Appion

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>

* make

* cp -v src/mpi.so /usr/lib64/python2.6/site-packages/

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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