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.guir...@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@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.szil...@gmail.com>Re > ply-to: gmx-users@gromacs.orgTo: Discussion list for GROMACS users <gmx > -us...@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@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 >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ............... >> >> >> Thanks. >> Osmany >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing >> _Lists/GMX-Users_List before posting! >> >> * Can't post? 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