Install Xmipp » History » Revision 50
Revision 49 (Amber Herold, 05/12/2011 02:21 PM) → Revision 50/61 (Amber Herold, 05/13/2011 12:33 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-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>
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, or source the environment script <pre> source /etc/profile.d/xmipp.sh</pre> 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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