Install Xmipp » History » Version 22
Neil Voss, 05/12/2010 02:39 PM
| 1 | 1 | Amber Herold | h1. Install Xmipp |
|---|---|---|---|
| 2 | |||
| 3 | 22 | Neil Voss | h2. Install Xmipp from source |
| 4 | |||
| 5 | 10 | Neil Voss | * Download the v2.4 source code from http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/InstallingTheSoftware |
| 6 | 12 | Neil Voss | * Unzip the source code: |
| 7 | <pre>tar zxvf Xmipp-2.4-src.tar.gz</pre> |
||
| 8 | 1 | Amber Herold | * Go into Xmipp source directory |
| 9 | * Find openmpi directory |
||
| 10 | <pre> |
||
| 11 | 11 | Neil Voss | locate libmpi.so |
| 12 | 15 | Neil Voss | /usr/lib64/openmpi/1.3.2-gcc/lib/libmpi.so |
| 13 | 1 | Amber Herold | </pre> |
| 14 | |||
| 15 | * Setup Xmipp to use openmpi by changing three lines in SConstruct |
||
| 16 | <pre> |
||
| 17 | 11 | Neil Voss | cp -v SConstruct SConstruct.orig |
| 18 | 1 | Amber Herold | </pre> |
| 19 | <pre> |
||
| 20 | opts.Add('MPI_INCLUDE', 'MPI headers dir ', '/usr/lib/openmpi/1.2.7-gcc/include/') |
||
| 21 | opts.Add('MPI_LIBDIR', 'MPI libraries dir ', '/usr/lib/openmpi/1.2.7-gcc/lib/') |
||
| 22 | opts.Add('MPI_LIB', 'MPI library', 'mpi') |
||
| 23 | </pre> |
||
| 24 | |||
| 25 | * Compile |
||
| 26 | <pre> |
||
| 27 | 11 | Neil Voss | sudo mpi-selector --yes --system --set `rpm --qf '%{NAME}-%{VERSION}-gcc-%{ARCH}\n' -q openmpi` |
| 28 | 15 | Neil Voss | export PATH=$PATH:/usr/lib64/openmpi/1.3.2-gcc/bin |
| 29 | 11 | Neil Voss | ./scons.configure |
| 30 | 1 | Amber Herold | </pre> |
| 31 | |||
| 32 | 5 | Amber Herold | * Look for the following line in the output: |
| 33 | 1 | Amber Herold | <pre> |
| 34 | * Checking for MPI ... yes |
||
| 35 | </pre> |
||
| 36 | |||
| 37 | 11 | Neil Voss | * Now compile the source code |
| 38 | 1 | Amber Herold | <pre> |
| 39 | 11 | Neil Voss | ./scons.compile |
| 40 | 1 | Amber Herold | </pre> |
| 41 | 8 | Amber Herold | |
| 42 | 17 | Neil Voss | * Move the main source code directory to global location, like @/usr/local@ |
| 43 | 19 | Neil Voss | <pre>sudo mv -v Xmipp-2.4-src /usr/local/Xmipp</pre> |
| 44 | 17 | Neil Voss | |
| 45 | 18 | Neil Voss | * Set environmental variables: |
| 46 | ** For bash, edit xmipp.sh: |
||
| 47 | 1 | Amber Herold | <pre> |
| 48 | 21 | Neil Voss | export XMIPPDIR=/usr/local/Xmipp |
| 49 | 18 | Neil Voss | export PATH=${XMIPPDIR}/bin:${PATH} |
| 50 | export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${XMIPPDIR}/lib |
||
| 51 | </pre> |
||
| 52 | ** For C shell, edit xmipp.csh: |
||
| 53 | <pre> |
||
| 54 | 1 | Amber Herold | setenv XMIPPDIR /usr/local/Xmipp |
| 55 | setenv PATH ${XMIPPDIR}/bin:${PATH} |
||
| 56 | setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${XMIPPDIR}/lib |
||
| 57 | </pre> |
||
| 58 | 18 | Neil Voss | ** Copy to /etc/profile.d |
| 59 | 17 | Neil Voss | <pre> |
| 60 | 18 | Neil Voss | sudo cp -v xmipp.sh /etc/profile.d/ |
| 61 | 20 | Neil Voss | sudo chmod 755 /etc/profile.d/xmipp.sh |
| 62 | 18 | Neil Voss | |
| 63 | sudo cp -v xmipp.csh /etc/profile.d/ |
||
| 64 | 20 | Neil Voss | sudo chmod 755 /etc/profile.d/xmipp.csh |
| 65 | 17 | Neil Voss | </pre> |
| 66 | 18 | Neil Voss | |
| 67 | 1 | Amber Herold | |
| 68 | 22 | Neil Voss | h2. Test Xmipp |
| 69 | <pre> |
||
| 70 | xmipp_ml_align2d |
||
| 71 | </pre> |
||
| 72 | <pre> |
||
| 73 | 2104:Argument -i not found or invalid argument |
||
| 74 | File: libraries/data/args.cpp line: 502 |
||
| 75 | Usage: ml_align2d [options] |
||
| 76 | -i <selfile> : Selfile with input images |
||
| 77 | -nref <int> : Number of references to generate automatically (recommended) |
||
| 78 | OR -ref <selfile/image> OR selfile with initial references/single reference image |
||
| 79 | [ -o <rootname> ] : Output rootname (default = "ml2d") |
||
| 80 | [ -mirror ] : Also check mirror image of each reference |
||
| 81 | [ -fast ] : Use pre-centered images to pre-calculate significant orientations |
||
| 82 | [ -thr <N=1> ] : Use N parallel threads |
||
| 83 | [ -more_options ] : Show all possible input parameters |
||
| 84 | </pre> |
||
| 85 | should appear |
||
| 86 | 8 | Amber Herold | ______ |
| 87 | 16 | Neil Voss | |
| 88 | 9 | Amber Herold | [[Compile Ace2|< Compile Ace2]] | [[Test Appion|Test Appion >]] |
| 89 | |||
| 90 | 1 | Amber Herold | ______ |