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=
> > <
> 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=
> >
> > > > >
> > > >
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_vaibhav-2Ddixit-2Db1a07a39_&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=cIXj9hu2SRpeUSqYWvphN1y8LpR_KD83pfCyrRLo3wI&s=n4cBvUz1hv7rjjmpGm_OjwldF1afVwaJ98Lfufc41rI&e=
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_vaibhav-2Ddixit-2Db1a07a39_&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=cIXj9hu2SRpeUSqYWvphN1y8LpR_KD83pfCyrRLo3wI&s=n4cBvUz1hv7rjjmpGm_OjwldF1afVwaJ98Lfufc41rI&e=
> >
> > > > >
> > > > > ORCID ID:
> > > >
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__orcid.org_0000-2D0003-2D4015-2D2941&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=cIXj9hu2SRpeUSqYWvphN1y8LpR_KD83pfCyrRLo3wI&s=GyD8MQ2vyCWMOJK3doUOUvSVjl3M-N1v69A7p-UeCno&e=
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__orcid.org_0000-2D0003-2D4015-2D2941&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=cIXj9hu2SRpeUSqYWvphN1y8LpR_KD83pfCyrRLo3wI&s=GyD8MQ2vyCWMOJK3doUOUvSVjl3M-N1v69A7p-UeCno&e=
> >
> > > > >
> > > > >
> > > >
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.google.co.in_citations-3Fuser-3DX876BKcAAAAJ-26hl-3Den-26oi-3Dsra&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=cIXj9hu2SRpeUSqYWvphN1y8LpR_KD83pfCyrRLo3wI&s=2-MLtTD74ywt136kQQ83KzpqxiPRoZD9VsOqE9sd6ec&e=
> > <
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> >
> > > > >
> > > > > P Please consider the environment before printing this e-mail
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> > > > >
> > > >
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=cIXj9hu2SRpeUSqYWvphN1y8LpR_KD83pfCyrRLo3wI&s=cSnjsnkMfHjetjjQLjst7XVaRAsvWQcCdfbUFa2NG64&e=
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=cIXj9hu2SRpeUSqYWvphN1y8LpR_KD83pfCyrRLo3wI&s=cSnjsnkMfHjetjjQLjst7XVaRAsvWQcCdfbUFa2NG64&e=
> >
> > > >
> > > > --
> > > > 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
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bits-2Dpilani.ac.in_pilani_vaibhavdixit_profile&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=yhsV48MY_njKx28BWI2knMo_99csBGjiZNEfL6DBWtA&s=6ZW35fbazyUsOxA0Ea0TU1oP7tWhvAEMTdQaArLx9PA&e=
> >
> > > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> > <
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> >
> > >
> > > ORCID ID: https://orcid.org/0000-0003-4015-2941
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__orcid.org_0000-2D0003-2D4015-2D2941&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=yhsV48MY_njKx28BWI2knMo_99csBGjiZNEfL6DBWtA&s=10JFQapxmJjdyVB5LBjRpERxU-F58ZwR99e3p8WKnc4&e=
> >
> > >
> > >
> > 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=
> >
> > >
> > > P Please consider the environment before printing this e-mail
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > <
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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>,
> > vaibhavadixit.gmail.com <mailto:vaibhavadixit.gmail.com>
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bits-2Dpilani.ac.in_pilani_vaibhavdixit_profile&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=yhsV48MY_njKx28BWI2knMo_99csBGjiZNEfL6DBWtA&s=6ZW35fbazyUsOxA0Ea0TU1oP7tWhvAEMTdQaArLx9PA&e=
> >
> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_vaibhav-2Ddixit-2Db1a07a39_&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=yhsV48MY_njKx28BWI2knMo_99csBGjiZNEfL6DBWtA&s=4fHP_yykcPV3y8tUTC01it8lGeSsZveuCOvqCj65Imo&e=
> >
> >
> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__orcid.org_0000-2D0003-2D4015-2D2941&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=yhsV48MY_njKx28BWI2knMo_99csBGjiZNEfL6DBWtA&s=10JFQapxmJjdyVB5LBjRpERxU-F58ZwR99e3p8WKnc4&e=
> >
> >
> > 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
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Tue Feb 09 2021 - 08:30:02 PST
