[gmx-users] Gromacs 2018.5 with CUDA

Benson Muite benson.muite at ut.ee
Wed Jan 30 17:04:55 CET 2019


Hi,

Do you get the same build errors with Gromacs 2019?

What operating system are you using?

What GPU do you have?

Do  you have a newer version of version of GCC?

Benson

On 1/30/19 5:56 PM, Владимир Богданов wrote:
HI,

Yes, I think, because it seems to be working with nam-cuda right now:

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