[gmx-users] Gromacs_GPU_Compiling_Problem
郭逸峰
guoyifengfdu at gmail.com
Tue Aug 22 10:20:18 CEST 2017
Dear users,
-->I have installed the gromacs on the linux-ubuntu16.04 system, but I
cannot get the GPU support to accelerate the calculations.
-->Can you tell me how to fix it.
-->When I input "gmx mdrun gpu_id=..........", it will give me this:
--Fatal error:
--GPU ID string set, but gmx was compiled without GPU support!
-->The main installation commands and mdrun results are shown below.(with
an mdrun example of He216)
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#1
user at user-desktop:/usr/local/gromacs/gromacs-5.1.4/build$ sudo cmake ..
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs-5.1.4
-DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/g++
-DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
[sudo] password for user:
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/gromacs/gromacs-5.1.4/build
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#2
user at user-desktop:/usr/local/gromacs/gromacs-5.1.4/build$ sudo make -j16[
0%] Built target view_objlib
[ 1%] Built target mdrun_objlib
[ 1%] Building NVCC (Device) object src/gromacs/CMakeFiles/libgrom
acs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o
[ 1%] Building NVCC (Device) object src/gromacs/CMakeFiles/libgrom
acs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_data_mgmt.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
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#Igoring the problem, I can still installing and running the gromacs, bur
cannot use GPU support.
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#3
*Here is the typical running step*
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user at user-desktop:~/Fubu/GYF/_day1/He216$ gmx mdrun
:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
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) 2001-2015, 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 5.1.2
Executable: /usr/bin/gmx
Data prefix: /usr
Command line:
gmx mdrun
Back Off! I just backed up md.log to ./#md.log.24#
Running on 1 node with total 8 cores, 16 logical cores
Hardware detected:
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: SSE2
Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this
machine, which is better
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 16 OpenMP threads
Back Off! I just backed up traj.trr to ./#traj.trr.15#
Back Off! I just backed up traj_comp.xtc to ./#traj_comp.xtc.15#
Back Off! I just backed up ener.edr to ./#ener.edr.15#
starting mdrun 'He Box'
100000 steps, 100.0 ps.
Writing final coordinates.
Back Off! I just backed up confout.gro to ./#confout.gro.15#
NOTE: 40 % of the run time was spent in pair search,
you might want to increase nstlist (this has no effect on accuracy)
Core t (s) Wall t (s) (%)
Time: 90.289 5.788 1559.9
(ns/day) (hour/ns)
Performance: 1492.740 0.016
gcq#184: "I Am a Poor Lonesome Cowboy" (Lucky Luke)
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#4
*Here is the trying to run on GPU!!!!!!!!!!!!*
user at user-desktop:~/Fubu/GYF/_day1/He216$ gmx mdrun -gpu_id
GPU-7a845104-091e-0e5c-d092-425457b38b3a
:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
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) 2001-2015, 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 5.1.2
Executable: /usr/bin/gmx
Data prefix: /usr
Command line:
gmx mdrun -gpu_id GPU-7a845104-091e-0e5c-d092-425457b38b3a
Back Off! I just backed up md.log to ./#md.log.25#
Running on 1 node with total 8 cores, 16 logical cores
Hardware detected:
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: SSE2
Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this
machine, which is better
Reading file topol.tpr, VERSION 5.1.2 (single precision)
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Program gmx mdrun, VERSION 5.1.2
Source code file: /build/gromacs-z6bPBg/gromacs-
5.1.2/src/gromacs/gmxlib/gmx_detect_hardware.cpp, line: 1161
Fatal error:
GPU ID string set, but gmx was compiled without GPU
support!*---------------------------------------------#Here
is the problem!*
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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