SPARX Tutorial Session


Please download file codim.tar.gz using link on page prior to Tuesday session, preferable before arriving to the workshop. The file is ~600Mb and may take awhile to upload.

Tuesday afternoon

By Tuesday, you should have EMAN2 installed and running. SPARX is part of the same installation package. To make sure it runs properly, at a prompt type

and ipython interpreter should appear. Should that fail, please change sparx script to executable by typing

Gentle introduction to sparx session is found at

MPI installation

SPARX extensively uses MPI parallelization. While many commands exists in both single and multiple CPU versions, non-parallel versions are maintained mainly for educational purposes and often are not most versions of the code. Therefore, it is recommended to run MPI versions even on low-end workstations. MPI might be preinstalled on many systems (for example, it is built in on Mac workstations), so MPI installation is separate from installation of EMAN2/SPARX. To do the installation, follow instructions in

On clusters, usage of MPI requires turning off cache option of bdb file format. This can be done either during installation of EMAN2 (see, or by setting flag

in file ~/EMAN2/lib/global.def

(Note that this is not required to use MPI in EMAN2, only in SPARX, and that this flag has no impact on e2*py programs, only sx*py programs)

codimPCA tutorial

We will follow detailed instructions given in:

Ws2011/Sparx (last edited 2011-03-09 05:04:13 by SteveLudtke)