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Install Xmipp » History » Version 42

Amber Herold, 05/21/2010 03:49 PM

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h1. Install Xmipp
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h2. Install documentation at Xmipp
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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.
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h2. Install Xmipp from source
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We recommend installing Xmipp from source to properly use the openmpi libraries that allows you to run on multiple processors
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h3. Download source code
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* Download the v2.4 source code from http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/InstallingTheSoftware
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* Unzip the source code:
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<pre>tar zxvf Xmipp-2.4-src.tar.gz</pre>
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h3. Prepare Xmipp make files
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* Go into Xmipp source directory
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* Find openmpi directory
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<pre>
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locate libmpi.so
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  /usr/lib64/openmpi/1.3.2-gcc/lib/libmpi.so
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</pre>
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 *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.
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* Setup Xmipp to use openmpi by changing three lines in SConstruct (creating a backup of the file first)
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<pre>
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cp -v SConstruct SConstruct.orig
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</pre><pre>
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opts.Add('MPI_INCLUDE', 'MPI headers dir ', '/usr/lib/openmpi/1.2.7-gcc/include/')
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opts.Add('MPI_LIBDIR', 'MPI libraries dir ', '/usr/lib/openmpi/1.2.7-gcc/lib/')
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opts.Add('MPI_LIB', 'MPI library', 'mpi')
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</pre>
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h3. Compile the source code
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* Configure
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 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:
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 export PATH=$PATH:/usr/lib/openmpi/1.4-gcc/bin
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<pre>
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sudo mpi-selector --verbose --yes --system --set `rpm --qf '%{NAME}-%{VERSION}-gcc-%{ARCH}\n' -q openmpi`
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export PATH=$PATH:/usr/lib64/openmpi/1.3.2-gcc/bin
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./scons.configure
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</pre>
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* Look for the following line in the output:
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<pre>
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* Checking for MPI ... yes
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</pre>
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* Now compile the source code
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<pre>
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./scons.compile
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</pre>
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* Move the main source code directory to global location, like @/usr/local@
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<pre>sudo mv -v Xmipp-2.4-src /usr/local/Xmipp</pre>
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h3. Setup environmental variables
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* For bash, edit xmipp.sh:
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<pre>
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export XMIPPDIR=/usr/local/Xmipp
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export PATH=${XMIPPDIR}/bin:${PATH}
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export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${XMIPPDIR}/lib
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</pre>
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* For C shell, edit xmipp.csh:
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<pre>
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setenv XMIPPDIR /usr/local/Xmipp
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setenv PATH ${XMIPPDIR}/bin:${PATH}
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setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${XMIPPDIR}/lib
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</pre>
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* Copy to /etc/profile.d
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<pre>
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sudo cp -v xmipp.sh /etc/profile.d/
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sudo chmod 755 /etc/profile.d/xmipp.sh
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- or -
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sudo cp -v xmipp.csh /etc/profile.d/
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sudo chmod 755 /etc/profile.d/xmipp.csh
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</pre>
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bq. You may need to log out and log back in for these changes to take place.
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h2. Test Xmipp
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Test Xmipp by running ml_align2d program
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<pre>
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xmipp_ml_align2d -h
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</pre>
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This result should appear
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<pre>
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2104:Argument -i not found or invalid argument
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File: libraries/data/args.cpp line: 502
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Usage:  ml_align2d [options] 
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   -i <selfile>                : Selfile with input images 
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   -nref <int>                 : Number of references to generate automatically (recommended)
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   OR -ref <selfile/image>         OR selfile with initial references/single reference image 
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 [ -o <rootname> ]             : Output rootname (default = "ml2d")
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 [ -mirror ]                   : Also check mirror image of each reference 
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 [ -fast ]                     : Use pre-centered images to pre-calculate significant orientations
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 [ -thr <N=1> ]                : Use N parallel threads 
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 [ -more_options ]             : Show all possible input parameters 
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</pre>
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[[Install SPIDER|< Install SPIDER]] | [[Install UCSF Chimera|Install UCSF Chimera >]]
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