AMBER Archive (2007)

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

From: Patrick McCarren (mccarren_at_chem.ucla.edu)
Date: Wed Apr 25 2007 - 18:44:15 CDT

Thanks for all the suggestions from everyone. It sounds like we will be
fine without these test cases working. It's great to have people to
turn to.

Patrick

Ross Walker wrote:
> Hi Patrick,
>
> It's a shame that turning off optimization doesn't work. Your best option is
> probably to just avoid using divcon and the related routines on the machine.
> At least for the time being. This essentially means that you can't use
> antechamber on the machine (at least to obtain charges) and you can't run
> QM/MM MD with idc>0. The antechamber issue is likely not a problem since I
> assume people don't use this machine interactively in which case they can
> build systems using amber9 installed on their own local machine and copy
> across the prmtop and inpcrd files to run production MD. Thus they wouldn't
> need to use antechamber on the AIX machine.
>
> As for QM/MM MD it is unlikely that you would want to run QM/MM simulations
> using the divcon interface. Sander now includes everything you need
> (excluding divide and conquor support) built in. Thus you will be able to
> run QM/MM simulations without a problem. The alternate divcon interface is
> enabled by setting idc>0 in the qmmm namelist but this then restricts you to
> non-periodic systems and you cannot run in parallel so you probably won't
> have a call to use it.
>
> Thus I would just stick with the installation you have (don't forget to
> build pmemd as well).
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu
>> [mailto:owner-amber_at_scripps.edu] On Behalf Of Patrick McCarren
>> Sent: Monday, April 23, 2007 14:52
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: AIX 5 test failures: -NaNQ
>>
>> 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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>>>>>>
>>>>>>
>>>>>>
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>>
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>>>>>
>>>>>
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>>>
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