Hello,
I have been porting AMBER4.1 to a dual PentiumIII 450. With some effort
I have manged to get things working well in serial and parallel (by
replacing SGI_MP directives with OpenMP directives supported by
the pgf77/pgcc compiler), except for one glitch which I can't seem to
overcome. I have been using the "bench" test suite provided with
the distribution to test things out. Perhaps someone can point
me in the right direction...
System: dual PIII450 running RedHat 6.0 (2.2.5-15smp kernel)
Both in serial and parallel, under every possible compiler/optimization
directive combination, using pgf77, g77 and even fort77,
I obtain the following (identical) differences at the first time step
for the dnawat/Ewald test case.:
b1_md4.out.dif:
188,189c188,189
< NSTEP = 1 TIME(PS) = 0.101 TEMP(K) = 249.75 PRESS =
-2047.64
< Etot = -24172.9092 EKtot = 3874.6436 EPtot =
-28047.5528
---
> NSTEP = 1 TIME(PS) = 0.101 TEMP(K) = 249.75 PRESS =
-2047.40
> Etot = -24172.8891 EKtot = 3874.6428 EPtot =
-28047.5319
329,334c329,334
< NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 5.65 PRESS =
630.69
< Etot = 22.8409 EKtot = 87.5834 EPtot =
108.6791
< BOND = 7.5226 ANGLE = 18.9307 DIHED =
7.8277
< 1-4 NB = 9.3561 1-4 EEL = 29.6332 VDWAALS =
209.7362
< EELEC = 320.7651 EHBOND = 2.0258 CONSTRAINT =
0.0000
< EKCMT = 54.8849 VIRIAL = 1149.1345 VOLUME =
381.2115
---
> NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 5.65 PRESS =
630.66
> Etot = 22.8213 EKtot = 87.5914 EPtot =
108.6732
> BOND = 7.5223 ANGLE = 18.9312 DIHED =
7.8272
> 1-4 NB = 9.3558 1-4 EEL = 29.6337 VDWAALS =
209.7410
> EELEC = 320.7652 EHBOND = 2.0259 CONSTRAINT =
0.0000
> EKCMT = 54.8862 VIRIAL = 1149.0809 VOLUME =
381.2251
336c336
< Ewald error estimate: 0.2978E-04
---
> Ewald error estimate: 0.7049E-04
Given that there are differences at the first time step, I am assuming
they
are not attributable to machine precision, but rather, that
there exists a more serious underlying problem. I assume that the
problem lies with the use of the Ewald routine for this test. I have
made bugfixes 32, 78, and 88, to no avail. The same code/test case
compiled and run our SGIs shows no such differences.
Has anyone observed similar discrepancies for Pentium based machines?
Thanks very much for your help,
Claudio Chuaqui
Rowland Institute for Science
Cambridge, MA
chuaqui_at_rowland.org
Received on Fri Aug 13 1999 - 10:33:54 PDT