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<meta name="description" content=" Building CentOS image (emphasis on Ubuntu host) Dec 27, 2016 / This recipe describes how to build a CentOS image using Singularity, with special emphasis for Ubuntu compatible host.NOTE: this tutorial is intended for Singularity release 2.2, and reflects standards for that version.The ProblemIn theory, an Ubuntu host can create/bootstrap a CentOS image by installing the yum package, which is a front-end controller for RPM. In order for this to work on Ubuntu, a software called Berkeley DB must be identical in version to the version expected by yum. Unfortunately, these two verisons tend to be different, and this situation poses a difficult challenge for Singularity to deal with. A perfectly working centos.def file that can bootstrap a CentOS image from a RHEL-compatible host will not work when executed on Ubuntu, yielding the following error:YumRepo Error: All mirror URLs are not using ftp, http[s] or file.Eg. Invalid release/removing mirrorlist with no valid mirrors: /var/cache/yum/x86_64/$releasever/base/mirrorlist.txtError: Cannot find a valid baseurl for repo: baseERROR: Aborting with RETVAL=255 The error above results during the bootstrap process, and happens because Ubuntu is trying to use its version of Berkeley DB to create the RPM database in the CentOS image. Because of a version conflict, subsequent use of yum fails because it is unable parse the Berkeley DB.This problem is not exclusive to Ubuntu. Other flavors of Linux likely have the same problem. In fact, building a CentOS image hosted by a newer CentOS host results in the same problem!Potential SolutionsThere are a number of solutions: Obtain db*_load that match the Berkeley DB version for the version of CentOS being imaged, and add a conversion step during the Singularity bootstrap process. Perform a double bootstrap process: First build a base container containg CentOS (e.g. import from docker) and then 2) use this image to build the final desired CentOS image. You can run a container from within another container with Singularity as long as you are root when you do it. Go to a CentOS machine and create a basic singularity image, and copy this image to the Ubuntu machine. Since such an image already has working /bin/sh, rpm, yum commands, and an RPM database with the correct version of Berkeley DB, a subsequent singularity bootstrap on this image can successfully run yum to update and add additional software to this image. Leverage singularity import centos.img docker://centos:6 to seed the CentOS image. Import the container from Singularity Hub, when this feature becomes available.Create an image on CentOS (Option 3) Identify a CentOS machine with the same major version of CentOS you want to build. Don’t use a CentOS-7 machine to build a CentOS-6 machine, because it won’t work. (Building a CentOS-7 image on a CentOS-6 host works, but the RPM DB would actually be using an older version of Berkeley DB) Install Singularity on this host. Locate the centos.def file from the example/ directory. Edit to your heart’s desire (eg change OSVersion). Create the image, bootstrap, and run:sudo singularity create /tmp/centos.imgBootstrap:sudo singularity bootstrap /tmp/centos.img centos.defCopy /tmp/centos.img to the host where you want to run the container (e.g. the Ubuntu host).On the Ubuntu host, you can execute the CentOS container:singularity shell centos.imgIf further update is desired on this image, update the centos.def as desired, then run:singularity bootstrap centos.img centos.defAt this stage, the bootstrap works because the container already has the minimum requirements to run yum from its own content. There isn’t a need to install yum on the Ubuntu host.Bootstrap a Docker Container (Option 4)Instead of building your own seed CentOS image, the docker image imported using Option 4 can be used as well. Subsequent singularity bootstrap on such .img file works.Pursuing Option 1 or 2You will need to find the binary for various versions of db_load, and perhaps rename them to things like db43_load, db47_load, etc. You will then need to update the build-yum.sh script that comes with the Singularity distribution, and add steps to convert the RPM DB files in /var/lib/rpm to the desired version of Berkeley DB utilized by the target OS release.For further details of the above steps, refer to this thread on the mailing list, and look for postings by Tru Huynh.Miscellaneous troubleshooting notes The RPM command is NOT needed on the host to carry out the Singularity bootstrap process Initial bootstrap from an empty image needs yum, but after a basic image with /bin/sh and yum in place, the yum installation from inside the container is called. The RPM containing db*_load are different in different OS. Here is a helpful list:OS rpm path to db*_load CentOS-6 db4-utils-4.7.25-20.el6_7.x86_64 /usr/bin/db_loadCentOS-6 compat-db43-4.3.29-15.el6.x86_64 /usr/bin/db42_loadCentOS-6 compat-db42-4.2.52-15.el6.x86_64 /usr/bin/db43_loadCentOS-7 libdb-utils-5.3.21-19.el7.x86_64 /usr/bin/db_load Unfortunately the file command provided by coreutils cannot give accurate version details of Berkeley DB used by the RPM database. file /var/lib/rpm/Packages returns “version 9” in both CentOS 6 and 7. Unfortunately the db_dump command provided by db4-utils doesn’t help either. db_dump -p /var/lib/rpm/Packages | head -1 always returns “VERSION=3”, for RPM DB found natively in RHEL-6 and 7 hosts.Be careful with yum releaseIf building CentOS image from an Ubuntu host, one can seemingly use yum --releasever=6 to get yum to work and get a container to build. This kind of works, but some packages may be installed twice while others may not be consistent, since yum is not able to properly query the RPM database created in the first stage of the bootstrap process. This approach is NOT recommended for any long-lived container images. Please enable JavaScript to view the comments powered by Disqus. Site last generated: Jul 26, 2017 ">
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<h1 class="post-title" itemprop="name headline">Building CentOS image (emphasis on Ubuntu host)</h1>
<p class="post-meta"><time datetime="2016-12-27T00:00:00-05:00" itemprop="datePublished">Dec 27, 2016</time> /
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<p>This recipe describes how to build a CentOS image using Singularity, with special emphasis for Ubuntu compatible host.</p>
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<p><strong>NOTE: this tutorial is intended for <a href="http://singularity.lbl.gov/release-2-2">Singularity release 2.2</a>, and reflects standards for that version.</strong></p>
<h2 id="the-problem">The Problem</h2>
<p>In theory, an Ubuntu host can create/bootstrap a CentOS image by installing the <code class="highlighter-rouge">yum</code> package, which is a front-end controller for <a href="https://en.wikipedia.org/wiki/RPM_Package_Manager">RPM</a>. In order for this to work on Ubuntu, a software called <a href="https://en.wikipedia.org/wiki/Berkeley_DB">Berkeley DB</a> must be identical in version to the version expected by <code class="highlighter-rouge">yum</code>. Unfortunately, these two verisons tend to be different, and this situation poses a difficult challenge for Singularity to deal with. A perfectly working <code class="highlighter-rouge">centos.def</code> file that can bootstrap a CentOS image from a RHEL-compatible host will not work when executed on Ubuntu, yielding the following error:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>YumRepo Error: All mirror URLs are not using ftp, http[s] or file.
Eg. Invalid release/
removing mirrorlist with no valid mirrors: /var/cache/yum/x86_64/<span class="nv">$releasever</span>/base/mirrorlist.txt
Error: Cannot find a valid baseurl <span class="k">for </span>repo: base
ERROR: Aborting with <span class="nv">RETVAL</span><span class="o">=</span>255
</code></pre>
</div>
<p>The error above results during the bootstrap process, and happens because Ubuntu is trying to use its version of Berkeley DB to create the RPM database in the CentOS image. Because of a version conflict, subsequent use of <code class="highlighter-rouge">yum</code> fails because it is unable parse the Berkeley DB.</p>
<p>This problem is not exclusive to Ubuntu. Other flavors of Linux likely have the same problem. In fact, building a CentOS image hosted by a newer CentOS host results in the same problem!</p>
<h2 id="potential-solutions">Potential Solutions</h2>
<p>There are a number of solutions:</p>
<ol>
<li>Obtain <code class="highlighter-rouge">db*_load</code> that match the Berkeley DB version for the version of CentOS being imaged, and add a conversion step during the Singularity bootstrap process.</li>
<li>Perform a double bootstrap process: First build a base container containg CentOS (e.g. import from docker) and then 2) use this image to build the final desired CentOS image. You can run a container from within another container with Singularity as long as you are root when you do it.</li>
<li>Go to a CentOS machine and create a basic singularity image, and copy this image to the Ubuntu machine. Since such an image already has working <code class="highlighter-rouge">/bin/sh</code>, <code class="highlighter-rouge">rpm</code>, <code class="highlighter-rouge">yum</code> commands, and an RPM database with the correct version of Berkeley DB, a subsequent <code class="highlighter-rouge">singularity bootstrap</code> on this image can successfully run <code class="highlighter-rouge">yum</code> to update and add additional software to this image.</li>
<li>Leverage <code class="highlighter-rouge">singularity import centos.img docker://centos:6</code> to seed the CentOS image.</li>
<li>Import the container from Singularity Hub, when this feature becomes available.</li>
</ol>
<h3 id="create-an-image-on-centos-option-3">Create an image on CentOS (Option 3)</h3>
<ol>
<li>Identify a CentOS machine with the same major version of CentOS you want to build. Don’t use a CentOS-7 machine to build a CentOS-6 machine, because it won’t work. (Building a CentOS-7 image on a CentOS-6 host works, but the RPM DB would actually be using an older version of Berkeley DB)</li>
<li>Install Singularity on this host. Locate the <a href="https://github.com/singularityware/singularity/blob/2.x/examples/centos.def">centos.def</a> file from the <code class="highlighter-rouge">example/</code> directory. Edit to your heart’s desire (eg change OSVersion).</li>
<li>Create the image, bootstrap, and run:</li>
</ol>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>sudo singularity create /tmp/centos.img
</code></pre>
</div>
<p>Bootstrap:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>sudo singularity bootstrap /tmp/centos.img centos.def
</code></pre>
</div>
<p>Copy <code class="highlighter-rouge">/tmp/centos.img</code> to the host where you want to run the container (e.g. the Ubuntu host).
On the Ubuntu host, you can execute the CentOS container:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity shell centos.img
</code></pre>
</div>
<p>If further update is desired on this image, update the <code class="highlighter-rouge">centos.def</code> as desired, then run:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity bootstrap centos.img centos.def
</code></pre>
</div>
<p>At this stage, the bootstrap works because the container already has the minimum requirements to run <code class="highlighter-rouge">yum</code> from its own content. There isn’t a need to install <code class="highlighter-rouge">yum</code> on the Ubuntu host.</p>
<h3 id="bootstrap-a-docker-container-option-4">Bootstrap a Docker Container (Option 4)</h3>
<p>Instead of building your own seed CentOS image, the docker image imported using Option 4 can be used as well. Subsequent <code class="highlighter-rouge">singularity bootstrap</code> on such .img file works.</p>
<h3 id="pursuing-option-1-or-2">Pursuing Option 1 or 2</h3>
<p>You will need to find the binary for various versions of <code class="highlighter-rouge">db_load</code>, and perhaps rename them to things like <code class="highlighter-rouge">db43_load</code>, <code class="highlighter-rouge">db47_load</code>, etc. You will then need to update the <code class="highlighter-rouge">build-yum.sh</code> script that comes with the Singularity distribution, and add steps to convert the RPM DB files in <code class="highlighter-rouge">/var/lib/rpm</code> to the desired version of Berkeley DB utilized by the target OS release.</p>
<p>For further details of the above steps,
refer to <a href="https://groups.google.com/a/lbl.gov/forum/#!topic/singularity/gb-m2sjOLkM">this thread</a> on the mailing list, and look for postings by Tru Huynh.</p>
<h2 id="miscellaneous-troubleshooting-notes">Miscellaneous troubleshooting notes</h2>
<ul>
<li>The RPM command is NOT needed on the host to carry out the Singularity bootstrap process</li>
<li>Initial bootstrap from an empty image needs <code class="highlighter-rouge">yum</code>, but after a basic image with <code class="highlighter-rouge">/bin/sh</code> and <code class="highlighter-rouge">yum</code> in place, the <code class="highlighter-rouge">yum</code> installation from inside the container is called.</li>
<li>The RPM containing <code class="highlighter-rouge">db*_load</code> are different in different OS. Here is a helpful list:</li>
</ul>
<div class="highlighter-rouge"><pre class="highlight"><code>OS rpm path to db*_load
CentOS-6 db4-utils-4.7.25-20.el6_7.x86_64 /usr/bin/db_load
CentOS-6 compat-db43-4.3.29-15.el6.x86_64 /usr/bin/db42_load
CentOS-6 compat-db42-4.2.52-15.el6.x86_64 /usr/bin/db43_load
CentOS-7 libdb-utils-5.3.21-19.el7.x86_64 /usr/bin/db_load
</code></pre>
</div>
<ul>
<li>Unfortunately the <code class="highlighter-rouge">file</code> command provided by coreutils cannot give accurate version details of Berkeley DB used by the RPM database. <code class="highlighter-rouge">file /var/lib/rpm/Packages</code> returns “version 9” in both CentOS 6 and 7.</li>
<li>Unfortunately the <code class="highlighter-rouge">db_dump</code> command provided by <code class="highlighter-rouge">db4-utils</code> doesn’t help either. <code class="highlighter-rouge">db_dump -p /var/lib/rpm/Packages | head -1</code> always returns “VERSION=3”, for RPM DB found natively in RHEL-6 and 7 hosts.</li>
</ul>
<h3 id="be-careful-with-yum-release">Be careful with yum release</h3>
<p>If building CentOS image from an Ubuntu host, one can seemingly use <code class="highlighter-rouge">yum --releasever=6</code> to get <code class="highlighter-rouge">yum</code> to work and get a container to build. This kind of works, but some packages may be installed twice while others may not be consistent, since <code class="highlighter-rouge">yum</code> is not able to properly query the RPM database created in the first stage of the bootstrap process. This approach is <em>NOT</em> recommended for any long-lived container images.</p>
</div>
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