Revision 55 - History - Install EMAN2 - Appion - Electron Microscopy Group

Install EMAN2 » History » Revision 55

Revision 54 (Neil Voss, 06/11/2013 01:07 PM) → Revision 55/87 (Amber Herold, 11/20/2013 04:46 PM)

h1. 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 The development trunk and future releases will require this software. 
 This documentation assumes you are using CentOS 6 (written as of CentOS 6.4) 6.2) 
 It is best to install EMAN2/SPARX from source, to avoid 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. 


 h2. Install pre-requisite packages 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> 

 h3. c shell 

 <pre>sudo nano /etc/profile.d/eman2.csh</pre> 

 <pre> 
 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 
 </pre> 


 h2. Install MyMPI 

 * Download source:  
 <pre>wget -O pydusa-1.15-sparx.tgz \ 
  'http://sparx-em.org/sparxwiki/MPI-installation?action=AttachFile&do=get&target=pydusa-1.15-sparx.tgz'</pre> 
 * Extract: 
 <pre>tar zxvf pydusa-1.15-sparx.tgz</pre> 
 * go into directory 
 <pre>cd pydusa-1.15-sparx</pre> 

 I had problems with the code finding the numpy headers: 

 <pre>nano configure</pre> 

 find the line: 
 <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> 
 and replace it with: 

 <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> 
 * Configure: 
 <pre> 
 setenv MPIROOT /usr/lib64/openmpi 
 setenv MPIINC /usr/include/openmpi-x86_64 
 setenv MPILIB ${MPIROOT}/lib 
 setenv MPIBIN ${MPIROOT}/bin 
 ./configure 
 </pre> 
 <pre> 
 export MPIROOT=/usr/lib64/openmpi 
 export MPIINC=/usr/include/openmpi-x86_64 
 export MPILIB=${MPIROOT}/lib 
 export MPIBIN=${MPIROOT}/bin 
 ./configure 
 </pre> 
 * compile the source: 
 <pre>make</pre> 
 * copy the mpi.so to site-packages with a different name: 
 <pre> 
 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 
 </pre> 
 * create a wrapper around the wrapper: 
 <pre>sudo nano /usr/lib64/python2.6/site-packages/mpi.py</pre> 
 <pre> 
 import ctypes 
 mpi = ctypes.CDLL('libmpi.so.1', ctypes.RTLD_GLOBAL) 
 from mympi.mpi import * 
 </pre> 
 This needs to be done to avoid the error: 
 <pre> 
 python: symbol lookup error:  
   /usr/lib64/openmpi/lib/openmpi/mca_paffinity_hwloc.so:  
     undefined symbol: mca_base_param_reg_int 
 </pre> 

 * test 1:  
 <pre> 
 python -c 'import mpi' 
 python -c 'import sys; from mpi import mpi_init; mpi_init(len(sys.argv), sys.argv)' 
 </pre> 

 * test 2:  
 <pre>sxisac.py start.hdf</pre> 
 (Note: start.hdf does not need to exist, if it does not exist then it should exit with file not found) 

 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 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> 

 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. 

 h2. Documentation 

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

 ______ 

 [[Install EMAN|< Install EMAN 1]] | [[Install SPIDER|Install SPIDER >]] 

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