[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument
Mark Abraham
mark.j.abraham at gmail.com
Thu Aug 29 14:02:59 CEST 2019
Hi,
Did you try doing em with the flag I mentioned? Simulation won't need any
change.
Mark
On Mon., 26 Aug. 2019, 22:25 Navneet Kumar Singh, <navneetcdl at gmail.com>
wrote:
> Thank You Sir.
>
> Again installed gromacs2016.6 (final version from gromacs2016.x).
> Throwing same error(HtoD cudaMemcpyAsync failed: invalid argument)
>
> . Its running on CPU, but not on GPU. Work of 3 days will take 15 days.
> Already completed simulation for other complexes. This complex creating
> problem due to vsites3. PLEASE HELP DEADLINE IS APPROACHING.
>
> On Tue, Aug 27, 2019 at 12:23 AM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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
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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
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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
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