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 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

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/HowToInstall
• Unzip the source code:
  

  tar zxvf Xmipp-2.4-src.tar.gz

Alternatively, you may download from the svn repo:

svn co http://newxmipp.svn.sourceforge.net/svnroot/newxmipp/tags/release-2.4/xmipp/ Xmipp-2.4-src

As of Nov 2013, this was required to compile the 2.4 source code.

Prepare Xmipp make files¶

• Go into Xmipp source directory
• Find openmpi directory
  

  locate libmpi.so
  /usr/lib/openmpi/1.2.7-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.

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

CentOS 5¶

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

CentOS 6¶

Note: If you are installing Xmipp on x86_64 CentOS 6, you can use the following commands instead.

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

• 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, or source the environment script:

 source /etc/profile.d/xmipp.sh

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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