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<channel>
    <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-34029] mongod get stuck after upgrade</title>
                <link>https://jira.mongodb.org/browse/SERVER-34029</link>
                <project id="10000" key="SERVER">Core Server</project>
                    <description>&lt;p&gt;One of our mongodb cluster has very weird issue. &lt;br/&gt;
I tried to upgrade our cluster from 3.4.1 to 3.6.3, after upgrade I noticed that one slave server gets stuck after a while, I can connect to that slave, some commands are working, but not all, e.g rs.printSlaveReplicationInfo() is not responding, also that slave starts lagging, there is no cpu usage or disk IO, server is idling.&lt;br/&gt;
And later even primary server got stuck (I suspect it is same issue, but not sure).&lt;br/&gt;
After primary got stuck I decided to rollback cluster to 3.4.13, same thing happened.&lt;br/&gt;
Rolled back whole cluster to 3.4.1, this version works.&lt;/p&gt;

&lt;p&gt;I started playing with one slave server, tried different versions, turned out that 3.4.4 is OK, but 3.4.5 is not. Using git bisect I found that following commit is causing issues for us: &lt;a href=&quot;https://github.com/mongodb/mongo/commit/c3fda2d13c2f60eb3a68564403985cb1c7e8aa43&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;https://github.com/mongodb/mongo/commit/c3fda2d13c2f60eb3a68564403985cb1c7e8aa43&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;Slave that gets stuck is also used for read-only queries, another slave that is not getting queries works fine.&lt;/p&gt;

&lt;p&gt;Every time slave gets stuck there is are few huge queries like following in log:&lt;/p&gt;
&lt;p/&gt;
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					&lt;pre style=&quot;font-size: 1em; margin: 0 10px;  margin-top: 10px;   width: auto; padding: 0;&quot;&gt;&amp;nbsp;&lt;/pre&gt;
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					&lt;pre style=&quot;font-size: 1em; margin: 0 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;2018-03-21T11:16:02.888+0000 I COMMAND  [conn124] warning: log line attempted (644kB) over max size (10kB), printing beginning and end ... command Baz.foocollection command: getMore { getMore: 120605126995, collection: &quot;foocollection&quot; } originatingCommand: { find: &quot;foocollection&quot;, filter: { $or: [ { fooObjectId: ObjectId(&apos;58931cae526107078bbf71f7&apos;), stamp: 1494514165.463685 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1494422652.740239 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1494422716.137933 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1494422723.481655 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1495113378.631109 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1494422718.830563 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1495113381.569376 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1495113388.42224 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1495113426.608498 }, { fooObjectId: ObjectId(&apos;58931cae526107078bbf71f7&apos;), stamp: 1493802053.254245 }, { fooObjectId: ObjectId(&apos;58931cae526107078bbf71f7&apos;), stamp: 1493802049.093342 }, { fooObjectId: ObjectId(&apos;58931cae526107078bbf71f7&apos;), stamp: 1493802054.233313 }, { fooObjectId: ObjectId(&apos;58931cae526107078bbf71f7&apos;), stamp: 1494329972.558202 }, { fooObjectId: ObjectId(&apos;58931cae526107078bbf71f7&apos;), stamp: 1493802055.457206 }, { stamp: 1487772816.953898, fooObjectId: ObjectId(&apos;5805bf6e74712800bb012f05&apos;) }, { fooObjectId: ObjectId(&apos;5805bf6e74712800bb012f05&apos;), stamp: 1487772831.640239 }, { fooObjectId: ObjectId(&apos;589c35934e89350783564909&apos;), stamp: 1496404387.08405 }, { fooObjectId: ObjectId(&apos;589c35934e89350783564909&apos;), stamp: 1496404383.584682 }, { fooObjectId: ObjectId(&apos;589c35934e89350783564909&apos;), stamp: 1496404357.338354 }, { fooObjectId: ObjectId(&apos;58931cae526107078bbf71f7&apos;), stamp: 1494513722.518675 }, { fooObjectId: ObjectId(&apos;58b412645e9206070a1dd06a&apos;), stamp: 1494423044.121071 }, { fooObjectId: ObjectId(&apos;58b412645e9206070a1dd06a&apos;), stamp: 1494423041.918467 }, { fooObjectId: ObjectId(&apos;58b412645e9206070a1dd06a&apos;), stamp: 1494423039.961413 }, { fooObjectId: ObjectId(&apos;58b412645e9206070a1dd06a&apos;), stamp: 1494423034.819859 }, { stamp: 1501573001.144575, fooObjectId: ObjectId(&apos;5812fc35b2a83a00b8c9061f&apos;) }, { fooObjectId: ObjectId(&apos;5812fc35b2a83a00b8c9061f&apos;), stamp: 1501573004.145434 }, { fooObjectId: ObjectId(&apos;5812fc35b2a83a00b8c9061f&apos;), stamp: 1501572997.895948 }, { fooObjectId: ObjectId(&apos;5812fc35b2a83a00b8c9061f&apos;), stamp: 1501573008.895141 }, { fooObjectId: ObjectId(&apos;5812fc35b2a83a00b8c9061f&apos;), stamp: 1501573005.394891 }, { fooObjectId: ObjectId(&apos;5812fc35b2a83a00b8c9061f&apos;), stamp: 1501090931.443829 }, { fooObjectId: ObjectId(&apos;58931cae526107078bbf71f7&apos;), stamp: 1497892396.056092 }, { stamp: 1493890957.166266, fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;) }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1493890819.475622 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1493890822.902208 }, { fooObjectId: ObjectId(&apos;57beea4dd93194b60029ee9a&apos;), stamp: 1490703301.703321 }, { stamp: 1487949706.666049, fooObjectId: ObjectId(&apos;5805c00f74712800bb01320a&apos;) }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1497550576.221023 }, { fooObjectId: ObjectId(&apos;58b412d65e9206070a1dd5f6&apos;), stamp: 1497550576.95499 }, { fooObjectId: ObjectId(&apos;58b412645e9206070a1dd06a&apos;), stamp: 1511271224.294596 }, { fooObjectId: ObjectId(&apos;58b412645e9206070a1dd06a&apos;), stamp: 15112712 .......... on.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 }, IXSCAN { stamp: 1, position.x: 1, position.y: 1 } cursorid:120605126995 keysExamined:34140 docsExamined:34140 cursorExhausted:1 numYields:307 nreturned:34140 reslen:11101775 locks:{ Global: { acquireCount: { r: 616 }, acquireWaitCount: { r: 146 }, timeAcquiringMicros: { r: 469372 } }, Database: { acquireCount: { r: 308 } }, Collection: { acquireCount: { r: 308 } } } protocol:op_query 1110ms&lt;/span&gt;&lt;/pre&gt;
			&lt;/td&gt;
		&lt;/tr&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-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;&lt;/span&gt;&lt;/pre&gt;
			&lt;/td&gt;
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			&lt;/tbody&gt;
&lt;/table&gt;
&lt;/div&gt;
&lt;p/&gt;

&lt;p&gt;It doesn&apos;t happen each time, most of the time these queries are successful.&lt;/p&gt;

&lt;p&gt;I can provide logs, but not sure how to do that privately as our logs can contain sensitive information.&lt;/p&gt;</description>
                <environment></environment>
        <key id="514457">SERVER-34029</key>
            <summary>mongod get stuck after upgrade</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="3">Duplicate</resolution>
                                        <assignee username="kelsey.schubert@mongodb.com">Kelsey Schubert</assignee>
                                    <reporter username="tarvip">Tarvi Pillessaar</reporter>
                        <labels>
                    </labels>
                <created>Wed, 21 Mar 2018 13:01:20 +0000</created>
                <updated>Mon, 23 Apr 2018 21:59:52 +0000</updated>
                            <resolved>Thu, 22 Mar 2018 19:45:10 +0000</resolved>
                                    <version>3.4.5</version>
                    <version>3.4.14</version>
                    <version>3.6.3</version>
                                                    <component>Querying</component>
                    <component>WiredTiger</component>
                                        <votes>0</votes>
                                    <watches>6</watches>
                                                                                                                <comments>
                            <comment id="1842498" author="thomas.schubert" created="Thu, 22 Mar 2018 19:44:25 +0000"  >&lt;p&gt;Hi &lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=tarvip&quot; class=&quot;user-hover&quot; rel=&quot;tarvip&quot;&gt;tarvip&lt;/a&gt;,&lt;/p&gt;

&lt;p&gt;Thank you for the stacks, I can confirm that issue you&apos;re encountering is being tracked in &lt;a href=&quot;https://jira.mongodb.org/browse/WT-3972&quot; title=&quot;Allow more than 64K cursors to be open on a data source simultaneously&quot; class=&quot;issue-link&quot; data-issue-key=&quot;WT-3972&quot;&gt;&lt;del&gt;WT-3972&lt;/del&gt;&lt;/a&gt;, and I expect that the fix will be backported into next release of MongoDB 3.4. As a workaround, I would suggest looking into whether you can modify your application to use $in queries rather than $or queries which should also have performance benefits as described by &lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-34012&quot; title=&quot;Planner&amp;#39;s logic for taking union of index bounds intervals is slow for large $or queries&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-34012&quot;&gt;&lt;del&gt;SERVER-34012&lt;/del&gt;&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;Kind regards,&lt;br/&gt;
Kelsey&lt;/p&gt;</comment>
                            <comment id="1841732" author="tarvip" created="Thu, 22 Mar 2018 12:02:19 +0000"  >&lt;p&gt;Hi Kelsey,&lt;/p&gt;

&lt;p&gt;files uploaded. From diagnostic data you can probably see, that it actually happened twice (first time it happened few hours earlier, first time I forgot to run gdb).&lt;br/&gt;
gdb output was following:&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;
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						&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;   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;gdb -p $(pidof mongod) -batch -ex &apos;thread apply all bt&apos; &amp;gt; gdb_`date +&quot;%Y%m%d_%H%M%S&quot;`.txt&lt;/span&gt;&lt;/pre&gt;
			&lt;/td&gt;
		&lt;/tr&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-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;185	../sysdeps/unix/sysv/linux/x86_64/pthread_cond_wait.S: No such file or directory.&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;Slave started lagging at ~11:39:05 UTC, so I guess something happened at that time.&lt;/p&gt;

&lt;p&gt;Also, if needed I can increase log verbosity for some components, at the moment verbosity is set to default.&lt;/p&gt;

&lt;p&gt;Thank you,&lt;br/&gt;
Tarvi Pillessaar&lt;/p&gt;</comment>
                            <comment id="1841165" author="thomas.schubert" created="Wed, 21 Mar 2018 19:05:21 +0000"  >&lt;p&gt;Hi &lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=tarvip&quot; class=&quot;user-hover&quot; rel=&quot;tarvip&quot;&gt;tarvip&lt;/a&gt;,&lt;/p&gt;

&lt;p&gt;Would you please upload the complete logs and diagnostic.data from an affected node? I&apos;ve created a &lt;a href=&quot;https://10gen-httpsupload.s3.amazonaws.com/upload_forms/1498c2db-aca8-41a4-ba3b-3cedeea7d780.html&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;secure portal&lt;/a&gt; for you to use.&lt;/p&gt;

&lt;p&gt;Additionally, if performance isn&apos;t critical, would you please collect gdb during this issue using the following command?&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;gdb -p $(pidof mongod) -batch -ex &apos;thread apply all bt&apos; &amp;gt;gdb.txt&lt;/span&gt;&lt;/pre&gt;
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		&lt;/tr&gt;
			&lt;/tbody&gt;
&lt;/table&gt;
&lt;/div&gt;
&lt;p/&gt;

&lt;p&gt;Please be sure to specify the time the &lt;tt&gt;gdb.txt&lt;/tt&gt; file was generated when you upload so we can correlate it to the mongod logs and diagnostic.data.&lt;/p&gt;

&lt;p&gt;Thank you,&lt;br/&gt;
Kelsey&lt;/p&gt;
</comment>
                            <comment id="1840622" author="tarvip" created="Wed, 21 Mar 2018 13:04:37 +0000"  >&lt;p&gt;Slave is running on:&lt;br/&gt;
OS: Ubuntu Xenial, 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux&lt;br/&gt;
HW: AWS VM c4.&lt;br/&gt;
Data volume: 1300GB gp2 c4.4xlarge&lt;/p&gt;

&lt;p&gt;Today I also tested 3.4.14, still not working.&lt;/p&gt;</comment>
                    </comments>
                <issuelinks>
                            <issuelinktype id="10010">
                    <name>Duplicate</name>
                                            <outwardlinks description="duplicates">
                                        <issuelink>
            <issuekey id="509405">WT-3972</issuekey>
        </issuelink>
                            </outwardlinks>
                                                        </issuelinktype>
                            <issuelinktype id="10012">
                    <name>Related</name>
                                            <outwardlinks description="related to">
                                        <issuelink>
            <issuekey id="514146">SERVER-34012</issuekey>
        </issuelink>
                            </outwardlinks>
                                                        </issuelinktype>
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