[gmx-developers] Coulomb LR energy totals on AMD???

[Anton Feenstra]

Hi,


We've seen a reproducible error here on our 32 single CPU AMD 1G cluster,
which appears *only* in the Coloumb LR energy totals (both in .log and .edr).
The values are bogus, jumping from e.g. -1e04 to -1e11 or even -1e35!
Averages are -inf, rmsd nan. Simulations run for several ns, so it appears
forces are not affected. These values do not occur on SGI, or our dual
1.3G AMD machines. It therefore smells like a nasty bug!

It appears the single AMD's use 3Dnow, as per md.log:
> Testing x86 processor CPUID...
> 
> Testing x86 SSE capabilities...
> No SSE support in CPU. Trying Extended 3DNow...
> 
> Testing x86 processor CPUID...
> 
> Testing x86 3DNow capabilities...
> CPU and OS support extended 3DNow.
> Using Gromacs 3DNow single precision assembly innerloops.

while the duals use SSE:
> Testing x86 processor CPUID...
> 
> Testing x86 SSE capabilities...
> CPU and OS support SSE.
> Using Gromacs SSE single precision assembly innerloops.

Below are cpuinfo, resp. hinv for the three machine flavours ('xtc01' is the
single AMD, 'xtc33' the dual and 'alanine' the SGI).


xtc01> cat /proc/cpuinfo
processor       : 0
vendor_id       : AuthenticAMD
cpu family      : 6
model           : 4
model name      : AMD Athlon(tm) Processor
stepping        : 2
cpu MHz         : 999.839
cache size      : 256 KB
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
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 mmx fxsr syscall mmxext 3dnowext 3dnow
bogomips        : 1966.08

xtc33> cat /proc/cpuinfo
processor       : 0
vendor_id       : AuthenticAMD
cpu family      : 6
model           : 6
model name      : AMD Athlon(tm) MP Processor 1500+
stepping        : 2
cpu MHz         : 1333.064
cache size      : 256 KB
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
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 mmx fxsr sse syscall mp mmxext 3dnowext 3dnow
bogomips        : 2637.82

processor       : 1
vendor_id       : AuthenticAMD
cpu family      : 6
model           : 6
model name      : AMD Athlon(tm) Processor
stepping        : 2
cpu MHz         : 1333.064
cache size      : 256 KB
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
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 mmx fxsr sse syscall mp mmxext 3dnowext 3dnow
bogomips        : 2662.40

alanine> hinv
2 360 MHZ IP30 Processors
CPU: MIPS R12000 Processor Chip Revision: 3.5
FPU: MIPS R12010 Floating Point Chip Revision: 0.0
Main memory size: 768 Mbytes
Xbow ASIC: Revision 1.4
Instruction cache size: 32 Kbytes
Data cache size: 32 Kbytes
Secondary unified instruction/data cache size: 2 Mbytes
Integral SCSI controller 0: Version QL1040B (rev. 2), single ended
   Disk drive: unit 1 on SCSI controller 0
Integral SCSI controller 1: Version QL1040B (rev. 2), single ended
IOC3 serial port: tty1
IOC3 serial port: tty2
IOC3 parallel port: plp1
Graphics board: V8
Integral Fast Ethernet: ef0, version 1, pci 2
Iris Audio Processor: version RAD revision 12.0, number 1

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Room P275  Tel: +31 20 44 47608  Fax: +31 20 44 47610 |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "Don't Push Me, Cause I'm Close to the Edge" (Tricky) |
|_____________|_______________________________________________________|