Install Xmipp » History » Revision 54
Revision 53 (Neil Voss, 02/22/2012 11:27 AM) → Revision 54/61 (Neil Voss, 02/22/2012 12:46 PM)
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:|_.yum package name|_.SuSE rpm name|
|gcc-c++||gcc-c++||
|openmpi-devel||openmpi-devel||
|libtiff-devel||libtiff-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-2.4svn/</pre>
As of Feb 2012, this was required to compile the 2.4 source code.
h3. Compile the source code
* Go into Xmipp source directory
* Add mpi compilers to your path.
<pre>
export PATH=/usr/lib64/openmpi/bin:$PATH
</pre>
*Note:* This example is for x86_64 CentOS 6. If you can not find the openmpi directory, make sure you have installed the openmpi package. The installation on CentOS using yum is: yum -y install openmpi-devel.
* Configure
<pre>
./scons.configure MPI_LIBDIR=/lib/usr/lib64/openmpi/lib MPI_LIB=mpi MPI_INCLUDE=/lib/usr/lib64/openmpi/include
</pre>
* Look for the following line in the output:
<pre>
* Checking for MPI ... yes
</pre>
* Now compile the source code
<pre>
./scons.compile
</pre>
* Move the main source code directory to global location, like @/usr/local@
<pre>sudo mv -v Xmipp-2.4-src /usr/local/Xmipp</pre>
h3. Setup environmental variables
* For bash, edit xmipp.sh:
<pre>
export XMIPPDIR=/usr/local/Xmipp
export PATH=${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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