SPARX Tutorial Session

Wed. Afternoon

By Wednesday, 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

codimPCA tutorial

We will follow detailed instructions given in:

• http://sparx-em.org/sparxwiki/codim