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Scipion configuration

Running scipion config

This is the command used to generate config files or analyze them if you already have them.

./scipion config

The configuration files generated with this command are in two locations:

  • ~/.config/scipion/scipion.conf contains the configuration specific for the current user.

  • <your-scipion-home>/config contains configuration files for this Scipion installation, which will be applied to everyone using it. There are three files stored here:

    • <your-scipion-home>/config/scipion.conf with general variables to run scipion, install and use external libraries, etc.

    • <your-scipion-home>/config/hosts.conf with the host configuration. You can find more about it in the host configuration page.

    • <your-scipion-home>/config/protocols.conf with the list of protocols available in the Scipion installation. Not to be messed with unless you’re a developer and have a good known reason to do so.

scipion config might tell you it is not able to find some of the paths. In this case, you should edit config/scipion.conf to reflect your system’s configuration. For example, below is an excerpt of config/scipion.conf adapted for an Ubuntu computer:

CC = gcc
CXX = g++
MPI_LIBDIR = /usr/lib
MPI_INCLUDE = /usr/include/mpi
MPI_BINDIR = /usr/bin
JAVA_HOME = /usr/lib/jvm/java-1.7.0-openjdk-amd64

Once config/scipion.conf is changed, run ./scipion config again.

If you have configuration files from previous installations, you may want to use this instead:

./scipion config --overwrite

GPU variables

To install the GPU programs, you will need to set CUDA to True in scipion.conf. If CUDA is installed in a non-standard location, you will need to specify where to find CUDA libraries. For this, you can use the LINKFLAGS variable of scipion.conf. For example:

CUDA = True
LINKFLAGS = -L/opt/CUDA/cuda-5.5/lib64

OpenCV flag

To install Xmipp without OpenCV and, then skipping the programs using it (Optical Alignment and Volume Enrich), you will need to set OPENCV to False in scipion.conf:

OPENCV = False

Running Scipion in multi-users environment

In the case we want to install Scipion on a Cluster for many users, it is convenient to have a single scipion.conf file for all of them, otherwise, the each user must have a config file under his home folder as described above.

We can launch Scipion with the –config parameter: --config <scipion.conf PATH>. This parameter tells Scipion to be use a configuration file in a specific path.


In this case, the config file must be a union of the ~/.config/scipion/scipion.conf and ``<your-scipion-home>/config` and be placed in an accessible path to all users.

./scipion --config <scipion.conf PATH>