AMBER Archive (2007)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Apr 19 2007 - 20:20:46 CDT

Dear Patrick,

All of the errors you are seeing are coming from test cases that make use of
Divcon. All the standard QMMM tests have passed (or differ only in the last
decimal place), however the crambin test case that uses divcon, rather than
sander's built in QM routines has failed with NANQ errors. 2pk4_stan is
another divcon test as is 2pk4. The Antechamber failures have come about
because this also calls divcon in order to calculate the AM1-BCC RESP
charges. Here divcon has failed and the errors have propogated through into
the parameter files produced by Antechamber.

The crambin_2 and amoeba_jac errors are innocuous.

Thus I suspect this is a compiler problem with miscompilation of the divcon
code. It could take a long time to track this down. A quicker alternative
maybe to turn off optimization for the divcon part of the code. This will
slow down antechamber but that probably won't cause too many problems. It
will also slow down QM/MM MD calculations that specifically use divcon (NOT
the default QMMM implementation) and it is probably unlikely that you will
want to run divcon QMMM MD so try the following:

edit $AMBERHOME/src/dcqtp/mod/Makefile

change line 122 from:

F90FLAGS = $(FOPTFLAGS) $(FREEFORMAT_FLAG) $(MODULEDIR)../../sander

to

F90FLAGS = $(FFLAGS) $(FREEFORMAT_FLAG) $(MODULEDIR)../../sander

Then I would suggest rebuilding everything from scratch just to be certain
that everything gets recompiled.

cd $AMBERHOME/src
make clean
make

Hopefully the test cases will then pass.

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 |

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Patrick McCarren
> Sent: Thursday, April 19, 2007 16:31
> To: amber_at_scripps.edu
> Subject: AMBER: AIX 5 test failures: -NaNQ
>
> 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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