From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Apr 05 2012 - 03:10:59 CDT
I forgot to mention that with the stable 2.8 I could now only get the
.log file, so that even an examination of the system at the crash
becomes impossible (contrary to the case with 2.9b2, where the
restart.coor file was obtained.
francesco
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Thu, Apr 5, 2012 at 10:02 AM
Subject: Fwd: namd-l: Line minimizerfailure because of IMPR?
To: Norman Geist <norman.geist_at_uni-greifswald.de>, NAMD <namd-l_at_ks.uiuc.edu>
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.
>
>> -----Ursprüngliche 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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