[gmx-users] mdrun GPU

Ragothaman Yennamalli ragothaman at gmail.com
Mon Nov 20 06:50:40 CET 2017 

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 (-:

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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
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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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