This is an extra exercise. It can not be run in Puhti. You will need access to a computer or a virtual machine where you have sudo rights and that has Singularity 3.x installed.
In this tutorial we create a Singularity container and install the same software as we installed in the tutorial Installing a simple C code from source You can see that tutorial for more information on the installation commands.
In this tutorial we only cover the basics. Detailed instructions can be found in the Singularity manual
One way to create a Singularity container is to do it in so-called sandbox mode. Instead of an read-only image file, we create a directory structure representing the file system of the container.
To start with we create a basic container from a definition file. To choose a suitable Linux distribution, you should check the documentation of the software you wish to install. If the the developers provide installation intructions for a specific distribution, it is usually easiest to start with that.
In this case there is no specific reason to choose one distribution over another, but from past experience I know the software installs without problems in CentOS, so we start with that.
We start from a very bare-bones definition file. Copy the following lines to
a file called centos.def.
Bootstrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include: yum
We the use that definition file to build teh container:
sudo singularity build --sandbox mcl centos.def
Note that instead of an image file, we created a directory called mcl. If
you need to include some reference files etc, you can copy them to correct subfolder.
We can then open a shell in that container. We need the container file system
to be writable, so we include option --writable:
sudo singularity shell --writable mcl
The command prompt should now be singularity>
If there is a need to make the container as small as possible, we should only install the dependencies we need. Usually the size is not that critical, so we may opt more for ease of use. In this case we install application group “Development tools” that includes most of the components we need (C, C++, make), but also things we don’t need in this case.
yum group install "Development Tools" -y
yum install wget -y
We are now ready to install.
Download and extract the distribuition package:
wget https://micans.org/mcl/src/mcl-latest.tar.gz
tar xf mcl-latest.tar.gz
cd mcl-14-137
Run configure:
./configure
Check the output of configure and install any missing dependencies
(In this case there should not be any.)
And finally run make:
make
make install
We can now test the application to see it works:
mcl --version
If everything works we can clean up:
cd ..
rm -rf mcl-*
We can also add a runscript:
echo '"$@"' >> /singularity
We can now exit the container:
exit
In order to run the container without sudo rights we need to build a production image from the sandbox:
sudo singularity build mcl.sif mcl
We can now test it. Note that we no longer need sudo:
singularity exec mcl.sif mcl --version
The above method is applicable as-is if you intend the container to be only used by you and your close collaborators. However, if you plan to distribute it wider, it’s best to write a definition file for it. That way the other users can, if they so choose, rebuild the production image.
A definition file will also make it easier to modify and re-use the container later. For example, software update can often be done simply by modifying the version number in the definition file and re-building the image.
To write the definition file we can start from the original bare-bones file and add various sections to it as necessary.
The installation commands go to section %post
%post
yum group install "Development Tools" -y
yum install wget -y
wget https://micans.org/mcl/src/mcl-latest.tar.gz
tar xf mcl-latest.tar.gz
cd mcl-14-137
./configure
make
make install
If you need to set any environment variables, they go to section %environment
If you need to include any files in the container they go to %files.
Runscript goes to %runscript.
There are also other sections available as necessary. More information can be found in the Definition file chapter of the Singularity manual
The final definition file will look like this:
Bootstrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include: yum
%post
yum group install "Development Tools" -y
yum install wget -y
wget https://micans.org/mcl/src/mcl-latest.tar.gz
tar xf mcl-latest.tar.gz
cd mcl-14-137
./configure
make
make install
cd ..
rm -rf mcl-*
%environment
export LC_ALL=C
%runscript
exec "$@"
In more complex cases it often helpful to first build the image in sandbox mode and make note of all the commands needed.