On Wed, Dec 12, 2012, ???? wrote:
> I'm using amber12 pmemd.cuda_SPFP to run MD simulation. But there is a
> fatal error.
>
>
> My input file and log file is as below:
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> md script
> &cntrl
> !irest=1, ntx=5, ! restart MD
> imin=0, ! run MD
> ntb=2, ntp=1, ! periodic box
> ntpr=5000, ntwr=10000, ntwx=5000,
> ntt=3, gamma_ln=2.0, tempi = 300.0, temp0 = 300.0,
> pres0=1.0, taup=2.0, ig=4052, ! rand number
> ntf=2, ntc=2, ! SHAKE
> nstlim=100000000, dt=0.002, ! steptime
> cut=8.0, ntr=1,
> ioutfm=1,
> /
> RESTRAINT
> 100.0
> RES 1 599
> END
> END
What happens if you set ntpr=1 and nstlim=100? What happens if you run the
same short job on a cpu? If those work, slowly increase the number of steps.
Also: you are running with the big step size and very strong restraints.
Once you get short jobs that work (or, more importantly, fail) consider
reducing the time step by a factor of 2 and the restraint weight by a factor
of 10.
Do you really want to run 200 ns of simulation with gigantic restraints on 600
residues? How many atoms is your total system? Note that the job above will
create 20,000 snapshots in the trajectory file; if you have 100,000 atoms in
your system (a wild guess, but you have 600 residues that are not even moving)
the file will be over 30 Gb in size. Consider breaking the job into smaller
pieces.
...dac
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> cudaMemcpy GpuBuffer::Download failed unspecified launch failure
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Any help will be appreciated. Thanks a lot!
>
>
>
>
> Yours,
> Jun
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David A. Case | case.biomaps.rutgers.edu
BioMaPS Institute and Dept. of |
Chemistry & Chemical Biology | fax: +1-732-445-4320
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Received on Wed Dec 12 2012 - 05:30:02 PST
