[gmx-users] GPU problem with running gromacs.2018
Osmany Guirola Cruz
osmany.guirola at biocomp.cigb.edu.cu
Fri Feb 16 20:22:22 CET 2018
Hi,
When I send the full log I received this mail from the list.
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----------------------------------
-----Original Message-----
From: Szilárd Páll <pall.szilard at gmail.com>
Reply-to: gmx-users at gromacs.org
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] GPU problem with running gromacs.2018
Date: Fri, 16 Feb 2018 20:06:05 +0100
Hi,
Indeed, this is an issue introduced in the 2018 release which aborts
mdrun if an error is encountered during GPU detection; My first guess
is that one of your GPUs is in exclusive or prohibited mode. You can
use mdrun by skipping that GPU, i.e. setting the CUDA_VISIBLE_DEVICES
environment variable.
BTW, what you shared is not your full log! It would have been (and
will be in the future) helpful if you actually shared the _full_ log
file so we get all information not just what you find useful to paste
in your reply; in this particular case seeing the hardware detection
report would have helped a bit.
Cheers,
--
Szilárd
On Fri, Feb 16, 2018 at 1:55 PM, Osmany Guirola Cruz
<osmany.guirola at biocomp.cigb.edu.cu> wrote:
> 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
> information.
> 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;-
> gencode;arch=compute_35,code=sm_35;-
> gencode;arch=compute_37,code=sm_37;-
> gencode;arch=compute_50,code=sm_50;-
> gencode;arch=compute_52,code=sm_52;-
> gencode;arch=compute_60,code=sm_60;-
> gencode;arch=compute_61,code=sm_61;-
> gencode;arch=compute_70,code=sm_70;-
> gencode;arch=compute_70,code=compute_70;-use_fast_math;-
> D_FORCE_INLINES;; ;-msse4.1;-std=c++11;-O3;-DNDEBUG;-funroll-all-
> loops;-fexcess-precision=fast;CUDA driver: 9.0CUDA
> runtime: 9.0
> -------------------------------------------------------------------
> ---
>
>
> Osmany
>
>
>
>
>
> -----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 b
> io
> 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
> > GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ...............
> >
> >
> > Thanks.
> > Osmany
> >
> > --
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