Add notes for 2019-04-14

content/posts/2019-04.md

@@ -621,4 +621,28 @@ $ ./delete-metadata-values.py -i /tmp/2019-04-11-delete-6-subjects.csv -db dspac
 
 ![Java GC during Solr indexing Solr 4.10.4 settings](/cgspace-notes/2019/04/visualvm-solr-indexing-solr-settings.png)
 
+## 2019-04-14
+
+- Change DSpace Test (linode19) to use the Java GC tuning from the Solr 4.14.4 startup script:
+
+```
+GC_TUNE="-XX:NewRatio=3 \
+    -XX:SurvivorRatio=4 \
+    -XX:TargetSurvivorRatio=90 \
+    -XX:MaxTenuringThreshold=8 \
+    -XX:+UseConcMarkSweepGC \
+    -XX:+UseParNewGC \
+    -XX:ConcGCThreads=4 -XX:ParallelGCThreads=4 \
+    -XX:+CMSScavengeBeforeRemark \
+    -XX:PretenureSizeThreshold=64m \
+    -XX:+UseCMSInitiatingOccupancyOnly \
+    -XX:CMSInitiatingOccupancyFraction=50 \
+    -XX:CMSMaxAbortablePrecleanTime=6000 \
+    -XX:+CMSParallelRemarkEnabled \
+    -XX:+ParallelRefProcEnabled"
+```
+
+- I need to remember to check the Munin JVM graphs in a few days
+- It might be placebo, but the site *does* feel snappier...
+
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docs/2015-11/index.html

@@ -65,8 +65,7 @@ $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspac
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docs/2015-12/index.html

@@ -67,8 +67,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
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docs/2016-01/index.html

@@ -57,8 +57,7 @@ Update GitHub wiki for documentation of maintenance tasks.
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docs/2016-02/index.html

@@ -71,8 +71,7 @@ Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE&r
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docs/2016-03/index.html

@@ -57,8 +57,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
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docs/2016-04/index.html

@@ -61,8 +61,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
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docs/2016-05/index.html

@@ -65,8 +65,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
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docs/2016-06/index.html

@@ -63,8 +63,7 @@ Working on second phase of metadata migration, looks like this will work for mov
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docs/2016-07/index.html

@@ -79,8 +79,7 @@ In this case the select query was showing 95 results before the update
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docs/2016-08/index.html

@@ -73,8 +73,7 @@ $ git rebase -i dspace-5.5
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docs/2016-09/index.html

@@ -65,8 +65,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=or
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docs/2016-10/index.html

@@ -73,8 +73,7 @@ I exported a random item’s metadata as CSV, deleted all columns except id
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docs/2016-11/index.html

@@ -57,8 +57,7 @@ Add dc.type to the output options for Atmire’s Listings and Reports module
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docs/2016-12/index.html

@@ -81,8 +81,7 @@ Another worrying error from dspace.log is:
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docs/2017-01/index.html

@@ -57,8 +57,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
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docs/2017-02/index.html

@@ -85,8 +85,7 @@ Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name
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docs/2017-03/index.html

@@ -89,8 +89,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
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docs/2017-04/index.html

@@ -75,8 +75,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Th
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docs/2017-05/index.html

@@ -45,8 +45,7 @@
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     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
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docs/2017-06/index.html

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     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
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docs/2017-07/index.html

@@ -69,8 +69,7 @@ We can use PostgreSQL’s extended output format (-x) plus sed to format the
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docs/2017-08/index.html

@@ -89,8 +89,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
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docs/2017-09/index.html

@@ -65,8 +65,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account
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docs/2017-10/index.html

@@ -69,8 +69,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
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docs/2017-11/index.html

@@ -89,8 +89,7 @@ COPY 54701
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docs/2017-12/index.html

@@ -59,8 +59,7 @@ The list of connections to XMLUI and REST API for today:
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docs/2018-01/index.html

@@ -197,8 +197,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
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docs/2018-02/index.html

@@ -59,8 +59,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-pl
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docs/2018-03/index.html

@@ -53,8 +53,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
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docs/2018-04/index.html

@@ -55,8 +55,7 @@ Catalina logs at least show some memory errors yesterday:
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docs/2018-05/index.html

@@ -67,8 +67,7 @@ Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked
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docs/2018-06/index.html

@@ -95,8 +95,7 @@ sys     2m7.289s
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docs/2018-07/index.html

@@ -73,8 +73,7 @@ There is insufficient memory for the Java Runtime Environment to continue.
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docs/2018-08/index.html

@@ -81,8 +81,7 @@ I ran all system updates on DSpace Test and rebooted it
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docs/2018-09/index.html

@@ -59,8 +59,7 @@ I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I
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docs/2018-10/index.html

@@ -55,8 +55,7 @@ I created a GitHub issue to track this #389, because I’m super busy in Nai
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docs/2018-11/index.html

@@ -69,8 +69,7 @@ Today these are the top 10 IPs:
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docs/2018-12/index.html

@@ -69,8 +69,7 @@ I noticed that there is another issue with PDF thumbnails on CGSpace, and I see
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docs/2019-01/index.html

@@ -81,8 +81,7 @@ I don’t see anything interesting in the web server logs around that time t
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docs/2019-02/index.html

@@ -109,8 +109,7 @@ sys     0m1.979s
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docs/2019-03/index.html

@@ -75,8 +75,7 @@ I think I will need to ask Udana to re-copy and paste the abstracts with more ca
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docs/2019-04/index.html

@@ -38,7 +38,7 @@ $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-04/" />
 <meta property="article:published_time" content="2019-04-01T09:00:43&#43;03:00"/>
-<meta property="article:modified_time" content="2019-04-11T14:23:30&#43;03:00"/>
+<meta property="article:modified_time" content="2019-04-13T12:15:55&#43;03:00"/>
 
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="April, 2019"/>
@@ -81,9 +81,9 @@ $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace
   "@type": "BlogPosting",
   "headline": "April, 2019",
   "url": "https:\/\/alanorth.github.io\/cgspace-notes\/2019-04\/",
-  "wordCount": "3655",
+  "wordCount": "3724",
   "datePublished": "2019-04-01T09:00:43\x2b03:00",
-  "dateModified": "2019-04-11T14:23:30\x2b03:00",
+  "dateModified": "2019-04-13T12:15:55\x2b03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -101,8 +101,7 @@ $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace
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     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
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@@ -890,6 +889,33 @@ $ ./delete-metadata-values.py -i /tmp/2019-04-11-delete-6-subjects.csv -db dspac
 
 <p><img src="/cgspace-notes/2019/04/visualvm-solr-indexing-solr-settings.png" alt="Java GC during Solr indexing Solr 4.10.4 settings" /></p>
 
+<h2 id="2019-04-14">2019-04-14</h2>
+
+<ul>
+<li>Change DSpace Test (linode19) to use the Java GC tuning from the Solr 4.14.4 startup script:</li>
+</ul>
+
+<pre><code>GC_TUNE=&quot;-XX:NewRatio=3 \
+    -XX:SurvivorRatio=4 \
+    -XX:TargetSurvivorRatio=90 \
+    -XX:MaxTenuringThreshold=8 \
+    -XX:+UseConcMarkSweepGC \
+    -XX:+UseParNewGC \
+    -XX:ConcGCThreads=4 -XX:ParallelGCThreads=4 \
+    -XX:+CMSScavengeBeforeRemark \
+    -XX:PretenureSizeThreshold=64m \
+    -XX:+UseCMSInitiatingOccupancyOnly \
+    -XX:CMSInitiatingOccupancyFraction=50 \
+    -XX:CMSMaxAbortablePrecleanTime=6000 \
+    -XX:+CMSParallelRemarkEnabled \
+    -XX:+ParallelRefProcEnabled&quot;
+</code></pre>
+
+<ul>
+<li>I need to remember to check the Munin JVM graphs in a few days</li>
+<li>It might be placebo, but the site <em>does</em> feel snappier&hellip;</li>
+</ul>
+
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docs/404.html

@@ -28,8 +28,7 @@
     <!-- combined, minified CSS -->
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+    <!-- RSS 2.0 feed -->
-
     
 
     

docs/categories/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
-    
     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/categories/index.xml" title="CGSpace Notes" />
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docs/categories/notes/index.html

@@ -29,11 +29,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
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     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/categories/notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/categories/notes/index.xml" title="CGSpace Notes" />
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docs/categories/page/2/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
-    
     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/categories/index.xml" title="CGSpace Notes" />
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docs/categories/page/3/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
-    
     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
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docs/categories/page/4/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
-    
     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/categories/index.xml" title="CGSpace Notes" />
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docs/categories/page/5/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
-    
     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/categories/index.xml" title="CGSpace Notes" />
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docs/cgiar-library-migration/index.html

@@ -46,8 +46,7 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
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+    <!-- RSS 2.0 feed -->
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docs/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
-    
     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/index.xml" title="CGSpace Notes" />
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docs/page/2/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
-    
     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/index.xml" title="CGSpace Notes" />
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docs/page/3/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
-    
     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/index.xml" title="CGSpace Notes" />
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docs/page/4/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
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     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/index.xml" title="CGSpace Notes" />
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docs/page/5/index.html

@@ -43,11 +43,8 @@
     <!-- combined, minified CSS -->
     <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
 
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     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
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docs/posts/index.html

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     <!-- combined, minified CSS -->
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-    <link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
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docs/posts/page/2/index.html

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     <!-- combined, minified CSS -->
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-    <link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
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docs/posts/page/3/index.html

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     <!-- combined, minified CSS -->
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     <!-- RSS 2.0 feed -->
-    <link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
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docs/posts/page/4/index.html

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     <!-- combined, minified CSS -->
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-    <link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/posts/index.xml" title="CGSpace Notes" />
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docs/posts/page/5/index.html

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     <!-- combined, minified CSS -->
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-    <link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
+    <link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/posts/index.xml" title="CGSpace Notes" />
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docs/sitemap.xml

@@ -4,30 +4,30 @@
   
   <url>
     <loc>https://alanorth.github.io/cgspace-notes/2019-04/</loc>
-    <lastmod>2019-04-11T14:23:30+03:00</lastmod>
+    <lastmod>2019-04-13T12:15:55+03:00</lastmod>
   </url>
   
   <url>
     <loc>https://alanorth.github.io/cgspace-notes/</loc>
-    <lastmod>2019-04-11T14:23:30+03:00</lastmod>
+    <lastmod>2019-04-13T12:15:55+03:00</lastmod>
     <priority>0</priority>
   </url>
   
   <url>
     <loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
-    <lastmod>2019-04-11T14:23:30+03:00</lastmod>
+    <lastmod>2019-04-13T12:15:55+03:00</lastmod>
     <priority>0</priority>
   </url>
   
   <url>
     <loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
-    <lastmod>2019-04-11T14:23:30+03:00</lastmod>
+    <lastmod>2019-04-13T12:15:55+03:00</lastmod>
     <priority>0</priority>
   </url>
   
   <url>
     <loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
-    <lastmod>2019-04-11T14:23:30+03:00</lastmod>
+    <lastmod>2019-04-13T12:15:55+03:00</lastmod>
     <priority>0</priority>
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docs/tags/index.html

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docs/tags/notes/index.html

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-    <link href="https://alanorth.github.io/cgspace-notes/tags/notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
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docs/tags/notes/page/2/index.html

@@ -29,11 +29,8 @@
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-    <link href="https://alanorth.github.io/cgspace-notes/tags/notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
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docs/tags/notes/page/3/index.html

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-    <link href="https://alanorth.github.io/cgspace-notes/tags/notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
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docs/tags/notes/page/4/index.html

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-    <link href="https://alanorth.github.io/cgspace-notes/tags/notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
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docs/tags/page/2/index.html

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docs/tags/page/3/index.html

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themes/hugo-theme-bootstrap4-blog

@@ -1 +1 @@
-Subproject commit c079c28841d7a28019a7b8df2b2862c56589de3a
+Subproject commit dedf1bd62c505828021be676dfab66add5b5d3c0