PyMOLer's & Friends,
For those of you considering a new PowerMac G5, a special
"native" PyMOL v0.91 for the G5 with some nice demonstrations has been
released: http://pymol.sf.net. This version contains an assortment of
G5 optimizations, and the next release will have even more. Current G4
users will benefit from these as well.
Although Apple's top-of-the-line 2.0 Ghz G5 systems aren't quite
shipping yet, they did let us run some PyMOL benchmarks on one, and the
numbers were very impressive. In my own hands, a dual 2.0 Ghz G5
effectively competes with a dual 3.0 Ghz Pentium 4 Xeon for generating
PyMOL ray-traced movies in head-to-head comparisons. OpenGL speed is
also top notch. So in my opinion, Mac/PC performance parity has finally
been achieved -- congratulations Apple!
By the way, Steve Jobs' controversial "twice as fast as a PC"
claim is only valid for code exploiting the Altivec vectorization unit.
PyMOL doesn't use that, but it can still render images equally as fast
on the dual-processor Mac as on the dual-processor PC. "Once as fast as
a PC is fast enough", I say, without any magic code.
Thus, the really good news for cross-platform developers (like
me) is that it is not necessary to write G5-specific code in order to
get good performance. In fact, most of the "G5 optimizations" we put
into PyMOL have equally helped the PC version (much to Apple's chagrin).
Code optimization is simply easier on a Mac using Apple's great free
tools (especially Shark
http://developer.apple.com/technotes/tn/tn2086.html#useshark ), and the
resulting code runs measurably faster on every platform.
So if you are looking to buy a fast dual-processor desktop
system, you may want to take a look at the G5 once the dual 2 Ghz
machines ship in a few weeks. Though you'll probably pay more for this
Mac than you will for a no-name x86 Linux setup, you will get concrete
value in return:
- freedom from Linux hardware configuration and OpenGL driver
hassles
- accountable vendor support
- a user-friendly operating system
- desktop applications such as Office, Photoshop, and
Illustrator.
- awesome developer tools (at no additional cost!)
- 64 bits
- stereo 3D graphics capability
- and of course, the unique Mac OS X "look and feel".
Plus, since Mac OS X is Unix, most computational chemistry,
bioinformatics, and structural biology research software already runs
well on it.
Whatever your platform disposition, it is absolutely in your
interest to learn about the many new options which exist before your
next big purchase. With ridiculously fast Pentium 4, G5, Athlon,
Itanium2, and Opteron hardware now entering the market, and with at
least four affordable or free operating systems to choose from, there
are plenty of ways to build a great system for relatively little money.
You should not spend the cost of a new car just to buy a desktop
computer (sadly, some companies I know STILL do this...).
These days, PyMOL can compile and run virtually anywhere, but
our focus will continue to be on x86 Windows, x86 Linux, and G4/G5 Macs,
with IRIX and Solaris support continuing as long as demand persists.
Please do speak up if/when native Itanium2 and Opteron binaries are
needed...
Does this sound like an Apple commercial? I hope not -- I aim
for long-term platform neutrality, but at the same time, I do want PyMOL
users and potential PyMOL users to be fully informed as to their
options. Plus, I am concerned about the distorting effect of dogmatic
anti-Mac prejudice which pervades some corporations. The goal behind
this message is to encourage everyone become aware of a unique new
hardware offering so that you will take the time to evaluate it and can
then make fully-informed decisions to buy whatever product best suits
your scientific needs.
Don't we owe it to ourselves and to the people who fund our
research to apply our finite resources judiciously? In keeping with
this, we should seek to reward those vendors who deliver the best values
and to avoid those who do not. To do anything less is to waste precious
resources or opportunities.
So take a look at the dual 2 Ghz G5 even if it means overcoming
historical anti-Mac bias within yourself or your organization. Sure,
"Macintosh" may have become synonymous with "molasses" during the last
couple of years, but that perception just doesn't apply to these
forthcoming dual 2 Ghz G5 systems. If you do run into static within
your IT department, remind them that these machines are long-sought
replacements for those expensive old SGI workstations and
"hard-to-support" Linux desktops, and that they pose no real threat to
the Windows corporate enterprise. They are tools for doing science just
like an X-ray diffractometer or an NMR, and who is IT to dictate what
tools scientists should use?
DISCLIAMER: Apple is NOT a financial sponsor of the PyMOL
project, but they have taken steps to promote PyMOL on Macintosh by
providing early access to hardware, exposure, and limited developer
assistance.
DISCLIAMER to the DISCLAIMER: So what? We're not afraid to
criticize Apple. Apart from the iPod, the dual 2 Ghz G5 PowerMac is the
ONLY system we recommend you purchase from the company at this time.
Their laptops, cluster nodes, single-processor G5s, and mid-range G4
systems are arguably still behind the competition, even after taking OS
X's advantages into account. I'm no Mac-addict, but I do like to
recognize and celebrate a good product when I see one. The dual 2 Ghz
G5 running Mac OS X is a "killer" desktop computer for research --
Apple's first in a long time, and hopefully more will come if we
appropriately reward this one with our business.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
