Subject: Summary: Alpha vs. SGI for Mol. Modelling.

From: "Dr. Mrigank" <[email-masked]>
Date: Fri, 7 Jan 94 13:09:21 +0530

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
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                        ----- 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:  [email-masked]
P O Box 1304, Sector 39A          \/UUCP:...!uunet!sangam!vikram!imtech!mrigank
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   point, however, is to change it.

============================ Original Responses  ===========================
_____________________________________________________________________________
From:	UUCP%"[email-masked]" 31-DEC-1993 02:17  

Please send me a summary of yourr responses. Thanks.
--Jonathan
---------
Jonathan G. Harris				    [email-masked]
Department of Chemical Engineering          	    tel(617)253-5273
Room 66-450, MIT, 25 Ames St, Cambridge, MA 02139   fax(617)253-9695
---------------------------------------------------------------------------
From:	UUCP%"[email-masked]" 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.
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From:	UUCP%"[email-masked]"  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
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From:	UUCP%"[email-masked]"  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.

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From:	UUCP%"[email-masked]"  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

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|New York, NY 10032	|   email: [email-masked]
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From:	UUCP%"[email-masked]"  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%"[email-masked]"  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::"[email-masked]" "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%"[email-masked]"  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
[.....]
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From:	UUCP%"[email-masked]"  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
[......]
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---------------------------------------------------------------------------
From:	UUCP%"[email-masked]"  3-JAN-1994 00:43

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From:	UUCP%"[email-masked]"  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:		[email-masked]
Department of Chemistry			Phone: 		(617) 495-0787
Harvard, Cambridge
Mass 02138
USA
---------------------------------------------------------------------------
From:	UUCP%"[email-masked]"  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%"[email-masked]"  3-JAN-1994 00:50

   I would be interested in the information you obtain about the best
modelling platform

Joe Landman
[email-masked]
---------------------------------------------------------------------------
From:	UUCP%"[email-masked]"  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: [email-masked]  *
*  Cincinnati, OH 45221-0172        *                                  *
************************************************************************
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