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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-19815] Improved mongod --repair option for WiredTiger</title>
                <link>https://jira.mongodb.org/browse/SERVER-19815</link>
                <project id="10000" key="SERVER">Core Server</project>
                    <description>&lt;div class=&quot;panel&quot; style=&quot;background-color: #EEEEEE;border-color: #ccc;border-width: 1px;&quot;&gt;&lt;div class=&quot;panelHeader&quot; style=&quot;border-bottom-width: 1px;border-bottom-color: #ccc;background-color: #6CB33F;&quot;&gt;&lt;b&gt;Issue Status as of October 1st, 2018&lt;/b&gt;&lt;/div&gt;&lt;div class=&quot;panelContent&quot; style=&quot;background-color: #EEEEEE;&quot;&gt;
&lt;p&gt;&lt;b&gt;ISSUE DESCRIPTION AND IMPACT&lt;/b&gt;&lt;br/&gt;
The &lt;tt&gt;mongod --repair&lt;/tt&gt; option was originally introduced for use with the MMAP storage engine; when it is used with WiredTiger, attempts to recover a corrupted &lt;tt&gt;dbpath&lt;/tt&gt; via &lt;tt&gt;mongod --repair&lt;/tt&gt; may fail under a number of specific scenarios.&lt;br/&gt;
Enhanced repair functionality allows &lt;tt&gt;mongod --repair&lt;/tt&gt; to successfully recover from a wider variety of faulty conditions that previously would have resulted in a repair failure. It&#8217;s important to note that these changes do not allow the &lt;tt&gt;mongod&lt;/tt&gt; to recover otherwise unretrievable data; instead, they ensure that the data set is returned to a working state with as much data as the process was able to salvage. &lt;br/&gt;
In addition to a more robust repair mechanism, this change adds the following new behavior:&lt;/p&gt;

&lt;ul class=&quot;alternate&quot; type=&quot;square&quot;&gt;
	&lt;li&gt;If the repair operation modifies data for a node in a replica set, it will not be able to rejoin the replica set until it has been fully resynced.  This behavior is designed to prevent an instance where a node with only partial data recovered via &lt;tt&gt;mongod --repair&lt;/tt&gt; could potentially become a replica set primary, as this would result in data effectively going missing.&lt;/li&gt;
	&lt;li&gt;If a repair operation fails for any reason, the node will not be able to start up again without the &lt;tt&gt;mongod --repair&lt;/tt&gt; option. This precaution is included to prevent instances where the &lt;tt&gt;mongod&lt;/tt&gt; is repeatedly restarted with a broken data set, potentially resulting in additional data corruption.&lt;/li&gt;
&lt;/ul&gt;


&lt;p&gt;&lt;b&gt;DIAGNOSIS AND AFFECTED VERSIONS&lt;/b&gt;&lt;br/&gt;
This issue is exhibited whenever a &lt;tt&gt;mongod --repair&lt;/tt&gt; command fails to start the &lt;tt&gt;mongod&lt;/tt&gt; and instead returns an error message. There are several error messages than can be returned - some of the most common:&lt;/p&gt;
&lt;p/&gt;
&lt;div id=&quot;syntaxplugin&quot; class=&quot;syntaxplugin&quot; style=&quot;border: 1px dashed #bbb; border-radius: 5px !important; overflow: auto; max-height: 30em;&quot;&gt;
&lt;table cellspacing=&quot;0&quot; cellpadding=&quot;0&quot; border=&quot;0&quot; width=&quot;100%&quot; style=&quot;font-size: 1em; line-height: 1.4em !important; font-weight: normal; font-style: normal; color: black;&quot;&gt;
		&lt;tbody &gt;
				&lt;tr id=&quot;syntaxplugin_code_and_gutter&quot;&gt;
						&lt;td  style=&quot; line-height: 1.4em !important; padding: 0em; vertical-align: top;&quot;&gt;
					&lt;pre style=&quot;font-size: 1em; margin: 0 10px;  margin-top: 10px;   margin-bottom: 10px;  width: auto; padding: 0;&quot;&gt;&lt;span style=&quot;color: black; font-family: &apos;Consolas&apos;, &apos;Bitstream Vera Sans Mono&apos;, &apos;Courier New&apos;, Courier, monospace !important;&quot;&gt;Fatal Assertion 28558 at src\mongo\db\storage\wiredtiger\wiredtiger_util.cpp &lt;/span&gt;&lt;/pre&gt;
			&lt;/td&gt;
		&lt;/tr&gt;
			&lt;/tbody&gt;
&lt;/table&gt;
&lt;/div&gt;
&lt;p/&gt;
&lt;p/&gt;
&lt;div id=&quot;syntaxplugin&quot; class=&quot;syntaxplugin&quot; style=&quot;border: 1px dashed #bbb; border-radius: 5px !important; overflow: auto; max-height: 30em;&quot;&gt;
&lt;table cellspacing=&quot;0&quot; cellpadding=&quot;0&quot; border=&quot;0&quot; width=&quot;100%&quot; style=&quot;font-size: 1em; line-height: 1.4em !important; font-weight: normal; font-style: normal; color: black;&quot;&gt;
		&lt;tbody &gt;
				&lt;tr id=&quot;syntaxplugin_code_and_gutter&quot;&gt;
						&lt;td  style=&quot; line-height: 1.4em !important; padding: 0em; vertical-align: top;&quot;&gt;
					&lt;pre style=&quot;font-size: 1em; margin: 0 10px;  margin-top: 10px;   margin-bottom: 10px;  width: auto; padding: 0;&quot;&gt;&lt;span style=&quot;color: black; font-family: &apos;Consolas&apos;, &apos;Bitstream Vera Sans Mono&apos;, &apos;Courier New&apos;, Courier, monospace !important;&quot;&gt;WiredTiger.wt: encountered an illegal file format or internal value&lt;/span&gt;&lt;/pre&gt;
			&lt;/td&gt;
		&lt;/tr&gt;
			&lt;/tbody&gt;
&lt;/table&gt;
&lt;/div&gt;
&lt;p/&gt;
&lt;p&gt;While these are only some of the most common, &lt;b&gt;most&lt;/b&gt; &lt;tt&gt;mongod --repair&lt;/tt&gt; operations that fail to boot the &lt;tt&gt;mongod&lt;/tt&gt; exhibit this issue. &lt;br/&gt;
This issue affects MongoDB versions 3.0 - 4.0.2 that use the WiredTiger storage engine.&lt;/p&gt;

&lt;p&gt;&lt;b&gt;REMEDIATION AND WORKAROUNDS&lt;/b&gt;&lt;br/&gt;
Currently, the only workaround available is to &lt;a href=&quot;https://docs.mongodb.com/manual/tutorial/resync-replica-set-member/&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;resync from a healthy node in a replica set&lt;/a&gt;, restore the &lt;tt&gt;dbpath&lt;/tt&gt; from an earlier backup, or open a &lt;a href=&quot;https://jira.mongodb.org/projects/SERVER/issues/&quot; class=&quot;external-link&quot; rel=&quot;nofollow&quot;&gt;SERVER project ticket&lt;/a&gt; to request a manual repair attempt of the WiredTiger metadata files. &lt;/p&gt;

&lt;p&gt;&lt;b&gt;FIX VERSIONS&lt;/b&gt;&lt;br/&gt;
This issue is fixed in MongoDB 4.0.3 as well as in 4.1.4, and will be available in the 4.2 production release. &lt;/p&gt;
&lt;/div&gt;&lt;/div&gt;

&lt;h6&gt;&lt;a name=&quot;Originaldescription&quot;&gt;&lt;/a&gt;Original description&lt;/h6&gt;

&lt;p&gt;The repair loop should be more forgiving about failures such as missing files and deal with collections or indexes missing from the catalog with a big warning message.&lt;/p&gt;</description>
                <environment></environment>
        <key id="224556">SERVER-19815</key>
            <summary>Improved mongod --repair option for WiredTiger</summary>
                <type id="4" iconUrl="https://jira.mongodb.org/secure/viewavatar?size=xsmall&amp;avatarId=14710&amp;avatarType=issuetype">Improvement</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="louis.williams@mongodb.com">Louis Williams</assignee>
                                    <reporter username="michael.cahill@mongodb.com">Michael Cahill</reporter>
                        <labels>
                            <label>nyc</label>
                    </labels>
                <created>Thu, 6 Aug 2015 23:12:14 +0000</created>
                <updated>Wed, 22 Jun 2022 17:44:28 +0000</updated>
                            <resolved>Tue, 18 Sep 2018 17:14:10 +0000</resolved>
                                    <version>3.0.5</version>
                                    <fixVersion>4.0.3</fixVersion>
                    <fixVersion>4.1.4</fixVersion>
                                    <component>WiredTiger</component>
                                        <votes>37</votes>
                                    <watches>52</watches>
                                                                                                                <comments>
                            <comment id="3288368" author="JIRAUSER1269864" created="Thu, 16 Jul 2020 16:52:48 +0000"  >&lt;p&gt;Hi &lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=louis.williams&quot; class=&quot;external-link&quot; rel=&quot;nofollow&quot;&gt;Louis Williams&#160;&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;Thanks, I have similar issue with 4.0.19 version, are the above fixes applicable in my version, can you please update.&lt;/p&gt;

&lt;p&gt;Thanks&lt;/p&gt;</comment>
                            <comment id="2010426" author="louis.williams" created="Fri, 21 Sep 2018 15:16:08 +0000"  >&lt;p&gt;All changes described in my previous comment have been backported to 4.0, with the exception of the removal of the repairDatabase command. This command&apos;s behavior remains unchanged in 4.0.&lt;/p&gt;</comment>
                            <comment id="2006773" author="louis.williams" created="Tue, 18 Sep 2018 17:14:10 +0000"  >&lt;p&gt;Starting mongod with --repair on a WiredTiger data directory now handles and recovers from the following scenarios:&lt;/p&gt;
&lt;ul&gt;
	&lt;li&gt;Corrupt .wt files (existing behavior)
	&lt;ul&gt;
		&lt;li&gt;Collections are salvaged by discarding corrupt data&lt;/li&gt;
		&lt;li&gt;Indexes are unconditionally rebuilt&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;Missing .wt data files (for both collections and indexes)
	&lt;ul&gt;
		&lt;li&gt;&lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-35627&quot; title=&quot;Repair should re-create missing collection data files from the existing metadata&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-35627&quot;&gt;&lt;del&gt;SERVER-35627&lt;/del&gt;&lt;/a&gt; A new, empty .wt file is created&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;Unsalvageable collection data files
	&lt;ul&gt;
		&lt;li&gt;&lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-35782&quot; title=&quot;Repair should move aside unsalvageable data files and create empty ones in their place&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-35782&quot;&gt;&lt;del&gt;SERVER-35782&lt;/del&gt;&lt;/a&gt; Repair moves aside unsalvageable data files and creates empty ones in their place&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;Corrupt WiredTiger metadata files
	&lt;ul&gt;
		&lt;li&gt;&lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-35629&quot; title=&quot;Use WiredTiger salvage API for repairing metadata files&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-35629&quot;&gt;&lt;del&gt;SERVER-35629&lt;/del&gt;&lt;/a&gt; Salvage corrupt WiredTiger.wt/WiredTiger.turtle files by discarding corrupt data&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;&#8220;Orphaned&#8221; data files
	&lt;ul&gt;
		&lt;li&gt;&lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-28734&quot; title=&quot;Recover WiredTiger data files when lacking metadata, but have _mdb_catalog data&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-28734&quot;&gt;&lt;del&gt;SERVER-28734&lt;/del&gt;&lt;/a&gt; Recover collection files missing from the WiredTiger metadata, but present in the _mdb_catalog&lt;/li&gt;
		&lt;li&gt;&lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-35696&quot; title=&quot;Provide a way to restore idents known by WiredTiger, but unknown to the _mdb_catalog&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-35696&quot;&gt;&lt;del&gt;SERVER-35696&lt;/del&gt;&lt;/a&gt; Recover collection files missing from the _mdb_catalog, but present in WiredTiger&lt;/li&gt;
		&lt;li&gt;&lt;em&gt;Note: there is no support for &quot;importing&quot; files that are missing from both metadata sources&lt;/em&gt;&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
&lt;/ul&gt;


&lt;p&gt;Additionally, --repair has the following new behavior:&lt;/p&gt;
&lt;ul&gt;
	&lt;li&gt;&lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-35731&quot; title=&quot;Prevent a repaired node from re-joining a replica set &quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-35731&quot;&gt;&lt;del&gt;SERVER-35731&lt;/del&gt;&lt;/a&gt; If a repair operation modifies data, the node will not be able to rejoin a replica set without a full resync
	&lt;ul&gt;
		&lt;li&gt;&lt;em&gt;Note: if a repair operation fails for any reason, the node will be unable to start up again without the --repair option.&lt;/em&gt;&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;&lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-28990&quot; title=&quot;when started with --repair mongod should not try to bind to a port&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-28990&quot;&gt;&lt;del&gt;SERVER-28990&lt;/del&gt;&lt;/a&gt; MongoDB will not bind to a port when started with --repair.&lt;/li&gt;
	&lt;li&gt;&lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-36208&quot; title=&quot;remove repairDatabase server command and shell helper&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-36208&quot;&gt;&lt;del&gt;SERVER-36208&lt;/del&gt;&lt;/a&gt; The repairDatabase command has been removed in 4.1&lt;/li&gt;
&lt;/ul&gt;
</comment>
                            <comment id="1613272" author="thomas.schubert" created="Tue, 4 Jul 2017 03:42:50 +0000"  >&lt;p&gt;Hi &lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=ccornel&quot; class=&quot;user-hover&quot; rel=&quot;ccornel&quot;&gt;ccornel&lt;/a&gt;,&lt;/p&gt;

&lt;p&gt;This issue would be best addressed in a new SERVER ticket. Would you please open one so we can investigate?&lt;/p&gt;

&lt;p&gt;Thank you,&lt;br/&gt;
Thomas&lt;/p&gt;</comment>
                            <comment id="1613230" author="ccornel" created="Tue, 4 Jul 2017 00:06:38 +0000"  >
&lt;p&gt;Hi&lt;br/&gt;
I tried the previous steps, but I have not been lucky with the wt tools tools, to repair the wiredtiger.wt file, what else can I recommend doing to extract the data?&lt;/p&gt;

&lt;p&gt;I hope someone can help please...&lt;/p&gt;

&lt;p&gt;my files &lt;br/&gt;
&lt;a href=&quot;https://drive.google.com/open?id=0BwyEAdclOsc_X0Nfa3RRd3RMT0k&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;https://drive.google.com/open?id=0BwyEAdclOsc_X0Nfa3RRd3RMT0k&lt;/a&gt;&lt;/p&gt;


&lt;p&gt;Regards &lt;/p&gt;

&lt;p&gt;Carlos&lt;/p&gt;</comment>
                            <comment id="1472176" author="alexander.gorrod" created="Sun, 8 Jan 2017 21:39:03 +0000"  >&lt;blockquote&gt;&lt;p&gt;Once I have .wt files, I should be able to recreate the database. Now there is no way I can recreate the database from the .wt files if I don&apos;t have the other files like WiredTiger ..&lt;/p&gt;&lt;/blockquote&gt;

&lt;p&gt;That is correct - you need the other files from the MongoDB database directory. Those files contain important metadata information that is necessary for WiredTiger to know which data is where, and how to access the data in those files.&lt;/p&gt;

&lt;p&gt;If the files in your database directory have become corrupted, there are several steps to take to get back online. The following options are listed in priority order:&lt;/p&gt;
&lt;ol&gt;
	&lt;li&gt;Re-sync from another node in an active replica set.&lt;/li&gt;
	&lt;li&gt;Restore the full database from a recent backup copy.&lt;/li&gt;
	&lt;li&gt;Start MongoDB with the repair option, and have it attempt to automatically recover data.&lt;/li&gt;
	&lt;li&gt;Manually retrieve data from the corrupted files, and attempt to reconstruct the original data set.&lt;/li&gt;
&lt;/ol&gt;


&lt;p&gt;The goal of this ticket is to move the line between options 3 and 4, so that automatic repair is possible in more cases.&lt;/p&gt;</comment>
                            <comment id="1472149" author="haris@baabte.com" created="Sun, 8 Jan 2017 19:04:09 +0000"  >&lt;p&gt;Once I have .wt files, I should be able to recreate the database. Now there is no way I can recreate the database from the .wt files if I don&apos;t have the other files like WiredTiger .. &lt;/p&gt;</comment>
                            <comment id="1303725" author="stefan.rogin" created="Thu, 23 Jun 2016 01:59:25 +0000"  >&lt;p&gt;Important feature, to ignore corrupt collections, when recovering a database with many collections and have only a tiny/recoverable one corrupt or out of alignment.&lt;/p&gt;</comment>
                            <comment id="1281551" author="asya" created="Wed, 1 Jun 2016 19:09:29 +0000"  >&lt;p&gt;Users have requested ability to start mongod to either manually or automatically to &quot;drop&quot; entities that don&apos;t have files/directories present. &lt;/p&gt;</comment>
                            <comment id="1063885" author="alexander.gorrod" created="Mon, 19 Oct 2015 05:15:41 +0000"  >&lt;p&gt;Thanks &lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=david.hows&quot; class=&quot;user-hover&quot; rel=&quot;david.hows&quot;&gt;david.hows&lt;/a&gt;. The categorization is taking shape now. Can you think of a way to test the different scenarios? Preferably as part of the regular MongoDB test suite.&lt;/p&gt;</comment>
                            <comment id="1059959" author="david.hows" created="Wed, 14 Oct 2015 04:47:08 +0000"  >&lt;p&gt;&lt;b&gt;Database files missing&lt;/b&gt;&lt;/p&gt;
&lt;ul class=&quot;alternate&quot; type=&quot;square&quot;&gt;
	&lt;li&gt;An entry for a file will exist in the catalogue, but on disk file is gone&lt;/li&gt;
	&lt;li&gt;Will be impossible to recover from, remove the entry from the catalogue&lt;/li&gt;
	&lt;li&gt;Warn the user strongly about this (Error message)&lt;/li&gt;
&lt;/ul&gt;


&lt;p&gt;&lt;b&gt;Database files corrupted&lt;/b&gt;&lt;/p&gt;
&lt;ul class=&quot;alternate&quot; type=&quot;square&quot;&gt;
	&lt;li&gt;An entry for a file will exist in the catalogue, but on disk file is unable to be opened&lt;/li&gt;
	&lt;li&gt;Attempt to rename the collection with WiredTiger to a new table that has some mention of it being corrupted in the name&lt;/li&gt;
	&lt;li&gt;Re-create the same collection with the same name (in order to continue repair)&lt;/li&gt;
	&lt;li&gt;Warn the user strongly about this problem, the creation of the new collection&lt;/li&gt;
&lt;/ul&gt;


&lt;p&gt;&lt;b&gt;Index files missing&lt;/b&gt;&lt;/p&gt;
&lt;ul class=&quot;alternate&quot; type=&quot;square&quot;&gt;
	&lt;li&gt;An entry will exist in the catalogue, but on disk file is gone&lt;/li&gt;
	&lt;li&gt;Build the index as part of repair&lt;/li&gt;
&lt;/ul&gt;


&lt;p&gt;&lt;b&gt;Index files corrupted&lt;/b&gt;&lt;/p&gt;
&lt;ul class=&quot;alternate&quot; type=&quot;square&quot;&gt;
	&lt;li&gt;An entry will exist in the catalogue, but on disk file is unable to be opened&lt;/li&gt;
	&lt;li&gt;Drop, then rebuild the index as part of repair&lt;/li&gt;
&lt;/ul&gt;


&lt;p&gt;&lt;b&gt;MongoDB catalogue metadata may be out of alignment with the WT files on disk&lt;/b&gt;&lt;/p&gt;
&lt;ul class=&quot;alternate&quot; type=&quot;square&quot;&gt;
	&lt;li&gt;When something is missing on disk, then this should be resolved by the changes above&lt;/li&gt;
	&lt;li&gt;When something is missing from the catalogue metadata but exists as a wt table on disk we have no recourse. We would need a user accessible function to import&lt;/li&gt;
	&lt;li&gt;If the WiredTiger metadata is corrupt, then the database is corrupt&lt;/li&gt;
&lt;/ul&gt;
</comment>
                    </comments>
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