Install EMAN2/SPARX¶

Before you begin:
Please note that Appion 2.2, Appion 2.2-redux and any earlier releases do not include any features that require EMAN2/SPARX to be installed. Appion 3.0, the development trunk and future releases will require this software.
This documentation assumes you are using CentOS 6 (written as of CentOS 6.4)
It is best to install EMAN2/SPARX from source, to avoid conflicts with having two different versions of python on your system. Binaries of EMAN2/SPARX all come with their own python pre-installed.

Install pre-requisite 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¶

1. To download the source code go to the link:
   • http://blake.bcm.edu/emanwiki/EMAN2
2. Click on "Main EMAN2 Download Page"
3. Click on "Download EMAN 2.0x", whichever is the latest minor release of 2.0.
4. Click to download the eman-source-2.xx.tar.gz file (as of November 2013, 2.xx is 2.07)

Work with the source¶

1. go to the directory with the source code
2. extract the archive:
   

   tar zxvf eman-source-2.06.tar.gz
   

3. go into directory
   

   cd EMAN2/src/build

4. start configure script:
   

   cmake ../eman2/

   • Note: alternatively you can run ccmake ../eman2/ and configure all the parameters
5. start compiling:
   

   make

6. 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

c shell¶

sudo nano /etc/profile.d/eman2.csh

setenv EMAN2DIR /usr/local/EMAN2
setenv PATH ${EMAN2DIR}/bin:${PATH}
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
setenv PYTHONPATH ${EMAN2DIR}/lib:${EMAN2DIR}/bin

Install MyMPI¶

• Download source:
  

  wget -O pydusa-1.15-sparx.tgz \
   'http://sparx-em.org/sparxwiki/MPI-installation?action=AttachFile&do=get&target=pydusa-1.15-sparx.tgz'

• Extract:
  

  tar zxvf pydusa-1.15-sparx.tgz

• go into directory
  

  cd pydusa-1.15-sparx

I had problems with the code finding the numpy headers:

nano configure

find the line:

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" 

and replace it with:

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" 

* Configure:

setenv MPIROOT /usr/lib64/openmpi
setenv MPIINC /usr/include/openmpi-x86_64
setenv MPILIB ${MPIROOT}/lib
setenv MPIBIN ${MPIROOT}/bin
./configure

export MPIROOT=/usr/lib64/openmpi
export MPIINC=/usr/include/openmpi-x86_64
export MPILIB=${MPIROOT}/lib
export MPIBIN=${MPIROOT}/bin
./configure

* compile the source:

make

* copy the mpi.so to site-packages with a different name:

sudo mkdir /usr/lib64/python2.6/site-packages/mympi/
sudo touch /usr/lib64/python2.6/site-packages/mympi/__init__.py
sudo cp -v src/mpi.so /usr/lib64/python2.6/site-packages/mympi/mpi.so

* create a wrapper around the wrapper:

sudo nano /usr/lib64/python2.6/site-packages/mpi.py

import ctypes
mpi = ctypes.CDLL('libmpi.so.1', ctypes.RTLD_GLOBAL)
from mympi.mpi import *

This needs to be done to avoid the error:

python: symbol lookup error: 
  /usr/lib64/openmpi/lib/openmpi/mca_paffinity_hwloc.so: 
    undefined symbol: mca_base_param_reg_int

• test 1:
  

  python -c 'import mpi'
  python -c 'import sys; from mpi import mpi_init; mpi_init(len(sys.argv), sys.argv)'
  

• test 2:
  

  sxisac.py start.hdf

  
  (Note: start.hdf does not need to exist, if it does not exist then it should exit with file not found)

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 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

This module was very difficult to get working, it seems to be a poorly supported python wrapper for MPI. So, what we are going to do is compile the module, rename it, and create a wrapper. So, essentially we are creating a wrapper around the wrapper. We can only hope they switch to [http://mpi4py.scipy.org/ mpi4py] in the future.

Documentation¶

• http://blake.bcm.edu/emanwiki/EMAN2/Install
• http://blake.bcm.edu/emanwiki/EMAN2/FAQ/eman2BuildFAQ

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