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Neil Voss, 08/14/2012 09:57 AM


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

  1. To download the source code go to the link:
  2. Click on "Current stable version - direct link"
  3. Go under the heading "Source" at bottom of page
  4. Click to download the eman-source-2.xx.tar.gz file (as of August 2012, 2.xx is 2.06)

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

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 1: python -c 'from mpi import mpi_init'
  • test 2: sxisac.py start.hdf (Note: start.hdf does not need to exist)

Documentation


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Updated by Neil Voss about 12 years ago · 41 revisions