Running scipion config¶
This is the command used to generate config files or analyze them if you already have them.
The configuration files generated with this command are in two locations:
~/.config/scipion/scipion.confcontains the configuration specific for the current user.
<your-scipion-home>/configcontains 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.confwith general variables to run scipion, install and use external libraries, etc.
<your-scipion-home>/config/hosts.confwith the host configuration. You can find more about it in the host configuration page.
<your-scipion-home>/config/protocols.confwith 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:
(...) [BUILD] 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 JAVA_BINDIR = %(JAVA_HOME)s/bin (...)
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
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
LINKFLAGS variable of
scipion.conf. For example:
CUDA = True LINKFLAGS = -L/opt/CUDA/cuda-5.5/lib64
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
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
``<your-scipion-home>/config` and be placed in an accessible path to all users.
./scipion --config <scipion.conf PATH>