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 6.5)
It is best to install EMAN2/SPARX from source to get MPI working on a cluster or 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 libjpeg-devel \
   PyQt4-devel cmake ipython hdf5-devel libtiff-devel libpng-devel libdb-devel \
   PyOpenGL ftgl-devel db4-devel python-argparse openmpi-devel python-pip
  

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 pip 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", whichever is the latest release of EMAN.
4. Scroll down to Source to download the eman2.1beta3.source.tar.gz

Work with the source¶

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

   tar zxvf eman2.1beta3.source.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
     

     -- The C compiler identification is GNU 4.4.7
     -- The CXX compiler identification is GNU 4.4.7
     -- Check for working C compiler: /usr/bin/cc
     -- Check for working C compiler: /usr/bin/cc -- works
     -- Detecting C compiler ABI info
     -- Detecting C compiler ABI info - done
     -- Check for working CXX compiler: /usr/bin/c++
     -- Check for working CXX compiler: /usr/bin/c++ -- works
     -- Detecting CXX compiler ABI info
     -- Detecting CXX compiler ABI info - done
     -- Looking for fseek64
     -- Looking for fseek64 - not found
     -- Looking for fseeko
     -- Looking for fseeko - found
     -- Looking for ftell64
     -- Looking for ftell64 - not found
     -- Looking for ftello
     -- Looking for ftello - found
     -- Configuring done
     -- Generating done
     -- Build files have been written to: /emg/sw/EMAN2/src/build
     

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¶

• First, add the openmpi module so that MyMPI can find it.
  

  module add openmpi-i386
  -or-
  module add openmpi-x86_64
  

• Download source:
  From the main software page: http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222 scroll to MPI Support.
  Click on Download MPI Support
  Click on pydusa-1.15es.tgz
• Extract:
  

  tar zxvf pydusa-1.15es.tgz

• go into directory
  

  cd pydusa-1.15es

  
   
  If you are on a 64bit machine, you may have 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
  

  
  Please ensure mpicc was found. If it is not found, a version of MPI will be installed that may cause errors. Look for the following error and correct this issue before moving on:
  

  configure: error: Unable to find mpicc! mpicc location can be specified with --with-mpicc
  

  
   
• 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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