[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

Mon Aug 26 20:51:17 CEST 2019

Hi,

If you have a reason to have to use 2016.x, then please get the latest
version (which is always advisable when starting new work) because this
issue is fixed there. You also don't have to run energy minimization on
GPUs, so you could just append -nb cpu to your mdrun command line to avoid
the problem.

Mark

On Mon, 26 Aug 2019 at 20:44, Navneet Kumar Singh <navneetcdl at gmail.com>
wrote:

> Currently I am using only gromacs16.5. As this have *"PLEASE NOTE* that the
> current versions do support lone pair construction on halogens, however the
> current construction is only compatible with GROMACS-2016.x and by using
> gmx grompp -maxwarn 1 to override the warning about lone pair
> construction."
>
> I was unable to understand this "For all other GROMACS versions, you will
> have to manually edit the topology to use "3fad" construction and
> appropriate atom numbers."as I was using 2018.4. So I switched to
> version-16. But now trapped in this HtoD cudaMemcpyAsync failed: invalid
> argumenterror.
>
> On Tue, Aug 27, 2019 at 12:09 AM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You're running 2016.x which had a bug, not the 2018.x you thought you
> were
> > using. Use GMXRC or your cluster's modules to select the version you want
> > to use in the terminal or script that you want to use.
> >
> > Mark
> >
> > On Mon, 26 Aug 2019 at 20:34, Navneet Kumar Singh <navneetcdl at gmail.com>
> > wrote:
> >
> > > What kind of error is this. Previously Gromacs 2018.4 version was
> running
> > > fine using GPU. But Now this error I am getting.
> > >
> > > _________________________________________________________
> > >
> > > gmx mdrun -v -deffnm em
> > >                       :-) GROMACS - gmx mdrun, 2016.5 (-:
> > >
> > >                             GROMACS is written by:
> > >      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
> > > Bjelkmar
> > >  Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit
> > Groenhof
> > >  Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios
> > > Karkoulis
> > >     Peter Kasson        Jiri Kraus      Carsten Kutzner      Per
> Larsson
> > >   Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff    Erik
> Marklund
> > >    Teemu Murtola       Szilard Pall       Sander Pronk      Roland
> Schulz
> > >   Alexey Shvetsov     Michael Shirts     Alfons Sijbers     Peter
> > Tieleman
> > >   Teemu Virolainen  Christian Wennberg    Maarten Wolf
> > >                            and the project leaders:
> > >         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> > >
> > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > > Copyright (c) 2001-2017, The GROMACS development team at
> > > Uppsala University, Stockholm University and
> > > the Royal Institute of Technology, Sweden.
> > > check out http://www.gromacs.org for more information.
> > >
> > > GROMACS is free software; you can redistribute it and/or modify it
> > > under the terms of the GNU Lesser General Public License
> > > as published by the Free Software Foundation; either version 2.1
> > > of the License, or (at your option) any later version.
> > >
> > > GROMACS:      gmx mdrun, version 2016.5
> > > Executable:   /usr/local/gromacs/bin/gmx
> > > Data prefix:  /usr/local/gromacs
> > > Working dir:  /home/nitttr/Desktop/Hydroxy_chloroquine
> > > Command line:
> > >   gmx mdrun -v -deffnm em
> > >
> > >
> > > Back Off! I just backed up em.log to ./#em.log.7#
> > >
> > > Running on 1 node with total 16 cores, 32 logical cores, 1 compatible
> GPU
> > > Hardware detected:
> > >   CPU info:
> > >     Vendor: Intel
> > >     Brand:  Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
> > >     SIMD instructions most likely to fit this hardware: AVX_512
> > >     SIMD instructions selected at GROMACS compile time: AVX_512
> > >
> > >   Hardware topology: Basic
> > >   GPU info:
> > >     Number of GPUs detected: 1
> > >     #0: NVIDIA Tesla P4, compute cap.: 6.1, ECC: yes, stat: compatible
> > >
> > > Reading file em.tpr, VERSION 2016.5 (single precision)
> > > Using 1 MPI thread
> > > Using 32 OpenMP threads
> > >
> > > 1 compatible GPU is present, with ID 0
> > > 1 GPU auto-selected for this run.
> > > Mapping of GPU ID to the 1 PP rank in this node: 0
> > >
> > > Application clocks (GPU clocks) for Tesla P4 are (3003,1531)
> > >
> > > Back Off! I just backed up em.trr to ./#em.trr.7#
> > >
> > > Back Off! I just backed up em.edr to ./#em.edr.7#
> > >
> > > Steepest Descents:
> > >    Tolerance (Fmax)   =  1.00000e+03
> > >    Number of steps    =        50000
> > >
> > > -------------------------------------------------------
> > > Program:     gmx mdrun, version 2016.5
> > > Source file: src/gromacs/gpu_utils/cudautils.cu (line 105)
> > >
> > > Fatal error:
> > > HtoD cudaMemcpyAsync failed: invalid argument
> > >
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > > -------------------------------------------------------
> > >
> > > --
> > >
> > >
> > >
> > >
> > >
> > >
> > >      Thanks & Regards
> > > _______________________________________________________
> > >
> > > [image: photo]
> > > *NAVNEET KUMAR*
> > > Doctoral Student
> > > Dept. of Pharmacoinformatics
> > > National Institute of Pharmaceutical Education and Research, Sector 67,
> > > S.A.S. Nagar - 160062, Punjab (INDIA)
> > > P +918017967647  <+918017967647> |
> > > E navneetcdl at gmail.com  <navneetcdl at gmail.com>
> > > <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> > > <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
> > >
> > > Please consider your environmental responsibility. Before printing this
> > > e-mail message, ask yourself whether you really need a hard copy.
> > > --
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>
> --
>
>
>
>
>
>
>      Thanks & Regards
> _______________________________________________________
>
> [image: photo]
> *NAVNEET KUMAR*
> Doctoral Student
> Dept. of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research, Sector 67,
> S.A.S. Nagar - 160062, Punjab (INDIA)
> P +918017967647  <+918017967647> |
> E navneetcdl at gmail.com  <navneetcdl at gmail.com>
> <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
>
> Please consider your environmental responsibility. Before printing this
> e-mail message, ask yourself whether you really need a hard copy.
> --
> Gromacs Users mailing list
>
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