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Use singularity
===============
Install singularity
-------------------
The `oficial installation instructions <https://sylabs.io/guides/3.0/user-guide/installation.html>`_ have many steps.
Please don't install NeuroDebian repo from the repo as it holds v2.6 and eic image require singularity > 3.0.
Instead. If you have ubuntu, there is a `debian repo with 3.5.2 version <https://packages.debian.org/source/sid/singularity-container>`_,
which works pretty nicely (You will have to install dependencies, it will print them...)
.. code::
wget http://ftp.fi.debian.org/debian/pool/main/s/singularity-container/singularity-container_3.5.2+ds1-1_amd64.deb
sudo dpkg -i singularity-container_3.5.2+ds1-1_amd64.deb
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Install work environment
------------------------
The below command automatically creates the right working environment for detector development.
It checks if there are CVMFS images available (which is true for JLab and BNL farms) and links them or downloads images (which is a scenario for users laptops).
It also creates eic_shell with the right environment setup, prepares the current dir to work with detector or etc.
.. code::
curl https://eicweb.phy.anl.gov/containers/eic_container/-/raw/master/install.sh | bash
CVMFS
-----
For farms like at BNL or JLab the image is automatically replicated to CVMS:
.. code::
singularity run /cvmfs/singularity.opensciencegrid.org/eicweb/jug_xl:3.0-stable
Custom work environment
-----------------------
#. Clone the repository and go into the directory
.. code-block:: bash
git clone https://eicweb.phy.anl.gov/containers/eic_container.git
cd eic_container
#. Run the install script ``install.py`` to install to your ``<PREFIX>`` of choice
(e.g. $HOME/local/opt/eic_container_1.0.4). By default the
modeuefile will be installed to ``$PREFIX/../../etc/modulefiles``.
You can use the ``-v`` flag to select the version you want to install, or omit the
flag if you want to install the master build. The recommended stable
release version is ``v2.6.1``.
.. code-block:: bash
./install.py -v 2.6.1 <PREFIX>
Available flags:
.. code-block:: bash
-v VERSION, --version VERSION
(opt.) project version. Default: current version (in repo).
-b BIND_PATHS, --bind-path BIND_PATHS
(opt.) extra bind paths for singularity.
-m MODULE_PATH, --module-path MODULE_PATH
(opt.) Root module path where you want to install a
modulefile. D: <prefix>/../../etc/modulefiles
-l, --local Local install, will not install the modulefiles (you will have
to run the launcher scripts from their relative paths).
-f, --force Force-overwrite already downloaded container with the same name.
#. To use the container in installed mode, you can load the modulefile,
and then use the included apps as if they are native apps on your system!
.. code-block:: bash
module load eic_container
#. To use the container in local mode, you can install the container with the ``-l`` flag,
and then use the runscripts (under ``$PREFIX/bin``\ ) manually.
.. code-block:: bash
./install.py $PREFIX -l
...
$PREFIX/bin/eic-shell
#. (Advanced) If you need to add additional bind directives for the internal singularity container,
you can add them with the ``-b`` flag. Run ``./install.py -h`` to see a list of all
supported options.
Modulefiles
^^^^^^^^^^^
Running the singularity development environment with modulefiles
#. Add the installed modulefile to your module path, e.g.,
.. code-block:: bash
module use <prefix>/../../etc/modulefiles
#. Load the eic container
.. code-block:: bash
module load eic_container
#. To start a shell in the container environment, do
.. code-block:: bash
eic-shell
Without modulefiles
^^^^^^^^^^^^^^^^^^^
Running the singularity development locally (without modulefiles)
1. This is assuming you installed with the ``-l`` flag to a prefix ``$PREFIX``\ :
.. code-block:: bash
./install.py $PREFIX
2. To start a shell in the container environment, do
.. code-block:: bash
$PREFIX/bin/eic-shell