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Add notes for 2016-02-09
Signed-off-by: Alan Orth <alan.orth@gmail.com>
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@ -109,3 +109,48 @@ $ ~/dspace/bin/dspace index-discovery -b
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## 2016-02-09
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- Re-sync DSpace Test with CGSpace
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- Help Sisay with OpenRefine
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- Enable HTTPS on DSpace Test using Let's Encrypt:
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```
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$ cd ~/src/git
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$ git clone https://github.com/letsencrypt/letsencrypt
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$ cd letsencrypt
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$ sudo service nginx stop
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# add port 443 to firewall rules
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$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
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$ sudo service nginx start
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$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
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```
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- We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: https://letsencrypt.org/howitworks/
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- I had to export some CIAT items that were being cleaned up on the test server and I noticed their `dc.contributor.author` fields have DSpace 5 authority index UUIDs...
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- To clean those up in OpenRefine I used this GREL expression: `value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")`
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- Getting more and more hangs on DSpace Test, seemingly random but also during CSV import
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- Logs don't always show anything right when it fails, but eventually one of these appears:
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```
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org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
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```
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- or
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```
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Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
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```
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- Right now DSpace Test's Tomcat heap is set to 1536m and we have quite a bit of free RAM:
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```
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# free -m
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total used free shared buffers cached
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Mem: 3950 3902 48 9 37 1311
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-/+ buffers/cache: 2552 1397
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Swap: 255 57 198
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```
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- So I'll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)
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@ -199,6 +199,57 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
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<p><img src="../images/2016/02/submit-button-ilri.png" alt="ILRI submission buttons" />
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<img src="../images/2016/02/submit-button-drylands.png" alt="Drylands submission buttons" /></p>
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<h2 id="2016-02-09:124a59adbaa8ef13e1518d003fc03981">2016-02-09</h2>
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<ul>
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<li>Re-sync DSpace Test with CGSpace</li>
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<li>Help Sisay with OpenRefine</li>
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<li>Enable HTTPS on DSpace Test using Let’s Encrypt:</li>
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</ul>
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<pre><code>$ cd ~/src/git
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$ git clone https://github.com/letsencrypt/letsencrypt
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$ cd letsencrypt
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$ sudo service nginx stop
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# add port 443 to firewall rules
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$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
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$ sudo service nginx start
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$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
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</code></pre>
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<ul>
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<li>We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: <a href="https://letsencrypt.org/howitworks/">https://letsencrypt.org/howitworks/</a></li>
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<li>I had to export some CIAT items that were being cleaned up on the test server and I noticed their <code>dc.contributor.author</code> fields have DSpace 5 authority index UUIDs…</li>
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<li>To clean those up in OpenRefine I used this GREL expression: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")</code></li>
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<li>Getting more and more hangs on DSpace Test, seemingly random but also during CSV import</li>
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<li>Logs don’t always show anything right when it fails, but eventually one of these appears:</li>
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</ul>
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<pre><code>org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>or</li>
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</ul>
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<pre><code>Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
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</code></pre>
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<ul>
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<li>Right now DSpace Test’s Tomcat heap is set to 1536m and we have quite a bit of free RAM:</li>
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</ul>
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<pre><code># free -m
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total used free shared buffers cached
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Mem: 3950 3902 48 9 37 1311
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-/+ buffers/cache: 2552 1397
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Swap: 255 57 198
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</code></pre>
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<ul>
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<li>So I’ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li>
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</ul>
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</section>
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<footer>
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@ -136,6 +136,57 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
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<p><img src="../images/2016/02/submit-button-ilri.png" alt="ILRI submission buttons" />
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<img src="../images/2016/02/submit-button-drylands.png" alt="Drylands submission buttons" /></p>
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<h2 id="2016-02-09:124a59adbaa8ef13e1518d003fc03981">2016-02-09</h2>
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<ul>
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<li>Re-sync DSpace Test with CGSpace</li>
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<li>Help Sisay with OpenRefine</li>
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<li>Enable HTTPS on DSpace Test using Let&rsquo;s Encrypt:</li>
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</ul>
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<pre><code>$ cd ~/src/git
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$ git clone https://github.com/letsencrypt/letsencrypt
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$ cd letsencrypt
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$ sudo service nginx stop
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# add port 443 to firewall rules
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$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
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$ sudo service nginx start
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$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
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</code></pre>
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<ul>
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<li>We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: <a href="https://letsencrypt.org/howitworks/">https://letsencrypt.org/howitworks/</a></li>
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<li>I had to export some CIAT items that were being cleaned up on the test server and I noticed their <code>dc.contributor.author</code> fields have DSpace 5 authority index UUIDs&hellip;</li>
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<li>To clean those up in OpenRefine I used this GREL expression: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,&quot;&quot;)</code></li>
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<li>Getting more and more hangs on DSpace Test, seemingly random but also during CSV import</li>
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<li>Logs don&rsquo;t always show anything right when it fails, but eventually one of these appears:</li>
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</ul>
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<pre><code>org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>or</li>
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</ul>
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<pre><code>Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
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</code></pre>
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<ul>
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<li>Right now DSpace Test&rsquo;s Tomcat heap is set to 1536m and we have quite a bit of free RAM:</li>
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</ul>
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<pre><code># free -m
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total used free shared buffers cached
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Mem: 3950 3902 48 9 37 1311
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-/+ buffers/cache: 2552 1397
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Swap: 255 57 198
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</code></pre>
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<ul>
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<li>So I&rsquo;ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li>
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</ul>
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</description>
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</item>
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@ -136,6 +136,57 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
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<p><img src="../images/2016/02/submit-button-ilri.png" alt="ILRI submission buttons" />
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<img src="../images/2016/02/submit-button-drylands.png" alt="Drylands submission buttons" /></p>
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<h2 id="2016-02-09:124a59adbaa8ef13e1518d003fc03981">2016-02-09</h2>
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<ul>
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<li>Re-sync DSpace Test with CGSpace</li>
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<li>Help Sisay with OpenRefine</li>
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<li>Enable HTTPS on DSpace Test using Let&rsquo;s Encrypt:</li>
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</ul>
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<pre><code>$ cd ~/src/git
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$ git clone https://github.com/letsencrypt/letsencrypt
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$ cd letsencrypt
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$ sudo service nginx stop
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# add port 443 to firewall rules
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$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
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$ sudo service nginx start
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$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
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</code></pre>
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<ul>
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<li>We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: <a href="https://letsencrypt.org/howitworks/">https://letsencrypt.org/howitworks/</a></li>
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<li>I had to export some CIAT items that were being cleaned up on the test server and I noticed their <code>dc.contributor.author</code> fields have DSpace 5 authority index UUIDs&hellip;</li>
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<li>To clean those up in OpenRefine I used this GREL expression: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,&quot;&quot;)</code></li>
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<li>Getting more and more hangs on DSpace Test, seemingly random but also during CSV import</li>
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<li>Logs don&rsquo;t always show anything right when it fails, but eventually one of these appears:</li>
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</ul>
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<pre><code>org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>or</li>
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</ul>
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<pre><code>Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
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</code></pre>
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<ul>
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<li>Right now DSpace Test&rsquo;s Tomcat heap is set to 1536m and we have quite a bit of free RAM:</li>
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</ul>
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<pre><code># free -m
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total used free shared buffers cached
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Mem: 3950 3902 48 9 37 1311
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-/+ buffers/cache: 2552 1397
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Swap: 255 57 198
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</code></pre>
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<ul>
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<li>So I&rsquo;ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li>
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</ul>
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</description>
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</item>
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