Subject: amber on linux

From: [email-masked] (Cezary Czaplewski)
Date: Mon, 3 Jul 1995 08:41:15 +0200 (MET DST)

Dear Netters,

Some time ago there was on CCL a letter with list of programs ported to linux.
As I remeber amber4.0 was on the list. Today I have just compile amber4.1.
It is prepared for f2c and I use it and also g77. And there are benchmark:

type of                DNA in water              DNA      DNA   Plastocyanin
compiler                                        in vacum  Gibbs   in water
         cutoff	8A	9/12A	12A	Ewald	 10A	  10A	   12A

g77		640	1095	-	-	 414	  882	    -

f2c
(with		733	1149	2466	-	 601	  +	    -
-DISTAR2)        

and just to compare:

DOS 6.2
NDP		1216	-	-	 -	  872	   -	    -
(with -DISTAR2)

All test were done on Pentium 90Mhz (SIS PCI 85C50X board with P54C-90
processor and 256 Kb L2 WB cache, 8Mb RAM 12MB swap, under Linux 1.2.8)
with g77 v0.5.14, f2c v0.10, gcc v2.6.3.

In DOS I used for test the same machine and NDP-486 fortran v3.2.0

Some benchmark indicated with "-" haven't been done becuse of lack of memory.
Gibbs4.1 "+" has no -DISTAR2 (integer*2) option and it wasn't compile with f2c.
g77 is faster but it has no integer*2 - with sander this option save a lot
of memory.

For compare with true workstations:
                     DNA in water                DNA      DNA   Plastocyanin
                                               in vacum  Gibbs   in water
    cutoff	8A	9/12A	12A	Ewald	 10A	  10A	   12A
sun5
usparc70MHz	696	1070	2189	2484	 706	  906	   3593

sun20
ssparc50MHz	459	699	1407	1243	 325	  561	   1837

SGI
R4000 150MHz	383	611	1303	1342	 316	  567	   1857

(sun20 and SGI results from SUMMARY in distribution of amber41)

I think that Pentium90 with Linux is a true low-end workstation. If we
compare price: sun5 costs about 4000$, PC Pentium90 about 2500$ with 
the same perypheries what winns ? Linux and gcc/g77 are free. For f77 
from Sun you must also pay about 500$ (academic price).
Of course today there are no comercial software fo linux :-((

				Cezary Czaplewski
				University of Gdansk
				Faculty of Chemistry