Dear Adrian, Carlos and All,
I'll get back to the list as soon as I have tried this modification with
the pmemd.cuda code.
It seems that this modification (if it works) would be necessary since the
sander quickly runs out of trajectories to work on before GPU code finishes
doing the MD.
thanks a lot for valuable suggestions and insights.
On Mon, Feb 8, 2021 at 9:35 PM Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi
>
> My advice depends a bit on how comfortable are you with changing the
> actual amber code and recompiling.
>
> If you feel you can, you can go into the pmemd code, find the part of
> the code where the mdcrd file is written, and add a flush command (or
> amflush, look for that in the code) right after the lien where amber
> writes that file.
>
>
> What happens is that in most operating systems, even if your program
> says 'write this', the file is not written at that moment but rather
> after the I/O buffer is full.
>
> Using a flush command makes the writing immediate.
>
> One thingsm, depending how often you write, you might experience a
> slowdown of the code, but should be ok.
>
> Adrian
>
>
>
> On 2/5/21 11:39 AM, Vaibhav Dixit wrote:
> > [External Email]
> >
> > Dear All,
> > Do the Amber MD codes lock the files that are in use or being written?
> > I'm running MD (pmemd.cuda) on GPU, then estimating SP energies with
> sander
> > on CPU.
> > Now since sander on CPU is slower than the GPU MD code (is it true for SP
> > sander vs MD on GPU? I think it is slower but not by a very large
> margin).
> > Is it possible to read an MD trajectory using sander (with -y option) to
> > estimate SP Es, while it is being written by the GPU code?
> > If this is possible, then what are the chances that sander will catch up
> > with the GPU code while reading trajectories that GPU code writes.
> >
> > Although this is not absolutely necessary, it might just save a few hours
> > of time, since one wouldn't have to wait for the GPU MD to finish before
> > starting the sander SP calculations.
> > Looking forward to valuable insights and suggestions from the list.
> > thank you and best regards.
> >
> > --
> >
> > Regards,
> >
> > Dr. Vaibhav A. Dixit,
> >
> > Visiting Scientist at the Manchester Institute of Biotechnology (MIB),
> The
> > University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> > AND
> > Assistant Professor,
> > Department of Pharmacy,
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> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > India.
> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> >
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> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Mon Feb 08 2021 - 21:00:03 PST
