[gmx-users] mdrun GPU

Szilárd Páll pall.szilard at gmail.com
Mon Nov 20 17:12:53 CET 2017 

On Mon, Nov 20, 2017 at 8:18 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> For NVIDIA GPUs you should use their drivers and a CUDA build. It looks
> like you are using other drivers and an OpenCL build, which is completely
> untested.
>

Note: the OpenCL acceleration using NVIDIA's proprietary library,
distributed with the GPU drivers, is *well-tested* (but useless due to the
terrible performance compared to CUDA -- ask NVIDIA why). However, here
it's a MESA driver/compiler that's reported to be used which is definitely
not tested (nor even sure if it works at all on NVIDIA).

Cheers,
--
Szilárd



>
> Mark
>
> On Mon, 20 Nov 2017 06:51 Ragothaman Yennamalli <ragothaman at gmail.com>
> wrote:
>
> > Hi,
> > I have been reading this (
> >
> > http://manual.gromacs.org/documentation/5.1/user-guide/
> mdrun-performance.html
> > )
> > and trying to run mdrun in a GPU based system. Unfortunately, I don't
> > understand what the error is and how to troubleshoot it. Copy pasted
> below
> > is the output I got for gmx mdrun.
> >
> > I tried assigning the GPU ids using the examples provided in the link
> above
> > but have been unsuccessful. Please help me in troubleshooting this.
> >
> > Thanks and Regards,
> > Raghu
> >
> > [student at localhost test]$ gmx mdrun -v -deffnm em
> >                       :-) GROMACS - gmx mdrun, 2016.4 (-:
> >
> >                             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 2016.4
> > Executable:   /usr/bin/gmx
> > Data prefix:  /usr
> > Working dir:  /home/student/test
> > Command line:
> >   gmx mdrun -v -deffnm em
> >
> >
> > Back Off! I just backed up em.log to ./#em.log.6#
> > X server found. dri2 connection failed!
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > X server found. dri2 connection failed!
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > cl_get_gt_device(): error, unknown device: 0
> > X server found. dri2 connection failed!
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > X server found. dri2 connection failed!
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > cl_get_gt_device(): error, unknown device: 0
> > X server found. dri2 connection failed!
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > cl_get_gt_device(): error, unknown device: 0
> > X server found. dri2 connection failed!
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> > Assuming 131072kB available aperture size.
> > May lead to reduced performance or incorrect rendering.
> > get chip id failed: -1 [22]
> > param: 4, val: 0
> > cl_get_gt_device(): error, unknown device: 0
> >
> > Running on 1 node with total 4 cores, 8 logical cores, 2 compatible GPUs
> > Hardware detected:
> >   CPU info:
> >     Vendor: Intel
> >     Brand:  Intel(R) Xeon(R) CPU E5-1620 v3 @ 3.50GHz
> >     SIMD instructions most likely to fit this hardware: AVX2_256
> >     SIMD instructions selected at GROMACS compile time: SSE2
> >
> >   Hardware topology: Full, with devices
> >   GPU info:
> >     Number of GPUs detected: 2
> >     #0: name: NV106, vendor: NVIDIA, device version: OpenCL 1.1 Mesa
> > 17.1.3, stat: compatible
> >     #1: name: NVF1, vendor: NVIDIA, device version: OpenCL 1.1 Mesa
> 17.1.3,
> > stat: compatible
> >
> > Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this
> > machine, which is better.
> >
> >
> > The current CPU can measure timings more accurately than the code in
> > gmx mdrun was configured to use. This might affect your simulation
> > speed as accurate timings are needed for load-balancing.
> > Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake
> > option.
> >
> > Reading file em.tpr, VERSION 2016.4 (single precision)
> > Using 2 MPI threads
> > Using 4 OpenMP threads per tMPI thread
> >
> > 2 compatible GPUs are present, with IDs 0,1
> > 2 GPUs auto-selected for this run.
> > Mapping of GPU IDs to the 2 PP ranks in this node: 0,1
> >
> >
> > -------------------------------------------------------
> > Program:     gmx mdrun, version 2016.4
> >
> > -------------------------------------------------------
> > Program:     gmx mdrun, version 2016.4
> > Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 273)
> > Function:    size_t gmx::ocl::getWarpSize(cl_context, cl_device_id)
> > Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 273)
> > Function:    size_t gmx::ocl::getWarpSize(cl_context, cl_device_id)
> > MPI rank:    0 (out of 2)
> >
> > Internal error (bug):
> > MPI rank:    1 (out of 2)
> >
> > Internal error (bug):
> > Failed to compile NBNXN kernels for GPU #NV106
> >   Could not build OpenCL program to determine warp size, error was
> >   CL_BUILD_PROGRAM_FAILURE
> > Failed to compile NBNXN kernels for GPU #NVF1
> >   Could not build OpenCL program to determine warp size, error was
> >   CL_BUILD_PROGRAM_FAILURE
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

More information about the gromacs.org_gmx-users mailing list