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Scipion Configuration

Jose Miguel de la Rosa Trevin edited this page Jan 3, 2016 · 1 revision

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

./scipion config --overwrite

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.

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
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