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MODULES

To be able to deal with numerous software/libraries/compilers and their versions, Ukko 2 uses a module system. With the module system you can easily customize your working environment to be exactly as you want it.

Modules system modifies the environment variables of the user's shell so that the correct versions of executables are in the path and linker can find the correct version of needed libraries. For example, the command mpicc points to different compilers depending of the loaded module.

Note that not all modules are compatible with each other.

Module system, programs and modules

To list all programs that have been installed:

rpm -qa

To list all available modules that are compatible with the modules that you have currently loaded:

module avail

To load a module:

module load <modulename>

To switch or swap between two modules:

module swap <module1> <module2>

To list all loaded modules:

module list

To get info about a module:

module help <module-name>

To list all available modules:

module spider

If you add the name or part of the name as an argument, you will get more information about matching modules. If a version number is provided, you also see that module's requirements.
module spider int

To unload a module:

module unload <module-name>

To unload all modules:

module purge

Virtual Environments

To create a virtual environment, in this example Python 3.5.2:

module load Python/3.5.2-foss-2016b
mkdir python352 # any directory name, for your virtual environment
virtualenv python352
cd python352
source bin/activate pip install biopython # etc, any python packages you need

You may also install additional packages with pip inside the virtualenv:

./configure --prefix=$HOME/python352
make
make install

If a module or a program you need is missing, contact the it support it4science@helsinki.fi