Ok, thanks. After running the test jobs with the recompiled code I got
no additional output in the TEST_FAILURES.diff. Also turning off all
optimization in the dcqtp/ Makefile did not get rid of the NaNQ values.
I'm not sure whether we'll need these sections or not but we are
planning to do QM/MM calculations. I apologize for the bad link on my
first message. I am including my diff files for the three compilations
I have tried. Maybe it will be helpful. Thanks again.
http://www.chem.ucla.edu/~mccarren/TEST_FAILURES.diff (all defaults
for XLF90_aix)
http://www.chem.ucla.edu/~mccarren/TEST_FAILURES.diff_debug
(make AMBERBUILDFLAGS='-g -qflttrap -qsigtrap')
http://www.chem.ucla.edu/~mccarren/TEST_FAILURES.diff_dcqtpNoOpt
($(FOPTFLAGS) removed from src/dcqtp Makefile)
Patrick
Scott Brozell wrote:
> Hi,
>
> These compiler options add code to trap exceptions and signals.
> If the failing tests are rerun as usual (ie, no debugger needed)
> then the executable will terminate when a signal occurs and
> produce a stack trace.
>
> Scott
>
>
> On Fri, 20 Apr 2007, Patrick McCarren wrote:
>
>
>> 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
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Received on Wed Apr 25 2007 - 06:07:25 PDT
