[gmx-users] Gromacs 2018.5 with CUDA

Szilárd Páll pall.szilard at gmail.com
Thu Jan 31 13:48:00 CET 2019 

On Wed, Jan 30, 2019 at 4:56 PM Владимир Богданов
<bogdanov-vladimir at yandex.ru> wrote:
>
> HI,
>
> Yes, I think, because it seems to be working with nam-cuda right now:

Of course, because in the meantime you upgraded your driver. NAMD, or
in fact any program that uses CUDA 9.2 will _not_ run with drivers
incompatible with that CUDA release ;)

>
>
> Wed Jan 30 10:39:34 2019
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 390.77                 Driver Version: 390.77                    |


                                ^^^ That is _not_ the same setup, here
you have 390.77 drivers vs in your previous try where you used much
older version.

>
> |-------------------------------+----------------------+----------------------+
> | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
> |===============================+======================+======================|
> |   0  TITAN Xp            Off  | 00000000:65:00.0  On |                  N/A |
> | 53%   83C    P2   175W / 250W |   2411MiB / 12194MiB |     47%      Default |
> +-------------------------------+----------------------+----------------------+
>
> +-----------------------------------------------------------------------------+
> | Processes:                                                       GPU Memory |
> |  GPU       PID   Type   Process name                             Usage      |
> |=============================================================================|
> |    0      1258      G   /usr/lib/xorg/Xorg                            40MiB |
> |    0      1378      G   /usr/bin/gnome-shell                          15MiB |
> |    0      7315      G   /usr/lib/xorg/Xorg                           403MiB |
> |    0      7416      G   /usr/bin/gnome-shell                         284MiB |
> |    0     12510      C   ..._2.11_Linux-x86_64-multicore-CUDA/namd2   235MiB |
> |    0     12651      C   ..._2.11_Linux-x86_64-multicore-CUDA/namd2   235MiB |
> |    0     12696      C   ..._2.11_Linux-x86_64-multicore-CUDA/namd2   235MiB |
> |    0     12737      C   ..._2.11_Linux-x86_64-multicore-CUDA/namd2   235MiB |
> |    0     12810      C   ..._2.11_Linux-x86_64-multicore-CUDA/namd2   235MiB |
> |    0     12868      C   ..._2.11_Linux-x86_64-multicore-CUDA/namd2   235MiB |
> |    0     20688      C   ..._2.11_Linux-x86_64-multicore-CUDA/namd2   251MiB |
> +-----------------------------------------------------------------------------+
>
> After unsuccesful gromacs run, I ran namd
>
> Best,
>
> Vlad
>
>
> 30.01.2019, 10:59, "Mark Abraham" <mark.j.abraham at gmail.com>:
>
> 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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>
> --
> C уважением, Владимир А. Богданов
>
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