Installing Scipion v3.0¶

Prepare installation¶

pip¶

You need to have python2 or 3 already and pip or pip3. There are several ways to test if pip is installed. Pip comes out of the box with conda, e.g.

conda activate

will bring you pip.

To test if you have pip available type:

python -m pip -V

Other alternatives would be:

python3 -m pip -V
pip -V
pip3 -V

If any of these commands works, you have pip. If you don’t have it please, check https://pip.pypa.io/en/stable/installing/ or use your package manager (yum, apt-get,…) to install pip or pip3.

CUDA (optional, highly recommended)¶

Many of the software that Scipion integrates use CUDA. You can have different CUDA versions installed and choose which CUDA to use for any particular software. Nevertheless, CUDA 10.1 seems to be compatible with the majority of them. We recommend to have CUDA 10.1 installed and being linked at /usr/local/cuda. By default scipion will use /usr/local/cuda and xmipp installation is done against this path.

Check the config guide for more detailed information.

Conda (optional, recommended if you are not admin)¶

Although conda is not a requirement, it provides most of the dependencies Scipion and Xmipp needs and can be installed without being admin/root.

Miniconda would be enough.

Scipion installation¶

We have prepared some recipes to install Scipion and its companion Xmipp in the most simplified way. Below you can find some installation hints that could help you to troubleshoot your case. Scipion can be installed using conda or virtualenv. Conda installation has one drawback: conda will not identify properly the fonts in your system and you will end up with a font we didn’t intend but readable and workable. Don’t worry there is a fix for this bellow.

If you have problems during the Scipion’s installation, please, check our Troubleshooting page.

To install Scipion in development mode, just add the -dev flag in the last command of each recipe below (git is needed in the development mode).

In addition, you can replace the last command of each recipe below by python -m scipioninstaller --help in order to figure out more options regarding the Scipion’s installation.

Ubuntu with conda¶

sudo apt-get install gcc-8 g++-8 libopenmpi-dev make
conda activate
export CXX_CUDA=g++-8
export PATH=$PATH:/usr/local/cuda/bin
pip install --user scipion-installer
python -m scipioninstaller /path/where/you/want/scipion -j 4

Ubuntu with virtualenv¶

sudo apt-get install gcc g++ make libopenmpi-dev python3-tk libfftw3-dev libhdf5-dev libtiff-dev libjpeg-dev libsqlite3-dev openjdk-8-jdk
export PATH=$PATH:/usr/local/cuda/bin
python -m pip install --user scipion-installer
python -m scipioninstaller /path/where/you/want/scipion -venv -j 4

CentOS with conda¶

sudo yum -y install epel-release
sudo yum-config-manager --enable epel
sudo yum -y install libzstd-devel hdf5-devel gcc gcc-c++ openmpi-devel
export PATH=$PATH:/usr/lib64/openmpi/bin/:/usr/local/cuda/bin
conda activate
pip install --user scipion-installer
python3 -m scipioninstaller /path/where/you/want/scipion -j 4

CentOS with virtualenv¶

CentOS 7¶

sudo yum -y install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
sudo yum install dnf
sudo dnf -y install libaec-devel
sudo yum install gcc gcc-c++ make openmpi-devel python3-devel python3-tkinter wget fftw-devel hdf5-devel libtiff-devel libjpeg-devel sqlite-devel.x86_64 java-1.8.0-openjdk-devel
export PATH=$PATH:/usr/lib64/openmpi/bin/:/usr/local/cuda/bin
python3 -m pip install --user scipion-installer
python3 -m scipioninstaller /path/where/you/want/scipion -venv -j 4

CentOS 8¶

sudo yum -y install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm
sudo yum install dnf
sudo dnf -y --enablerepo=PowerTools install libaec-devel
sudo yum install gcc gcc-c++ make openmpi-devel python3-devel python3-tkinter wget fftw-devel hdf5-devel libtiff-devel libjpeg-devel sqlite-devel.x86_64 java-1.8.0-openjdk-devel
export PATH=$PATH:/usr/lib64/openmpi/bin/:/usr/local/cuda/bin
python3 -m pip install --user scipion-installer
python3 -m scipioninstaller /path/where/you/want/scipion -venv -j 4

Launching scipion3¶

Installation should have created a launching file at <SCIPION_HOME>/scipion3. For convenience, create an alias in the .bashrc file located in /home/<user>/.bashrc that allows you to launch Scipion from any location on your computer.

alias scipion3='<SCIPION_HOME>/scipion3'

You can always launch it like <SCIPION_HOME>/scipion3 or ./scipion3 (if you are already in scipion’s installation folder)

Installing other EM Plugins¶

Scipion3 can use many EM plugins.

If you intend to develop a plugin, check the For developers section below. However, if you only want to use the plugin, just follow the For users section below.

For users¶

Scipion installation includes also the Xmipp installation, by default.

To list and install more plugins you can use the plugin manager (recommended) or, alternatively, use the command line tool.

To open the plugin manager, please run Scipion

scipion3

and choose Others > Plugin manager on the top bar. There, any plugin can be easily installed.

Please, refer to the Plugin manager guide to get more details about plugin installation options.

For developers¶

Scipion installation also includes the Xmipp installation, by default. If you have installed Scipion in devel mode, Xmipp should be also installed in devel mode at <SCIPION_HOME>/xmipp-bundle. See the Xmipp structure guide for more information regarding Xmipp.

You might also want to check how to install plugins from the command line in order to also install some other plugins in development mode. Notice that some plugins can be installed in production mode (see section above) while others can be in devel mode. To learn specific instructions regarding a devel installation of a given plugin, please, check the ‘Readme’ file in its github repository (usually at scipion-em github account under its plugin’s name).

Optional steps¶

Fixing fonts in a conda installation¶

This will fix the fonts issue when using conda installation

conda activate .scipion3env
conda remove tk --force
wget https://anaconda.org/scipion/tk/8.6.10/download/linux-64/tk-8.6.10-h14c3975_1005.tar.bz2
conda install tk-8.6.10-h14c3975_1005.tar.bz2

Configure¶

In Scipion3, configuration step is optional. Without a configuration file, Scipion and the plugins will run with default values and what is available in the system (usually what is exposed with PATH and LD_LIBRARY_PATH).

Please, check Scipion’s configuration page for more details.

Linking existing software¶

If you have an existing installation you want Scipion to use instead of the one that scipion installs. Please, check Linking existing software for more details.

Test the installation and learn how to use Scipion¶

Test your installation by running at least the Small and Medium tests mentioned in verify installation page.
Complete some of the Scipion Tutorials.

Cleaning up¶

After Scipion is installed and properly working (see how to run tests in the previous section) one could clean some temporary files to free some disk space after installation.

Remove the files under software/tmp folder (if exists):

rm -rf sofware/tmp/*

The downloaded .tgz files of the EM packages can also be removed:

rm -rf sofware/em/*.tgz