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Add notes for 2018-04-10
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@ -21,7 +21,7 @@ Catalina logs at least show some memory errors yesterday:
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<meta property="article:published_time" content="2018-04-01T16:13:54+02:00"/>
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<meta property="article:modified_time" content="2018-04-04T15:57:34+03:00"/>
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<meta property="article:modified_time" content="2018-04-04T17:01:08+03:00"/>
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@ -43,7 +43,7 @@ Catalina logs at least show some memory errors yesterday:
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"/>
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<meta name="generator" content="Hugo 0.38" />
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<meta name="generator" content="Hugo 0.38.2" />
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@ -53,9 +53,9 @@ Catalina logs at least show some memory errors yesterday:
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"@type": "BlogPosting",
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"headline": "April, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-04/",
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"wordCount": "423",
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"wordCount": "1005",
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"datePublished": "2018-04-01T16:13:54+02:00",
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"dateModified": "2018-04-04T15:57:34+03:00",
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"dateModified": "2018-04-04T17:01:08+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -206,8 +206,162 @@ $ git rebase -i dspace-5.8
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</ul></li>
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<li>… but somehow git knew, and didn’t include them in my interactive rebase!</li>
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<li>I need to send this branch to Atmire and also arrange payment (see <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">ticket #560</a> in their tracker)</li>
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<li>Fix Sisay’s SSH access to the new DSpace Test server (linode19)</li>
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</ul>
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<h2 id="2018-04-05">2018-04-05</h2>
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<ul>
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<li>Fix Sisay’s sudo access on the new DSpace Test server (linode19)</li>
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<li>The reindexing process on DSpace Test took <em>forever</em> yesterday:</li>
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</ul>
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<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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real 599m32.961s
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user 9m3.947s
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sys 2m52.585s
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</code></pre>
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<ul>
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<li>So we really should not use this Linode block storage for Solr</li>
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<li>Assetstore might be fine but would complicate things with configuration and deployment (ughhh)</li>
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<li>Better to use Linode block storage only for backup</li>
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<li>Help Peter with the GDPR compliance / reporting form for CGSpace</li>
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<li>DSpace Test crashed due to memory issues again:</li>
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</ul>
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<pre><code># grep -c 'java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
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16
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</code></pre>
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<ul>
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<li>I ran all system updates on DSpace Test and rebooted it</li>
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<li>Proof some records on DSpace Test for Udana from IWMI</li>
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<li>He has done better with the small syntax and consistency issues but then there are larger concerns with not linking to DOIs, copying titles incorrectly, etc</li>
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</ul>
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<h2 id="2018-04-10">2018-04-10</h2>
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<ul>
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<li>I got a notice that CGSpace CPU usage was very high this morning</li>
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<li>Looking at the nginx logs, here are the top users today so far:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "10/Apr/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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282 207.46.13.112
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286 54.175.208.220
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287 207.46.13.113
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298 66.249.66.153
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322 207.46.13.114
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780 104.196.152.243
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3994 178.154.200.38
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4295 70.32.83.92
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4388 95.108.181.88
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7653 45.5.186.2
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</code></pre>
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<ul>
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<li>45.5.186.2 is of course CIAT</li>
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<li>95.108.181.88 appears to be Yandex:</li>
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</ul>
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<pre><code>95.108.181.88 - - [09/Apr/2018:06:34:16 +0000] "GET /bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg HTTP/1.1" 200 2638 "-" "Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)"
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</code></pre>
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<ul>
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<li>And for some reason Yandex created a lot of Tomcat sessions today:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=95.108.181.88' dspace.log.2018-04-10
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4363
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</code></pre>
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<ul>
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<li>70.32.83.92 appears to be some harvester we’ve seen before, but on a new IP</li>
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<li>They are not creating new Tomcat sessions so there is no problem there</li>
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<li>178.154.200.38 also appears to be Yandex, and is also creating many Tomcat sessions:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=178.154.200.38' dspace.log.2018-04-10
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3982
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</code></pre>
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<ul>
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<li>I’m not sure why Yandex creates so many Tomcat sessions, as its user agent should match the Crawler Session Manager valve</li>
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<li>Let’s try a manual request with and without their user agent:</li>
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</ul>
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<pre><code>$ http --print Hh https://cgspace.cgiar.org/bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg 'User-Agent:Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)'
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GET /bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg HTTP/1.1
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Accept: */*
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Accept-Encoding: gzip, deflate
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Connection: keep-alive
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Host: cgspace.cgiar.org
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User-Agent: Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)
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HTTP/1.1 200 OK
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Connection: keep-alive
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Content-Language: en-US
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Content-Length: 2638
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Content-Type: image/jpeg;charset=ISO-8859-1
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Date: Tue, 10 Apr 2018 05:18:37 GMT
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Expires: Tue, 10 Apr 2018 06:18:37 GMT
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Last-Modified: Tue, 25 Apr 2017 07:05:54 GMT
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Server: nginx
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Strict-Transport-Security: max-age=15768000
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Vary: User-Agent
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X-Cocoon-Version: 2.2.0
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X-Content-Type-Options: nosniff
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X-Frame-Options: SAMEORIGIN
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X-XSS-Protection: 1; mode=block
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$ http --print Hh https://cgspace.cgiar.org/bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg
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GET /bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg HTTP/1.1
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Accept: */*
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Accept-Encoding: gzip, deflate
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Connection: keep-alive
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Host: cgspace.cgiar.org
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User-Agent: HTTPie/0.9.9
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HTTP/1.1 200 OK
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Connection: keep-alive
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Content-Language: en-US
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Content-Length: 2638
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Content-Type: image/jpeg;charset=ISO-8859-1
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Date: Tue, 10 Apr 2018 05:20:08 GMT
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Expires: Tue, 10 Apr 2018 06:20:08 GMT
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Last-Modified: Tue, 25 Apr 2017 07:05:54 GMT
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Server: nginx
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Set-Cookie: JSESSIONID=31635DB42B66D6A4208CFCC96DD96875; Path=/; Secure; HttpOnly
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Strict-Transport-Security: max-age=15768000
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Vary: User-Agent
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X-Cocoon-Version: 2.2.0
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X-Content-Type-Options: nosniff
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X-Frame-Options: SAMEORIGIN
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X-XSS-Protection: 1; mode=block
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</code></pre>
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<ul>
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<li>So it definitely looks like Yandex requests are getting assigned a session from the Crawler Session Manager valve</li>
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<li>And if I look at the DSpace log I see its IP sharing a session with other crawlers like Google (66.249.66.153)</li>
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<li>Indeed the number of Tomcat sessions appears to be normal:</li>
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</ul>
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<p><img src="/cgspace-notes/2018/04/jmx_dspace_sessions-week.png" alt="Tomcat sessions week" /></p>
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<ul>
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<li>Looks like the number of total requests processed by nginx in March went down from the previous months:</li>
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</ul>
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<pre><code># time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Mar/2018"
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2266594
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real 0m13.658s
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user 0m16.533s
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sys 0m1.087s
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</code></pre>
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