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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-5845] Cursor can get deleted because of timeout at the finish stage of a sharded map reduce</title>
                <link>https://jira.mongodb.org/browse/SERVER-5845</link>
                <project id="10000" key="SERVER">Core Server</project>
                    <description>&lt;p&gt;When I run one of MR job, the second time fail with error:&lt;/p&gt;
&lt;p/&gt;
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&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;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;{&quot;errmsg&quot;:&quot;exception: getMore: cursor didn&apos;t exist on server, possible restart or timeout?&quot;,&quot;code&quot;:13127,&quot;ok&quot;:0}&lt;/span&gt;&lt;/pre&gt;
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&lt;p/&gt;

&lt;p&gt;And by logs, I see that in final stage (when it iterate over &quot;CollectionByWhatMapReduceRun_IntNumber&quot;), it not handle connections&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;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;// conn178752 - MR job connection&lt;/span&gt;&lt;/pre&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;   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;
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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;   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;Mon May 14 17:48:35 [conn178752] getmore Database.CollectionByWhatMapReduceRun_IntNumber cursorid:4899920544814319828 ntoreturn:0 keyUpdates:0 nreturned:4316 reslen:5621110 142ms&lt;/span&gt;&lt;/pre&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;   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;
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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;   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;Mon May 14 17:48:51 [initandlisten] connection accepted from 127.0.0.1:33015 #559035 (446 connections now open)&lt;/span&gt;&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;Mon May 14 17:48:51 [initandlisten] connection accepted from 127.0.0.1:33016 #559036 (447 connections now open)&lt;/span&gt;&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;...&lt;/span&gt;&lt;/pre&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;   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;Mon May 14 18:23:14 [conn178752]                52200/108636    48%&lt;/span&gt;&lt;/pre&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;   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;
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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;   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;Mon May 14 18:23:14 [conn180633] SocketException handling request, closing client connection: 9001 socket exception [2] server [127.0.0.1:60746]&lt;/span&gt;&lt;/pre&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;   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;
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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;   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;Mon May 14 18:24:11 [initandlisten] connection refused because too many open connections: 819&lt;/span&gt;&lt;/pre&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;   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;Mon May 14 18:24:11 [initandlisten] connection accepted from 127.0.0.1:59086 #754273 (820 connections now open)&lt;/span&gt;&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;...&lt;/span&gt;&lt;/pre&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-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;Mon May 14 18:24:16 [conn178752] getMore: cursorid not found Database.CollectionByWhatMapReduceRun_IntNumber 4899920544814319828&lt;/span&gt;&lt;/pre&gt;
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&lt;p/&gt;

&lt;p&gt;And after - number of connection decrements&lt;/p&gt;

&lt;p&gt;But another type of MR job is runs okay.&lt;/p&gt;

&lt;p&gt;Any ideas?&lt;/p&gt;</description>
                <environment></environment>
        <key id="38723">SERVER-5845</key>
            <summary>Cursor can get deleted because of timeout at the finish stage of a sharded map reduce</summary>
                <type id="4" iconUrl="https://jira.mongodb.org/secure/viewavatar?size=xsmall&amp;avatarId=14710&amp;avatarType=issuetype">Improvement</type>
                                            <priority id="2" iconUrl="https://jira.mongodb.org/images/icons/priorities/critical.svg">Critical - P2</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="randolph@mongodb.com">Randolph Tan</assignee>
                                    <reporter username="azat">Azat Khuzhin</reporter>
                        <labels>
                    </labels>
                <created>Tue, 15 May 2012 07:59:36 +0000</created>
                <updated>Mon, 11 Jul 2016 18:32:35 +0000</updated>
                            <resolved>Thu, 30 Aug 2012 23:01:05 +0000</resolved>
                                    <version>2.1.1</version>
                                    <fixVersion>2.3.0</fixVersion>
                                    <component>MapReduce</component>
                                        <votes>0</votes>
                                    <watches>2</watches>
                                                                                                                <comments>
                            <comment id="158787" author="auto" created="Thu, 30 Aug 2012 22:57:44 +0000"  >&lt;p&gt;Author:&lt;/p&gt;
{u&apos;date&apos;: u&apos;2012-08-30T15:54:30-07:00&apos;, u&apos;name&apos;: u&apos;Randolph Tan&apos;, u&apos;email&apos;: u&apos;randolph@10gen.com&apos;}
&lt;p&gt;Message: &lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-5845&quot; title=&quot;Cursor can get deleted because of timeout at the finish stage of a sharded map reduce&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-5845&quot;&gt;&lt;del&gt;SERVER-5845&lt;/del&gt;&lt;/a&gt; Cursor can get deleted because of timeout at the finish stage of a sharded map reduce&lt;br/&gt;
Branch: master&lt;br/&gt;
&lt;a href=&quot;https://github.com/mongodb/mongo/commit/374289bb6e043b16fe9bf613bc18e56f6df14a81&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;https://github.com/mongodb/mongo/commit/374289bb6e043b16fe9bf613bc18e56f6df14a81&lt;/a&gt;&lt;/p&gt;</comment>
                            <comment id="126961" author="azat" created="Wed, 6 Jun 2012 10:32:01 +0000"  >&lt;p&gt;See my pull request&lt;br/&gt;
&lt;a href=&quot;https://github.com/mongodb/mongo/pull/231&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;https://github.com/mongodb/mongo/pull/231&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;I&apos;v add only QueryOption_NoCursorTimeout&lt;/p&gt;

&lt;p&gt;But need to add yielding ( maybe only if nonAtomic is set? )&lt;br/&gt;
And maybe better to use just &quot;update&quot;/&quot;insert&quot; instead of &quot;upsert&quot;, because it run &quot;findOne&quot; command twice^&lt;br/&gt;
first in &quot;State::postProcessCollectionNonAtomic&quot;&lt;br/&gt;
second in &quot;Helpers::upsert&quot;&lt;/p&gt;</comment>
                            <comment id="126951" author="azat" created="Wed, 6 Jun 2012 10:14:18 +0000"  >&lt;p&gt;And why you are using upsert, if you already check exist it or not in &quot;State::postProcessCollectionNonAtomic&quot;?&lt;/p&gt;</comment>
                            <comment id="126949" author="azat" created="Wed, 6 Jun 2012 10:12:11 +0000"  >&lt;p&gt;Line mongo/db/commands/mr.cpp:507 (State::postProcessCollectionNonAtomic) must have QueryOption_NoCursorTimeout&lt;br/&gt;
And must yielding&lt;/p&gt;</comment>
                            <comment id="126947" author="azat" created="Wed, 6 Jun 2012 10:09:19 +0000"  >&lt;p&gt;It fails at stage&lt;br/&gt;
&quot;m/r: reduce post processing 1154/55614 2&quot;&lt;br/&gt;
after 20 seconds&lt;br/&gt;
&quot;m/r: reduce post processing 1159/55614 2%&quot;&lt;br/&gt;
It merge &quot;inc&quot; collection with &quot;out&quot; collection (but too slow, &quot;out&quot; collection has ~2.5 million of rows, not so much I think)&lt;/p&gt;

&lt;p&gt;Db is locked &quot;lockType&quot; : &quot;W&quot;, but I use &quot;nonAtomic&quot; flag, when running mapreduce&lt;br/&gt;
CPU usage 100%&lt;br/&gt;
No io activity&lt;/p&gt;

&lt;p&gt;New clients arrived, but not served, so connections accumulated&lt;br/&gt;
And the it fails&lt;/p&gt;</comment>
                            <comment id="126404" author="azat" created="Tue, 5 Jun 2012 15:28:08 +0000"  >&lt;p&gt;Attach log&lt;br/&gt;
3k lines before starting MR job&lt;br/&gt;
some lines after failed MR job&lt;/p&gt;</comment>
                            <comment id="126384" author="renctan" created="Tue, 5 Jun 2012 14:48:33 +0000"  >&lt;p&gt;It should be fine because the cursor has been initialized with QueryOption_NoCursorTimeout. It would be best to post the entire log, but 3k lines before might be enough. The grep output might be enough too.&lt;/p&gt;</comment>
                            <comment id="126358" author="azat" created="Tue, 5 Jun 2012 14:12:15 +0000"  >&lt;p&gt;If I grep by &quot;conn34700&quot; is it enough?&lt;/p&gt;</comment>
                            <comment id="126357" author="renctan" created="Tue, 5 Jun 2012 14:11:11 +0000"  >&lt;p&gt;Can you post the complete new log?&lt;/p&gt;</comment>
                            <comment id="126355" author="azat" created="Tue, 5 Jun 2012 14:10:45 +0000"  >&lt;p&gt;About cursor already not exist:&lt;/p&gt;

&lt;p&gt;Maybe because of &lt;a href=&quot;https://github.com/mongodb/mongo/blob/a105cf0bb3b8bc8aac662441f53deae5e4e83462/src/mongo/db/commands/mr.cpp#L760&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;https://github.com/mongodb/mongo/blob/a105cf0bb3b8bc8aac662441f53deae5e4e83462/src/mongo/db/commands/mr.cpp#L760&lt;/a&gt;&lt;br/&gt;
And if there is 100 objects (~16mb) = 1600mb ?&lt;/p&gt;

&lt;p&gt;And maybe better to yield on every 100mb ?&lt;/p&gt;</comment>
                            <comment id="126349" author="azat" created="Tue, 5 Jun 2012 14:02:30 +0000"  >&lt;p&gt;Now I have the same error (maybe because of data set increase)&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;
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					&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;Sun May 27 17:13:15 [conn34700] getMore: cursorid not found seoquake_ad_api.tmp.mr.ad_statistics_6 4879762645212462063&lt;/span&gt;&lt;/pre&gt;
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					&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;Sun May 27 17:13:15 [conn34700] mr failed, removing collection :: caused by :: 13127 getMore: cursor didn&apos;t exist on server, possible restart or timeout?&lt;/span&gt;&lt;/pre&gt;
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&lt;p/&gt;

&lt;p&gt;And what about data inconsistency?&lt;/p&gt;</comment>
                            <comment id="125630" author="azat" created="Mon, 4 Jun 2012 12:01:43 +0000"  >&lt;p&gt;But in my case no sharding is used&lt;/p&gt;</comment>
                            <comment id="124542" author="renctan" created="Wed, 30 May 2012 21:30:08 +0000"  >&lt;p&gt;I have confirmed that this is a bug and this happens because the cursor used by the shard doesn&apos;t use notimeout when querying over the map reduce results of individual shards (when mapreduce.shardedfinish is called).&lt;/p&gt;</comment>
                            <comment id="123532" author="azat" created="Mon, 28 May 2012 08:14:31 +0000"  >&lt;p&gt;BTW if it iterate over &quot;CollectionByWhatMapReduceRun_IntNumber&quot; is it write to &quot;out&quot; collection?&lt;br/&gt;
If so, and it fails - than this cause inconsistency&lt;/p&gt;</comment>
                            <comment id="123135" author="azat" created="Fri, 25 May 2012 15:37:42 +0000"  >&lt;p&gt;This cursor create in mapreduce. I can&apos;t set noTimeout flag for it.&lt;br/&gt;
But it already create with it&lt;/p&gt;

&lt;p/&gt;
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&lt;p/&gt;</comment>
                            <comment id="122834" author="renctan" created="Thu, 24 May 2012 18:02:36 +0000"  >&lt;p&gt;The server cleans up cursors that has been idle for 10 minutes unless you set the no timeout flag. Assuming that you posted everything for conn178752 between 17:48:35 and 18:24:16, the cursor has been untouched for more than 10 mins.&lt;/p&gt;</comment>
                            <comment id="120422" author="azat" created="Thu, 17 May 2012 09:23:59 +0000"  >&lt;p&gt;I think that it can be because of too many connections.&lt;br/&gt;
And when mongo kill it (timeout ?) it kills this cursor, or something like this&lt;/p&gt;

&lt;p&gt;Now I add replicaset and I successfully run this MR job&lt;/p&gt;</comment>
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