AMBER Archive (2007)

Subject: Re: AMBER: AIX 5 test failures: -NaNQ

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Apr 19 2007 - 19:13:54 CDT

Hi,

It could be useful to see what source code lines are causing the
floating point issues; rebuild with
make AMBERBUILDFLAGS='-g -qflttrap -qsigtrap'
and rerun the tests.

Some will probably be innocuous and are probably caused floating point
optimization settings, but some may be bugs.

Scott

On Thu, 19 Apr 2007, Patrick McCarren wrote:

> AMBER 9 (patched up to bug 34) compiled with no errors on an IBM P655+
> machine running AIX 5.2.0.0 with xlf enterprise edition 10.1 at ARSC,
> but some tests failed: crambin_divcon, 2pk4_stan, amoeba_jac, tp.mol2,
> ash.mol2, sustiva.mol2, fluorescein.mol2, frcmod, DGN.mol2 with NaNQ
> values. We didn't have this problem on our commodity intel and opteron
> machines. See http://www.chem.ucla.edu/~mccarren/TEST_FAILURES.dff.txt
> and a selection of messages below. Does anyone have any ideas on how to
> fix this or what's causing it? Thanks,
>
> Patrick McCarren
> UCLA
>
> /wrkdir/mccarren/amber9/test/qmmm2/crambin
> 82c86
> < 1 1.580E+3 2.654E+2 4.228E+3 SG 373
> ---
> > 1 -NaNQ -NaNQ 8.351E+1 CG 592
> 114,118c93,97
> < 5 1.283E+3 2.307E+2 3.670E+3 SG 373
> < BOND = 52.706 ANGLE = 71.855 DIHED = 175.646
> < VDWAALS = 1829.840 EEL = -3263.747 EGB = 0.
> < 1-4 VDW = 179.449 1-4 EEL = 2324.257 RESTRAINT = 0.
> < PM3ESCF = -86.627
> ---
> > 1 -NaNQ -NaNQ 8.351E+1 CG 592
> > BOND = 53.126 ANGLE = 71.909 DIHED =
> 175.658
> > VDWAALS = 2120.633 EEL = -3258.619 EGB = 0.
> > 1-4 VDW = 179.433 1-4 EEL = 2324.264 RESTRAINT = 0.
> > PM3ESCF = -NaNQ
> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> /wrkdir/mccarren/amber9/test/qmmm2/2pk4
> 89a90,93
> > QMMM: Warning: No Convergence in SCF Calculation;
> > QMMM: Maximum Iteraction Count Has Been Reached
> > QMMM: Job will continue with unconverged SCF
> > QMMM: Energies and forces this step will not be accurate
> 91c95
> < 1 -2.732E+2 4.788E+1 1.156E+3 SG 319
> ---
> > 1 -NaNQ -NaNQ 0. N 1
> 95,120c99
> < AM1ESCF = -275.132
> < NSTEP ENERGY RMS GMAX NAME NUMBER
> < 2 -3.068E+2 4.566E+1 1.088E+3 SG 319
> < BOND = 102.150 ANGLE = 358.630 DIHED = 679.810
> < VDWAALS = 370.536 EEL = -3985.345 EGB = 0.
> < 1-4 VDW = 320.744 1-4 EEL = 2123.792 RESTRAINT = 0.
> < AM1ESCF = -277.206
> < NSTEP ENERGY RMS GMAX NAME NUMBER
> < 3 -3.452E+2 4.318E+1 1.013E+3 SG 319
> < BOND = 100.813 ANGLE = 357.771 DIHED = 679.722
> < VDWAALS = 337.058 EEL = -3985.319 EGB = 0.
> < 1-4 VDW = 320.794 1-4 EEL = 2123.643 RESTRAINT = 0.
> < AM1ESCF = -279.749
> < NSTEP ENERGY RMS GMAX NAME NUMBER
> < 4 -3.886E+2 4.046E+1 9.323E+2 SG 319
> < BOND = 99.172 ANGLE = 356.699 DIHED = 679.612
> < VDWAALS = 299.751 EEL = -3985.285 EGB = 0.
> < 1-4 VDW = 320.852 1-4 EEL = 2123.454 RESTRAINT = 0.
> < AM1ESCF = -282.872
> < NSTEP ENERGY RMS GMAX NAME NUMBER
> < 5 -4.370E+2 3.751E+1 8.450E+2 SG 319
> < BOND = 97.154 ANGLE = 355.354 DIHED = 679.472
> < VDWAALS = 258.742 EEL = -3985.238 EGB = 0.
> < 1-4 VDW = 320.916 1-4 EEL = 2123.214 RESTRAINT = 0.
> < AM1ESCF = -286.709
> < Maximum number of minimization cycles reached.
> ---
> > AM1ESCF = -NaNQ
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> /wrkdir/mccarren/amber9/test/antechamber/tp
> 7,19c7,19
> < 1 CG -1.959 0.102 0.795 ca 1 TP -0.118
> < 2 CD1 -1.249 0.602 -0.303 ca 1 TP -0.113
> < 3 CD2 -2.071 0.865 1.963 ca 1 TP 0.016
> < 4 CE1 -0.646 1.863 -0.234 ca 1 TP -0.137
> < 5 C6 -1.472 2.129 2.031 ca 1 TP -0.145
> < 6 CZ -0.759 2.627 0.934 ca 1 TP -0.112
> < 7 HE2 -1.558 2.719 2.931 ha 1 TP 0.129
> < 8 S15 -2.782 0.365 3.060 sh 1 TP -0.254
> < 9 H19 -3.541 0.979 3.274 hs 1 TP 0.191
> < 10 H29 -0.787 -0.043 -0.938 ha 1 TP 0.134
> < 11 H30 0.373 2.045 -0.784 ha 1 TP 0.133
> < 12 H31 -0.092 3.578 0.781 ha 1 TP 0.133
> < 13 H32 -2.379 -0.916 0.901 ha 1 TP 0.143
> ---
> > 1 CG -1.959 0.102 0.795 ca 1 TP -NaNQ
> > 2 CD1 -1.249 0.602 -0.303 ca 1 TP -NaNQ
> > 3 CD2 -2.071 0.865 1.963 ca 1 TP -NaNQ
> > 4 CE1 -0.646 1.863 -0.234 ca 1 TP -NaNQ
> > 5 C6 -1.472 2.129 2.031 ca 1 TP -NaNQ
> > 6 CZ -0.759 2.627 0.934 ca 1 TP -NaNQ
> > 7 HE2 -1.558 2.719 2.931 ha 1 TP -NaNQ
> > 8 S15 -2.782 0.365 3.060 sh 1 TP -NaNQ
> > 9 H19 -3.541 0.979 3.274 hs 1 TP -NaNQ
> > 10 H29 -0.787 -0.043 -0.938 ha 1 TP -NaNQ
> > 11 H30 0.373 2.045 -0.784 ha 1 TP -NaNQ
> > 12 H31 -0.092 3.578 0.781 ha 1 TP -NaNQ
> > 13 H32 -2.379 -0.916 0.901 ha 1 TP -NaNQ
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