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Neil Voss, 08/13/2012 09:54 PM
Install EMAN2/SPARX¶
It is best to install EMAN2/SPARX from source, so that do not have conflicts with having two different versions of python on your system. Binaries of EMAN2/SPARX all come with their own python pre-installed.
This documentation assumes you are using CentOS 6 (written as of CentOS 6.2)
Install require pre-packages for EMAN2 compiling¶
yum based packages¶
- Make sure EPEL is install, if not go here: Download additional Software (CentOS Specific)
- Use yum to install devel libraries:
sudo yum install fftw-devel gsl-devel boost-python numpy \ PyQt4-devel cmake ipython hdf5-devel libtiff-devel libpng-devel \ PyOpenGL ftgl-devel db4-devel python-argparse openmpi-devel
bsddb3¶
Additionally you need to install the python-bsddb3 library (not available via YUM). I just use the pypi easy_installer, yum will never know.
sudo easy_install bsddb3
Download the source¶
- To download the source code go to the link:
- Click on "Current stable version - direct link"
- Go under the heading "Source" at bottom of page
- Click to download the eman-source-2.xx.tar.gz file (as of August 2012, 2.xx is 2.06)
Work with the source¶
- go to the directory with the source code
- extract the archive:
tar zxvf eman-source-2.06.tar.gz
- go into directory
cd EMAN2/src/build
- start configure script:
cmake ../eman2/
- Note: alternatively you can run
ccmake ../eman2/
and configure all the parameters
- Note: alternatively you can run
- start compiling:
make
- install to directory:
sudo make install
Set environmental variables¶
bash¶
sudo nano /etc/profile.d/eman2.sh
export EMAN2DIR=/usr/local/EMAN2 export PATH=${EMAN2DIR}/bin:${PATH} export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin
Test to see if code works¶
see http://blake.bcm.edu/emanwiki/EMAN2/FAQ/EMAN2_unittest
cd EMAN2/test/rt ./rt.py
Install MyMPI for SPARX MPI functions¶
see http://sparx-em.org/sparxwiki/MPI-installation
or https://www.nbcr.net/pub/wiki/index.php?title=MyMPI_Setup
This fixes this problem:
from mpi import mpi_init ImportError: No module named mpi
to install
- Download source
- tar zxvf
- cd directory
- setenv MPIINC /usr/include/openmpi-x86_64/
- ./configure --with-mpicc=/usr/lib64/openmpi/bin/mpicc
- if it fails you need to change these lines in configure
nano configure
elif test -d ${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include; then
PY_HEADER_NUMPY="-I${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include"
elif test -d ${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include; then
PY_HEADER_NUMPY="-I${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include"
- make
- cp -v src/mpi.so /usr/lib64/python2.6/site-packages/
- test: python -c 'from mpi import mpi_init'
- if it fails you need to change these lines in configure
nano configure
elif test -d ${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include; then PY_HEADER_NUMPY="-I${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include"
elif test -d ${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include; then PY_HEADER_NUMPY="-I${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include"
Documentation¶
< Install EMAN 1 | Install SPIDER >
Updated by Neil Voss about 12 years ago · 39 revisions