Install Xmipp¶

Install documentation at Xmipp¶

Biocomputing Unit at the Spanish National Center of Biotechnology (CNB-CSIC) provides detailed documentation on how to install Xmipp on various systems. Below we cover our way to get it working on your system.

Install Xmipp from source¶

We recommend installing Xmipp from source to properly use the openmpi libraries that allows you to run on multiple processors

Download source code¶

• Download the v2.4 source code from http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/InstallingTheSoftware
• Unzip the source code:
  

  tar zxvf Xmipp-2.4-src.tar.gz

Prepare Xmipp make files¶

• Go into Xmipp source directory
• Find openmpi directory
  

  locate libmpi.so
    /usr/lib64/openmpi/1.3.2-gcc/lib/libmpi.so
  

  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)
  

  cp -v SConstruct SConstruct.orig
  

  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')
  

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

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

• Look for the following line in the output:

* Checking for MPI ... yes

• Now compile the source code

./scons.compile

• Move the main source code directory to global location, like /usr/local

sudo mv -v Xmipp-2.4-src /usr/local/Xmipp

Setup environmental variables¶

• For bash, edit xmipp.sh:
  

  export XMIPPDIR=/usr/local/Xmipp
  export PATH=${XMIPPDIR}/bin:${PATH}
  export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${XMIPPDIR}/lib
  

• For C shell, edit xmipp.csh:
  

  setenv XMIPPDIR /usr/local/Xmipp
  setenv PATH ${XMIPPDIR}/bin:${PATH}
  setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${XMIPPDIR}/lib
  

• Copy to /etc/profile.d
  

  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
  

You may need to log out and log back in for these changes to take place.

Test Xmipp¶

Test Xmipp by running ml_align2d program

xmipp_ml_align2d -h

This result should appear

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 

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