Hello Laura,
The test I mentioned previously can be found in the current version of AmberTools. Nevertheless, I will send it to you on a separate e-mail for your convenience.
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: Monday, February 28, 2022 3:26 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,
Thank you very much for your suggestion.
In my $AMBERHOME/test/cuda/remd I found the tests: *h_rem, hrem_4rep_gb,
mrem_4rep_gb, multid_remd, rem_2rep_gb, rem_2rep_pme, rem_4rep_gb,
rem_gb_2rep, rem_gb_4rep* and *rem_wat*. All of them worked well. Moreover,
I ran the tests in $AMBERHOME/test/cuda/cnstph/ and they also worked
smoothly.
However, I am not able to find the tests for CUDA/pH-REMD. If you have such
information, could you please provide me with the bunch of files for
running the test pH-REMD in explicit solvent? Otherwise, I would really
appreciate it if you can kindly provide me with the corresponding input
files for one of the simulations that you ran in the past using Amber18. I
would like to check if one example that works for you also runs in my
installation.
Thanks again for your help.
Best regards,
Laura
On Fri, Feb 25, 2022 at 10:03 PM Vinicius Wilian Cruzeiro <
vwcruz.stanford.edu> wrote:
> Hello Laura,
>
> I double checked here and indeed the test I indicated did not exist back
> in Amber18. Sorry about that... Nevertheless, pH-REMD should work fine. I
> have ran multiple pH-REMD simulations in the past using Amber18.
>
> So, try running these tests here instead then, which exist in Amber18:
> $AMBERHOME/test/cuda/remd . Let me know if these pass.
>
> 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 12:48 PM
> 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,
>
> 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
> _______________________________________________
> 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 Mon Feb 28 2022 - 10:00:03 PST
