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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Received on Thu Feb 24 2022 - 15:30:03 PST
