AMBER Archive (2003)

Subject: Re: AMD opteron

From: Tru Huynh (tru_at_pasteur.fr)
Date: Wed May 28 2003 - 08:08:51 CDT

On Tue, May 27, 2003 at 10:57:39AM -0500, Hai-Long Wang wrote:
> Hi, All
>
> I got an opteron dual cpu (1.4GHz) box, and want to try amber on it. I had
> PGI 5.0 beta2 compiler and gcc3 on it. Does any one has an idea to compile
> the amber on opteron? Thanks

Hi,

Here is the MACHINE file I have used for amber7 and the GNU compilers:
<cut>
setenv MACHINE "linux/FreeBSD/Windows PC/Mac OSX"
setenv MACH Linux
setenv MACHINEFLAGS " "
setenv CPP "cpp -traditional "
setenv CC gcc
setenv SYSDIR Machines/standard
setenv LOAD "g77 -O2 -m64"
setenv LOADLIB "-lm"
setenv G77_COMPAT "-Wno-globals -fno-globals -ff90 -funix-intrinsics-hide"
setenv G77_OPT "-O2 -m64"
setenv L0 "g77 -c -g $G77_COMPAT"
setenv L1 "g77 -c $G77_OPT $G77_COMPAT"
setenv L2 "g77 -c $G77_OPT $G77_COMPAT"
setenv L3 "g77 -c $G77_OPT $G77_COMPAT"
setenv RANLIB ranlib
<cut>

Amber7 compiles and run pretty fast on the opteron when you have the chance
to get your hands on one. <SHAMELESS ADV> Thank you Alineos :) </ADV>
On one cpu it is comparable to one HP/Compaq/Digital ev67_at_1GHz.

Joint CHAMM/AMBER benchmarks:

with gcc-3.3:
/home/tru/bin/sander_amber7-gcc-3.3

real 17m19.601s
user 17m17.800s
sys 0m1.530s

with system gcc-3.2.2
/home/tru/bin/sander_amber7-gnu_rh

real 17m32.467s
user 17m32.050s
sys 0m0.140s

Other figures at: http://www.scripps.edu/brooks/Benchmarks/

No figures for PGI because of:
BETA LICENSE CONDITIONS
...
 
  iv. In the absense of explicit permission from STMicroelectronics,
      The Portland Group Compiler Technology, performance results
      obtained using this Software will not be published or presented
      in a public forum
...

More details about the configuration.
------------------------------------

[tru_at_rio242 src]$ cat /etc/redhat-release
Red Hat Linux release 8.0.95 (GinGin64)
[tru_at_rio242 src]$ uname -a
Linux rio242 2.4.20-9.2smp #1 SMP Thu Apr 10 11:54:33 EDT 2003 x86_64 x86_64 x86_64 GNU/Linux
[tru_at_rio242 src]$ rpm -q gcc
gcc-3.2.2-10
[tru_at_rio242 src]$ rpm -q glibc
glibc-2.3.2-27.9
[tru_at_rio242 jac]$ cat /proc/cpuinfo
processor : 0
vendor_id : AuthenticAMD
cpu family : 15
model : 5
model name : AMD Opteron(tm) Processor 242
stepping : 0
cpu MHz : 1603.652
cache size : 1024 KB
fpu : yes
fpu_exception : yes
cpuid level : 1
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow
bogomips : 3198.15
TLB size : 1088 4K pages
clflush size : 64
address sizes : 40 bits physical, 48 bits virtual
power management: ts ttp

processor : 1
vendor_id : AuthenticAMD
cpu family : 15
model : 5
model name : AMD Opteron(tm) Processor 242
stepping : 0
cpu MHz : 1603.652
cache size : 1024 KB
fpu : yes
fpu_exception : yes
cpuid level : 1
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow
bogomips : 3204.71
TLB size : 1088 4K pages
clflush size : 64
address sizes : 40 bits physical, 48 bits virtual
power management: ts ttp

[tru_at_rio242 jac]$ cat /proc/meminfo
        total: used: free: shared: buffers: cached:
Mem: 1044918272 1013727232 31191040 0 159260672 535695360
Swap: 4293554176 13565952 4279988224
MemTotal: 1020428 kB
MemFree: 30460 kB
MemShared: 0 kB
Buffers: 155528 kB
Cached: 521452 kB
SwapCached: 1688 kB
Active: 390928 kB
Inactive: 378668 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 1020428 kB
LowFree: 30460 kB
SwapTotal: 4192924 kB
SwapFree: 4179676 kB

==> jac-amber7.sander_amber7-gcc-3.3.20030528_11h29.opteron242.out <==

| Setup wallclock 2 seconds
| Nonsetup wallclock 1038 seconds

==> jac-amber7.sander_amber7-gnu_rh.20030528_11h46.opteron242.out <==

| Setup wallclock 1 seconds
| Nonsetup wallclock 1051 seconds

More figures at: http://www.alineos.com/Benchs/bench3_eng.html
Caveat, they were collected on an other opteron board and different cpu speed (240/1400MHz)

Best regards,

Tru 

-- 
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru_at_pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France