Appion

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 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.

h2. Install pre-requisite 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 libjpeg-devel \

 PyQt4-devel cmake ipython hdf5-devel libtiff-devel libpng-devel \

 PyOpenGL db4-devel python-argparse openmpi-devel python-pip

</pre>

h2. Download the source

# To download the source code go to the link:

#* http://blake.bcm.edu/emanwiki/EMAN2

# Click on *"Main EMAN2 Download Page"*

# Click on *"Download EMAN 2"*, whichever is the latest release of EMAN. 

# Scroll down to *Source* to download the *eman2.1beta3.source.tar.gz* 

h2. Work with the source

# go to the directory with the source code

# extract the archive:

<pre>

tar zxvf eman2.12.source.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

#* I had to disable ftgl (fonts in OpenGL) to get 2.12 to compile.

<pre>

-- 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

</pre>

# 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

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

<pre>

module add openmpi-i386

-or-

module add openmpi-x86_64

</pre>

* 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:

<pre>tar zxvf pydusa-1.15es.tgz</pre>

* go into directory

<pre>cd pydusa-1.15es</pre>

 

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

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:

<pre>

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

</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

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

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