|
|
| From: |
"Dr. Mrigank" <mrigank -AatT- imtech.ernet.in> |
| Date: |
Fri, 7 Jan 94 13:09:21 +0530 |
| Subject: |
Summary: Alpha vs. SGI for Mol. Modelling. |
Hi
I posted following querry some time back
______________________ORIGINAL MESSAGE______________________________
Hi
We are about to place an order for a computer system for a newly
established molecular modelling laboratory. Our initial survey zeroed downs
to select DEC alpha. I have following questions
1. Which sysstem is better for this work, SGI(Indigo2, Challenge),
Alpha (DEC 3000 AXP 600, 800), IBM RS/6000, Sun, HP 735 etc.
2. How are they score in
a)Number Crunching? b) Graphics Hardware? c) Graphics Software?
3. In case of AXP, is it which graphics option is better, PXG,
Kubota, any other. Is it worth spending money in Kubota (More
than Half the price of DEC 3000 AXP 600)
4. What is the price performance ratio, how much RAM generally
needed and diskspace.
5. What all support OpenGL now?
6. Which OS is better for Alpha OSF/1 or OpenVMS?
7. What CASE tools avaiable on Alpha?
8. Any Benchmarks ?
Thanks in advance, Please reply by mail to save bandwidht, if sufficent
interest, I will summrize.
Mrigank
----
Dr. Mrigank \/Phone +91 172 45004 x216
Institute of Microbial Technology /\Email: mrigank &$at$& imtech.ernet.in
P O Box 1304, Sector 39A \/UUCP:...!uunet!sangam!vikram!imtech!mrigank
Chandigarh 160 014 India. /\
==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+
-- When I feed the poor, they call me saint. When I ask why the poors do
not have food, they call me communist - Archbishop Camaran
----- End of the message -----
I think from the responses upto now, one can deduce the following:
1. For number crunching, Alpha is better,[ a few suggested HP 735 etc,
but not many have them and is not very popular]. IBM is also good
but Alpha scores in Price/performance.
2. For Graphics SGI is best. But many graphics option with Alpha
makes it competetive. And with faster CPU, The difference is not
notciable.
3. Most of the software, partcular;y graphics based is avialable
on SGI. But then Alpha is a new comer, and porting has already
started.
4. SUN is inferior to alpha in number crunching and infereior to
SGI in graphics.
There are other opinion also, but I concluded from the majority. It still may
not be the right opinion. I have included all the message in original below,
except one, who wanted to be so. Some message are edited to delete long
portion avialable otherwise. If it is not accessible to you, please let me
know, I will mail.
Hope this will be useful. It has helped me a lot.
Mrigank
----
Dr. Mrigank \/Phone +91 172 45004 x216
Institute of Microbial Technology /\Email: mrigank \\at// imtech.ernet.in
P O Box 1304, Sector 39A \/UUCP:...!uunet!sangam!vikram!imtech!mrigank
Chandigarh 160 014 India. /\
==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+
-- Various phillosphers have interpreted the world in varios ways. The
point, however, is to change it.
============================ Original Responses ===========================
_____________________________________________________________________________
From: UUCP%"harris "-at-" MIT.EDU" 31-DEC-1993 02:17
Please send me a summary of yourr responses. Thanks.
--Jonathan
---------
Jonathan G. Harris harris (+ at +) athena.mit.edu
Department of Chemical Engineering tel(617)253-5273
Room 66-450, MIT, 25 Ames St, Cambridge, MA 02139 fax(617)253-9695
---------------------------------------------------------------------------
From: UUCP%"eloranta - at - tukki.jyu.fi" 31-DEC-1993 02:23
Well, I'll just describe what we have here.
>We are about to place an order for a computer system for a newly
>established molecular modelling laboratory. Our initial survey zeroed downs
>to select DEC alpha. I have following questions
>
>1. Which sysstem is better for this work, SGI(Indigo2, Challenge),
> Alpha (DEC 3000 AXP 600, 800), IBM RS/6000, Sun, HP 735 etc.
>
We have sun sparc 4/670 (upto 4 cpus) and sun sparc 10 (upto 4 cpus).
Both machines are setup as servers. Displays are Tektronix X terminals and
MS windows machines with Xvision X windows emulator.
>2. How are they score in
> a)Number Crunching? b) Graphics Hardware? c) Graphics Software?
a) below high end alphas and sgis. MD runs can use many cpus.
b) we're just using regular X terminals - nothing fancy (but cheap).
c) any X windows stuff. We usually run sybyl 6.0 and couple of PD X windows
programs (rasmol, etc.)
>4. What is the price performance ratio, how much RAM generally
> needed and diskspace.
Suns need at least 32 MB. Our server has abt. 200 meg. The disk space
is almost 10 GB. and 2 GB on our ss10.
>
>5. What all support OpenGL now?
>
Sun itself doesn't support opengl and X terminals don't support opengl.
I'd like too see X11R5 3d libs being used more by chemistry packages so
that these could be run on variety of machines and displays.
>6. Which OS is better for Alpha OSF/1 or OpenVMS?
>
I think that VMS is dying. OSF/1 is sort of ok, but at least the version
that we had had quite fatal bugs (cc and csh dumping core!).
>8. Any Benchmarks ?
>
Try to run your own code. Some machines look very attractive in specint92
and specfp92 but real code doesn't then run very well. I've noticed with
math dept. HPs that these machines can't get stuff fast enough from memory.
Also note that administration etc. of UNIX machines are different from
machine to machine. If you have one sort of machines and you get another
brand then you add administrative work.
Most of the chem software is available for SGIs. If you want raw CPU power
then HP is the best choice.
Regards,
jussi
ps. sun is in transition from solaris 1.x to solaris 2.x which can cause
problems.
---------------------------------------------------------------------------
From: UUCP%"nmdl-: at :-rlmtc.DNET.hcc.com" 2-JAN-1994 23:32
The question boils down to what software will you be running. Then you
must get benchmarks for each applications. In some cases SGI is better
in others DEC and yet others IBM. If you are starting from scratch
and you will be writing all you own code, the best choice is probably
the DEC with the Kubota graphics. If you need transferability across
a wide array of users, you probably want SGI. I hope this helps.
All the best
Sol JAcobson
Hoechst Celanese
---------------------------------------------------------------------------
From: UUCP%"hongma -8 at 8- mcnc.org" 2-JAN-1994 23:32
Software availability is also very important. Almost all molecular modeling
programs run on SGI, but not Alpha. We have DEC Alpha's in our training
room and it has limited our ability to do molecular modeling workshops.
Of the three major molecular modeling programs, only QUANTA/CHARMm
currently run on DEC Alpha.
--------------------------------------------------------------------------
Hong Ma MCNC / Information Technologies Division !
Scientific Support Analyst PO Box 12889 !
919/248-1176 3021 Cornwallis Road !
hongma.,at,.ncsc.org Research Triangle Park, NC 27709-2889 !
--------------------------------------------------------------------------
---------------------------------------------------------------------------
From: UUCP%"windemut()at()cumbnd.bioc.columbia.edu" 2-JAN-1994 23:35
I have benchmarks of my molecular dynamics program (PMD)
on all of the above systems. This is in seconds per step with
23,975 atoms and all interactions, using a multiple timestep
method and the fast multipole algorithm. The relative results
agree quite well with all floating point specmarks that I have
seen.
(fastest first)
1. HP 9000/735 (c89 -O) 6.5
2. IBM R6000/550 (cc -O) 10.0
3. DEC alpha (cc -O2) 12.08
4. SGI Indigo 2 R4400 (cc -O -mips2 -lfastm) 14.6
5. SUN SPARCstation 10 (cc -O) 16.65
This is in seconds per timestep.
Note:
I am not sure what type alpha that was, but believe it is the fastest.
You can get a 150MHz Indigo now, which is 1.5 times faster (gives 9.41)
You can get a better, faster HP in January (I have no details, yet)
The HP is more than 2 times faster than the Indigo at the same clock speed
The sun seems to be quite left in the dust
Conclusion:
- If you have a lot of numbers to crunch, take the HP.
- If you need to display tons of polygons fast, think about the Indigo.
- if you need to buy IBM, buy IBM.
- don't even think about anything else :-)
I hope this helps,
--
Andreas Windemuth
+--------------------------------------------------------------------
|Columbia University, Dept. of Biochemistry and Biophysics, BB-221
|630 West 168th St. | tel: (212)-305-6884, fax: 6926, NeXTmail
|New York, NY 10032 | email: windemut { *at * } cumbne.bioc.columbia.edu
+--------------------------------------------------------------------
---------------------------------------------------------------------------
From: UUCP%"ross \\at// cgl.ucsf.edu" 2-JAN-1994 23:35
Here are some Amber benchmarks. Unfortunately, it won't help
w/ selecting the amount of memory.
In spite of the slightly faster speed under vms, I would still
get Unix.
Bill Ross
Molecular Mechanics/Dynamics Benchmarks
The following benchmarks may be of interest, not only for the
thrill of watching the price/performance competition, but also
for insights into architectures and for clues about what the
molecular modelling community might request of designers. It may
be useful to construct a set of comp chem benchmarks, including
cases such as these along with QM and semiempirical cases.
Two cases are considered: a "small," 274-atom solute in a large
periodic bath of water molecules and ions; and a "large," 4282-atom
molecule in vacuum. For simplicity, both systems are DNA. The code
used is Amber 4.0.
Although the measurements have not been taken under controlled
conditions, the trials that were repeated yielded quite similar
results, probably varying by less than 2%. Formal benchmarks would
require a 'bare' machine and might well include wallclock times
and running multiple copies of a benchmark simultaneously to force
paging. In any case, the numbers that follow must be treated as
anecdotal and informal.
The form of dielectric constant has a surprising effect on performance:
using the normal form (dependent on 1/r) exacts as much as a 30% penalty
over the "distance-dependent" form (1/r^2) on architectures that have
less support for the square root operation (most notably the SGI series
and rs6000). Clearly this is one architectural feature that the comp chem
community may want to lobby for.
Only one parallel architecture was tested as such: an old 8-processor
Alliant - using only compiler optimization - obtained correct results
on the more tested, older code. The speedup (2.3) is harder to evaluate
given the uncontrolled conditions (I don't know how many processors
were used).
The cases include energy minimization, dynamics, and a free energy
calculation. Eventually I expect to run the same cases for the solvated
system as for the vacuum one.
My thanks to George Seibel and David Case for helpful observations
on architectures and factors affecting program speed.
Note: The minmd program contains the traditional energy minimization and
molecular dynamics capabilities of Amber. Sander is essentially the same,
as used here. (Both programs have significant other features which are not
exercised by the benchmarks.) Gibbs is the Amber free energy perturbation
program.
Amber 4.0 Benchmarks
These benchmarks are for larger systems than the other demo cases and
are intended to compare machine performance on more realistic problems.
The order is roughly that of performance for the fastest machine in a
product line. All times are CPU seconds measured by system calls in the
programs; wallclock times may not correspond. All results except for
the Alliant are for a single processor. These are single observations.
Note: benchmarks supplied by manufacturers are indicated by a leading
'-'.
dna/Run.bench dna/Run.bench2
DNA hexamer in periodic 68 DNA base pairs in vacuum.
water box, constant volume. 4282 atoms, 10A cutoff on all
7682 atoms: 274 dna, 10 nonbonded pairs. Distance-
counterions, 2466 waters. dependent dielectric.
All solute interactions;
8A cutoff otherwise. Constant
dielectric.
______________________________ ______________________________
min min+md sander sander gibbs
min md
______________________________ ______________________________
Cray
C90 - /49 - /56 - /57 - /25 - /25 59
Y-MP(ncsc) - /80 - /92 - /90 - /44 - /44 96
Y-MP(sdsc) - /91 - /104 - /104 - /44 - /44 98
Y-MP EL - /445 - /498 - /500 - /282 - /278 535
Fujitsu
VP2200 52/54 62/64 63/64 26/24 26/25 92
HP
735 173/172 197/193 216/190 112/109 109/106 186
730 336/327 367/363 337/363 205/220 200/216 409
720/50MHz 434/462 480/512 476/503
DEC-alpha
3000/500vms 232/275 249/294 247/286 154/191 151/191 258
3000/500osf 285/363 320/397 298/335 160/195 163/197 271
iris**
-Chall150.1 209/262 221/277 221/275 153/195 160/191 314
-Chall150.2 117/155 136/170 150/167 104/138 102/128 199
-Chall150.4 88/108 111/124 92/118 79/104 77/104 159
Challenge.1 298/382 322/415 324/405 228/287 228/287 460
Challenge.2 173/219 194/243 193/242 160/196 153/193 298
Challenge.4 108/137 132/182 130/163 118/151 115/147 229
-Challeng.8 79/95 99/120 101/120
-Crimson 308/426 332/455 346/479
-Indigo/R4 310/416 335/448 348/488
Crimson 352/421 341/452 379/468 224/281 226/282 479
w/fastm** 337/416 358/447 325/439 219/273 216/268 481
4d/410vgx 730/1129 779/1180 768/1156
indigo3000 868/1253 881/1391 866/1300 490/629 461/623 1269
4d/310vgx 956/1618 1015/1704 993/1560 578/809 578/804 1244
personal 1722/2830 1724/3371 1724/2846
4d/80gt 1901/3542 1996/4006 2006/3201
rs6000
560 376/347 400/372 405/399
530 859/844 912/895 915/858 516/391 501/378 630
vax 9000
vector 365/468 399/520 390/524 229/311 219/296
no vector 654/774 /865 948/917 462/497 454/794 789
convex
c2 479/516 549/597 562/603 279/303 277/304 767
fps
500 744/774 855/865 921/915
mips
rc6280 723/1133 758/1191 731/1101 565/869 564/867 888
decstation
5000/200 1112/1585 1173/1657 1168/1638 670/884 663/871 1325
alliant
FX/8* 1772/1876 2016/2160 2034/2184
1-process 4270
IBM 3090
200J vector - /1999 - /2051
200J scalar - /6059 - /6143
sun
sparc2 1798/2145 1834/2312 1627/2299
sparc
4/280 2528/3830 2700/4062 2708/4018
PROGRAM NOTES
Run.bench
min: 100 steps minimization
minmd: 20 steps min, 80 steps md
sander: 100 steps gradual warming
Run.bench2
sander/min: 100 steps minimization
sander/md: 100 steps gradual warming
gibbs: 100 steps of dynamic windows perturbation (double-wide sampling)
note: gibbs4 does not have vectorization directives
note: gibbs4 is double precision
One interesting thing that came to light when developing bench2
was that the distance-dependent (1/r^2) dielectric was significantly
faster than the normal (1/r) one. This effect, attributed to the taking
of the square root, was more pronounced when hardware arithmetic
support was lacking. Representative results (double precision sander
minimization):
SGI Crim32M MIPS IBM Convex HP Cray Fujitsu
diel Crim32M -lfastm RC6280 530 C2 730 Y-MP VP220
1/r^2 347 346 616 391 303 220 44 24
1/r 594 495 869 576 313 240 49 29
ratio .584 .699 .709 .679 .968 .917 .898 .828
When the SGI Crimson32M used -lfastm, the double precision version
was faster than the single for the 1/r^2 dielectric: 566 single,
495 double on minimization.
MACHINE NOTES
The Fujitsu VP2200 is a 32-bit machine with 64-bit arithmetic.
The Cray Y-MP is a 64-bit machine, so single precision results are irrelevant.
ncsc = North Carolina Supercomputing Center
sdsc = San Diego Supercomputing Center
The Convex C2 was running under IEEE Floating Point default mode.
-----
Cray hpm (hardware performance monitor) results
________ Y-MP ncsc___ ________ C90 ________
Run.bench Run.bench2 Run.bench Run.bench2
MFlops 61.5 72.7 109.0 116.6
MIPS 36.9 37.8 59.0 63.2
M_Mem/sec 70.9 91.2 115.1 142.3
ClockCyc/Inst 4.5 4.4 4.1 3.8
-----
Memory (Mb) Data Cache Instruction Cache Cache
c2 1024
fps500 128
alliant 64 512K
mips 64
rs6000/530 16
dec5000/200 32
Challenge 1024 16k (100MHz) 16k Sec Cache 1MB
Chall150 1024 16k (150MHz) 16k Sec Cache 1MB
iris4d/Crim 96 8K 8K Sec Cache 1MB
iris4d/indigoR4000 32 8K 8K Sec Cache 1MB
iris4d/410vgx 128 64K 64K Sec Cache 1MB
iris4d/310vgx 32 64K 64K Sec Cache 256KB
irisPersonal 12 32K 64K
iris4d/80gt 8 32K 64K
*Automatic parallelization directives were invoked in the
Alliant compilation. The machine has 8 processors. I do not
know what the parallel timings mean, but am impressed that
correct results were obtained on all tests except polarization. -Bill Ross
** SGI:
Multiprocessor results are from a version of code parallelized by SGI,
available on request from UCSF, currently being integrated in the
standard release. -lfastm = "fastmath" lib. Energy results
were exactly the same after 100 steps min + 100 steps md. -BR
----
Bill Ross
---------------------------------------------------------------------------
From: UUCP%"desimone "at@at" akocoa.enet.dec.com" 3-JAN-1994 00:28
I have attached some bm's recently sent over the net. Did you see them ?
I will also send you some electronic structure bm's for GAMESS in a separate
message.
Some answers to your questions:
o Using the OSF/1 OS, OpenGL is now available for the PXG boards. You
might want to consider the newly announced ZLX-M1 or ZLX-M2 boards
which will have OpenGL support by the end of March. They are priced
around $8K and $12K list US.
o I believe, for most computational chemistry simulations(calculations)
, the Alpha AXP systems offer the best performance or best
price/performance vs SGI , HP, IBM, or Sun. The model 600, and
800 pick up some additional performance on some of the popular
ab initio codes (depending on the problem) because of their larger
on board caches.
o Both OpenVMS and OSF/1 are good OS's. OSF/1 , can handle
larger than 2 GB UNIX file sizes, which no other desktop UNIX can.
Sometimes these large file sizes are advantageous for certain ab initio
calculations.
o It is difficult to suggest memory and disk requirements without
knowing what kind of problems you are handling. The best thing you
can do here is to ask the authors of any computational chemistry
software you are using.
Bill DeSimone
Edu & Research Business Unit
Digital Equip. Corp.
Molecular Sciences
---------------------------------------------------------------------------
From: US1RMC::"berkley $#at#$ wubs.wustl.edu" "Mr. Berkley Shands" 8-DEC-1993
14:47:56.61
*******************************************************************************
Benchmarks of the complete ACE series of 71 molecules Modified scan factors
*******************************************************************************
---------------------------------------------------------------------------%
====== Internet headers and postmarks (see DECWRL::GATEWAY.DOC) ======
From: UUCP%"desimone <-at-> akocoa.enet.dec.com" 3-JAN-1994 00:29
Here are some benchmarks that include a model 400S Alpha AXP, which is quite
a bit slower than the models your are considering. You will have to
estimate times for the newer Alpha's.
Already posted on net. Please pick from there. - Mrigank
[.....]
---------------------------------------------------------------------------
From: UUCP%"afj -x- at -x- chem.ucla.edu" 3-JAN-1994 00:33
I have some benchmark data you may be able to use.
This is a collection of stuff from the last year or so.
The newest stuff is at the bottom.
Good luck,
-A.J.
Collectable from archieve. Pick from there. - Mrigank
[......]
---------------------------------------------------------------------------
---------------------------------------------------------------------------
From: UUCP%"gene # - at - # jersey.cray.com" 3-JAN-1994 00:43
---------------------------------------------------------------------------
From: UUCP%"nagle[ AT ]tammy.harvard.edu" 3-JAN-1994 00:48
mrigank> We are about to place an order for a computer system for a newly
mrigank> established molecular modelling laboratory. Our initial survey zeroed
downs
mrigank> to select DEC alpha. I have following questions
mrigank>
mrigank> 1. Which sysstem is better for this work, SGI(Indigo2, Challenge),
mrigank> Alpha (DEC 3000 AXP 600, 800), IBM RS/6000, Sun, HP 735 etc.
For standalone number crunching, Dec Alpha is best. Depending on your
budget and computation needs, but also dependent of the software you
will be running, you may be interested in cluster performance which is
a different story.
For graphics, SGI is far and away the best, not necessarily because of
their graphics environment (and its performance) but because it has
the greatest number of tuned applications.
mrigank> 2. How are they score in
mrigank> a)Number Crunching? b) Graphics Hardware? c) Graphics Software?
See above. If you're writing your own software, I can give you more
details.
mrigank> 3. In case of AXP, is it which graphics option is better, PXG,
mrigank> Kubota, any other. Is it worth spending money in Kubota (More
mrigank> than Half the price of DEC 3000 AXP 600)
This depends greatly on the applications you will be runing and how
well they've been tuned for the different graphics environments. Run
a benchmark. If you're writing you're own software, write a benchmark
and run it.
mrigank> 4. What is the price performance ratio, how much RAM generally
mrigank> needed and diskspace.
Depends on application.
mrigank> 5. What all support OpenGL now?
Careful here. If it's just OpenGL, then DEC has support now. BUT
many of the older applications use features of GL which were not
included in the definition of OpenGl but were to be part of the
compatibility set. In other words, YMMV.
mrigank> 6. Which OS is better for Alpha OSF/1 or OpenVMS?
Depends on application.
mrigank> 8. Any Benchmarks ?
There are a variety of sources of benchmark information. UNIX review
periodically performs detailed comparisons of machines. They had at
least one in depth review of Dec ALPHA in 1993 - but I can't remember
which issue. These reviews are fairly comprehensive covering a
variety of floating point, integer, windowing, graphics, disk and
network performance (usually with comparisons to ostensibly equivalent
machines).
For SpecInt and SpecFP information, try the FAQ on comp.parallel (if
that fails I can get you a copy).
I have run a series of benchmarks of CHARMM dynamics simulations on a
variety of machines - if interested let me know. Some of the vendors
(both the hardware vendors and the commercial software vendors (MSI,
BIOSYM etc) have detailed performance information, if you can get them
to release it to you.
hope this helps.
Disclaimer: I was formerly general manager of MSI but have no
current affiliation with any commercial hardare or software supplier for
computational chemisty.
RN
-------------------------------------------------------------------------------
Robert J. Nagle Email: nagle;at;tammy.harvard.edu
Department of Chemistry Phone: (617) 495-0787
Harvard, Cambridge
Mass 02138
USA
---------------------------------------------------------------------------
From: UUCP%"arne #*at*# escher.mbi.ucla.edu" 3-JAN-1994 00:48
My (biased) opinions are:
>1. Which sysstem is better for this work, SGI(Indigo2, Challenge),
> Alpha (DEC 3000 AXP 600, 800), IBM RS/6000, Sun, HP 735 etc.
SGI is the clear leader for graphics, but alpha is the price
perfoemance leader for number crunching.
>2. How are they score in
> a)Number Crunching? b) Graphics Hardware? c) Graphics Software?
a) Price/Mflops is probably the cheapest AXP
b) All should have something good enough.
c) A lot of software will only run on SGI (for instance MIDAS/SCARECROW)
4. What is the price performance ratio, how much RAM generally
needed and diskspace.
> When I run MD (mainly rather small proteins) i Found that
32 MB is good enough on IBM but not on alpha, even with 64 MB
I only get 50% of the CPU speed for a system of 8000 Atoms
and a 14A cutoff running charmm.
6. Which OS is better for Alpha OSF/1 or OpenVMS?
OSF
8. Any Benchmarks ?
SpecFP/Spec Int should be available somewhere.
arne
---------------------------------------------------------------------------
From: UUCP%"landman { *at * } hal.physics.wayne.edu" 3-JAN-1994 00:50
I would be interested in the information you obtain about the best
modelling platform
Joe Landman
landman \\at// hal.physics.wayne.edu
---------------------------------------------------------------------------
From: UUCP%"Jeffrey.Nauss #*at*# UC.Edu" 4-JAN-1994 00:21
While the Dec Alpha has better performance for number crunching than a
comparable SGI computer, I doubt that you will find much in the way of
molecular graphics software for the Alpha. Also, the graphics on an
Alpha are not as good as with an SGI. In my opinion, if you want
graphics and visualization of yuor data, SGI is the best choice.
Jeff Nauss
************************************************************************
* Dr. Jeffrey L. Nauss * Telephone: 513-556-0148 *
* Department of Chemistry * Fax: 513-556-9239 *
* University of Cincinnati * e-mail: nauss "at@at" ucmodl.che.uc.edu *
* Cincinnati, OH 45221-0172 * *
************************************************************************
---------------------------------------------------------------------------
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