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
> > > > > > 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>
> > > > > >
> > > > >
> > > >
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bits-2Dpilani.ac.in_pilani_vaibhavdixit_profile&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=cIXj9hu2SRpeUSqYWvphN1y8LpR_KD83pfCyrRLo3wI&s=NKKVTB6vgRW9RZDbQ0-f5qnb_Qtf8zNBiM1xFcFS5L8&e=
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> > >
> > > > > >
> > > > > > ORCID ID:
> > > > >
> > > >
> > >
> >
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> > >
> > > > > >
> > > > > > P Please consider the environment before printing this e-mail
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
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> > > > > >
> > > > >
> > > >
> > >
> >
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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>
> > > > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > > <
> >
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> > >
> > > >
> > > > ORCID ID: https://orcid.org/0000-0003-4015-2941
> > > <
> >
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> > >
> > > >
> > > >
> > >
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> > > <
> >
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> > >
> > > >
> > > > P Please consider the environment before printing this e-mail
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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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> > >
> > >
> > > ORCID ID: https://orcid.org/0000-0003-4015-2941
> > > <
> >
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> > >
> > >
> > > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> > > <
> >
> 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=
> > >
> > >
> > > PPlease consider the environment before printing this e-mail
> > >
> > --
> > Dr. Adrian E. Roitberg
> > V.T. and Louise Jackson Professor in Chemistry
> > Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> > 352-392-6972
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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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, 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 - 03:00:02 PST
