Install EMAN2 » History » Revision 35
Revision 34 (Neil Voss, 08/13/2012 09:43 PM) → Revision 35/87 (Neil Voss, 08/13/2012 09:46 PM)
h1. 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)
h2. Install require pre-packages for EMAN2 compiling
h3. yum based packages
* Make sure EPEL is install, if not go here: [[Download additional Software (CentOS Specific)]]
* Use yum to install devel libraries:
<pre>
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
</pre>
h3. 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.
<pre>
sudo easy_install bsddb3
</pre>
h2. Download the source
# To download the source code go to the link:
#* http://blake.bcm.edu/emanwiki/EMAN2
# 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)
h2. Work with the source
# go to the directory with the source code
# extract the archive:
<pre>
tar zxvf eman-source-2.06.tar.gz
</pre>
# go into directory
<pre>cd EMAN2/src/build</pre>
# start configure script:
<pre>cmake ../eman2/</pre>
#* Note: alternatively you can run @ccmake ../eman2/@ and configure all the parameters
# start compiling:
<pre>make</pre>
# install to directory:
<pre>sudo make install</pre>
h2. Set environmental variables
h3. bash
<pre>sudo nano /etc/profile.d/eman2.sh</pre>
<pre>
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
</pre>
h2. Test to see if code works
see http://blake.bcm.edu/emanwiki/EMAN2/FAQ/EMAN2_unittest
<pre>
cd EMAN2/test/rt
./rt.py
</pre>
h2. 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:
<pre>
from mpi import mpi_init
ImportError: No module named mpi
</pre>
h3. 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
<pre>nano configure</pre>
<pre>
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"
</pre><pre>
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"
</pre>
h2. Documentation
* http://blake.bcm.edu/emanwiki/EMAN2/Install
* http://blake.bcm.edu/emanwiki/EMAN2/FAQ/eman2BuildFAQ
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[[Install EMAN|< Install EMAN 1]] | [[Install SPIDER|Install SPIDER >]]
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