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<!DOCTYPE html>
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<meta name="description" content=" Getting Started with Bootstrap Previous Next Bootstrapping a ContainerBootstrapping is the process where we install an operating system and then configure it appropriately for a specified need. To do this we use a bootstrap definition file which is a recipe of how to specifically build the container and explained in detail in the previous section.For the purpose of this example, we will use the portions of the bootstrap definition file above, and assemble it into a complete definition file:# Bootstrap definition example for Centos-7 with the latest Open MPI from GitHub masterBootStrap: yumOSVersion: 7MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/Include: yum%setup echo "Looking in directory '$SINGULARITY_ROOTFS' for /bin/sh" if [ ! -x "$SINGULARITY_ROOTFS/bin/sh" ]; then echo "Hrmm, this container does not have /bin/sh installed..." exit 1 fi exit 0%post echo "Installing Development Tools YUM group" yum -y groupinstall "Development Tools" echo "Installing OpenMPI into container..." mkdir /tmp/git cd /tmp/git git clone https://github.com/open-mpi/ompi.git cd ompi ./autogen.pl ./configure --prefix=/usr/local make make install /usr/local/bin/mpicc examples/ring_c.c -o /usr/bin/mpi_ring cd / rm -rf /tmp/git exit 0%runscript echo "Arguments received: $*" exec /usr/bin/python "$@"%test /usr/local/bin/mpirun --allow-run-as-root /usr/bin/mpi_ringTaking this particular definition file as the example, we can use this to create our container.The Singularity bootstrap command syntax is as follows:$ singularity bootstrapUSAGE: singularity [...] bootstrap <container path> <definition file>The <container path> is the path to the Singularity image file, and the <definition file> is the location of the definition file (the recipe) we will use to create this container. The process of building a container should always be done by root so that the correct file ownership and permissions are maintained. Also, so installation programs check to ensure they are the root user before proceeding. The bootstrap process may take anywhere from one minute to one hour depending on what needs to be done and how fast your network connection is.Here are the steps necessary to create a container using the above definition file:$ sudo singularity create --size 2048 /tmp/Centos7-ompi.imgCreating a new image with a maximum size of 2048MiB...Executing image create helperFormatting image with ext3 file systemDone.$ sudo singularity bootstrap /tmp/Centos7-ompi.img centos7-ompi_master.def Bootstrap initializationChecking bootstrap definitionExecuting Prebootstrap moduleExecuting Bootstrap 'yum' module...+ /usr/local/bin/mpicc examples/ring_c.c -o /usr/bin/mpi_ring+ cd /+ rm -rf /tmp/git+ exit 0+ /usr/local/bin/mpirun --allow-run-as-root /usr/bin/mpi_ringProcess 0 sending 10 to 1, tag 201 (4 processes in ring)Process 0 sent to 1Process 0 decremented value: 9Process 0 decremented value: 8Process 0 decremented value: 7Process 0 decremented value: 6Process 0 decremented value: 5Process 0 decremented value: 4Process 0 decremented value: 3Process 0 decremented value: 2Process 0 decremented value: 1Process 0 decremented value: 0Process 0 exitingProcess 1 exitingProcess 2 exitingProcess 3 exitingYou can see from the output above, that the container has been built and the %test section has executed as expected. Our container has now been bootstrapped.For more examples we recommend that you look at the examples folder for the most up-to-date examples. Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<h2 id="bootstrapping-a-container">Bootstrapping a Container</h2>
<p>Bootstrapping is the process where we install an operating system and then configure it appropriately for a specified need. To do this we use a bootstrap definition file which is a recipe of how to specifically build the container and explained in detail in the previous section.</p>
<p>For the purpose of this example, we will use the portions of the bootstrap definition file above, and assemble it into a complete definition file:</p>
<div class="highlighter-rouge"><pre class="highlight"><code># Bootstrap definition example for Centos-7 with the latest Open MPI from GitHub master
BootStrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include: yum
%setup
echo "Looking in directory '$SINGULARITY_ROOTFS' for /bin/sh"
if [ ! -x "$SINGULARITY_ROOTFS/bin/sh" ]; then
echo "Hrmm, this container does not have /bin/sh installed..."
exit 1
fi
exit 0
%post
echo "Installing Development Tools YUM group"
yum -y groupinstall "Development Tools"
echo "Installing OpenMPI into container..."
mkdir /tmp/git
cd /tmp/git
git clone https://github.com/open-mpi/ompi.git
cd ompi
./autogen.pl
./configure --prefix=/usr/local
make
make install
/usr/local/bin/mpicc examples/ring_c.c -o /usr/bin/mpi_ring
cd /
rm -rf /tmp/git
exit 0
%runscript
echo "Arguments received: $*"
exec /usr/bin/python "$@"
%test
/usr/local/bin/mpirun --allow-run-as-root /usr/bin/mpi_ring
</code></pre>
</div>
<p>Taking this particular definition file as the example, we can use this to create our container.</p>
<p>The Singularity bootstrap command syntax is as follows:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity bootstrap
USAGE: singularity <span class="o">[</span>...] bootstrap <container path> <definition file>
</code></pre>
</div>
<p>The <code class="highlighter-rouge"><container path></code> is the path to the Singularity image file, and the <code class="highlighter-rouge"><definition file></code> is the location of the definition file (the recipe) we will use to create this container. The process of building a container should always be done by root so that the correct file ownership and permissions are maintained. Also, so installation programs check to ensure they are the root user before proceeding. The bootstrap process may take anywhere from one minute to one hour depending on what needs to be done and how fast your network connection is.</p>
<p>Here are the steps necessary to create a container using the above definition file:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>sudo singularity create --size 2048 /tmp/Centos7-ompi.img
Creating a new image with a maximum size of 2048MiB...
Executing image create helper
Formatting image with ext3 file system
Done.
<span class="gp">$ </span>sudo singularity bootstrap /tmp/Centos7-ompi.img centos7-ompi_master.def
Bootstrap initialization
Checking bootstrap definition
Executing Prebootstrap module
Executing Bootstrap <span class="s1">'yum'</span> module
...
+ /usr/local/bin/mpicc examples/ring_c.c -o /usr/bin/mpi_ring
+ <span class="nb">cd</span> /
+ rm -rf /tmp/git
+ <span class="nb">exit </span>0
+ /usr/local/bin/mpirun --allow-run-as-root /usr/bin/mpi_ring
Process 0 sending 10 to 1, tag 201 <span class="o">(</span>4 processes <span class="k">in </span>ring<span class="o">)</span>
Process 0 sent to 1
Process 0 decremented value: 9
Process 0 decremented value: 8
Process 0 decremented value: 7
Process 0 decremented value: 6
Process 0 decremented value: 5
Process 0 decremented value: 4
Process 0 decremented value: 3
Process 0 decremented value: 2
Process 0 decremented value: 1
Process 0 decremented value: 0
Process 0 exiting
Process 1 exiting
Process 2 exiting
Process 3 exiting
</code></pre>
</div>
<p>You can see from the output above, that the container has been built and the <code class="highlighter-rouge">%test</code> section has executed as expected. Our container has now been bootstrapped.</p>
<p><br />For more <strong>examples</strong> we recommend that you look at the <a href="https://github.com/singularityware/singularity/tree/master/examples" target="_blank">examples</a> folder for the most up-to-date examples.</p>
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