Dear all,
I am contacting you because I am obtaining a strange error during a
simulation on GPU (I obtain the same error both with C2050 and GTX580).
My system has inside a gadolinium DOTA molecule - the Gd atom has 8
coordination bonds parametrized according to literature.
The problem is that the system passes successfully the minimization step
with reasonable energy and everything seems to be ok.
When MD is started I obtain the following error:
Error: unspecified launch failure launching kernel kReduceForces
cudaFree GpuBuffer::Deallocate failed unspecified launch failure
At line 109 of file inpcrd_dat.f90 (unit = 9, file = 'heat1_G3_DOTA.rst')
Fortran runtime error: End of file
STOP PMEMD Terminated Abnormally!
The input file of MD 1st step is:
&cntrl
imin=0,
irest=0,
ntx=1,
nstlim=10000,
dt=0.001,
ntc=2,
ntf=2,
cut=8.0,
ntb=1,
ntpr=1000,
ntwx=1000,
ntt=3,
gamma_ln=2.0,
temp0=60,
ntr=1,
ig=-1,
ioutfm=1,
/
2.0
RES 1 109
END
END
The strange thing is that the error is the same in presence or absence of
iwrap=1 (which was indicated recently as possible source of such an error on
this mailing list
http://archive.ambermd.org/201111/0272.html).
Another strange thing is that if the same MD step is run with pmemd instead
of pmemd.cuda, no error is reported.
Curiously, however the energies reported are quite different!
In fact PMEMD reports "usual/safe" negative values, while pmemd.cuda reports
a "worse" energetic situation.
PMEMD.CUDA run:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = 1108141.2453 EKtot = 0.0000 EPtot =
1108141.2453
BOND = 9126.0102 ANGLE = 3780.4845 DIHED =
2107.0903
1-4 NB = 1401.2256 1-4 EEL = -42904.2608 VDWAALS =
1773510.4445
EELEC = -638879.7492 EHBOND = 0.0000 RESTRAINT =
0.0000
----------------------------------------------------------------------------
--
Normal PMEMD run:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -585383.3566 EKtot = 0.0000 EPtot =
-585383.3566
BOND = 9126.0102 ANGLE = 3780.4845 DIHED =
2107.0903
1-4 NB = 1401.2256 1-4 EEL = -42904.2608 VDWAALS =
72165.7215
EELEC = -631059.6280 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.2749E-03
----------------------------------------------------------------------------
--
This looks like a pmemd/pmemd.cuda problem rather than something wrong with
the system (but maybe I am wrong).
How is it possible that starting from the very same configuration, the same
system reports energies that are so big?
Is this somehow related to the error encountered and reported above?
Am I missing something?
I hope really that you have any suggestion on all this.
Looking forward to receive your prompt feedback on this issue.
Have a nice day,
Bye
giovanni
Dr. Giovanni M. Pavan
Laboratory of Applied Mathematics and Physics (LaMFI)
University of Applied Sciences of Southern Switzerland (SUPSI)
Centro Galleria 2, Manno 6928, Switzerland.
e-mail: giovanni.pavan.supsi.ch
web: http://www.dti.supsi.ch/~pavan/
skype: giovanni_pavan
phone: +41 58 666 65 60
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Received on Mon Apr 02 2012 - 04:00:03 PDT
