Re: [AMBER] curiosity about sander reading a traj being written by GPU code

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Wed, 10 Feb 2021 16:21:53 +0530

Here I'm assuming that 2m should be sufficient for the GPU code to dump any
remaining coordinates in the trajectory file.
Please do suggest if I should increase the time-limit to be on the safe
side.
Thank you and best regards.

On Wed, Feb 10, 2021 at 4:11 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:

> Dear Kenneth and all,
> Thanks for the suggestion about using a loop.
> I wrote a while bash-loop for this, which started soon after the GPU code
> finished.
> A modified version is pasted below in case it is helpful to another
> new-bee (like myself) on the list.
> thank you and best regards.
>
> while [ $(awk '{print $6}' mdinfo | tail -2 | head -1) != seconds. ]
> do
> sleep 2m
> done
> echo creating stripped trajectories
> cpptraj -i cpptraj.in
> echo "running sander jobs"
> ./run-sander-jobs.sh
> .
>
> On Tue, Feb 9, 2021 at 9:46 PM Kenneth Huang <kennethneltharion.gmail.com>
> wrote:
>
>> Just to chime in, I'll second Adrian's suggestion- I'm doing a similar
>> thing only with R, but since your setup doesn't rely on the MD portion to
>> make a choice on the next step, you could have a parallel script that
>> periodically checks using the estimated time of finish for a condtional
>> (line count? EOF on output?) in python/shell/language of choice before
>> running sander? So maybe like
>>
>> some loop
>> >
>> >> if grep -q EOFflag "mdout"; then
>> >> run sander, etc
>> >>
>> > fi
>> >>
>> > close loop
>> >
>>
>> Best,
>>
>> Kenneth
>>
>>
>> On Tue, Feb 9, 2021 at 10:40 AM Adrian Roitberg <roitberg.ufl.edu> wrote:
>>
>> > 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
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>> > > > > > Email: vaibhav.dixit.pilani.bits-pilani.ac.in
>> > > <mailto:vaibhav.dixit.pilani.bits-pilani.ac.in>,
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>> > > > > >
>> > > > > > P Please consider the environment before printing this
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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>,
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>> > > > ​http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
>> > > <
>> >
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>> > >
>> > > >
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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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>> > >
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>> > > <
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.google.co.in_citations-3Fuser-3DX876BKcAAAAJ-26hl-3Den-26oi-3Dsra&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=yhsV48MY_njKx28BWI2knMo_99csBGjiZNEfL6DBWtA&s=xrllHABNmEZZ36Vb7ywzOyljRDPiet4TZQm2UGqr3IQ&e=
>> > >
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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
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>> > 352-392-6972
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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, 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
>
> P Please consider the environment before printing this e-mail
>
>

-- 
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
P Please consider the environment before printing this e-mail
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Received on Wed Feb 10 2021 - 03:00:03 PST
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