Dear Vinícius,
Thanks for your reply, it was indeed useful to realize that I do not have
the folders for such tests in my $AMBERHOME/test/cuda/ path. As I specified
in my first post, I am using Amber18/AmberTools18. More specifically:
AmberTools 18 Applied Patches:
------------------------------
update.1, update.2, update.3, update.4, update.5, update.6, update.7,
update.8, update.9, update.10,
update.11, update.12, update.13, update.14
Amber 18 Applied Patches:
-------------------------
update.1, update.2, update.3, update.4, update.5, update.6, update.7,
update.8, update.9, update.10,
update.11, update.12, update.13, update.14, update.15, update.16, update.17
Could you please let me know if a more updated version or a different patch
is needed for CUDA MPI pH-REMD calculations?
Thanks again!
Best,
Laura
On Fri, Feb 25, 2022 at 7:47 PM Vinicius Wilian Cruzeiro <
vwcruz.stanford.edu> wrote:
> Hello Laura,
>
> Thank you. I am not sure why your simulation is failing, but I can think
> on a few things you could test. For starters, could try running the pH-REMD
> CUDA tests and see if these work? They are located at
> $AMBERHOME/test/cuda/cnstph_remd
>
> All the best,
>
> Vinícius Wilian D. Cruzeiro, PhD
> Postdoctoral Researcher
> Department of Chemistry
> Stanford University
> Twitter: @vwcruzeiro
> ________________________________
> From: Laura Milena Pedraza-González <la.pedrazagonzalez.gmail.com>
> Sent: Friday, February 25, 2022 3:30 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent,
> using CUDA MPI in AMBER 18
>
> Dear Vinícius,
>
> I have checked that the code is using 4 different GPUs, one for each
> pH-REMD replica. Please, find attached below the information shown by the
> mdout file.
>
> |------------------- GPU DEVICE INFO --------------------
>
> |
>
> | Task ID: 0
>
> | CUDA_VISIBLE_DEVICES: 0,1,2,3
>
> | CUDA Capable Devices Detected: 4
>
> | CUDA Device ID in use: 0
>
> | CUDA Device Name: Tesla V100-PCIE-16GB
>
> | CUDA Device Global Mem Size: 16160 MB
>
> | CUDA Device Num Multiprocessors: 80
>
> | CUDA Device Core Freq: 1.38 GHz
>
> |
>
> |--------------------------------------------------------
>
>
>
> |---------------- GPU PEER TO PEER INFO -----------------
>
> |
>
> | Peer to Peer support: ENABLED
>
> |
>
> |--------------------------------------------------------
>
>
>
>
>
> | Conditional Compilation Defines Used:
>
> | MPI
>
> | PUBFFT
>
> | BINTRAJ
>
> | CUDA
>
> | EMIL
>
>
> Bests,
>
>
> Laura
>
> On Fri, Feb 25, 2022 at 10:55 AM Laura Milena Pedraza-González <
> la.pedrazagonzalez.gmail.com> wrote:
>
> > Dear Vinícius,
> >
> > In fact, I am using a machine with 8 GPUs (Tesla V100-PCIE-16GB). Do you
> > know if any specific setup on the GPUs is needed before running pH-REMD?
> >
> > Thanks and regards,
> >
> > Laura
> >
> > On Fri, Feb 25, 2022 at 12:18 AM Vinicius Wilian Cruzeiro <
> > vwcruz.stanford.edu> wrote:
> >
> >> Hello Laura,
> >>
> >> Are you running this pH-REMD test in a machine with 4 GPUs? REMD
> requires
> >> one GPU per replica.
> >>
> >> Best,
> >>
> >> Vinícius Wilian D. Cruzeiro, PhD
> >> Postdoctoral Researcher
> >> Department of Chemistry
> >> Stanford University
> >> Twitter: @vwcruzeiro
> >> ________________________________
> >> From: Laura Milena Pedraza-González <la.pedrazagonzalez.gmail.com>
> >> Sent: Thursday, February 24, 2022 6:33 AM
> >> To: amber.ambermd.org <amber.ambermd.org>
> >> Subject: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent,
> >> using CUDA MPI in AMBER 18
> >>
> >> Dear Amber users,
> >>
> >> I am interested in doing constant pH replica exchange MD (pH-REMD) in
> >> explicit solvent, using CUDA MPI in AMBER 18. As far as I know, such
> >> methodology has been implemented and recently employed (e.g., J. Phys.
> >> Chem. B 2021, 125, 9168−9185). In this regard, I ran the test
> >> amber18/test/cnstph_remd/Explicit_pHREM/, that works correctly when
> using
> >> both sander.MPI and pmemd.MPI. However, when using pmemd.cuda.MPI (i.e.,
> >> mpirun -np 4 pmemd.cuda.MPI -ng 4 -groupfile groupfile -rem 4 -remlog
> >> rem.log), the calculation crashes after the first protonation state
> change
> >> attempt (e.g., at NSTEP 4 with ntcnstph=5), without printing any error
> >> different to the standard:
> >>
> >> ".Primary job terminated normally, but 1 process returned
> >>
> >> a non-zero exit code. Per user-direction, the job has been aborted.
> >>
> --------------------------------------------------------------------------
> >>
> --------------------------------------------------------------------------
> >> mpirun detected that one or more processes exited with non-zero status,
> >> thus causing
> >> the job to be terminated. The first process to do so was:
> >>
> >> Process name: [[42377,1],0]
> >> Exit code: 174"
> >>
> >> On the other hand, I tested my pmemd.cuda.MPI AMBER installation by
> >> running
> >> the test of temperatura REMD (
> >> https://ambermd.org/tutorials/advanced/tutorial7/index.php) and it
> worked
> >> smoothly. Moreover, I have some experience computing normal CpHMD with
> >> pmemd.cuda and the methodology works well in my installation.
> >> Do you have any idea about which would be the problem associated with
> >> pmemd.cuda.MPI in pH-REMD?
> >>
> >> Thanks in advance for your help.
> >>
> >> Best regards,
> >>
> >> Laura
> >>
> >> --
> >> *Dr. Laura Pedraza-González*
> >> Postdoctoral Researcher
> >> MoLECoLab (Modeling Light & Environment in Complex Systems)
> >> Department of Chemistry and Industrial Chemistry
> >> University of Pisa
> >> Via Moruzzi 13, 56124, Pisa, ITALY
> >> Tel. +39-331-2760784
> >>
> >> https://molecolab.dcci.unipi.it/people/laura-pedraza.html
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> > *Dr. Laura Pedraza-González*
> > Postdoctoral Researcher
> > MoLECoLab (Modeling Light & Environment in Complex Systems)
> > Department of Chemistry and Industrial Chemistry
> > University of Pisa
> > Via Moruzzi 13, 56124, Pisa, ITALY
> > Tel. +39-331-2760784
> >
> > https://molecolab.dcci.unipi.it/people/laura-pedraza.html
> >
>
>
> --
> *Dr. Laura Pedraza-González*
> Postdoctoral Researcher
> MoLECoLab (Modeling Light & Environment in Complex Systems)
> Department of Chemistry and Industrial Chemistry
> University of Pisa
> Via Moruzzi 13, 56124, Pisa, ITALY
> Tel. +39-331-2760784
>
> https://molecolab.dcci.unipi.it/people/laura-pedraza.html
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Laura Pedraza-González*
Postdoctoral Researcher
MoLECoLab (Modeling Light & Environment in Complex Systems)
Department of Chemistry and Industrial Chemistry
University of Pisa
Via Moruzzi 13, 56124, Pisa, ITALY
Tel. +39-331-2760784
https://molecolab.dcci.unipi.it/people/laura-pedraza.html
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Received on Fri Feb 25 2022 - 13:00:02 PST
