Subject: Re: CCL:PCI vs. SCSI and Linux

From: Taisung Lee <[email-masked]>
Date: Sat, 27 Sep 1997 21:55:53 -0400 (EDT)

Dear CCLers,

   There is a little misunstanding in Cavallo's article.  
A PCI bus is a bus between CPU and the world outside it.  
A SCSI interface is the bridge between the system bus and 
your HD or other devices.  You can not compare these two 
just as you can not say "My CPU is faster than your hard 
disk."

   Although this issue is not directly related to 
computational chemistry, PC's can be much cheaper 
choices to us CCLers. We shall to know little more about PC. 

   A PC internal structure looks like:

      CPU<---L2 Cache<---Main Memory
       |
       |
     System Bus------------------------------
      |            |           |            |
      |            |           |            |
     Video       Keyboard     SCSI       IDE interface
     Interface   , mouse....  interface  |
      |                        |         |
     Video device             SCSI       IDE  device
                              device

    To let your PC fly, the first thing to do is get a 
fast CPU.  To do computations, Pentium Pro-200 or Pentium 
II's will be good choice.  The second thing is get as much 
memory as you can.  Give the current price ~$3.5 /MB, ther 
is no reason to cut your memory.

    For other parts of the system, PCI is one kind of
System bus.  Curreny PCI standard has highest possible
bandwith of 133 MB/s in 32 bit mode and 266 MB/s in 64 bit
mode.  Almost new PCs come with PCI bus otherwise it is too
old to keep or it is too new...  We probably don't have
other choices now. 

    For people doing visualization, a good video card is 
necessary.  Remember only get a PCI version video card.  
You may see 'ISA' version.  ISA is old standard of system 
bus which has the bandwith of 8 MB/s.  Most PC's keep some 
ISA slots.  But don't buy an ISA video card or you will 
feel your Pentium PC is slower than a 486 when you run Rasmol.

    As Luigi Cavallo said, HD is another important part to 
look at.  The most popular HDs are IDE (or its variation, 
EIDE and Ultra-IDE, ATA-2, ATA-3,..) HD and SCSI HD.  SCSI 
HDs used to be much faster than IDEs.  But it is not the 
case anymore.  However, SCSI still has some advantages.  
We need to understand what are the factors to affect the 
HD performace.

    The first factor, of course, is the spinning speed of 
the HD.  Most HDs has the spinning speed ~5400 RPM.  High 
end SCSI HDs have 7200 RPM.  Seagate has the fastest HD in 
the world with 10000 RPM.  (Don't expect your workstation 
has better HDs than a new PC...)  HDs have buffer memory 
to store data when do reading/writing.  So the other 
factors will be the size of buffer memory and the data 
transfer rate between disks and buffer (called internal 
transfer rate).  You sholud get a HD with buffer no less 
than 256KB (except IBM's, they can make very fast HD with 
128KB buffer and nobody knows why...) and internal 
transfer rate no less than 100 Mbit/s.  

    High spinning HDs are all SCSI (>7200RPM) but not all
SCSI HDs are high spinning.  Be careful about tis point. 
You can buy an Ultra-Wide SCSI HD with only 4500RPM ( and
for sure it is slow).  SCSI and IDE HD have similar buffer
size and internal transfer rate. 

    The last factor (notice: I say it is the LAST factor) 
is the data transfer rate between HD buffer and the system 
bus.  It is important only when you have very slow 
interface or your have multiple HDs.  Following is a list 
of maximum transfer of different interfaces:
   IDE:
             normal IDE: 5MB/s (?) 
   ATA-2, EIDE (mode 4): 16.6 MB/s
   ATA-3, UIDE         : 33.2 MB/s

   SCSI:
      SCSI  :2.5 MB/s
      SCSI-2:5 MB/s
      fast-SCSI-2:10MB/s
      wide-SCSI-2:10MB/s
      fast,wide-SCSI-2:20MB/s
      ultra,wide-SCSI:40MB/s

   Like chemical reactions, the HD performance has a 
'rate-determining' step.  Say you have a HD with internal 
transfer rate 120Mbit/s=15 MB/s (which is very good) and 
you get an UW-SCSI interface and PCI system bus 
(133MB/s).  You will find your system is not faster at all 
compared with a similar HD with FW-SCSI interface.  If you 
buy an 4500RPM, internal transfer rate=50Mbit/s HD and buy 
an UW-SCSI card, you may just waste your money.
   
   I don't want to write too much here.  To be short, don't be
fooled by the bandwith of IDE and SCSI.  A good EIDE HD
will be as faster as a FW-SCSI/UW-SCSI HD.  The HD
performace of a new PC is very likely better than the
workstation in your lab.  However, if you want to get very
very good performance, SCSI is the only way.  The best HDs
are still SCSI (with a doubled price).  A well-develped
technique called RAID allows system to write/read data
to/from several SCSI HDs at the same time.  Using RAID you
can reach 150MB/s easily ( at that time, the PCI bus
becomes the bottleneck).  And you can expect 10 times more 
money will be gone...  

   I already wrote too much.   If there is any interest on 
this topic, I will post more about it.  Such as the  sync. 
transfer and multiple commands of SCSI bus.  

   My suggestion on HD for PC.  Get a new 5400RPM EIDE one 
and you will be happy.  If you can spend at least as twice 
money, get a high end SCSI. 

my $0.02 opinion

Taisung Lee

 > Dear CCLers,
> 
> Recent discussions on the list "seem" to assess that the PPro 256kb
> should be the best buy, in terms of performance/costs ratio.
> 
> Anyhow, the PCs are not simply made by the CPU. We know that another
> bottleneck can be the HD. A PCI bus should be more or less comparable
> to a FAST SCSI 2. Better performances can be obtained on going to
> Ultra Wide etc. SCSI stuff. Anyhow, prices increase.
> 
> What the experience here ? 
> 
> Are those (more) expensive last generation SCSI pieces really needed ?
> 
> Any comments appreciated
> 
> Best regards,
> 
> Luigi
> 
> -----------------------------------
> Luigi Cavallo
> Dept. of Chemistry
> Univ. of Naples
> Email [email-masked]
> -----------------------------------
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