[gmx-users] mdrun GPU
Mark Abraham
mark.j.abraham at gmail.com
Mon Nov 20 08:18:28 CET 2017
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.
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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