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:
(...)
[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
(...)
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.
IMPORTANT!!!!!
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>