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Install EMAN2 » History » Version 71

Neil Voss, 02/12/2016 01:09 PM

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h1. Install EMAN2/SPARX
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*Before you begin:*
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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.
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This documentation assumes you are using CentOS 6 (written as of CentOS 6.5)
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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.
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h2. Install pre-requisite packages for EMAN2 compiling
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h3. yum based packages
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* Make sure EPEL is install, if not go here: [[Download additional Software (CentOS Specific)]]
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* Use yum to install devel libraries:
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<pre>
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sudo yum install fftw-devel gsl-devel boost-python numpy libjpeg-devel \
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 PyQt4-devel cmake ipython hdf5-devel libtiff-devel libpng-devel libdb-devel \
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 PyOpenGL ftgl-devel db4-devel python-argparse openmpi-devel python-pip
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</pre>
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h3. bsddb3
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Additionally you need to install the python-bsddb3 library (not available via YUM). I just use the pypi easy_installer, yum will never know.
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<pre>
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sudo pip install bsddb3
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</pre>
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h2. Download the source
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# To download the source code go to the link:
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#* http://blake.bcm.edu/emanwiki/EMAN2
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# Click on *"Main EMAN2 Download Page"*
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# Click on *"Download EMAN 2"*, whichever is the latest release of EMAN. 
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# Scroll down to *Source* to download the *eman2.1beta3.source.tar.gz* 
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h2. Work with the source
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# go to the directory with the source code
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# extract the archive:
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<pre>
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tar zxvf eman2.12.source.tar.gz
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</pre>
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# go into directory
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<pre>cd EMAN2/src/build</pre>
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# start configure script:
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<pre>cmake ../eman2/</pre>
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#* Note: alternatively you can run @ccmake ../eman2/@ and configure all the parameters
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<pre>
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-- The C compiler identification is GNU 4.4.7
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-- The CXX compiler identification is GNU 4.4.7
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-- Check for working C compiler: /usr/bin/cc
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-- Check for working C compiler: /usr/bin/cc -- works
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-- Detecting C compiler ABI info
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-- Detecting C compiler ABI info - done
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-- Check for working CXX compiler: /usr/bin/c++
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-- Check for working CXX compiler: /usr/bin/c++ -- works
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-- Detecting CXX compiler ABI info
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-- Detecting CXX compiler ABI info - done
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-- Looking for fseek64
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-- Looking for fseek64 - not found
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-- Looking for fseeko
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-- Looking for fseeko - found
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-- Looking for ftell64
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-- Looking for ftell64 - not found
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-- Looking for ftello
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-- Looking for ftello - found
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-- Configuring done
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-- Generating done
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-- Build files have been written to: /emg/sw/EMAN2/src/build
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</pre>
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# start compiling:
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<pre>make</pre>
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# install to directory:
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<pre>sudo make install</pre>
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h2. Set environmental variables
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h3. bash
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<pre>sudo nano /etc/profile.d/eman2.sh</pre>
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<pre>
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export EMAN2DIR=/usr/local/EMAN2
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export PATH=${EMAN2DIR}/bin:${PATH}
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export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
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export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin
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</pre>
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h3. c shell
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<pre>sudo nano /etc/profile.d/eman2.csh</pre>
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<pre>
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setenv EMAN2DIR /usr/local/EMAN2
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setenv PATH ${EMAN2DIR}/bin:${PATH}
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setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
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setenv PYTHONPATH ${EMAN2DIR}/lib:${EMAN2DIR}/bin
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</pre>
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h2. Install MyMPI
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* First, add the openmpi module so that MyMPI can find it.
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<pre>
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module add openmpi-i386
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-or-
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module add openmpi-x86_64
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</pre>
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* Download source: 
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From the main software page: http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222 scroll to *MPI Support*.
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Click on *Download MPI Support*
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Click on *pydusa-1.15es.tgz*
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* Extract:
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<pre>tar zxvf pydusa-1.15es.tgz</pre>
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* go into directory
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<pre>cd pydusa-1.15es</pre>
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&nbsp;
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If you are on a 64bit machine, you may have problems with the code finding the numpy headers:
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&nbsp;
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<pre>nano configure</pre>
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&nbsp;
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find the line:
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<pre>
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elif test -d ${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include; then
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   PY_HEADER_NUMPY="-I${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include"
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</pre>
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and replace it with:
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&nbsp;
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<pre>
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elif test -d ${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include; then
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   PY_HEADER_NUMPY="-I${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include"
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</pre>
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* Configure:
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<pre>
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setenv MPIROOT /usr/lib64/openmpi
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setenv MPIINC /usr/include/openmpi-x86_64
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setenv MPILIB ${MPIROOT}/lib
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setenv MPIBIN ${MPIROOT}/bin
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./configure
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</pre>
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<pre>
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export MPIROOT=/usr/lib64/openmpi
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export MPIINC=/usr/include/openmpi-x86_64
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export MPILIB=${MPIROOT}/lib
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export MPIBIN=${MPIROOT}/bin
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./configure
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</pre>
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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:
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<pre>
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configure: error: Unable to find mpicc! mpicc location can be specified with --with-mpicc
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</pre>
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&nbsp;
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* compile the source:
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<pre>make</pre>
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* copy the mpi.so to site-packages with a different name:
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<pre>
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sudo mkdir /usr/lib64/python2.6/site-packages/mympi/
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sudo touch /usr/lib64/python2.6/site-packages/mympi/__init__.py
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sudo cp -v src/mpi.so /usr/lib64/python2.6/site-packages/mympi/mpi.so
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</pre>
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* create a wrapper around the wrapper:
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<pre>sudo nano /usr/lib64/python2.6/site-packages/mpi.py</pre>
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<pre>
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import ctypes
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mpi = ctypes.CDLL('libmpi.so.1', ctypes.RTLD_GLOBAL)
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from mympi.mpi import *
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</pre>
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This needs to be done to avoid the error:
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<pre>
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python: symbol lookup error: 
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  /usr/lib64/openmpi/lib/openmpi/mca_paffinity_hwloc.so: 
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    undefined symbol: mca_base_param_reg_int
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</pre>
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* test 1: 
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<pre>
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python -c 'import mpi'
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python -c 'import sys; from mpi import mpi_init; mpi_init(len(sys.argv), sys.argv)'
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</pre>
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* test 2: 
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<pre>sxisac.py start.hdf</pre>
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(Note: start.hdf does not need to exist, if it does not exist then it should exit with file not found)
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h2. Test to see if code works
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see http://blake.bcm.edu/emanwiki/EMAN2/FAQ/EMAN2_unittest
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<pre>
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cd EMAN2/test/rt
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./rt.py
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</pre>
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h2. Install MyMPI for MPI functions
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see http://sparx-em.org/sparxwiki/MPI-installation
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or https://www.nbcr.net/pub/wiki/index.php?title=MyMPI_Setup
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This fixes this problem:
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<pre>
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    from mpi import mpi_init
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ImportError: No module named mpi
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</pre>
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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.
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h2. Documentation
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* http://blake.bcm.edu/emanwiki/EMAN2/Install
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* http://blake.bcm.edu/emanwiki/EMAN2/FAQ/eman2BuildFAQ
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______
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[[Install EMAN|< Install EMAN 1]] | [[Install SPIDER|Install SPIDER >]]
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______