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 supporting packages

|_.Name:|_.Download site:|_.CentOS package name|_.Fedora package name|_.SuSE rpm name|

|gcc-c++||gcc-c++||

|openmpi-devel||openmpi-devel||

|libtiff-devel||libtiff-devel||

|libjpeg-devel||libjpeg-devel|libjpeg-turbo-devel||

|zlib-devel||zlib-devel||

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>

Alternatively, you may download from the svn repo:

<pre>svn co http://newxmipp.svn.sourceforge.net/svnroot/newxmipp/tags/release-2.4/xmipp/ Xmipp-2.4-src</pre>

As of Feb 2012, this was required to compile the 2.4 source code.

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> 

*Note:* If you are installing Xmipp on x86_64 CentOS 6, you can use the following commands instead.

<pre>

export PATH=/usr/lib64/openmpi/bin:$PATH

./scons.configure \

 MPI_LIBDIR=/lib/usr/lib64/openmpi/lib \

 MPI_INCLUDE=/lib/usr/lib64/openmpi/include \

 MPI_LIB=mpi

</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, or source the environment script: <pre> source /etc/profile.d/xmipp.sh</pre>

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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