AMBER Archive (2007)

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

From: Patrick McCarren (mccarren_at_chem.ucla.edu)
Date: Fri Apr 20 2007 - 18:01:53 CDT

Thanks for the response. I recompiled with those options but I don't
really know what to look for with TotalView. I don't have any
experience with debuggers. Do you have any hints? I will keep that
compiled code separate and make a separate build with lower optimization
levels for the crambin_divcon section next. Thanks,

Patrick

Scott Brozell wrote:
> 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
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu