AMBER Archive (2007)

Subject: Re: AMBER: AMBER8 compiler with intel 9.1 compiler

From: Peter Z. Qin (pzq_at_usc.edu)
Date: Fri May 18 2007 - 19:53:29 CDT

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, May 17, 2007 6:38 PM
Subject: Re: AMBER: AMBER8 compiler with intel 9.1 compiler

> 2. If so, try just compiling ew_fft.f (and/or ew_recip.f) at low
> optimization, everything else at high optimzation. My guess is that
> ew_fft.f
> is the culprit...there seem to be things in there that the intel
> optimizers
> don't like.
>
I modified the ew_fft.f by removing "! <compile=optimized>" and also applied
budfix64. Then I recompile with optimization on. However, failures occur at
the same cases (cytosine, dhfr, etc.)

>
> If you want, the next thing to do is to try to figure out which routine
> doesn't
> work with optimization turned on. Here is a suggested path, (for you or
> someone else):
>
> 1. Do dhfr one step with verbose=2 in the &ewald namelist. Look at the
> differences between optimized and unoptimzed code. If you are lucky, the
> differences will be in the reciprocal contribution to the electrostatic
> energy.

With verbose=2, I have ran dhfr/Run.dhfr. Part of the difference between
mdout.dhfr is listed below. The version with MPI flag is compiled without
optimization, and the version with no Flags is compiled as indicated above.

The big difference seems to be Eevir vs. Ecoulomb.

188,189c191,192
< Iso virial = -187936.116173447459
< Eevir vs. Ecoulomb = 0.000535006138 

---
>      Iso virial             =     -187933.775401700172
>      Eevir vs. Ecoulomb     =           0.000037834768

What next?

-peter

[pzq_at_hpc-login1 dhfr]$ more dif.op_nonop
6c6
< | Run on 05/18/2007 at 17:25:32
---
> | Run on 05/18/2007 at 17:31:37
43c43
< | Flags:
---
> | Flags: MPI
80c80
< |      Integer memory used by local nonb=    1113175
---
> |      Integer memory used by local nonb=     855625
83c83
< |    MAX NONBOND PAIRS =    7643333
---
> |    MAX NONBOND PAIRS =    3821666
86c86
< |     Real             1587417
---
> |     Real             1656247
88,90c88,90
< |     Integer          1822718
< |     Max Pairs        7643333
< |     Max Rstack       1147486
---
> |     Integer          1565168
> |     Max Pairs        3821666
> |     Max Rstack       1017678
92c92
< |       Total            59355 kbytes
---
> |       Total            42944 kbytes
151a152,155
> |  Atom division among processors:
> |         0   11467   22930
> |  Running AMBER/MPI version on    2 nodes
>
178,179c182
<  listtot =      4721242
< | Local SIZE OF NONBOND LIST =    4721242
---
> | Local SIZE OF NONBOND LIST =    2351245
183c186
<      Evdw                   =        8109.389249773295
---
>      Evdw                   =        8109.389249773089
185c188
<      Ecoulomb               =      -89881.644058586680
---
>      Ecoulomb               =      -89881.644058587204
188,189c191,192
<      Iso virial             =     -187936.116173447459
<      Eevir vs. Ecoulomb     =           0.000535006138
---
>      Iso virial             =     -187933.775401700172
>      Eevir vs. Ecoulomb     =           0.000037834768
192,194c195,197
<                      (rec)  =         791.295774837328
<                      (dir)  =      -70279.214671935872
<                      (adj)  =      463442.359416397696
---
>                      (rec)  =         791.295774837370
>                      (dir)  =      -70279.214671936992
>                      (adj)  =      463442.359416398278
196,198c199,201
<      MOLECULAR VIRIAL:  -.61556609E+05 -.73132351E+03 0.16272816E+03
<      MOLECULAR VIRIAL:  -.73132351E+03 -.63437371E+05 0.39174475E+03
<      MOLECULAR VIRIAL:  0.16272816E+03 0.39174475E+03 -.62942136E+05
---
>      MOLECULAR VIRIAL:  -.61554269E+05 -.73132351E+03 0.16272816E+03
>      MOLECULAR VIRIAL:  -.73132351E+03 -.63460369E+05 0.39174475E+03
>      MOLECULAR VIRIAL:  0.16272816E+03 0.39174475E+03 -.62919138E+05
200,201c203,204
<  NSTEP =        1   TIME(PS) =     510.051  TEMP(K) =   301.30  PRESS = 
0.0
<  Etot   =    -57751.4656  EKtot   =     14110.8966  EPtot 
  =    -71862.3622
---
>  NSTEP =        1   TIME(PS) =     510.051  TEMP(K) =   301.29  PRESS = 
> 0.0
>  Etot   =    -57751.8286  EKtot   =     14110.5335  EPtot 
>   =    -71862.3622
205c208
<  Ewald error estimate:   0.5350E-03
---
>  Ewald error estimate:   0.3783E-04
208c211
<  NET FORCE PER ATOM:   -0.2246E-04   0.1758E-04  -0.4452E-05
---
>  NET FORCE PER ATOM:   -0.2246E-04   0.1757E-04  -0.4451E-05
210c213
<      Evdw                   =        8112.296676774401
---
>      Evdw                   =        8112.287287794546
212c215
<      Ecoulomb               =      -89882.083206685784
---
>      Ecoulomb               =      -89882.066896236734
215,216c218,219
<      Iso virial             =     -187985.022914657660
<      Eevir vs. Ecoulomb     =           0.000546464804
---
>      Iso virial             =     -187983.277227977349
>      Eevir vs. Ecoulomb     =           0.000026650466
219,221c222,224
<                      (rec)  =         789.943303354934
<                      (dir)  =      -70279.067483709237
<                      (adj)  =      463443.125551554316
---
>                      (rec)  =         789.940498351458
>                      (dir)  =      -70279.064612572838
>                      (adj)  =      463443.141795870382
223,225c226,228
<      MOLECULAR VIRIAL:  -.61574500E+05 -.71646918E+03 0.18477125E+03
<      MOLECULAR VIRIAL:  -.71646918E+03 -.63433957E+05 0.36468806E+03
<      MOLECULAR VIRIAL:  0.18477125E+03 0.36468806E+03 -.62976566E+05
---
>      MOLECULAR VIRIAL:  -.61573011E+05 -.71651922E+03 0.18472266E+03
>      MOLECULAR VIRIAL:  -.71651922E+03 -.63455503E+05 0.36481257E+03
>      MOLECULAR VIRIAL:  0.18472266E+03 0.36481257E+03 -.62954763E+05

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