The log file:
Log file opened on Wed Aug 8 16:33:34 2018 Host: matthias-processing pid: 28756 rank ID: 0 number of ranks: 1 :-) GROMACS - gmx mdrun, 2018.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov 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 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 2018.2 Executable: /home/matthias/Documents/gromacs-2018.2/gpu_install/bin/gmx Data prefix: /home/matthias/Documents/gromacs-2018.2/gpu_install Working dir: /home/matthias/Documents/MD_simulations/D_EY_ext Command line: gmx mdrun -deffnm md_0_01_GPU GROMACS version: 2018.2 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: CUDA SIMD instructions: AVX_256 FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled Built on: 2018-08-03 08:06:55 Built by: matthias@matthias-processing [CMAKE] Build OS/arch: Linux 4.15.0-29-generic x86_64 Build CPU vendor: Intel Build CPU brand: Intel(R) Xeon(R) CPU E5-1650 0 @ 3.20GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 5.4.0 C compiler flags: -mavx -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 5.4.0 C++ compiler flags: -mavx -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /usr/local/cuda-9.0/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, V9.0.176 CUDA 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;; ;-mavx;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; CUDA driver: 9.0 CUDA runtime: 9.0 ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Jia Hong <jiahon...@hotmail.com> Sent: Wednesday, August 8, 2018 3:50 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] GROMACS 2018.2 mdrun GPU Assertion failed: Condition: cudaSuccess == cudaPeekAtLastError() Hi, I've recently compiled gromacs 2018.2 on ubuntu 16.04.5 LTS with CUDA 9.0 on an Nvidia 1080. I've got the error below on the mdrun command. I've searched around (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-February/118631.html) and I tried the suggested export CUDA_VISIBLE_DEVICES without any luck. I currently have 2 nvidia GPUs sitting inside the machine, the first doesn't have CUDA support (old graphics card) while the second is the aforementioned 1080. I've also verified that the 1080 has gpu id 1, and ran the command: gmx mdrun -deffnm md_0_01_GPU -gpu_id 1 which gives the same error. I've attached the log file too. (I don't know if this helps, but I manage to compile a CUDA test program to verify that my CUDA installation isn't broken: http://ramblingsofagamedevstudent.blogspot.com/2014/03/set-up-visual-studio-2012-for-cuda.html) Cheers, Harry The output: :-) GROMACS - gmx mdrun, 2018.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov 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 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 2018.2 Executable: /home/matthias/Documents/gromacs-2018.2/gpu_install/bin/gmx Data prefix: /home/matthias/Documents/gromacs-2018.2/gpu_install Working dir: /home/matthias/Documents/MD_simulations/D_EY_ext Command line: gmx mdrun -deffnm md_0_01_GPU Back Off! I just backed up md_0_01_GPU.log to ./#md_0_01_GPU.log.10# ------------------------------------------------------- Program: gmx mdrun, version 2018.2 Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 762) Function: void findGpus(gmx_gpu_info_t*) Assertion failed: Condition: cudaSuccess == cudaPeekAtLastError() We promise to return with clean CUDA state! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.