BTW: I just thought about something.
Depending on what you want to do with sander, you can use pysander,
write a python script to read the mdcrd file from pmemd and compute
whatever you want in sander, but in python I presume you can add some
code that will wait for the mdcrd file to be updated to run sander, then
wait for the next update, etc etc.
Adrian
On 2/9/21 7:14 AM, Vaibhav Dixit wrote:
> *[External Email]*
>
> Dear All,
> At present, I'm trying to save time by noting the expected time
> printed in the mdinfo file and using simple batch command e.g. "at 3
> am tonight" to submit the sander jobs in the queue.
> But based on my experience I think this estimated time is not very
> precise, thus just giving an hour extra looks ok at the moment.
> Can you please comment on the variation w.r.t. the system size in the
> expected and the actual time that one can expect for pmemd.cuda GPU jobs?
>
> I'm keeping the idea to run sander and pmemd.cuda simultaneously (with
> some delay) on hold for the moment till I figure out how I want to do
> the benchmarking since the system sizes that I'm investigating range
> from 140 to 480 AAs.
>
> Looking forward to your valuable comments and suggestions.
> Thanks all, Carlos and Adrian.
> Best regards.
> Vaibhav
>
>
>
> On Tue, Feb 9, 2021 at 5:06 PM Carlos Simmerling
> <carlos.simmerling.gmail.com <mailto:carlos.simmerling.gmail.com>> wrote:
>
> adding the flush might help, but might not. I think the issue
> you're going
> to run into is that pmemd is faster than sander, but in the
> sander step here you're only having to calculate energies for the
> snapshots
> in the trajectory, and that might be faster or slower than the MD run
> depending on how frequently you save frames to the mdcrd file (by
> setting
> ntwx). If ntwx=1000 for example, pmemd has to calculate
> energies/forces
> 1000x as often as sander will be doing, and it might not keep up.
> I suppose
> you could benchmark both and adjust ntwx such that sander is just
> a little
> slower.. depends on what your project needs. certainly sander could be
> faster than pmemd in this particular example.
>
> On Mon, Feb 8, 2021 at 11:40 PM Vaibhav Dixit
> <vaibhavadixit.gmail.com <mailto:vaibhavadixit.gmail.com>>
> wrote:
>
> > 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
> <mailto: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,
> > > > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > > > 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
> <mailto:vaibhav.dixit.pilani.bits-pilani.ac.in>,
> vaibhavadixit.gmail.com <mailto:vaibhavadixit.gmail.com>
> > > >
> > >
> >
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> > > >
> > > > P Please consider the environment before printing this e-mail
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> > >
> >
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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 <mailto: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
> <mailto:vaibhav.dixit.pilani.bits-pilani.ac.in>,
> vaibhavadixit.gmail.com <mailto:vaibhavadixit.gmail.com>
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>
>
> --
>
> 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
> <mailto:vaibhav.dixit.pilani.bits-pilani.ac.in>,
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> PPlease consider the environment before printing this e-mail
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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
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