Biomedical Engineering Reference
In-Depth Information
Fig. 3. SAXS profile reconstruction example
. Comparison of the reference profiles
I
(
q
)
com-
puted by CRYSOL from the all atom structure (light gray) and by the two body model (dark
line). Error shade indicates the simulated “experimental” error. PDB code 1JET (520 residues).
Cartoon made with PyMOL [20].
units, which are composed of one or more processing elements and, in some cases, local
memory.
The host program coordinates the execution of the kernels, and can be written in any
programming language. Kernels are written in a variant of the latest released C language
standard (C99) and are compiled at run time to device-specific instructions. A kernel
describes the operations of a single work-item, or thread, and is run simultaneously by
a set of work-items called a work-group.
The local memory of a compute unit, if present, is shared by all work-items in a
work-group and provides an efficient communication channel among them. It has very
low latency and is usually implemented with a full crossbar interface, but is limited in
size and does not retain its state between kernel executions.
Kernels execute most efficiently when the size of the work-group matches the size
of the compute unit on the OpenCL device and when all work-items in a work-group
follow the same execution path.
2.5
Efficient GPGPU Implementation
Parallel Page-Tile SAXS Algorithm.
The computation of a SAXS profile is experi-
mentally discretized in a set of
q
points, and thus naturally provides the first level of
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