in a 25gb db&lt;/p&gt;

&lt;p&gt;Fri Sep 16 11:55:33 is when the command was sent.&lt;/p&gt;

&lt;p&gt;this is the log&lt;/p&gt;

&lt;p&gt;mongodb_monru02.zip&lt;/p&gt;

</comment>
                            <comment id="54033" author="eliot" created="Wed, 14 Sep 2011 15:23:48 +0000"  >&lt;p&gt;Can you update the logs?&lt;br/&gt;
There were a number of changes.&lt;/p&gt;</comment>
                            <comment id="53989" author="pbrumm" created="Wed, 14 Sep 2011 13:41:50 +0000"  >&lt;p&gt;we upgraded to latest 2.0 release.   and when we do a repairDatabase .   the results return in seconds instead of the many minutes.&lt;/p&gt;

&lt;p&gt;does mongodb doing something differently on repair?&lt;/p&gt;</comment>
                            <comment id="53279" author="pbrumm" created="Fri, 9 Sep 2011 20:42:18 +0000"  >&lt;p&gt;we will give it a shot.   We won&apos;t be able to kick it off until monday though.&lt;/p&gt;</comment>
                            <comment id="53275" author="eliot" created="Fri, 9 Sep 2011 20:31:36 +0000"  >&lt;p&gt;Can you run with -vvvvvvv  &lt;/p&gt;</comment>
                            <comment id="53271" author="pbrumm" created="Fri, 9 Sep 2011 20:16:07 +0000"  >&lt;p&gt;we can reproduce this pretty easily&lt;/p&gt;

&lt;p&gt;if you have a debug build we could try it and report back&lt;/p&gt;</comment>
                            <comment id="52785" author="pbrumm" created="Wed, 7 Sep 2011 15:03:20 +0000"  >&lt;p&gt;disk space was not an issue&lt;/p&gt;

&lt;p&gt;here is the crash from the windows system log&lt;/p&gt;


&lt;p&gt;Faulting application name: mongod.exe, version: 0.0.0.0, time stamp: 0x4e607d02&lt;br/&gt;
Faulting module name: mongod.exe, version: 0.0.0.0, time stamp: 0x4e607d02&lt;br/&gt;
Exception code: 0x40000015&lt;br/&gt;
Fault offset: 0x0000000000287635&lt;br/&gt;
Faulting process id: 0xe2c&lt;br/&gt;
Faulting application start time: 0x01cc6cb7e2182d95&lt;br/&gt;
Faulting application path: c:\mongodb\bin\mongod.exe&lt;br/&gt;
Faulting module path: c:\mongodb\bin\mongod.exe&lt;br/&gt;
Report Id: 0b08ce59-d8ac-11e0-b471-180373f1d279&lt;/p&gt;


</comment>
                            <comment id="52692" author="eliot" created="Tue, 6 Sep 2011 21:53:57 +0000"  >&lt;p&gt;Was there an error in the system log or anywhere else when it crashed?&lt;br/&gt;
In the log you send, it just seems to go away.&lt;br/&gt;
Also, can you verify there is enough disk space&lt;/p&gt;</comment>
                            <comment id="52611" author="pbrumm" created="Tue, 6 Sep 2011 17:36:37 +0000"  >&lt;p&gt;here are the logs with the crash. &lt;/p&gt;

&lt;p&gt;mongodb_logs_20110906.4-crash.zip&lt;/p&gt;


&lt;p&gt;it starts at 12:10 on 03.   &lt;/p&gt;

&lt;p&gt;the other logs are from other replica set boxes and start a little earlier.&lt;/p&gt;

&lt;p&gt;we made 03 master and issued the repairDatabase command.   it took a few minutes then crashed.  and because of a missing file in the repair it continually restarts after first crash.&lt;/p&gt;

&lt;p&gt;we also are using jumbo frames on our switches and run on a vlan  &lt;/p&gt;</comment>
                            <comment id="52329" author="eliot" created="Sat, 3 Sep 2011 03:35:50 +0000"  >&lt;p&gt;I&apos;m not seeing any errors in that log, are things working right now?&lt;/p&gt;</comment>
                            <comment id="52323" author="pbrumm" created="Fri, 2 Sep 2011 23:21:17 +0000"  >&lt;p&gt;this is a log of starting up 2 to sync from 1 and issuing to 1 a stepdown.&lt;/p&gt;

&lt;p&gt;then we opened a console to 2 and issued the repairdatabase&lt;/p&gt;

&lt;p&gt;I need to look at the logs.  this may not show the restart.   just the recursive lock.   will reproduce more on tuesday&lt;/p&gt;</comment>
                            <comment id="52320" author="eliot" created="Fri, 2 Sep 2011 21:40:32 +0000"  >&lt;p&gt;Can you wipe the database again, and send the entire log from when it starts to resync till it hits an error.&lt;/p&gt;</comment>
                            <comment id="52293" author="pbrumm" created="Fri, 2 Sep 2011 18:51:47 +0000"  >&lt;p&gt;even after stopping 1 and copying files to 2 and restarting &lt;/p&gt;

&lt;p&gt;after making 2 master &lt;/p&gt;

&lt;p&gt;and running repairdatabase it returns this&lt;/p&gt;


&lt;ul&gt;
	&lt;li&gt;
	&lt;ul&gt;
		&lt;li&gt;
		&lt;ul&gt;
			&lt;li&gt;
			&lt;ul&gt;
				&lt;li&gt;
				&lt;ul&gt;
					&lt;li&gt;SERVER RESTARTED *****&lt;/li&gt;
				&lt;/ul&gt;
				&lt;/li&gt;
			&lt;/ul&gt;
			&lt;/li&gt;
		&lt;/ul&gt;
		&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
&lt;/ul&gt;



&lt;p&gt;Fri Sep 02 13:45:56 BackgroundJob starting: DataFileSync&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; MongoDB starting : pid=6972 port=27017 dbpath=M:\mongodb\Data\db 64-bit host=MONRU02&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; db version v2.0.0-rc1, pdfile version 4.5&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; git version: b5dd192afa9ad59e45b660f7193e0d80c59dc6d5&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; build info: windows (6, 1, 7601, 2, &apos;Service Pack 1&apos;) BOOST_LIB_VERSION=1_42&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; options: &lt;/p&gt;
{ config: &quot;c:\mongodb\bin\mongodb.conf&quot;, dbpath: &quot;M:\mongodb\Data\db&quot;, journal: &quot;true&quot;, logappend: &quot;true&quot;, logpath: &quot;M:\mongodb\logs\mongodb.log&quot;, oplogSize: 16384, pidfilepath: &quot;C:\mongodb\bin\mongodb.pid&quot;, replSet: &quot;prod_rudy&quot;, rest: &quot;true&quot;, service: true, verbose: &quot;true&quot; }
&lt;p&gt;Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; journal dir=M:/mongodb/Data/db/journal&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; recover begin&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; recover lsn: 192033&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; recover M:/mongodb/Data/db/journal/j._2&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; recover skipping application of section seq:115311 &amp;lt; lsn:192033&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; recover skipping application of section seq:153781 &amp;lt; lsn:192033&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; recover M:/mongodb/Data/db/journal/j._3&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; exception during recovery&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; exception in initAndListen std::exception: boost::filesystem::file_size: The system cannot find the path specified: &quot;M:\mongodb\Data\db\$tmp_repairDatabase_0\pr_blue_spruce.ns&quot;, terminating&lt;br/&gt;
Fri Sep 02 13:45:56 dbexit: &lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; shutdown: going to close listening sockets...&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; shutdown: going to flush diaglog...&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; shutdown: going to close sockets...&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; shutdown: waiting for fs preallocator...&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; shutdown: lock for final commit...&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; shutdown: final commit...&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; shutdown: closing all files...&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; closeAllFiles() finished&lt;br/&gt;
Fri Sep 02 13:45:56 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; shutdown: removing fs lock...&lt;br/&gt;
Fri Sep 02 13:45:56 dbexit: really exiting now&lt;/p&gt;

</comment>
                    </comments>
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                                        <issuelink>
            <issuekey id="22459">SERVER-3891</issuekey>
        </issuelink>
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                <attachments>
                            <attachment id="12964" name="mongodb_logs_20110906.4-crash.zip" size="317876" author="pbrumm" created="Tue, 6 Sep 2011 17:36:37 +0000"/>
                            <attachment id="13180" name="mongodb_monru02.zip" size="99270" author="pbrumm" created="Fri, 16 Sep 2011 19:28:26 +0000"/>
                            <attachment id="12952" name="mongodb_repairdatabase.log" size="17435240" author="pbrumm" created="Fri, 2 Sep 2011 23:21:17 +0000"/>
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