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<li class="toctree-l1 current"><a class="current reference internal" href="#">1. Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#prequisites">1.1. Prequisites</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#run-time">1.1.1. Run time</a></li>
<li class="toctree-l3"><a class="reference internal" href="#build-time">1.1.2. Build time</a></li>
<li class="toctree-l3"><a class="reference internal" href="#test-suite">1.1.3. Test suite</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#docker-install-tips">1.2. Docker install tips</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#understand-the-security-implications-of-docker">1.2.1. Understand the security implications of Docker</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#docker-equals-root">1.2.1.1. <code class="code docutils literal"><span class="pre">docker</span></code> equals root</a></li>
<li class="toctree-l4"><a class="reference internal" href="#images-can-contain-bad-stuff">1.2.1.2. Images can contain bad stuff</a></li>
<li class="toctree-l4"><a class="reference internal" href="#containers-run-as-root">1.2.1.3. Containers run as root</a></li>
<li class="toctree-l4"><a class="reference internal" href="#docker-alters-your-network-configuration">1.2.1.4. Docker alters your network configuration</a></li>
<li class="toctree-l4"><a class="reference internal" href="#docker-installs-services">1.2.1.5. Docker installs services</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#configuring-for-a-proxy">1.2.2. Configuring for a proxy</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#install-charliecloud">1.3. Install Charliecloud</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#download">1.3.1. Download</a></li>
<li class="toctree-l3"><a class="reference internal" href="#build">1.3.2. Build</a></li>
<li class="toctree-l3"><a class="reference internal" href="#install-optional">1.3.3. Install (optional)</a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="#test-charliecloud">1.4. Test Charliecloud</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id1">1.4.1. Build</a></li>
<li class="toctree-l3"><a class="reference internal" href="#run">1.4.2. Run</a></li>
<li class="toctree-l3"><a class="reference internal" href="#examples">1.4.3. Examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="#quick-and-multiple-phase-tests">1.4.4. Quick and multiple-phase tests</a></li>
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<div class="section" id="installation">
<h1>1. Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last"><strong>If you are installing on a Cray</strong> and have not applied the patch for Cray
case #188073, you must use the <a class="reference external" href="https://github.com/hpc/charliecloud/compare/cray">cray branch</a> to avoid crashing
nodes during job completion. This is a Cray bug that Charliecloud happens
to tickle. Non-Cray build boxes and others at the same site can still use
the master branch.</p>
</div>
<div class="contents local topic" id="contents">
<ul class="simple">
<li><a class="reference internal" href="#prequisites" id="id2">Prequisites</a><ul>
<li><a class="reference internal" href="#run-time" id="id3">Run time</a></li>
<li><a class="reference internal" href="#build-time" id="id4">Build time</a></li>
<li><a class="reference internal" href="#test-suite" id="id5">Test suite</a></li>
</ul>
</li>
<li><a class="reference internal" href="#docker-install-tips" id="id6">Docker install tips</a><ul>
<li><a class="reference internal" href="#understand-the-security-implications-of-docker" id="id7">Understand the security implications of Docker</a></li>
<li><a class="reference internal" href="#configuring-for-a-proxy" id="id8">Configuring for a proxy</a></li>
</ul>
</li>
<li><a class="reference internal" href="#install-charliecloud" id="id9">Install Charliecloud</a><ul>
<li><a class="reference internal" href="#download" id="id10">Download</a></li>
<li><a class="reference internal" href="#build" id="id11">Build</a></li>
<li><a class="reference internal" href="#install-optional" id="id12">Install (optional)</a></li>
</ul>
</li>
<li><a class="reference internal" href="#test-charliecloud" id="id13">Test Charliecloud</a><ul>
<li><a class="reference internal" href="#id1" id="id14">Build</a></li>
<li><a class="reference internal" href="#run" id="id15">Run</a></li>
<li><a class="reference internal" href="#examples" id="id16">Examples</a></li>
<li><a class="reference internal" href="#quick-and-multiple-phase-tests" id="id17">Quick and multiple-phase tests</a></li>
</ul>
</li>
</ul>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">These are general installation instructions. If you’d like specific,
step-by-step directions for CentOS 7, section <a class="reference internal" href="virtualbox.html"><span class="doc">VirtualBox appliance</span></a> has these
for a VirtualBox virtual machine.</p>
</div>
<div class="section" id="prequisites">
<h2><a class="toc-backref" href="#id2">1.1. Prequisites</a><a class="headerlink" href="#prequisites" title="Permalink to this headline">¶</a></h2>
<p>Charliecloud is a simple system with limited prerequisites. If your system
meets these prerequisites but Charliecloud doesn’t work, please report that as
a bug.</p>
<div class="section" id="run-time">
<h3><a class="toc-backref" href="#id3">1.1.1. Run time</a><a class="headerlink" href="#run-time" title="Permalink to this headline">¶</a></h3>
<p>Systems used for running images in the standard unprivileged mode need:</p>
<ul class="simple">
<li>Recent Linux kernel with <code class="code docutils literal"><span class="pre">CONFIG_USER_NS=y</span></code>. We recommend version 4.4
or higher.</li>
<li>C compiler and standard library</li>
<li>POSIX shell and utilities</li>
</ul>
<p>Some distributions need configuration changes to enable user namespaces. For
example, Debian Stretch needs sysctl
<code class="code docutils literal"><span class="pre">kernel.unprivileged_userns_clone=1</span></code>, and RHEL and CentOS 7.4 need both
a <a class="reference external" href="https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux_atomic_host/7/html-single/getting_started_with_containers/#user_namespaces_options">kernel command line option and a sysctl</a>
(that put you into “technology preview”).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">An experimental setuid mode is also provided that does not need user
namespaces. This should run on most currently supported Linux
distributions.</p>
</div>
</div>
<div class="section" id="build-time">
<h3><a class="toc-backref" href="#id4">1.1.2. Build time</a><a class="headerlink" href="#build-time" title="Permalink to this headline">¶</a></h3>
<p>Systems used for building images need the run-time prerequisites, plus:</p>
<ul class="simple">
<li>Bash 4.1+</li>
</ul>
<p>and optionally:</p>
<ul class="simple">
<li><a class="reference external" href="https://www.docker.com/">Docker</a> 17.03+</li>
<li>internet access or Docker configured for a local Docker hub</li>
<li>root access using <code class="code docutils literal"><span class="pre">sudo</span></code></li>
</ul>
<p>Older versions of Docker may work but are untested. We know that 1.7.1 does
not work.</p>
</div>
<div class="section" id="test-suite">
<h3><a class="toc-backref" href="#id5">1.1.3. Test suite</a><a class="headerlink" href="#test-suite" title="Permalink to this headline">¶</a></h3>
<p>In order to run the test suite on a run or build system (you can test each
mode independently), you also need:</p>
<ul class="simple">
<li>Bash 4.1+</li>
<li>Python 2.6+</li>
<li><a class="reference external" href="https://github.com/sstephenson/bats">Bats</a> 0.4.0</li>
<li>wget</li>
</ul>
<p>Note that without Docker on the build system, some of the test suite will be
skipped.</p>
<p>Bats can be installed at the system level or embedded in the Charliecloud
source code. If it’s in both places, the latter is used.</p>
<p>To embed Bats, either:</p>
<ul class="simple">
<li>Download Charliecloud using <code class="code docutils literal"><span class="pre">git</span> <span class="pre">clone</span> <span class="pre">--recursive</span></code>, which will check
out Bats as a submodule in <code class="code docutils literal"><span class="pre">test/bats</span></code>.</li>
<li>Unpack the Bats zip file or tarball in <code class="code docutils literal"><span class="pre">test/bats</span></code>.</li>
</ul>
<p>To check an embedded Bats:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> test/bats/bin/bats --version
<span class="go">Bats 0.4.0</span>
</pre></div>
</div>
</div>
</div>
<div class="section" id="docker-install-tips">
<h2><a class="toc-backref" href="#id6">1.2. Docker install tips</a><a class="headerlink" href="#docker-install-tips" title="Permalink to this headline">¶</a></h2>
<p>Tnstalling Docker is beyond the scope of this documentation, but here are a
few tips.</p>
<div class="section" id="understand-the-security-implications-of-docker">
<h3><a class="toc-backref" href="#id7">1.2.1. Understand the security implications of Docker</a><a class="headerlink" href="#understand-the-security-implications-of-docker" title="Permalink to this headline">¶</a></h3>
<p>Because Docker (a) makes installing random crap from the internet really easy
and (b) is easy to deploy insecurely, you should take care. Some of the
implications are below. This list should not be considered comprehensive nor a
substitute for appropriate expertise; adhere to your moral and institutional
responsibilities.</p>
<div class="section" id="docker-equals-root">
<h4>1.2.1.1. <code class="code docutils literal"><span class="pre">docker</span></code> equals root<a class="headerlink" href="#docker-equals-root" title="Permalink to this headline">¶</a></h4>
<p>Anyone who can run the <code class="code docutils literal"><span class="pre">docker</span></code> command or interact with the Docker
daemon can <a class="reference external" href="http://reventlov.com/advisories/using-the-docker-command-to-root-the-host">trivially escalate to root</a>.
This is considered a feature.</p>
<p>For this reason, don’t create the <code class="code docutils literal"><span class="pre">docker</span></code> group, as this will allow
passwordless, unlogged escalation for anyone in the group.</p>
</div>
<div class="section" id="images-can-contain-bad-stuff">
<h4>1.2.1.2. Images can contain bad stuff<a class="headerlink" href="#images-can-contain-bad-stuff" title="Permalink to this headline">¶</a></h4>
<p>Standard hygiene for “installing stuff from the internet” applies. Only work
with images you trust. The official Docker Hub repositories can help.</p>
</div>
<div class="section" id="containers-run-as-root">
<h4>1.2.1.3. Containers run as root<a class="headerlink" href="#containers-run-as-root" title="Permalink to this headline">¶</a></h4>
<p>By default, Docker runs container processes as root. In addition to being poor
hygiene, this can be an escalation path, e.g. if you bind-mount host
directories.</p>
</div>
<div class="section" id="docker-alters-your-network-configuration">
<h4>1.2.1.4. Docker alters your network configuration<a class="headerlink" href="#docker-alters-your-network-configuration" title="Permalink to this headline">¶</a></h4>
<p>To see what it did:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> ifconfig <span class="c1"># note docker0 interface</span>
<span class="gp">$</span> brctl show <span class="c1"># note docker0 bridge</span>
<span class="gp">$</span> route -n
</pre></div>
</div>
</div>
<div class="section" id="docker-installs-services">
<h4>1.2.1.5. Docker installs services<a class="headerlink" href="#docker-installs-services" title="Permalink to this headline">¶</a></h4>
<p>If you don’t want the service starting automatically at boot, e.g.:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> systemctl is-enabled docker
<span class="go">enabled</span>
<span class="gp">$</span> systemctl disable docker
<span class="gp">$</span> systemctl is-enabled docker
<span class="go">disabled</span>
</pre></div>
</div>
</div>
</div>
<div class="section" id="configuring-for-a-proxy">
<h3><a class="toc-backref" href="#id8">1.2.2. Configuring for a proxy</a><a class="headerlink" href="#configuring-for-a-proxy" title="Permalink to this headline">¶</a></h3>
<p>By default, Docker does not work if you have a proxy, and it fails in two
different ways.</p>
<p>The first problem is that Docker itself must be told to use a proxy. This
manifests as:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> sudo docker run hello-world
<span class="go">Unable to find image 'hello-world:latest' locally</span>
<span class="go">Pulling repository hello-world</span>
<span class="go">Get https://index.docker.io/v1/repositories/library/hello-world/images: dial tcp 54.152.161.54:443: connection refused</span>
</pre></div>
</div>
<p>If you have a systemd system, the <a class="reference external" href="https://docs.docker.com/engine/admin/systemd/#http-proxy">Docker documentation</a> explains how to
configure this. If you don’t have a systemd system, then
<code class="code docutils literal"><span class="pre">/etc/default/docker</span></code> might be the place to go?</p>
<p>The second problem is that Docker containers need to know about the proxy as
well. This manifests as images failing to build because they can’t download
stuff from the internet.</p>
<p>The fix is to set the proxy variables in your environment, e.g.:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="go">export HTTP_PROXY=http://proxy.example.com:8088</span>
<span class="go">export http_proxy=$HTTP_PROXY</span>
<span class="go">export HTTPS_PROXY=$HTTP_PROXY</span>
<span class="go">export https_proxy=$HTTP_PROXY</span>
<span class="go">export ALL_PROXY=$HTTP_PROXY</span>
<span class="go">export all_proxy=$HTTP_PROXY</span>
<span class="go">export NO_PROXY='localhost,127.0.0.1,.example.com'</span>
<span class="go">export no_proxy=$NO_PROXY</span>
</pre></div>
</div>
<p>You also need to teach <code class="code docutils literal"><span class="pre">sudo</span></code> to retain them. Add the following to
<code class="code docutils literal"><span class="pre">/etc/sudoers</span></code>:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="go">Defaults env_keep+="HTTP_PROXY http_proxy HTTPS_PROXY https_proxy ALL_PROXY all_proxy NO_PROXY no_proxy"</span>
</pre></div>
</div>
<p>Because different programs use different subsets of these variables, and to
avoid a situation where some things work and others don’t, the Charliecloud
test suite (see below) includes a test that fails if some but not all of the
above variables are set.</p>
</div>
</div>
<div class="section" id="install-charliecloud">
<h2><a class="toc-backref" href="#id9">1.3. Install Charliecloud</a><a class="headerlink" href="#install-charliecloud" title="Permalink to this headline">¶</a></h2>
<div class="section" id="download">
<h3><a class="toc-backref" href="#id10">1.3.1. Download</a><a class="headerlink" href="#download" title="Permalink to this headline">¶</a></h3>
<p>See our GitHub project: <a class="reference external" href="https://github.com/hpc/charliecloud">https://github.com/hpc/charliecloud</a></p>
<p>The recommended download method is <code class="code docutils literal"><span class="pre">git</span> <span class="pre">clone</span> <span class="pre">--recursive</span></code>.</p>
</div>
<div class="section" id="build">
<h3><a class="toc-backref" href="#id11">1.3.2. Build</a><a class="headerlink" href="#build" title="Permalink to this headline">¶</a></h3>
<p>To build in the standard, unprivileged mode (recommended):</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make
</pre></div>
</div>
<p>To build in setuid mode (for testing if your kernel doesn’t support the user
namespace):</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make <span class="nv">SETUID</span><span class="o">=</span>yes
</pre></div>
</div>
<p>To build the documentation, see <code class="code docutils literal"><span class="pre">doc-src/README</span></code>.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Do not build as root. This is unsupported and may introduce security
problems.</p>
</div>
</div>
<div class="section" id="install-optional">
<h3><a class="toc-backref" href="#id12">1.3.3. Install (optional)</a><a class="headerlink" href="#install-optional" title="Permalink to this headline">¶</a></h3>
<p>You can run Charliecloud from the source directory, and it’s recommended you
at least run the test suite before installation to establish that your system
will work.</p>
<p>To install (FHS-compliant):</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make install <span class="nv">PREFIX</span><span class="o">=</span>/foo/bar
</pre></div>
</div>
<p>Note that <code class="code docutils literal"><span class="pre">PREFIX</span></code> is required; it does not default to
<code class="code docutils literal"><span class="pre">/usr/local</span></code> like many packages.</p>
</div>
</div>
<div class="section" id="test-charliecloud">
<span id="install-test-charliecloud"></span><h2><a class="toc-backref" href="#id13">1.4. Test Charliecloud</a><a class="headerlink" href="#test-charliecloud" title="Permalink to this headline">¶</a></h2>
<p>Charliecloud comes with a fairly comprehensive Bats test suite, in
<code class="code docutils literal"><span class="pre">test</span></code>. Go there:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> <span class="nb">cd</span> <span class="nb">test</span>
</pre></div>
</div>
<p>To check location and version of Bats used by the tests:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make where-bats
<span class="go">which bats</span>
<span class="go">/usr/bin/bats</span>
<span class="go">bats --version</span>
<span class="go">Bats 0.4.0</span>
</pre></div>
</div>
<p>Just like for normal use, the Charliecloud test suite is split into build and
run phases, and there is an additional phase that runs the examples’ test
suites. These phases can be tested independently on different systems.</p>
<p>Testing is coordinated by <code class="code docutils literal"><span class="pre">make</span></code>. The test targets run one or more test
suites. If any test suite has a failure, testing stops with an error message.</p>
<p>The tests need three work directories with several gigabytes of free space, in
order to store image tarballs, unpacked image directories, and permission test
fixtures. These are configured with environment variables:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> <span class="nb">export</span> <span class="nv">CH_TEST_TARDIR</span><span class="o">=</span>/var/tmp/tarballs
<span class="gp">$</span> <span class="nb">export</span> <span class="nv">CH_TEST_IMGDIR</span><span class="o">=</span>/var/tmp/images
<span class="gp">$</span> <span class="nb">export</span> <span class="nv">CH_TEST_PERMDIRS</span><span class="o">=</span><span class="s1">'/var/tmp /tmp'</span>
</pre></div>
</div>
<p><code class="code docutils literal"><span class="pre">CH_TEST_PERMDIRS</span></code> can be set to <code class="code docutils literal"><span class="pre">skip</span></code> in order to skip the file
permissions tests.</p>
<p>(Strictly speaking, the build phase needs only the first, and the example test
phase does not need the last one. However, for simplicity, the tests will
demand all three for all phases.)</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Bats will wait until all descendant processes finish before exiting, so if
you get into a failure mode where a test suite doesn’t clean up all its
processes, Bats will hang.</p>
</div>
<div class="section" id="id1">
<h3><a class="toc-backref" href="#id14">1.4.1. Build</a><a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
<p>In this phase, image building and associated functionality is tested.</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make test-build
<span class="go">bats build.bats build_auto.bats build_post.bats</span>
<span class="go"> ✓ create tarball directory if needed</span>
<span class="go"> ✓ documentations build</span>
<span class="go"> ✓ executables seem sane</span>
<span class="go">[...]</span>
<span class="go"> ✓ ch-build obspy</span>
<span class="go"> ✓ ch-docker2tar obspy</span>
<span class="go"> ✓ docker pull dockerpull</span>
<span class="go"> ✓ ch-docker2tar dockerpull</span>
<span class="go"> ✓ nothing unexpected in tarball directory</span>
<span class="go">41 tests, 0 failures</span>
</pre></div>
</div>
<p>Note that with an empty Docker cache, this test can be quite lengthy, half an
hour or more, because it builds all the examples as well as several basic
Dockerfiles for common Linux distributions and tools (in <code class="code docutils literal"><span class="pre">test</span></code>). With a
full cache, expect more like 1–2 minutes.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p>The easiest way to update the Docker images used in this test is to simply
delete all Docker containers and images, and let them be rebuilt:</p>
<div class="last highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> sudo docker rm <span class="k">$(</span>sudo docker ps -aq<span class="k">)</span>
<span class="gp">$</span> sudo docker rmi -f <span class="k">$(</span>sudo docker images -q<span class="k">)</span>
</pre></div>
</div>
</div>
</div>
<div class="section" id="run">
<h3><a class="toc-backref" href="#id15">1.4.2. Run</a><a class="headerlink" href="#run" title="Permalink to this headline">¶</a></h3>
<p>The run tests require the contents of <code class="code docutils literal"><span class="pre">$CH_TEST_TARDIR</span></code> produced by a
successful, complete build test. Copy this directory to the run
system.</p>
<p>Additionally, the user running the tests needs to be a member of at least 2
groups.</p>
<p>File permission enforcement is tested against specially constructed fixture
directories. These should include every meaningful mounted filesystem, and
they cannot be shared between different users. To create them:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> <span class="k">for</span> d in <span class="nv">$CH_TEST_PERMDIRS</span><span class="p">;</span> <span class="k">do</span> sudo ./make-perms-test <span class="nv">$d</span> <span class="nv">$USER</span> nobody<span class="p">;</span> <span class="k">done</span>
</pre></div>
</div>
<p>To skip this test (e.g., if you don’t have root), set
<code class="code docutils literal"><span class="pre">$CH_TEST_PERMDIRS</span></code> to <code class="code docutils literal"><span class="pre">skip</span></code>.</p>
<p>To run the tests:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make test-run
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h3><a class="toc-backref" href="#id16">1.4.3. Examples</a><a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
<p>Some of the examples include test suites of their own. This Charliecloud runs
those test suites, using a Slurm allocation if one is available or a single
node (localhost) if not.</p>
<p>These require that the run tests have been completed successfully.</p>
<p>Note that this test can take quite a while, and that single tests from
the Charliecloud perspective include entire test suites from the example’s
perspective, so be patient.</p>
<p>To run the tests:</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make test-test
</pre></div>
</div>
</div>
<div class="section" id="quick-and-multiple-phase-tests">
<h3><a class="toc-backref" href="#id17">1.4.4. Quick and multiple-phase tests</a><a class="headerlink" href="#quick-and-multiple-phase-tests" title="Permalink to this headline">¶</a></h3>
<p>We also provide the following additional test targets:</p>
<blockquote>
<div><ul class="simple">
<li><code class="code docutils literal"><span class="pre">test-quick</span></code>: key subset of build and run phases (nice for development)</li>
<li><code class="code docutils literal"><span class="pre">test</span></code>: build and run phases</li>
<li><code class="code docutils literal"><span class="pre">test-all</span></code>: all three phases</li>
</ul>
</div></blockquote>
<p>We recommend that a build box pass all phases so it can be used to run
containers for testing and development.</p>
</div>
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