Install Xmipp » History » Revision 60
Revision 59 (Neil Voss, 08/07/2012 02:22 PM) → Revision 60/61 (Amber Herold, 11/25/2013 04:08 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:|_.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/HowToInstall 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/lib/openmpi/1.2.7-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. h3. Compile the source code * Setup Xmipp to use openmpi by the following command. 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=$PATH:/usr/lib64/openmpi/bin h4. CentOS 5 <pre> export PATH=$PATH:/usr/lib64/openmpi/1.3.2-gcc/bin ./scons.configure \ MPI_LIBDIR=/usr/lib/openmpi/1.2.7-gcc/lib/ \ MPI_INCLUDE=/usr/lib/openmpi/1.2.7-gcc/include/ \ MPI_LIB=mpi </pre> h4. CentOS 6 *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> ______ [[Install SPIDER|< Install SPIDER]] | [[Install UCSF Chimera|Install UCSF Chimera >]] ______