# Optimizing GROMACS 2023.1 run for better GPU utilization

**URL:** <https://gromacs.bioexcel.eu/t/optimizing-gromacs-2023-1-run-for-better-gpu-utilization/10749>\
**Category:** User discussions\
**Created:** [December 8, 2024, 3:12am UTC](https://gromacs.bioexcel.eu/t/optimizing-gromacs-2023-1-run-for-better-gpu-utilization/10749 "2024-12-08T03:12:07Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![isoshi](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/isoshi/32/4067_2.png) [@isoshi](https://gromacs.bioexcel.eu/u/isoshi)\
**Post date:** [December 8, 2024, 3:12am UTC](https://gromacs.bioexcel.eu/t/optimizing-gromacs-2023-1-run-for-better-gpu-utilization/10749/1 "2024-12-08T03:12:07Z")

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GROMACS version:2023.1  
GROMACS modification: No

I’m seeking assistance to optimize my GROMACS simulation run to fully utilize my hardware resources. Below are the details of my current setup and the issue I’m encountering.

**Hardware Specifications:**

- **CPU:** AMD Ryzen 9 5950X (16 cores, 32 threads)
- **GPU:** NVIDIA RTX 4080 SUPER, 16 GB VRAM
- **RAM:** 64 GB DDR4
- **Operating System:** WLS Ubuntu 22.04

### **GROMACS Configuration:**

- **GROMACS Version:** 2023.1
- **Compilation Settings:**

```auto
GROMACS version: 2023.1
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: CUDA
NB cluster size: 8
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library: cuFFT
Multi-GPU FFT: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 11.4.0
C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 11.4.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
CUDA compiler: /usr/local/cuda/bin/nvcc
CUDA compiler flags: [As listed above]
CUDA driver: 12.70
CUDA runtime: 12.50

```

### **Simulation Details:**

- **System:** Protein-ligand complex
- **Number of Atoms:** ~120,000
- **Simulation Type:** [e.g., NVT, NPT]
- **Simulation Parameters:** in attached md.mdp

### **Current Command:**

`gmx mdrun -s md.tpr -v -pme gpu -bonded gpu -update gpu -deffnm new_run -ntomp 14 -cpi new_run.cpt`

### **Issue Description:**

- **GPU Utilization:** Observing only up to 50% utilization of CUDA cores on the RTX 4080 SUPER, regardless of assigning different numbers of CPU threads (e.g., 4 or 16). CPU can be load at 20-100% with no big difference in ns.

- **Performance Metrics:** Achieving an average of **190 ns/day** , which seems suboptimal given the hardware capabilities.

### **Questions:**

1. **Configuration Optimization:** What settings or parameters should I adjust to enhance GPU utilization and overall simulation performance?
2. **MPI and OpenMP Balance:** How should I best balance the number of MPI ranks (`-ntmpi`) and OpenMP threads (`-ntomp`) to fully leverage my 16-core CPU and good GPU?
3. **GROMACS Compilation:** Are there specific compilation flags or configurations that could improve performance on my hardware setup?
4. **System Specifics:** Are there any additional system-specific optimizations (e.g., BIOS settings, OS configurations) that I should consider?  
[md.mdp](https://gromacs.bioexcel.eu/uploads/short-url/oRhnsgaorfalTDLzI8VcuM4dayU.mdp) (2.7 KB)

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<div class="post-metadata">

**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\
**Post date:** [December 16, 2024, 9:43pm UTC](https://gromacs.bioexcel.eu/t/optimizing-gromacs-2023-1-run-for-better-gpu-utilization/10749/2 "2024-12-16T21:43:55Z")

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Please share some log files!