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
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>
--
*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 - 02:00:02 PST
