[gmx-users] GPU problem with running gromacs.2018

Osmany Guirola Cruz osmany.guirola at biocomp.cigb.edu.cu
Fri Feb 16 13:53:27 CET 2018

This is the output with gromacs 2018 and cuda 9
-------------------------------------------------------Program:     gmx
mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu
(line 735)Function:    void findGpus(gmx_gpu_info_t*)
Assertion failed:Condition: cudaSuccess == cudaPeekAtLastError()Should
be cudaSuccess
For more information and tips for troubleshooting, please check the
GROMACSwebsite at http://www.gromacs.org/Documentation/Errors----------

and this is the log
Log file opened on Fri Feb 16 07:49:19 2018Host: draco  pid:
20855  rank ID: 0  number of ranks:  1                       :-)
GROMACS - gmx mdrun, 2018 (-:
                            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    Viveca Lindahl    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
atUppsala University, Stockholm University andthe Royal Institute of
Technology, Sweden.check out http://www.gromacs.org for more
GROMACS is free software; you can redistribute it and/or modify itunder
the terms of the GNU Lesser General Public Licenseas published by the
Free Software Foundation; either version 2.1of the License, or (at your
option) any later version.
GROMACS:      gmx mdrun, version
2018Executable:   /usr/local/gromacs/bin/gmxData
prefix:  /usr/local/gromacsWorking
dir:  /home/osmany/Downloads/RASCommand line:  gmx mdrun -deffnm md
GROMACS version:    2018Precision:          singleMemory
model:       64 bitMPI library:        thread_mpiOpenMP
support:     enabled (GMX_OPENMP_MAX_THREADS = 64)GPU
support:        CUDASIMD instructions:  SSE4.1FFT library:        fftw-
3.3.7-sse2-avxRDTSCP usage:       disabledTNG
support:        enabledHwloc support:      hwloc-1.11.6Tracing
support:    disabledBuilt on:           2018-02-14 14:05:11Built
by:           osmany at draco [CMAKE]Build OS/arch:      Linux 4.14.0-3-
amd64 x86_64Build CPU vendor:   IntelBuild CPU brand:    Intel(R)
Core(TM)2 Quad CPU    Q9650  @ 3.00GHzBuild CPU family:   6   Model:
23   Stepping: 10Build CPU features: apic clfsh cmov cx8 cx16 intel
lahf mmx msr pdcm pse sse2 sse3 sse4.1 ssse3C
compiler:         /usr/bin/gcc-6 GNU 6.4.0C compiler flags:    -
msse4.1     -O3 -DNDEBUG -funroll-all-loops -fexcess-
precision=fast  C++ compiler:       /usr/bin/g++-6 GNU 6.4.0C++
compiler flags:  -msse4.1    -std=c++11   -O3 -DNDEBUG -funroll-all-
loops -fexcess-precision=fast  CUDA compiler:      /usr/lib/nvidia-
cuda-toolkit/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright
(c) 2005-2017 NVIDIA Corporation;Built on
Fri_Sep__1_21:08:03_CDT_2017;Cuda compilation tools, release 9.0,
V9.0.176CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-
D_FORCE_INLINES;; ;-msse4.1;-std=c++11;-O3;-DNDEBUG;-funroll-all-
loops;-fexcess-precision=fast;CUDA driver:        9.0CUDA
runtime:       9.0


-----Original Message-----From: Szilárd Páll <pall.szilard at gmail.com>Re
ply-to: gmx-users at gromacs.orgTo: Discussion list for GROMACS users <gmx
-users at gromacs.org>Subject: Re: [gmx-users] GPU problem with running
gromacs.2018Date: Thu, 15 Feb 2018 18:23:05 +0100
Please provide a full log file output.--Szilárd

On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz<osmany.guirola at bio
comp.cigb.edu.cu> wrote:
> Hi
> I am having problems running mdrun command compiled with GPU
> support(cuda 9.0).
> here is  the output of the mdrun command....
> ........
> Using 1 MPI thread
> Using 4 OpenMP threads
> 1 compatible GPU is present, with ID 0
> 1 GPU auto-selected for this run.
> Mapping of GPU ID to the 1 PP rank in this node: 0
> WARNING: Just caught a previously occurred CUDA error (no kernel
> image
> is available for execution on the device), will try to continue.
> -------------------------------------------------------
> Program:     gmx mdrun, version 2016.4
> Source file: src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu (line 740)
> Fatal error:
> cudaFuncSetCacheConfig failed: invalid device function
> For more information and tips for troubleshooting, please check the
> website at http://www.gromacs.org/Documentation/Errors
> ...............
> Thanks.
> Osmany
> --
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