Biomedical Engineering Reference
In-Depth Information
Xeon 550MHz processors, 512 kb on-chip cache, and 2 Gb RAM. The nodes are
coupled with a fast Myrinet network.
The other cluster is a heterogeneous COW (heteroCOW) comprising 12 different
SUN Ultra workstations with between one and three CPUs, a total of 15 processors.
The machines have CPU clock rates ranging from 143 to 440MHz and with memory
capacities between 128 and 1024Mb per processor (see Table 15.2 for more detail).
A total number of 15 processors is available. The communication between the nodes
is handled by 100Mbit Fast Ethernet.
15.3.2 Data Sets
To study the effects of problem size, granularity, and scheduling on the parallel per-
formance, data sets with different alignment lengths (192, 384, 768, and 1536 bp)
and numbers of sequences (16, 32, 64, and 128 sequences) were generated using the
Seq-Gen program [32].
The implementation was also applied on two biological data sets: data derived
from the set of small-subunit ribosomal RNA sequences from Rhodophyta in the
European rRNA Database [33] and another data set of Cadherin protein sequences
(HBG003908) was collected from the Hovergen database [34].
15.3.3 Scheduling Algorithms
To distribute the tasks, a scheduling strategy is required, which facilitates an even load
balancing while simultaneously keeping the communication overhead low. The latter
is especially important for COWs where a large number of concurrent communication
operations cannot be executed very fast.
Scheduling algorithms distribute a set of
N
tasks to the
p
processors executing
the parallel processes. The two naïve scheduling algorithms are distributing the
N
independent tasks to the
p
processes, either in equally sized packages of
B
=
N/p
tasks or in an one-by-one scheme (
B
1). Whenever a processor finished a batch of
tasks, it receives a new batch until all tasks are done. The former algorithm,
static
chunking
(SC) [35], although having a lowcommunication overhead, usually performs
=
TABLE 15.2 Specifications of the Heterogeneous COW
No. of CPU No. of System Clock Memory Cache
Machines Speed (MHz) CPUs
(MHz)
(Mb)
(Mb)
Type
2
143
1
71
160
0.5
Sun Ultra 1 SBus
2
167
1
84
288-448
0.5
Sun Ultra 1 SBus
1
200
2
100
2048
2
×
1.0 Sun Ultra 2 UPA
/
SBus
3
270
1
90
128
0.2
Sun Ultra 5
/
10
2
360
1
90
320
0.2
Sun Ultra 5
/
10
1
400
3
100
4096
4
×
4.0 Sun Enterprise 450
1
440
1
111
384
2.0
Sun Ultra 5
/
10
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