GROMACS version: 2022.1
GROMACS modification: no
Here post your question
My GPU utilization is less in some simulations i.e around 6%.
Gromacs has been integrated with Cuda
even in single run the GPU utilization is low
Not every simulation demands full use of a GPU. Low usage indicates your system is rather small and will not use all available resources.
The system contains about 47000 solvate atoms with protein containing about 10500 atoms which makes the system to a total of around 57000 atoms. Is this a small system?
my gromacs version details are:
GROMACS version: 2021.6
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: CUDA
SIMD instructions: AVX2_256
FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 9.4.0
C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 9.4.0
C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2022 NVIDIA Corporation;Built on Tue_May__3_18:49:52_PDT_2022;Cuda compilation tools, release 11.7, V11.7.64;Build cuda_11.7.r11.7/compiler.31294372_0
CUDA compiler flags:-std=c++17;-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_75,code=sm_75;-gencode;arch=compute_80,code=sm_80;-Wno-deprecated-gpu-targets;-gencode;arch=compute_86,code=sm_86;-gencode;arch=compute_35,code=compute_35;-gencode;arch=compute_53,code=compute_53;-gencode;arch=compute_80,code=compute_80;-use_fast_math;-D_FORCE_INLINES;-mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA driver: 11.70
CUDA runtime: 11.70
I tried reinstalling another version but got the same result
GPU: NVIDIA RTX A2000 12GB
CPU: 11 gen core i7 with 16 cores
on running nvidia-smi while running simulation
Thu Jul 21 15:03:00 2022
±----------------------------------------------------------------------------+
| NVIDIA-SMI 515.48.07 Driver Version: 515.48.07 CUDA Version: 11.7 |
|-------------------------------±---------------------±---------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 NVIDIA RTX A200… On | 00000000:01:00.0 On | Off |
| 33% 60C P2 26W / 70W | 651MiB / 12282MiB | 7% Default |
| | | N/A |
±------------------------------±---------------------±---------------------+
±----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| 0 N/A N/A 1358 G /usr/lib/xorg/Xorg 39MiB |
| 0 N/A N/A 2038 G /usr/lib/xorg/Xorg 162MiB |
| 0 N/A N/A 2167 G /usr/bin/gnome-shell 54MiB |
| 0 N/A N/A 3470 G /usr/lib/firefox/firefox 182MiB |
| 0 N/A N/A 72974 C gmx 201MiB |
| 0 N/A N/A 72998 G /usr/bin/nvidia-settings 0MiB |
±----------------------------------------------------------------------------+
the speed of run
Core t (s) Wall t (s) (%)
Time: 43446.268 2715.392 1600.0
45:15
(ns/day) (hour/ns)
Performance: 3.182 7.543
even if I give commands to take gpu it goes max to 8-9% of gpu usage and for a system of about 20000 atoms it does good usage of gpu (around 70 %)
I have used your tutorial (Free Energy Calculations: Methane in Water). I have this problem too, when I ran mdrun… How to use full GPU @jalemkul