===== SPARX Tutorial Session =====
==== Note ====
** Please download file codim.tar.gz using link on page http://sparx-em.org/sparxwiki/codim** **//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
 . //sparx//
and ipython interpreter should appear.  Should that fail, please change //sparx// script to executable by typing
 . chmod +x ~/EMAN2/bin/sparx
Gentle introduction to sparx session is found at
 . http://sparx-em.org/sparxwiki/HowToUseSparx

===== 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
 . http://sparx-em.org/sparxwiki/MPI-installation
On clusters, usage of MPI requires turning off cache option of bdb file format.  This can be done either during installation of EMAN2 (see http://sparx-em.org/sparxwiki/Installer), or by setting flag
 . CACHE_DISABLE = True
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:
 . http://sparx-em.org/sparxwiki/codim