Appion

h1. Install Xmipp

* Download the v2.4 source code from http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/InstallingTheSoftware

* Unzip the source code:

<pre>tar zxvf Xmipp-2.4-src.tar.gz</pre>

* Go into Xmipp source directory

* Find openmpi directory

<pre>

locate libmpi.so

  /usr/lib64/openmpi/1.3.2-gcc/lib/libmpi.so

</pre>

* Setup Xmipp to use openmpi by changing three lines in SConstruct

<pre>

cp -v SConstruct SConstruct.orig

</pre>

<pre>

opts.Add('MPI_INCLUDE', 'MPI headers dir ', '/usr/lib/openmpi/1.2.7-gcc/include/')

opts.Add('MPI_LIBDIR', 'MPI libraries dir ', '/usr/lib/openmpi/1.2.7-gcc/lib/')

opts.Add('MPI_LIB', 'MPI library', 'mpi')

</pre>

* Compile

<pre>

sudo mpi-selector --yes --system --set `rpm --qf '%{NAME}-%{VERSION}-gcc-%{ARCH}\n' -q openmpi`

export PATH=$PATH:/usr/lib64/openmpi/1.3.2-gcc/bin

./scons.configure

</pre>

* Look for the following line in the output:

<pre>

* Checking for MPI ... yes

</pre>

* Now compile the source code

<pre>

./scons.compile

</pre>

* Move the main source code directory to global location, like @/usr/local@

<pre>sudo mv -v Xmipp-2.4-src /usr/local/Xmipp</pre>

* Set environmental variables:

** For bash, edit xmipp.sh:

<pre>

export XMIPPDIR=/usr/local/Xmipp

export PATH=${XMIPPDIR}/bin:${PATH}

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${XMIPPDIR}/lib

</pre>

** For C shell, edit xmipp.csh:

<pre>

setenv XMIPPDIR /usr/local/Xmipp

setenv PATH ${XMIPPDIR}/bin:${PATH}

setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${XMIPPDIR}/lib

</pre>

** Copy to /etc/profile.d

<pre>

sudo cp -v xmipp.sh /etc/profile.d/

sudo chmod 755 /etc/profile.d/xmipp.sh

sudo cp -v xmipp.csh /etc/profile.d/

sudo chmod 755 /etc/profile.d/xmipp.csh

</pre>

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[[Compile Ace2|< Compile Ace2]] | [[Test Appion|Test Appion >]]

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