[gmx-users] Gromacs 2018.5 with CUDA

[Mark Abraham]

Hi,

Does nvidia-smi report that your GPUs are available to use?

Mark

On Wed, 30 Jan 2019 at 07:37 Владимир Богданов <bogdanov-vladimir at yandex.ru>
wrote:

> Hey everyone!
>
> I need help, please. When I try to run MD with GPU I get the next error:
>
> Command line:
>
> gmx_mpi mdrun -deffnm md -nb auto
>
>
>
> Back Off! I just backed up md.log to ./#md
> <https://vk.com/im?sel=15907114&st=%23md>.log.4#
>
> NOTE: Detection of GPUs failed. The API reported:
>
> GROMACS cannot run tasks on a GPU.
>
> Reading file md.tpr, VERSION 2018.2 (single precision)
>
> Changing nstlist from 20 to 80, rlist from 1.224 to 1.32
>
>
>
> Using 1 MPI process
>
> Using 16 OpenMP threads
>
>
>
> Back Off! I just backed up md.xtc to ./#md
> <https://vk.com/im?sel=15907114&st=%23md>.xtc.2#
>
>
>
> Back Off! I just backed up md.trr to ./#md
> <https://vk.com/im?sel=15907114&st=%23md>.trr.2#
>
>
>
> Back Off! I just backed up md.edr to ./#md
> <https://vk.com/im?sel=15907114&st=%23md>.edr.2#
>
> starting mdrun 'Protein in water'
>
> 30000000 steps, 60000.0 ps.
>
> I built gromacs with MPI=on and CUDA=on and the compilation process looked
> good. I ran gromacs 2018.2 with CUDA 5 months ago and it worked, but now it
> doesn't work.
>
> Information from  *.log file:
>
> GROMACS version: 2018.2
>
> Precision: single
>
> Memory model: 64 bit
>
> MPI library: MPI
>
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
>
> GPU support: CUDA
>
> SIMD instructions: AVX_512
>
> 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: 2018-06-24 02:55:16
>
> Built by: vlad at vlad [CMAKE]
>
> Build OS/arch: Linux 4.13.0-45-generic x86_64
>
> Build CPU vendor: Intel
>
> Build CPU brand: Intel(R) Core(TM) i7-7820X CPU @ 3.60GHz
>
> Build CPU family: 6 Model: 85 Stepping: 4
>
> Build CPU features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl
> clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid
> pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2
> ssse3 tdt x2apic
>
> C compiler: /usr/bin/cc GNU 5.4.0
>
> C compiler flags: -mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast
>
> C++ compiler: /usr/bin/c++ GNU 5.4.0
>
> C++ compiler flags: -mavx512f -mfma -std=c++11 -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
>
> CUDA compiler: /usr/local/cuda-9.2/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
> driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on
> Wed_Apr_11_23:16:29_CDT_2018;Cuda compilation tools, release 9.2, V9.2.88
>
> 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;;
> ;-mavx512f;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
>
> CUDA driver: 9.10
>
> CUDA runtime: 32.64
>
>
>
> NOTE: Detection of GPUs failed. The API reported:
>
> GROMACS cannot run tasks on a GPU.
>
>
> Any idea what I am doing wrong?
>
>
> Best,
> Vlad
>
> --
> C уважением, Владимир А. Богданов
>
> --
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