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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