Installing Xmipp

There are several ways of getting Xmipp installed on your computer:

Step 1: Download

Latest stable release

Fill in the XMIPP DOWNLOAD FORM (note we will not share your information with anyone!) to download precompiled (Linux) binaries or the platform-independent source.

Possibly unstable developmental version

Programmers contributing to Xmipp may download the latest (possibly unstable) development version from SVN (see also xmipp@sourceforge). Note that this option is NOT recommended for standard users, and we cannot give feed-back on bugs in the development version.

svn co http://newxmipp.svn.sourceforge.net/svnroot/newxmipp/trunk/xmipp

If you are a developer and want to submit changes, download with

svn co https://newxmipp.svn.sourceforge.net/svnroot/newxmipp/trunk/xmipp

Step 2: Install

If you just want to run on your Linux desktop machine, the precompiled binaries will probably work for you, and are definitely the easiest way to install. If you are installing Xmipp on a cluster (using MPI for parallelization), then you will most probably have to compile from source.

Using precompiled binaries

Uncompress the tarball in the directory where you wish to install Xmipp:

$ tar zxvf Xmipp-2.3-i386.tar.gz

Building from source

Uncompress the tarball, go to the directory, configure and compile the entire package by typing:

$ tar zxvf Xmipp-2.3-src.tar.gz
$ cd Xmipp-2.3
$ ./scons.configure
$ ./scons.compile

Please read the BuildingWithSCons page for detailed instructions on how to compile using SCons. Note that the scons compilation no longer works with python2.6, so use an older version of python to compile. At TheCNBCorner you may find example instructions for xmipp compilations on a range of different machines we use. Keep in mind that complete Xmipp compilation depends on the external qt3-devel, tiff-devel and mpi packages.

Step 3: Edit the environment setup

Finally, inform each user's shell of Xmipp's existence. By default, the binaries are in the bin and lib subdirectories of the Xmipp directory structure.

For csh or tcsh:

$ setenv LD_LIBRARY_PATH /home/Xmipp_user/Xmipp_directory/lib:$LD_LIBRARY_PATH
$ setenv PATH            /home/Xmipp_user/Xmipp_directory/bin:$PATH
$ setenv XMIPP_BROWSER WWW_BROWSER

For bash:

$ export LD_LIBRARY_PATH=/home/Xmipp_user/Xmipp_directory/lib:$LD_LIBRARY_PATH
$ export PATH=/home/Xmipp_user/Xmipp_directory/bin:$PATH
$ export XMIPP_BROWSER=WWW_BROWSER

where WWW_BROWSER is your favorite web browser such as firefox, mozilla, ... Add those lines to the .cshrc or .bash_profile file in the user's home directory for permanent setup.

Step 4: (only for clusters) Configure your parallel environment for the protocols

Some of the protocols can be run in parallel on large computer clusters. Since every cluster is different, this requires some additional configuring.

Choose a SystemFlavour

First, edit the file applications/scripts/protocols/protocol_setup.py (from your Xmipp top directory) and modify the line that says SystemFlavour = ''. Choose a SystemFlavour that suits your system as explained in the ParallelPage. If your system is not included, you may also modify the applications/scripts/protocols/launch_job.py to add your own system.

After modifying these files, recompile them by typing in the Xmipp top directory:

./scons.compile

Make a job submission script

Second, to ease job submission by the users, we recommend making a job submission script to submit xmipp protocols using your particular queueing system. Again, see the ParallelPage for detailed instructions. An example script (for TORQUE queues) may be found at the QsubPyCrunchy page. After making the script for your system, call it qsub.py, make it executable, and place it in a directory that is in your $PATH (e.g. XMIPP_directory/bin.)

A note on other dependies

Apart from the external libraries needed to compile and install Xmipp, one also needs python installed to run the protocols, and python-tk to have the graphical interface to the protocols xmipp_protocols. You can check whether these libraries are present using:

python

And then inside the python shell typing import Tkinter should not give an error. If it does, ask your system administrator to install python-tk (also called tkinter).

Then, for displaying some results, Xmipp sometimes depends on the external gnuplot program. It is not strictly necessary, but you may want to install this program as well.

-- AlfredoSolano - 15 Jan 2007