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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-16642] Error repairing database</title>
                <link>https://jira.mongodb.org/browse/SERVER-16642</link>
                <project id="10000" key="SERVER">Core Server</project>
                    <description>&lt;p&gt;Hi Team , &lt;/p&gt;

&lt;p&gt;Could you advise how can I track on the issue ?&lt;/p&gt;

&lt;p&gt;I am doing an incremental backup on the database , but failed when fetching the oplogs , so I run the repair command and fails again.&lt;br/&gt;
below is the error message.&lt;/p&gt;


&lt;p&gt;2014-12-23T13:53:44.007+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;FileAllocator&amp;#93;&lt;/span&gt; allocating new datafile /home/ISH/Data/_tmp_repairDatabase_0/local/local.41, filling with zeroes...&lt;br/&gt;
2014-12-23T13:53:44.023+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;FileAllocator&amp;#93;&lt;/span&gt; done allocating datafile /home/ISH/Data/_tmp_repairDatabase_0/local/local.41, size: 2047MB,  took 0.016 secs&lt;br/&gt;
2014-12-23T13:53:44.024+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;FileAllocator&amp;#93;&lt;/span&gt; allocating new datafile /home/ISH/Data/_tmp_repairDatabase_0/local/local.42, filling with zeroes...&lt;br/&gt;
2014-12-23T13:53:44.059+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;FileAllocator&amp;#93;&lt;/span&gt; done allocating datafile /home/ISH/Data/_tmp_repairDatabase_0/local/local.42, size: 2047MB,  took 0.034 secs&lt;br/&gt;
2014-12-23T13:53:44.108+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; warning Listener::getElapsedTimeMillis returning 0ms&lt;br/&gt;
2014-12-23T13:53:44.174+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; warning Listener::getElapsedTimeMillis returning 0ms&lt;br/&gt;
2014-12-23T13:53:44.245+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; Assertion: 10334:BSONObj size: 1634624622 (0x616E646E) is invalid. Size must be between 0 and 16793600(16MB) First element: e: ?type=109&lt;br/&gt;
2014-12-23T13:53:44.332+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; local.oplog.rs 0x11e6111 0x1187e49 0x116c9f6 0x116cf4c 0x77329b 0x8b6d28 0xe016bf 0x767d4e 0x76aa0c 0x76c62f 0x76cedb 0x76d475 0x76d699 0x31dc81ed1d 0x764329 &lt;br/&gt;
 mongod(_ZN5mongo15printStackTraceERSo+0x21) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x11e6111&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod(_ZN5mongo10logContextEPKc+0x159) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x1187e49&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod(_ZN5mongo11msgassertedEiPKc+0xe6) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x116c9f6&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod() &lt;span class=&quot;error&quot;&gt;&amp;#91;0x116cf4c&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod(_ZNK5mongo7BSONObj14_assertInvalidEv+0x41b) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x77329b&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod(_ZN5mongo10Collection6docForERKNS_7DiskLocE+0x68) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x8b6d28&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod(_ZN5mongo14repairDatabaseESsbb+0x24ef) &lt;span class=&quot;error&quot;&gt;&amp;#91;0xe016bf&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod(_ZN5mongo11doDBUpgradeERKSsPNS_14DataFileHeaderE+0x5e) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x767d4e&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod() &lt;span class=&quot;error&quot;&gt;&amp;#91;0x76aa0c&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod(_ZN5mongo14_initAndListenEi+0x5df) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x76c62f&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod(_ZN5mongo13initAndListenEi+0x1b) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x76cedb&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod() &lt;span class=&quot;error&quot;&gt;&amp;#91;0x76d475&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod(main+0x9) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x76d699&amp;#93;&lt;/span&gt;&lt;br/&gt;
 /lib64/libc.so.6(__libc_start_main+0xfd) &lt;span class=&quot;error&quot;&gt;&amp;#91;0x31dc81ed1d&amp;#93;&lt;/span&gt;&lt;br/&gt;
 mongod() &lt;span class=&quot;error&quot;&gt;&amp;#91;0x764329&amp;#93;&lt;/span&gt;&lt;br/&gt;
2014-12-23T13:53:44.341+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; cleaning up failed repair db: local path: /home/ISH/Data/_tmp_repairDatabase_0&lt;br/&gt;
2014-12-23T13:53:46.279+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; exception in initAndListen: 10334 BSONObj size: 1634624622 (0x616E646E) is invalid. Size must be between 0 and 16793600(16MB) First element: e: ?type=109, terminating&lt;br/&gt;
2014-12-23T13:53:46.279+0800 &lt;span class=&quot;error&quot;&gt;&amp;#91;initandlisten&amp;#93;&lt;/span&gt; dbexit: &lt;/p&gt;


&lt;p&gt;Thanks in Advance&lt;/p&gt;

&lt;p&gt;Carl Dong&lt;/p&gt;</description>
                <environment></environment>
        <key id="175901">SERVER-16642</key>
            <summary>Error repairing database</summary>
                <type id="6" iconUrl="https://jira.mongodb.org/secure/viewavatar?size=xsmall&amp;avatarId=14720&amp;avatarType=issuetype">Question</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="9">Done</resolution>
                                        <assignee username="ramon.fernandez@mongodb.com">Ramon Fernandez Marina</assignee>
                                    <reporter username="carl.dong@windfindtech.com">carl dong</reporter>
                        <labels>
                    </labels>
                <created>Tue, 23 Dec 2014 06:18:52 +0000</created>
                <updated>Thu, 8 Jan 2015 22:33:13 +0000</updated>
                            <resolved>Thu, 8 Jan 2015 22:33:13 +0000</resolved>
                                    <version>2.4.9</version>
                    <version>2.6.4</version>
                                                    <component>Storage</component>
                                        <votes>0</votes>
                                    <watches>3</watches>
                                                                                                                <comments>
                            <comment id="800658" author="ramon.fernandez" created="Thu, 8 Jan 2015 22:32:46 +0000"  >&lt;p&gt;Thanks for the update &lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=carl.dong%40windfindtech.com&quot; class=&quot;user-hover&quot; rel=&quot;carl.dong@windfindtech.com&quot;&gt;carl.dong@windfindtech.com&lt;/a&gt;, happy to hear that your replica set is working well again.&lt;/p&gt;

&lt;p&gt;I forgot to ask whether you would have considered uploading your database files; in the absence of system logs pointing to storage issues, analyzing the database files may help determine how the BSON corruption happened. Note also that if this was a hardware issue and you didn&apos;t replace your storage the issue may appear again. If that happens feel free to re-open this ticket.&lt;/p&gt;

&lt;p&gt;Regards,&lt;br/&gt;
Ram&#243;n.&lt;/p&gt;</comment>
                            <comment id="798655" author="carl.dong@windfindtech.com" created="Wed, 7 Jan 2015 01:38:57 +0000"  >&lt;p&gt;I don&apos;t find any disk error meessage in my system log , so I remove all data files and sync from another node , now my DB works fine .&lt;/p&gt;

&lt;p&gt;Thanks for your help .&lt;/p&gt;</comment>
                            <comment id="798401" author="ramon.fernandez" created="Tue, 6 Jan 2015 20:19:29 +0000"  >&lt;p&gt;&lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=carl.dong%40windfindtech.com&quot; class=&quot;user-hover&quot; rel=&quot;carl.dong@windfindtech.com&quot;&gt;carl.dong@windfindtech.com&lt;/a&gt;, something that may help would be to search the system logs for error messages pointing to disk issues. That way we can be sure we&apos;ve found the true cause of the problem. Can you please take a look at your system logs and post any error messages you may find?&lt;/p&gt;</comment>
                            <comment id="797346" author="ramon.fernandez" created="Mon, 5 Jan 2015 18:59:42 +0000"  >&lt;p&gt;&lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=carl.dong%40windfindtech.com&quot; class=&quot;user-hover&quot; rel=&quot;carl.dong@windfindtech.com&quot;&gt;carl.dong@windfindtech.com&lt;/a&gt;, the error message is indicative of data corruption on disk, often caused by flaky storage. At this stage you may need to re-sync from a healthy node after making sure your storage is healthy.&lt;/p&gt;</comment>
                            <comment id="796555" author="carl.dong@windfindtech.com" created="Sun, 4 Jan 2015 03:50:41 +0000"  >&lt;p&gt;Anyone advise on the issue ? &lt;/p&gt;</comment>
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