Subject: Alpha + Linux ?

From: "M. Nicklaus" <[email-masked]>
Date: Mon, 4 Aug 1997 17:25:56 -0400 (EDT)

On Fri, 1 Aug 1997, Cheol Choi  <[email-masked]> wrote:

> According to the SPEC benchmark, Dec Alpha seems to be the
> fastest processor currently.
> And I know some companies are selling Alpha workstations with Linux OS at
> very reasonable price.
> Is there anyone who has good experience with Alpha + Linux combination?

We've had some experience with Alpha + Linux recently, and are going to 
have more very soon.  Has it been good?  Yes and no.

The Alpha chip is indeed a very fast processor.  The new motherboards 
with the DEC Pyxis chip set promise to be even faster, 600 MHz systems
are selling (albeit still quite expensive), and processors with clock
rates of 800 MHz and higher are in the pipeline.

What's the drawback then?  Mostly the software.  The Linux for the Alpha
(axp-linux) is much less matuer and stable than Linux for the x86 type
processors.  A big problem are the compilers.  f2c is plain buggy, and
gcc and the linker also have their problems.  If you want to know more
(probably more than you want to know...) about these technical axp-linux
issues, you can follow the discussion on the mailing list [email-masked]
(to subscribe: send e-mail to [email-masked] with 'subscribe'
as the subject), or check the newsgroup comp.os.linux.alpha.

The software we tested on axp-linux was:
CHARMM       runs
GAMESS       runs
AMSOL        runs
Gaussian 94  doesn't compile (see also previous postings on the CCL)

When I last checked some of the Web sites on scientific applications for Linux, 
such as http://SAL.kachinatech.com/Z/2 or http://chpc06.ch.unito.it/chem_linux.html,
I counted more than 70 Chemistry/Biology related programs.  We sure haven't
tested them all, but I'd guess if you get the source code for them, you could
give it a shot at compiling them on an Alpha Linux system.  If you have access
to a Digital Unix system, you can actually compile your program on the DEC
system and then run it on the Alpha Linux machine -- the executables are binary
compatible (if you use static linking for the libraries).  This doesn't always
work (didn't work for G94), but we've used this method repeatedly for other
programs.

The benchmarks we ran showed very nice results indeed.  The speedup we saw
for various application relative to a Pentium PRO 200 MHz system running under
Linux was between 1.5 and 2.2.  From the clock rates, you would expect 2.5
(we used a 500 MHz Alpha chip).  The advanced chip architecture itself might
allow even higher numbers.  The reason we havent't seen those numbers (yet)
are most likely compiler issues.  I can only recommend that you test various 
compiler options (optimization etc.) if not different compilers to see which
gives you the fastest code.

The bottom line, from my point of view, is:  It's a great platform, but 
still in its early stages.  So, if you like to patch operating system source
code, rebuild the kernel, tweak the compilers, and do other system 'hacking'
regularly, go for it (...it's not really that bad, but you get my drift).
We *are* using such a system to do real comp.chem. work.  However, if you
want a system that is totally out-of-the-box, runs every known application
without a problem, has plenty of stable compilers, etc., then you'd probably
want to wait a little bit longer.

Marc

------------------------------------------------------------------------
 Marc C. Nicklaus                        National Institutes of Health
 E-mail: [email-masked]               Bldg 37, Rm 5B29
 Phone:  (301) 402-3111                  BETHESDA, MD 20892-4255    USA
 Fax:    (301) 496-5839    http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM
    Laboratory of Medicinal Chemistry, National Cancer Institute,  &
 Lab. of Structural Biology, Div. of Computer Research and Technology
------------------------------------------------------------------------