Installing pydusa for EMAN2/SPARX MPI Support

Note: Before 4/19/2013, EMAN2 and SPARX required different libraries to enable MPI support. After this date, we switched to a common system, which is based on the pydusa project. These instructions cover installing pydusa. Actually using MPI still differs somewhat between the packages. Once you have pydusa installed, please see:

Unfortunately, given the wide variations in MPI libraries used on different clusters and other computers, it is impractical to try and distribute precompiled MPI libraries with the EMAN2/SPARX binaries. Luckily, the pydusa project went to considerable effort to make installation from source easy on the vast majority of computers. Note that we do not directly support running using MPI on Windows. This system is primarily targeted at Linux clusters, though presumably it could also be used on individual Linux/Mac workstations. In EMAN2, however, there are alternative strategies (http://blake.bcm.edu/emanwiki/EMAN2/Parallel) which are more efficient in this situation.

Pydusa Download

The modified version of Pydusa is available for download from the main EMAN2/SPARX download pages, here: http://ncmi.bcm.edu/ncmi/software/counter_222/software_121 While we don't expect this package itself to require frequent updates, you will need to rerun the installation script if you update your version of EMAN2/SPARX. That is, after installing pydusa, we suggest keeping the installation directory, so you can rerun the installer in the future with minimum hassle.

Installing Pydusa

The package is provided as a compressed TAR archive. If you aren't familiar with these, they are easily unpacked using a single command shown below. EMAN2/SPARX must already be installed in your home directory for this to work properly. On most systems you should be able to simply:

tar -xvzf pydusa-1.15es.tgz
cd pydusa-1.15es
./install_mpi.py

Assuming your cluster has MPI installed, this will generally be able to find and use it automatically.

Notes:

When you have the library installed remember to refer to the EMAN2/SPARX specific pages listed above for usage information.