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Installing Scipion v3.0

Prepare installation


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.

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 does not fail, you have pip. If you don’t have it please, check or use your package manager (yum, apt-get,…) to install pip or pip3.

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.

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 install 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

sudo yum -y install
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 some 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

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

To open the plugin manager, please run Scipion

cd scipion

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

Developers might want to build xmipp from the latest development version, please head here if this is your case. You might also want to check how to install plugins from the command line.

Optional steps

Fixing fonts in a conda installation

This will fix the fonts issue when using a conda installation

conda activate .scipion3env (all commands below are inside this env)
conda remove tk --force (removes bad tk)
conda install tk-8.6.10-h14c3975_1005.tar.bz2

Test the installation and learn how to use Scipion

We also provide some tests and tutorials to check that all is fine and to learn how to use Scipion.


Scipion3 can be run without any configuration file. If you want to know what are the default values type:

scipion3 printenv

If you are installing Scipion in a cluster or you want to change the default values you can proceed to generate the configuration files. If you had a previous Scipion installation, it is a good idea to make a copy of your current home config file ~/.config/scipion/scipion.conf Now run:

./scipion3 config

You will be asked to share scipion usage only data. Sharing usage data will help to make Scipion better.

This command will generate 3 configuration files at <SCIPION_HOME>/config.

If everything is OK (all green in the output) you can proceed to the next step. If there is a problem (red colored output), you will need to edit config/scipion.conf file in your preferred text editor and run ./scipion3 config again.

One known change for Ubuntu 18 and CentOS are the MPI paths in <your_scipion_home>/config/scipion.conf:

For Ubuntu 18:

MPI_LIBDIR = /usr/lib/x86_64-linux-gnu/openmpi/lib
MPI_INCLUDE = /usr/lib/x86_64-linux-gnu/openmpi/include/

For CentOS:

MPI_BINDIR = /usr/lib64/openmpi/bin
MPI_LIBDIR = /usr/lib64/openmpi/lib
MPI_INCLUDE = /usr/include/openmpi-x86_64

Read more about editing the configuration file.

The file config/hosts.conf contains some properties of the execution machine. This configuration file is particularly important for clusters that use a Queue System. If you are installing Scipion on a cluster, you probably will want to check how to configure an execution host.

If you have problems compiling Scipion, see Troubleshooting page.

Cleaning up (Optional)

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

Remove the files under software/tmp folder:

rm -rf sofware/tmp/*

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

rm -rf sofware/em/*.tgz

Tests and tutorials