Install Xmipp » History » Revision 27
Revision 26 (Neil Voss, 05/13/2010 09:20 AM) → Revision 27/61 (Neil Voss, 05/13/2010 09:22 AM)
h1. Install Xmipp h2. Install Xmipp from source 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> * Setup Xmipp to use openmpi by changing three lines in SConstruct <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 <pre> sudo mpi-selector --yes --system --set `rpm --qf '%{NAME}-%{VERSION}-gcc-%{ARCH}\n' -q openmpi` export PATH=$PATH:/usr/lib64/openmpi/1.3.2-gcc/bin ./scons.configure </pre> * Look for the following line in the output: <pre> * Checking for MPI ... yes </pre> * Now compile the source code <pre> ./scons.compile </pre> * Move the main source code directory to global location, like @/usr/local@ <pre>sudo mv -v Xmipp-2.4-src /usr/local/Xmipp</pre> h3. Setup * Set environmental variables * variables: ** For bash, edit xmipp.sh: <pre> export XMIPPDIR=/usr/local/Xmipp export PATH=${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. 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]] | [[Compile FindEM|Compile FindEM >]] ______