[gmx-users] mdrun GPU
Mark Abraham
mark.j.abraham at gmail.com
Mon Nov 20 17:59:07 CET 2017
Hi,
Indeed. NVIDIA driver plus OpenCL is fine. Non-NVIDIA driver is untested.
Mark
On Mon, 20 Nov 2017 17:17 Szilárd Páll <pall.szilard at gmail.com> wrote:
> 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
> > > -------------------------------------------------------
> > > --
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