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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>
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<item>
            <title>[SERVER-12375] Improper file access</title>
                <link>https://jira.mongodb.org/browse/SERVER-12375</link>
                <project id="10000" key="SERVER">Core Server</project>
                    <description>&lt;p&gt;Attempting to use a db with approximately 50 collections using 604GB of disk space.  Running db.stats() abruptly fails along with clients going into a &quot;waiting&quot; state. &lt;/p&gt;

&lt;p&gt;/var/log/mongodb/mongo.log includes the line:&lt;br/&gt;
&lt;span class=&quot;error&quot;&gt;&amp;#91;conn1&amp;#93;&lt;/span&gt;        getFile(304) _files.size:304 /var/lib/mongodb/preannotation.304&lt;/p&gt;

&lt;p&gt;That file doesn&apos;t exist:&lt;/p&gt;

&lt;p&gt;mongodb@stsia0408:/var/log/mongodb&amp;gt; ls /var/lib/mongodb/preannotation.30*&lt;br/&gt;
/var/lib/mongodb/preannotation.30   /var/lib/mongodb/preannotation.301  /var/lib/mongodb/preannotation.303&lt;br/&gt;
/var/lib/mongodb/preannotation.300  /var/lib/mongodb/preannotation.302&lt;/p&gt;

&lt;p&gt;Wed Jan 15 17:06:30.062 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; MongoDB starting : pid=15707 port=27017 dbpath=/var/lib/mongodb 64-bit host=stsia0408&lt;br/&gt;
Wed Jan 15 17:06:30.062 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; db version v2.4.3&lt;br/&gt;
Wed Jan 15 17:06:30.062 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; git version: nogitversion&lt;br/&gt;
Wed Jan 15 17:06:30.062 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; build info: Linux stsia0508 2.6.34-12-desktop #1 SMP PREEMPT 2010-06-29 02:39:08 +0200 x86_64 BOOST_LIB_VERSION=1_49&lt;br/&gt;
Wed Jan 15 17:06:30.062 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; allocator: tcmalloc&lt;br/&gt;
Wed Jan 15 17:06:30.062 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; options: &lt;/p&gt;
{ config: &quot;/etc/mongodb.conf&quot;, dbpath: &quot;/var/lib/mongodb&quot;, fork: &quot;true&quot;, logappend: &quot;true&quot;, logpath: &quot;/var/log/mongodb/mongodb.log&quot;, nohttpinterface: &quot;true&quot;, oplogSize: 8192, quiet: true }
&lt;p&gt;Wed Jan 15 17:06:30.073 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; journal dir=/var/lib/mongodb/journal&lt;br/&gt;
Wed Jan 15 17:06:30.073 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; recover : no journal files present, no recovery needed&lt;br/&gt;
Wed Jan 15 17:06:30.113 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; waiting for connections on port 27017&lt;br/&gt;
Wed Jan 15 17:06:42.119 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn1&amp;#93;&lt;/span&gt; error: getFile() called in a read lock, yet file to return is not yet open&lt;br/&gt;
Wed Jan 15 17:06:42.120 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn1&amp;#93;&lt;/span&gt;        getFile(304) _files.size:304 /var/lib/mongodb/preannotation.304&lt;br/&gt;
Wed Jan 15 17:06:42.120 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn1&amp;#93;&lt;/span&gt;        context ns: preannotation.&lt;br/&gt;
Wed Jan 15 17:06:42.120 &lt;span class=&quot;error&quot;&gt;&amp;#91;conn1&amp;#93;&lt;/span&gt;  preannotation. Assertion failure false src/mongo/db/database.cpp 300&lt;br/&gt;
0xda0006 0xd48e6f 0x8f6577 0x8e2d92 0xa899ae 0x9087d5 0x8fe52f 0x90032a 0x900d1b 0xaa2a8a 0xaa72e4 0xa2d1b1 0x73a131 0xd82520 0x7f65530d0a4f 0x7f6551eaf82d&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo15printStackTraceERSo+0x26) &lt;span class=&quot;error&quot;&gt;&amp;#91;0xda0006&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo12verifyFailedEPKcS1_j+0xbf) &lt;span class=&quot;error&quot;&gt;&amp;#91;0xd48e6f&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo8Database7getFileEiib+0x317) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x8f6577&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo11DataFileMgr9getExtentERKNS_7DiskLocE+0x42) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x8e2d92&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZNK5mongo16NamespaceDetails11storageSizeEPiPNS_16BSONArrayBuilderE+0x1e) &lt;span class=&quot;error&quot;&gt;&amp;#91;0xa899ae&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo7DBStats3runERKSsRNS_7BSONObjEiRSsRNS_14BSONObjBuilderEb+0x2d5) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x9087d5&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo12_execCommandEPNS_7CommandERKSsRNS_7BSONObjEiRSsRNS_14BSONObjBuilderEb+0x2f) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x8fe52f&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo7Command11execCommandEPS0_RNS_6ClientEiPKcRNS_7BSONObjERNS_14BSONObjBuilderEb+0xb4a) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x90032a&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo12_runCommandsEPKcRNS_7BSONObjERNS_11_BufBuilderINS_16TrivialAllocatorEEERNS_14BSONObjBuilderEbi+0x5bb) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x900d1b&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo11runCommandsEPKcRNS_7BSONObjERNS_5CurOpERNS_11_BufBuilderINS_16TrivialAllocatorEEERNS_14BSONObjBuilderEbi+0x3a) &lt;span class=&quot;error&quot;&gt;&amp;#91;0xaa2a8a&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(&lt;em&gt;ZN5mongo8runQueryERNS_7MessageERNS_12QueryMessageERNS_5CurOpES1&lt;/em&gt;+0xce4) &lt;span class=&quot;error&quot;&gt;&amp;#91;0xaa72e4&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo16assembleResponseERNS_7MessageERNS_10DbResponseERKNS_11HostAndPortE+0xc91) &lt;span class=&quot;error&quot;&gt;&amp;#91;0xa2d1b1&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo16MyMessageHandler7processERNS_7MessageEPNS_21AbstractMessagingPortEPNS_9LastErrorE+0xd1) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x73a131&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /usr/sbin/mongod(_ZN5mongo17PortMessageServer17handleIncomingMsgEPv+0x480) &lt;span class=&quot;error&quot;&gt;&amp;#91;0xd82520&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /lib64/libpthread.so.0(+0x6a4f) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x7f65530d0a4f&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /lib64/libc.so.6(clone+0x6d) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x7f6551eaf82d&amp;#93;&lt;/span&gt;&lt;/p&gt;</description>
                <environment>Linux stsia0408 2.6.34-12-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux (suse)</environment>
        <key id="106281">SERVER-12375</key>
            <summary>Improper file access</summary>
                <type id="1" iconUrl="https://jira.mongodb.org/secure/viewavatar?size=xsmall&amp;avatarId=14703&amp;avatarType=issuetype">Bug</type>
                                            <priority id="3" iconUrl="https://jira.mongodb.org/images/icons/priorities/major.svg">Major - P3</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="-1">Unassigned</assignee>
                                    <reporter username="bill@scripps">Bill Shipman</reporter>
                        <labels>
                            <label>database.cpp</label>
                            <label>files,</label>
                            <label>server</label>
                    </labels>
                <created>Thu, 16 Jan 2014 01:23:59 +0000</created>
                <updated>Wed, 10 Dec 2014 23:18:07 +0000</updated>
                            <resolved>Thu, 3 Jul 2014 17:34:42 +0000</resolved>
                                    <version>2.4.3</version>
                                                    <component>Storage</component>
                                        <votes>0</votes>
                                    <watches>3</watches>
                                                                                                                <comments>
                            <comment id="647656" author="thomasr" created="Thu, 3 Jul 2014 17:34:42 +0000"  >&lt;p&gt;Hi Bill, &lt;/p&gt;

&lt;p&gt;as mentioned I&apos;m resolving this as &quot;cannot reproduce&quot; since we don&apos;t have enough information to diagnose. Please feel free to re-open the issue if this should happen again. &lt;/p&gt;

&lt;p&gt;Thanks,&lt;br/&gt;
Thomas&lt;/p&gt;</comment>
                            <comment id="635696" author="thomasr" created="Thu, 26 Jun 2014 22:10:17 +0000"  >&lt;p&gt;Hi Bill,&lt;/p&gt;

&lt;p&gt;Thanks for your additional input. Unfortunately, without any more details it&apos;s hard to track down the issue. Has this happened again since? If not, I think we have to mark the ticket as &quot;cannot reproduce&quot; for now, and you can re-open it if the problem appears again and you are able to collect fresh information.&lt;/p&gt;

&lt;p&gt;Thanks,&lt;br/&gt;
Thomas&lt;/p&gt;</comment>
                            <comment id="635547" author="bill@scripps" created="Thu, 26 Jun 2014 20:52:13 +0000"  >&lt;p&gt;It seems like we ran the repair tool maybe twice and it cleared it up.  At this point I don&apos;t clearly recall what we did. Looking in my email from January it looks like we first ran a repair and then a ? mongodump repair ?&lt;/p&gt;

&lt;p&gt;No nothing should have purged that file, it&apos;s in a limited access file tree on a machine with only 3 users in total.  Myself, another programmer and the sysadmin.  It is configured as a high availability replication cluster so that would have been the only thing migrating data other than a few (&amp;lt;10) processes doing inserts on the master but those are heavy loads.&lt;/p&gt;
</comment>
                            <comment id="635503" author="thomasr" created="Thu, 26 Jun 2014 20:30:31 +0000"  >&lt;p&gt;Hi Bill,&lt;/p&gt;

&lt;p&gt;Sorry for the delay on this issue. It appears that the file /var/lib/mongodb/preannotation.304 was deleted somehow, as it doesn&apos;t show up on the &lt;tt&gt;ls&lt;/tt&gt; anymore. I&apos;m not aware of any reports of files being deleted due to a bug caused by MongoDB. Are you aware of anything that could have deleted the file? Any data migration, permission issues etc?&lt;/p&gt;

&lt;p&gt;Have you recovered from this situation since reporting this?&lt;/p&gt;

&lt;p&gt;Regards,&lt;br/&gt;
Thomas&lt;/p&gt;</comment>
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