Biomedical Engineering Reference
In-Depth Information
bioinformatics is another application area that can benefit from the hybrid computing
concept.
We have built a hybrid MIMD-SIMD architecture from general available com-
ponents (Fig. 7.1). The MIMD part of the system is a cluster of 16 PCs (PentiumII,
450 MHz) running Linux. The machines are connected via a gigabit-per-second LAN
(using Myrinet M2F-PCI32 as network interface cards and Myrinet M2L-SW16 as a
switch). For application development, we use the MPI library MPICH v. 1.1.2. For
the SIMD part, we plugged a Systola 1024 PCI board [21] into each PC. Systola
1024 contains an ISA of size 32
32. ISAs have been developed to combine the
speed and simplicity of systolic arrays with flexible programmability [20]. Origi-
nally, the main application field of ISAs was supposed to be scientific computing.
However, in the mid-90s, the suitability of the ISA architecture for other applications
was recognized, for example, [10, 27-31].
×
7.2.1 Principle of the ISA
The ISA [20] is a mesh-connected processor grid, where the processors are controlled
by three streams of control information: instructions, row selectors, and column selec-
tors (Fig. 7.2). The instructions are input in the upper left corner of the processor array
and from there they move step by step in horizontal and vertical direction through the
array. This guarantees that within each diagonal of the array, the same instruction is
active during each clock cycle. In clock cycle,
k
+
+
+
1 processor
(i
1,
j)
and
(i
,
j
1
)
execute the instruction that has been executed by processor
(i
,
j)
in clock cycle
k
.
The selectors also move systolically through the array: the row selectors horizon-
tally from left to right and column selectors vertically from top to bottom. Selectors
mask the execution of the instructions within the processors, that is, an instruction is
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Systola 1024 board architecture
PCI bus
Northern board
RAM
Conroller
Northern IP
High speed Myrinet switch
Western
IP
ISA
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Systola
1024
Figure 7.1
Architecture of our hybrid system: A cluster of 16 PCs with 16 Systola 1024 PCI
boards (left). The data paths in Systola 1024 are depicted (right).
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