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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-32146] Log slow oplog entry application</title>
                <link>https://jira.mongodb.org/browse/SERVER-32146</link>
                <project id="10000" key="SERVER">Core Server</project>
                    <description>&lt;p&gt;We log slow operations on the primary, it would also be helpful to log slow oplog application to see what&apos;s using system resources.&lt;/p&gt;</description>
                <environment></environment>
        <key id="467104">SERVER-32146</key>
            <summary>Log slow oplog entry application</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="13201">Fixed</resolution>
                                        <assignee username="vesselina.ratcheva@mongodb.com">Vesselina Ratcheva</assignee>
                                    <reporter username="judah.schvimer@mongodb.com">Judah Schvimer</reporter>
                        <labels>
                            <label>SWDI</label>
                            <label>neweng</label>
                    </labels>
                <created>Fri, 1 Dec 2017 21:19:31 +0000</created>
                <updated>Mon, 30 Oct 2023 23:10:13 +0000</updated>
                            <resolved>Thu, 25 Oct 2018 22:17:50 +0000</resolved>
                                                    <fixVersion>3.6.11</fixVersion>
                    <fixVersion>4.0.6</fixVersion>
                    <fixVersion>4.1.5</fixVersion>
                                    <component>Diagnostics</component>
                    <component>Replication</component>
                                        <votes>2</votes>
                                    <watches>14</watches>
                                                                                                                <comments>
                            <comment id="2125392" author="xgen-internal-githook" created="Thu, 24 Jan 2019 04:10:29 +0000"  >&lt;p&gt;Author:&lt;/p&gt;
{&apos;username&apos;: &apos;vessy-mongodb&apos;, &apos;email&apos;: &apos;vesselina.ratcheva@10gen.com&apos;, &apos;name&apos;: &apos;Vesselina Ratcheva&apos;}
&lt;p&gt;Message: &lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-32146&quot; title=&quot;Log slow oplog entry application&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-32146&quot;&gt;&lt;del&gt;SERVER-32146&lt;/del&gt;&lt;/a&gt; Log slow oplog entry application&lt;/p&gt;

&lt;p&gt;(cherry picked from commit 66434ba0a7930efedbe5e06a098ab8e7bb659cfa)&lt;br/&gt;
Branch: v3.6&lt;br/&gt;
&lt;a href=&quot;https://github.com/mongodb/mongo/commit/afb213ced669a328c90e0a0fb0b7e06bf92c0ccb&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;https://github.com/mongodb/mongo/commit/afb213ced669a328c90e0a0fb0b7e06bf92c0ccb&lt;/a&gt;&lt;/p&gt;</comment>
                            <comment id="2113138" author="xgen-internal-githook" created="Fri, 11 Jan 2019 23:50:13 +0000"  >&lt;p&gt;Author:&lt;/p&gt;
{&apos;username&apos;: &apos;vessy-mongodb&apos;, &apos;email&apos;: &apos;vesselina.ratcheva@10gen.com&apos;, &apos;name&apos;: &apos;Vesselina Ratcheva&apos;}
&lt;p&gt;Message: &lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-32146&quot; title=&quot;Log slow oplog entry application&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-32146&quot;&gt;&lt;del&gt;SERVER-32146&lt;/del&gt;&lt;/a&gt; Log slow oplog entry application&lt;/p&gt;

&lt;p&gt;(cherry picked from commit 66434ba0a7930efedbe5e06a098ab8e7bb659cfa)&lt;br/&gt;
Branch: v4.0&lt;br/&gt;
&lt;a href=&quot;https://github.com/mongodb/mongo/commit/3e27146079106a97aaea9d84109c7d699de75540&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;https://github.com/mongodb/mongo/commit/3e27146079106a97aaea9d84109c7d699de75540&lt;/a&gt;&lt;/p&gt;</comment>
                            <comment id="2042736" author="xgen-internal-githook" created="Thu, 25 Oct 2018 21:41:55 +0000"  >&lt;p&gt;Author:&lt;/p&gt;
{&apos;name&apos;: &apos;Vesselina Ratcheva&apos;, &apos;email&apos;: &apos;vesselina.ratcheva@10gen.com&apos;, &apos;username&apos;: &apos;vessy-mongodb&apos;}
&lt;p&gt;Message: &lt;a href=&quot;https://jira.mongodb.org/browse/SERVER-32146&quot; title=&quot;Log slow oplog entry application&quot; class=&quot;issue-link&quot; data-issue-key=&quot;SERVER-32146&quot;&gt;&lt;del&gt;SERVER-32146&lt;/del&gt;&lt;/a&gt; Log slow oplog entry application&lt;br/&gt;
Branch: master&lt;br/&gt;
&lt;a href=&quot;https://github.com/mongodb/mongo/commit/66434ba0a7930efedbe5e06a098ab8e7bb659cfa&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;https://github.com/mongodb/mongo/commit/66434ba0a7930efedbe5e06a098ab8e7bb659cfa&lt;/a&gt;&lt;/p&gt;</comment>
                            <comment id="2041059" author="vesselina.ratcheva" created="Wed, 24 Oct 2018 20:24:56 +0000"  >&lt;p&gt;In a different discussion, we considered whether we should support logging all oplog application (not just slow operations) at log level 1, similar to how slow commands are logged. We decided against this, as we have no real use for logging for non-slow operations on secondaries, especially given that the primary already has the ability to log that generously on its own end. Instead, we&apos;re more concerned with keeping the logs cleaner and minimizing the perf impact, so we&apos;re only going to log slow ops on secondaries.&lt;/p&gt;

&lt;p&gt;We&apos;ve seen no reason to diverge from the usage of &quot;slowMS&quot;, however, so we chose to use that threshold for secondary application logging as well.&lt;/p&gt;</comment>
                            <comment id="2030862" author="tess.avitabile" created="Thu, 11 Oct 2018 22:46:41 +0000"  >&lt;p&gt;Thanks for the clarification. I agree that the secondary performance does not look like it is significantly impacted. It looks like mostly we are seeing noise in sys-perf, since performance went up in some cases and down in others. And since the call to &lt;tt&gt;now()&lt;/tt&gt; did not show up in your linux-perf sample, it must not have been very lengthly. I am happy for you to proceed with this work.&lt;/p&gt;</comment>
                            <comment id="2030362" author="vesselina.ratcheva" created="Thu, 11 Oct 2018 17:37:47 +0000"  >&lt;p&gt;&lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=tess.avitabile&quot; class=&quot;user-hover&quot; rel=&quot;tess.avitabile&quot;&gt;tess.avitabile&lt;/a&gt;, these are all good questions! I&apos;m sorry if I wasn&apos;t clear.&lt;/p&gt;

&lt;p&gt;1) Both of the patches have the same changes. I just ran more than one to be sure, as the waterfall was a bit noisy.&lt;/p&gt;

&lt;p&gt;2) The output metric itself represents secondary performance, measured by the number of documents applied per second. The workload disables replication on the secondary, only re-enabling it after the primary is done receiving and flushing all the writes, so that the secondary has to replicate them all at once. (More info here: &lt;a href=&quot;http://sys-perf-workloads.s3-website-us-east-1.amazonaws.com/module-workloads_secondary_performance.html&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;documentation&lt;/a&gt;.)&lt;br/&gt;
On each row, the &quot;size_N&quot; suffix represents the document size, and &quot;count_N&quot; describes the number of documents. We should expect to see the clock reads have a more noticeable impact on the perf measurements for smaller documents. &lt;br/&gt;
The comparison is made against commits on the waterfall (I put down four to reduce noise).&lt;/p&gt;

&lt;p&gt;3) Of course! I wrote a bare-bones clock-reads-only version to POC/test this, which can be found &lt;a href=&quot;https://evergreen.mongodb.com/task/sys_perf_linux_3_node_replSet_secondary_performance_patch_60e75c2b8fc57478382efb38759d22b33bea8fae_5bbb974fc9ec447a2ebf58d3_18_10_08_17_44_25##%257B%2522compare%2522%253A%255B%257B%2522hash%2522%253A%252260e75c2b8fc57478382efb38759d22b33bea8fae%2522%257D%252C%257B%2522hash%2522%253A%25221d608%2522%257D%252C%257B%2522hash%2522%253A%25227a9b1%2522%257D%252C%257B%2522hash%2522%253A%2522b272b%2522%257D%252C%257B%2522hash%2522%253A%2522ba38c%2522%257D%255D%252C%2522perftab%2522%253A1%257D&quot; class=&quot;external-link&quot; target=&quot;_blank&quot; rel=&quot;nofollow noopener&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;

&lt;p&gt;4) It didn&apos;t show up in my output. &lt;/p&gt;

&lt;p&gt;Feel free to chime in if you have further questions/comments. The perf impact doesn&apos;t seem scary to me, but I&apos;m totally open to discussion. &lt;/p&gt;</comment>
                            <comment id="2030125" author="tess.avitabile" created="Thu, 11 Oct 2018 14:48:31 +0000"  >&lt;p&gt;Thanks, &lt;a href=&quot;https://jira.mongodb.org/secure/ViewProfile.jspa?name=vesselina.ratcheva&quot; class=&quot;user-hover&quot; rel=&quot;vesselina.ratcheva&quot;&gt;vesselina.ratcheva&lt;/a&gt;! I have a few follow-up questions.&lt;/p&gt;

&lt;p&gt;1) Is there a difference between the Evergreen runs #1 and #2?&lt;/p&gt;

&lt;p&gt;2) What does the output metric represent in the sys-perf tests?&lt;/p&gt;

&lt;p&gt;3) Can I please see the patch build, so that I can see where and how the clock read was done?&lt;/p&gt;

&lt;p&gt;4) Is it possible to see the clock read function call itself in the linux perf output, or was it so small that it didn&apos;t show up?&lt;/p&gt;</comment>
                            <comment id="2029686" author="vesselina.ratcheva" created="Wed, 10 Oct 2018 22:22:49 +0000"  >&lt;p&gt;I ran some perf measurements for adding two clock reads to every op application and the effect on performance seemed somewhat noticeable, but not worrisome in my opinion. I chose to use the &quot;fast clock source&quot;, since it offers acceptable precision for its low impact. &lt;/p&gt;

&lt;p&gt;Here are the secondary throughput results from Evergreen: (1:  &lt;span class=&quot;image-wrap&quot; style=&quot;&quot;&gt;&lt;a id=&quot;198479_thumb&quot; href=&quot;https://jira.mongodb.org/secure/attachment/198479/198479_evg1.png&quot; title=&quot;evg1.png&quot; file-preview-type=&quot;image&quot; file-preview-id=&quot;198479&quot; file-preview-title=&quot;evg1.png&quot;&gt;&lt;img src=&quot;https://jira.mongodb.org/secure/thumbnail/198479/_thumb_198479.png&quot; style=&quot;border: 0px solid black&quot; role=&quot;presentation&quot;/&gt;&lt;/a&gt;&lt;/span&gt; , 2:  &lt;span class=&quot;image-wrap&quot; style=&quot;&quot;&gt;&lt;a id=&quot;198480_thumb&quot; href=&quot;https://jira.mongodb.org/secure/attachment/198480/198480_evg2.png&quot; title=&quot;evg2.png&quot; file-preview-type=&quot;image&quot; file-preview-id=&quot;198480&quot; file-preview-title=&quot;evg2.png&quot;&gt;&lt;img src=&quot;https://jira.mongodb.org/secure/thumbnail/198480/_thumb_198480.png&quot; style=&quot;border: 0px solid black&quot; role=&quot;presentation&quot;/&gt;&lt;/a&gt;&lt;/span&gt; ). Those were obtained by running the secondary_performance suite in the Linux 3-node variant (that particular suite only uses 2 nodes).&lt;/p&gt;

&lt;p&gt;Local measurements were taken by running replica_sets_jscore_passthrough (which has 1 secondary) and waiting 15 seconds before intercepting the secondary&apos;s process with the linux perf tool. I&apos;ve filtered in only the &quot;syncApply&quot; measurements (that&apos;s the affected method), showing the top 30 lines. (base:  &lt;span class=&quot;image-wrap&quot; style=&quot;&quot;&gt;&lt;a id=&quot;198481_thumb&quot; href=&quot;https://jira.mongodb.org/secure/attachment/198481/198481_base.png&quot; title=&quot;base.png&quot; file-preview-type=&quot;image&quot; file-preview-id=&quot;198481&quot; file-preview-title=&quot;base.png&quot;&gt;&lt;img src=&quot;https://jira.mongodb.org/secure/thumbnail/198481/_thumb_198481.png&quot; style=&quot;border: 0px solid black&quot; role=&quot;presentation&quot;/&gt;&lt;/a&gt;&lt;/span&gt; , with reads:  &lt;span class=&quot;image-wrap&quot; style=&quot;&quot;&gt;&lt;a id=&quot;198482_thumb&quot; href=&quot;https://jira.mongodb.org/secure/attachment/198482/198482_withreads.png&quot; title=&quot;withreads.png&quot; file-preview-type=&quot;image&quot; file-preview-id=&quot;198482&quot; file-preview-title=&quot;withreads.png&quot;&gt;&lt;img src=&quot;https://jira.mongodb.org/secure/thumbnail/198482/_thumb_198482.png&quot; style=&quot;border: 0px solid black&quot; role=&quot;presentation&quot;/&gt;&lt;/a&gt;&lt;/span&gt; ) &lt;/p&gt;</comment>
                            <comment id="1875216" author="tess.avitabile" created="Thu, 26 Apr 2018 17:19:55 +0000"  >&lt;p&gt;Re-triaging this ticket, since it was in the Support Grab Bag.&lt;/p&gt;</comment>
                            <comment id="1752320" author="milkie" created="Thu, 14 Dec 2017 19:42:09 +0000"  >&lt;p&gt;For this, we&apos;ll need to be careful not to impact performance by adding another two clock reads for every oplog entry.&lt;/p&gt;</comment>
                            <comment id="1741817" author="asya" created="Mon, 4 Dec 2017 18:31:23 +0000"  >&lt;p&gt;Agreed, it&apos;s rather difficult to debug (for example) secondary reads when you have to look on the primary logs to guess which replicated writes might be slow and therefore impacting read performance.&lt;/p&gt;</comment>
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