● In fall 2002 and spring 2003, we added two dual Xeon processor
(2.4GHz) x 2cpu units to our PC cluster machine.
○ The Xeon processor is equiped with the hyperthreading technology,
which is claimed to increase the performance up to 30% by time slicing
of each processor. However, our ab initio molecular dynamics program
which highly requires parallel tasking did not perform well under the HT
technology. This is primarily becausei manipulation of the equal-sized
subtasks and the MPI communication overhead added more load than
a speedup.
○ Thus, we switched off the HT technology at the boot time, and got the
gain of 2.2 times (at the maximum) in the computation speed with Xeon
(2.4GHz) compared to Pentium III (1 GHz). However, this performance
is highly job-size dependent, probably due to the CPU-main memory
data transfer rate.
● The great advantage of a PC cluster is its high performance and low
costs compared to other alternatives including the RISC machines.
However, its reliability is somewhat low for some hardwares including
hard-disk drives. It is advised to adopt the data backup (redundant
write) systems such as the RAID to avoid sudden data loss.
Also, self-made PC's are frequently noisier than factory-designed
PC's, and need more air-conditioning in summer time.
● The Linux is an excellent operating system as the free UNIX when
we construct the PC clusters. However, some new versions of the
Linux OS come frequently with new bugs and non-prepatch of the
previous versions, which is a nightmare of introducing version ups.
Bugs: Scalapack on Red Hat Linux 7.3 or later
● We look forward to the near future shift from the 32-bits to 64-bits
processors, intensification of the CPU-main memory data transfer rate,
and the development of applications that make full use of the power of
the 64-bits processors.
Recent Expansion: Pentium 4 and its performance
Methods of Molecular Dynamics and PC Clusters
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