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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-31905] in 3.6, __wt_update_obsolete_check, uses significant cpu</title>
                <link>https://jira.mongodb.org/browse/SERVER-31905</link>
                <project id="10000" key="SERVER">Core Server</project>
                    <description>&lt;p&gt;the calls to __wt_update_obsolete_check from __col_instantiate and __row_instantiate were not in 3.4. between 3.4 and 3.6-r2 these calls were added and, as a result, __wt_update_obsolete_check cpu usage builds to over 20% of system&lt;/p&gt;</description>
                <environment></environment>
        <key id="457056">SERVER-31905</key>
            <summary>in 3.6, __wt_update_obsolete_check, uses significant cpu</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="keith.bostic@mongodb.com">Keith Bostic</assignee>
                                    <reporter username="jvf">Jim Van Fleet</reporter>
                        <labels>
                    </labels>
                <created>Fri, 10 Nov 2017 14:25:12 +0000</created>
                <updated>Tue, 12 Dec 2017 04:32:42 +0000</updated>
                            <resolved>Tue, 21 Nov 2017 02:20:22 +0000</resolved>
                                    <version>3.6.0-rc3</version>
                                                    <component>WiredTiger</component>
                                        <votes>0</votes>
                                    <watches>10</watches>
                                                                                                                <comments>
                            <comment id="1731217" author="keith.bostic" created="Tue, 21 Nov 2017 01:26:19 +0000"  >&lt;p&gt;Fixed by &lt;a href=&quot;https://jira.mongodb.org/browse/WT-3752&quot; title=&quot;WiredTiger can walk long update chains for hot rows.&quot; class=&quot;issue-link&quot; data-issue-key=&quot;WT-3752&quot;&gt;&lt;del&gt;WT-3752&lt;/del&gt;&lt;/a&gt;.&lt;/p&gt;</comment>
                            <comment id="1731216" author="keith.bostic" created="Tue, 21 Nov 2017 01:24:55 +0000"  >&lt;p&gt;Thank you, &lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=jvf&quot; class=&quot;user-hover&quot; rel=&quot;jvf&quot;&gt;jvf&lt;/a&gt;!&lt;/p&gt;

&lt;p&gt;I&apos;ll go ahead and close this report then, please don&apos;t hesitate to re-open it if there are any follow-on issues.&lt;/p&gt;</comment>
                            <comment id="1731190" author="jvf" created="Tue, 21 Nov 2017 00:14:40 +0000"  >&lt;p&gt;Keith &amp;#8211; I just tried this fix &amp;#8211; I think it takes care of the problem that I reported.  I want to do some more testing and will finish up tomorrow &amp;#8211; nice job!&lt;/p&gt;</comment>
                            <comment id="1730178" author="keith.bostic" created="Mon, 20 Nov 2017 12:36:05 +0000"  >&lt;p&gt;&lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=jvf&quot; class=&quot;user-hover&quot; rel=&quot;jvf&quot;&gt;jvf&lt;/a&gt;, there&apos;s a change we put into place last night that I believe may fix this problem, would you be able to test if it fixes the problem you&apos;re seeing?&lt;/p&gt;

&lt;p&gt;I&apos;ve attached the diff to this ticket (&lt;tt&gt;ba357b7.diff&lt;/tt&gt;), and the patch would be applied in the directory &lt;tt&gt;mongo/src/third_party/wiredtiger/src/btree/&lt;/tt&gt;, to the file &lt;tt&gt;&amp;#95;&amp;#95;row_modify.c&lt;/tt&gt;.&lt;/p&gt;</comment>
                            <comment id="1727107" author="jvf" created="Wed, 15 Nov 2017 23:06:04 +0000"  >&lt;p&gt;I slightly lied - we&apos;re using workload &quot;mixed&quot; not workloada (they are &lt;br/&gt;
both 50% read, 50% write)&lt;/p&gt;

&lt;p&gt;I included another snippet of perf top, the start-script,  the ycsb &lt;br/&gt;
workloads in the script, in the attached file:&lt;/p&gt;

&lt;p&gt;the script is generally started something like&lt;/p&gt;

&lt;p&gt; sh tesCursor.sh  localhost 27017 20 3_6fix&lt;/p&gt;

&lt;p&gt;Jim&lt;/p&gt;




</comment>
                            <comment id="1727027" author="keith.bostic" created="Wed, 15 Nov 2017 21:57:04 +0000"  >&lt;p&gt;&lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=jvf&quot; class=&quot;user-hover&quot; rel=&quot;jvf&quot;&gt;jvf&lt;/a&gt;, would you please post a copy of the workloada that you&apos;re running, and any command-line arguments?&lt;/p&gt;

&lt;p&gt;Thanks!&lt;/p&gt;</comment>
                            <comment id="1726990" author="jvf" created="Wed, 15 Nov 2017 21:24:03 +0000"  >&lt;p&gt;Hi Keith &amp;#8211;&lt;/p&gt;

&lt;p&gt;My bad &amp;#8211; what I sent was a snippet from perf top and somehow I put &lt;br/&gt;
&quot;localhost....*&quot; where __wt_update_obsolete_check should have been &amp;#8211; it &lt;br/&gt;
is the 16%+ item.&lt;/p&gt;

&lt;p&gt;My appolgies&lt;/p&gt;

&lt;p&gt;Jim&lt;/p&gt;
</comment>
                            <comment id="1726961" author="keith.bostic" created="Wed, 15 Nov 2017 21:04:56 +0000"  >&lt;p&gt;Hi, &lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=jvf&quot; class=&quot;user-hover&quot; rel=&quot;jvf&quot;&gt;jvf&lt;/a&gt;. You said:&lt;/p&gt;

&lt;blockquote&gt;&lt;p&gt;the calls to __wt_update_obsolete_check from __col_instantiate and __row_instantiate were not in 3.4. between 3.4 and 3.6-r2 these calls were added and, as a result, __wt_update_obsolete_check cpu usage builds to over 20% of system&lt;/p&gt;&lt;/blockquote&gt;

&lt;p&gt;But I&apos;m not seeing __row_instantiate or __wt_update_obsolete_check in the perf report? I&apos;m sure there&apos;s something obvious I&apos;m missing &amp;#8211; it makes sense to me that if the lookaside file is getting involved they could be there, but I don&apos;t see them?&lt;/p&gt;

&lt;p&gt;&lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=alexander.gorrod&quot; class=&quot;user-hover&quot; rel=&quot;alexander.gorrod&quot;&gt;alexander.gorrod&lt;/a&gt;, this is a zipfian distribution with modify, so yes, I suspect it&apos;s similar to &lt;a href=&quot;https://jira.mongodb.org/browse/WT-3739&quot; title=&quot;Some workloads see more transaction conflicts with WT_CURSOR::modify&quot; class=&quot;issue-link&quot; data-issue-key=&quot;WT-3739&quot;&gt;&lt;del&gt;WT-3739&lt;/del&gt;&lt;/a&gt;.&lt;/p&gt;</comment>
                            <comment id="1726095" author="alexander.gorrod" created="Wed, 15 Nov 2017 05:33:04 +0000"  >&lt;p&gt;&lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=keith.bostic&quot; class=&quot;user-hover&quot; rel=&quot;keith.bostic&quot;&gt;keith.bostic&lt;/a&gt; I&apos;ve assigned this ticket to you because I believe it may be a different manifestation of the issue outlined in &lt;a href=&quot;https://jira.mongodb.org/browse/WT-3739&quot; title=&quot;Some workloads see more transaction conflicts with WT_CURSOR::modify&quot; class=&quot;issue-link&quot; data-issue-key=&quot;WT-3739&quot;&gt;&lt;del&gt;WT-3739&lt;/del&gt;&lt;/a&gt; - since it is running the same workload. I haven&apos;t had a chance to look at the diagnostic data yet, but I thought pairing the tickets might help circle around to the underlying cause for the performance regression.&lt;/p&gt;</comment>
                            <comment id="1724498" author="jvf" created="Mon, 13 Nov 2017 20:39:03 +0000"  >&lt;p&gt;[attachment &quot;diag_log_3_6rc3.tar.gz&quot; deleted by Jim Van &lt;br/&gt;
Fleet/Austin/Contr/IBM] &lt;br/&gt;
[attachment &quot;diag_log_3,4.tar.gz&quot; deleted by Jim Van &lt;br/&gt;
Fleet/Austin/Contr/IBM] &lt;/p&gt;</comment>
                            <comment id="1724241" author="jvf" created="Mon, 13 Nov 2017 17:45:04 +0000"  >&lt;p&gt;Sorry, used 3.6.0-rc3  &amp;#8211; what I have seen is similar behavior in &lt;br/&gt;
localhost_27017_20171113&lt;/p&gt;

&lt;p&gt;ycsb workloada &amp;#8211; 50% read, 50% write&lt;/p&gt;

&lt;p&gt;FYI &amp;#8211; throughput for rc3 is 163173; for 3.4 is 300110&lt;/p&gt;

&lt;p&gt;perf top output &amp;#8211; rc3&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;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;   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;      23.67%  [kernel]                 [k] snooze_loop&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;  16.33%  mongod                   [.] __wt_update_obsolete_check&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;   7.88%  [kernel]                 [k] _raw_spin_lock&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;   1.13%  mongod                   [.] __wt_row_search&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;   0.72%  mongod                   [.] __rec_txn_read&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;   0.63%  mongod                   [.] __wt_row_modify&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;   0.56%  mongod                   [.] tc_deletearray_nothrow&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;   0.55%  [kernel]                 [k] find_busiest_group&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;   0.54%  mongod                   [.] __wt_txn_get_snapshot&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;perf top output &amp;#8211; 3.4&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;  20.27%  [kernel]                 [k] snooze_loop&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;   1.71%  [kernel]                 [k] _raw_spin_lock&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;   1.58%  mongod                   [.] snappy::internal::CompressFragment&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;   1.57%  mongod                   [.] __wt_row_search&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;   1.07%  libc-2.24.so             [.] __memcpy_power7&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;   0.94%  mongod                   [.] tc_deletearray_nothrow&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;   0.71%  mongod                   [.] __wt_txn_get_snapshot&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;   0.58%  libpthread-2.24.so       [.] pthread_mutex_unlock&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;   0.49%  [kernel]                 [k] _raw_spin_lock_irqsave&lt;/span&gt;&lt;/pre&gt;
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&lt;p/&gt;</comment>
                            <comment id="1723678" author="alexander.gorrod" created="Mon, 13 Nov 2017 00:11:40 +0000"  >&lt;p&gt;&lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=jvf&quot; class=&quot;user-hover&quot; rel=&quot;jvf&quot;&gt;jvf&lt;/a&gt; Thanks for trying out the release candidate and sending feedback.&lt;/p&gt;

&lt;p&gt;Could you please:&lt;/p&gt;
&lt;ul&gt;
	&lt;li&gt;Give us details of the YCSB workload you were running&lt;/li&gt;
	&lt;li&gt;Give us details of the MongoDB configuration and setup you are using&lt;/li&gt;
	&lt;li&gt;Upload the content of the &lt;tt&gt;diagnostic.data&lt;/tt&gt; subdirectories and mongod log files from a run with &lt;tt&gt;3.4&lt;/tt&gt; and &lt;tt&gt;3.6-rc2&lt;/tt&gt;&lt;/li&gt;
&lt;/ul&gt;
</comment>
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