Appion

h1. Install Xmipp

h2. Install documentation at Xmipp

Biocomputing Unit at the Spanish National Center of Biotechnology (CNB-CSIC) provides "detailed documentation":http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/InstallingTheSoftware on how to install Xmipp on various systems. Below we cover _our way_ to get it working on your system.

h2. Install Xmipp from source

We recommend installing Xmipp from source to properly use the openmpi libraries that allows you to run on multiple processors

h3. Download source code

* 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>

h3. Prepare Xmipp make files

* Go into Xmipp source directory

* Find openmpi directory

<pre>

locate libmpi.so

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

</pre>

 *Note:* If you can not find the openmpi directory, make sure you have installed the openmpi package. The installation on CentOS using yum is: yum -y install openmpi-devel.

* Setup Xmipp to use openmpi by changing three lines in SConstruct (creating a backup of the file first)

<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>

h3. Compile the source code

* Configure

Be sure to modify the path in the second command as needed. For example, on a 32 bit machine using 1.4-gcc the command is:

export PATH=$PATH:/usr/lib/openmpi/1.4-gcc/bin

<pre>

sudo mpi-selector --verbose --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>

h3. Setup 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

- or -

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

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

</pre>

bq. You may need to log out and log back in for these changes to take place.

h2. Test Xmipp

Test Xmipp by running ml_align2d program

<pre>

xmipp_ml_align2d -h

</pre>

This result should appear

<pre>

2104:Argument -i not found or invalid argument

File: libraries/data/args.cpp line: 502

Usage:  ml_align2d [options] 

   -i <selfile>                : Selfile with input images 

   -nref <int>                 : Number of references to generate automatically (recommended)

   OR -ref <selfile/image>         OR selfile with initial references/single reference image 

 [ -o <rootname> ]             : Output rootname (default = "ml2d")

 [ -mirror ]                   : Also check mirror image of each reference 

 [ -fast ]                     : Use pre-centered images to pre-calculate significant orientations

 [ -thr <N=1> ]                : Use N parallel threads 

 [ -more_options ]             : Show all possible input parameters 

</pre>

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[[Install SPIDER|< Install SPIDER]] | [[Install UCSF Chimera|Install UCSF Chimera >]]

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