AW: Line minimizerfailure because of IMPR?

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Apr 05 2012 - 03:28:14 CDT

Was this a CUDA build?

> -----Urspr√ľngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Francesco Pietra
> Gesendet: Donnerstag, 5. April 2012 10:02
> An: Norman Geist; NAMD
> Betreff: Fwd: namd-l: Line minimizerfailure because of IMPR?
>
> Hello:
>
> I tried the same files with stable namd 2.8, getting partly the same
> error message. I.e., now the minimization halted, at least for 20
> minutes, without getting the Linux prompt
>
> Start/end of log file:
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE
> VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 131516.3834 15951.4182 1089.1031
> 80.7094 -208823.8451 4021786.0851 0.0000
> 0.0000 0.0000 3961599.8541 0.0000
> 3961599.8541 3961599.8541 0.0000 1373635.0459
> 1388330.3068 672033.8185 1373635.0459 1388330.3068
> .................................
> ENERGY: 2131 9062.5391 6886.1278 1019.7076
> 53.3039 -304342.7936 31732.7361 0.0000
> 0.0000 0.0000 -255588.3792 0.0000
> -255588.3792 -255588.3792 0.0000 -5055.1933
> -4902.4727 672033.8185 -5055.1933 -4902.4727
>
> LINE MINIMIZER BRACKET: DX 0.000500355 0.00100071 DU -2.41055 117.048
> DUDX -44805.5 35123.5 200226
>
> ---------------------------
> Confusing enough, the gradient trend was now better:
>
> MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM 9.95266e+08 TO 995266
> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
> ....................
> LINE MINIMIZER REDUCING GRADIENT FROM 128305 TO 128.305
> LINE MINIMIZER REDUCING GRADIENT FROM 131691 TO 131.691
> LINE MINIMIZER REDUCING GRADIENT FROM 123700 TO 123.7
>
> ----------------------
> Could you please suggest how to check from where the high VdW and
> IMPR come? (I mean in terms of interatomic clashes, however, having no
> indication as what atoms are flying out, I do not know where to look
> for). This means that I believe that these problems come from a still
> incorrect parameter files.
>
> thanks a lot
>
> francesco
>
>
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Thu, Apr 5, 2012 at 8:59 AM
> Subject: Re: namd-l: Line minimizerfailure because of IMPR?
> To: Norman Geist <norman.geist_at_uni-greifswald.de>
>
>
> Hello Norman:
> I was thinking to IMPR because the value is increasing, as you may
> notice from what I reported. As it is a new (complex) parameterization
> ..
> Also, you may have noticed that VdW decreases in the first couple of
> minimization steps, then no more, until the simulation crashes.
>
> I changed a little the IMPR parameters, getting the same error on
> minimization, this type at step 209.
>
> At any event - although 2.9b2 in my hands and same hardware and
> min.conf proved quite OK with another metalloprotein - your
> suggestion to try with a stable version of NAMD has to be followed.
> I'll come back soon.
>
> thanks
>
> francesco
>
> On Thu, Apr 5, 2012 at 8:08 AM, Norman Geist
> <norman.geist_at_uni-greifswald.de> wrote:
> > Hi,
> >
> > it's possible that there's a bug in the new implementation of the
> minimization on the gpu. But I have seen this error before on a broken
> gpu. Just to be sure, does this error occur on different gpus and only
> with 2.9b2? I don't think it's a wrong setting for IMPR because that
> would IMHO cause a unstable simulation and the simulation would just
> crash with a message like "Simulation has become unstable", but this
> message shows a missed answer from a gpu and could indicate a hardware
> issue, or it was just happenstance. Is the error reproducible?
> >
> > Best wishes
> > Norman Geist.
> >
> >> -----Urspr√ľngliche Nachricht-----
> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> >> Auftrag von Francesco Pietra
> >> Gesendet: Mittwoch, 4. April 2012 17:02
> >> An: NAMD
> >> Betreff: namd-l: Line minimizerfailure because of IMPR?
> >>
> >> Hi:
> >> with cuda v 2.9b2 and 27 FF, I was trying to minimize a new system
> >> comprising a new transition metal cluster. Minimization failed as
> >> indicated by the start/end of .log file and gradient trend:
> >>
> >> .log file:
> >>
> >> ETITLE: TS BOND ANGLE DIHED
> >> IMPRP ELECT VDW BOUNDARY
> MISC
> >> KINETIC TOTAL TEMP POTENTIAL
> >> TOTAL3 TEMPAVG PRESSURE GPRESSURE
> >> VOLUME PRESSAVG GPRESSAVG
> >>
> >> ENERGY: 0 131516.3834 15951.4182 1089.1031
> >> 80.7094 -208823.8452 4021786.0851 0.0000
> >> 0.0000 0.0000 3961599.8541 0.0000
> >> 3961599.8541 3961599.8541 0.0000 1373635.0459
> >> 1388330.3068 672033.8185 1373635.0459 1388330.3068
> >> ..................................................................
> >>
> >> LINE MINIMIZER BRACKET: DX 1.62748e-48 1.80832e-43 DU -2.26438e-05
> >> 8.74043e-06 DUDX 521930 521930 521930
> >> ENERGY: 608 121296.7924 15556.9336 1102.0259
> >> 130.0208 -214468.6419 18560.8579 0.0000
> >> 0.0000 0.0000 -57822.0113 0.0000
> >> -57822.0113 -57822.0113 0.0000 -14967.9037
> >> -1012.7549 672033.8185 -14967.9037 -1012.7549
> >>
> >> LINE MINIMIZER BRACKET: DX 1.62748e-49 1.80832e-43 DU -1.45298e-05
> >> 8.74043e-06 DUDX 521930 521930 521930
> >> LINE MINIMIZER REDUCING GRADIENT FROM 4.44643e+08 TO 444643
> >> FATAL ERROR: cuda_check_remote_progress polled 1000000 times over
> >> 101.723663 s on step 609
> >>
> >>
> >>
> >>
> >> Gradient:
> >>
> >> MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
> >> LINE MINIMIZER REDUCING GRADIENT FROM 9.95266e+08 TO 995266
> >> ............................
> >> LINE MINIMIZER REDUCING GRADIENT FROM 4.44643e+08 TO 444643
> >>
> >>
> >> The structure, at the end of the crashed minimization, does not show
> >> any major distortion. From the above files my impression is of a
> wrong
> >> setting of IMPR. I would be very grateful for confirming my feeling
> ,
> >> or suggesting otherwise.
> >>
> >> francesco pietra
> >
> >

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