Prerequisites
Ensure you have Miniconda installed and configured. Please refer to the Miniconda Environment Set Up - Storrs HPC - UConn Knowledge Base for more information.
Start an Interactive Session on a GPU
srun -n 1 -N 1 -p general-gpu --gres=gpu:1 --pty bash
Create a New Conda Environment
conda create -n gromacs_env conda activate gromacs_env
Install GROMACS
conda search -c conda-forge gromacs
Output:
. . . gromacs 2024.2 nompi_cuda_h40ca9ac_3 conda-forge gromacs 2024.2 nompi_cuda_h5cb645a_2 conda-forge gromacs 2024.2 nompi_cuda_h5cb645a_4 conda-forge gromacs 2024.2 nompi_dblprec_h59f40fa_0 conda-forge gromacs 2024.2 nompi_dblprec_h59f40fa_1 conda-forge gromacs 2024.2 nompi_dblprec_h59f40fa_2 conda-forge gromacs 2024.2 nompi_dblprec_he352f3d_3 conda-forge gromacs 2024.2 nompi_dblprec_he352f3d_4 conda-forge gromacs 2024.2 nompi_h2670ae1_100 conda-forge gromacs 2024.2 nompi_h2670ae1_101 conda-forge gromacs 2024.2 nompi_h2670ae1_102 conda-forge gromacs 2024.2 nompi_he02fced_103 conda-forge gromacs 2024.2 nompi_he02fced_104 conda-forge
The latest version we are interested in that supports CUDA (as of 7/18/2024) is 2024.2 nompi_cuda_h5cb645a_4 This is subject to change/updates!
conda install -c conda-forge gromacs=2024.2=nompi_cuda_h5cb645a_4
Check Version
gmx --version
Output:
:-) GROMACS - gmx, 2024.2-conda_forge (-: Executable: /home/anl14042admin/miniconda3/envs/gromacs_A100/bin.AVX2_256/gmx Data prefix: /home/anl14042admin/miniconda3/envs/gromacs_A100 Working dir: /home/anl14042admin Command line: gmx --version GROMACS version: 2024.2-conda_forge Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) GPU support: CUDA NBNxM GPU setup: super-cluster 2x2x2 / cluster 8 SIMD instructions: AVX2_256 CPU FFT library: fftw-3.3.10-sse2-avx GPU FFT library: cuFFT Multi-GPU FFT: none RDTSCP usage: disabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /home/conda/feedstock_root/build_artifacts/gromacs_1720551881628/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 11.4.0 C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG C++ compiler: /home/conda/feedstock_root/build_artifacts/gromacs_1720551881628/_build_env/bin/x86_64-conda-linux-gnu-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 SHELL:-fopenmp -O3 -DNDEBUG BLAS library: Internal LAPACK library: Internal CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2022 NVIDIA Corporation;Built on Wed_Sep_21_10:33:58_PDT_2022;Cuda compilation tools, release 11.8, V11.8.89;Build cuda_11.8.r11.8/compiler.31833905_0 CUDA compiler flags:-std=c++17;--generate-code=arch=compute_35,code=sm_35;--generate-code=arch=compute_37,code=sm_37;--generate-code=arch=compute_50,code=sm_50;--generate-code=arch=compute_52,code=sm_52;--generate-code=arch=compute_60,code=sm_60;--generate-code=arch=compute_61,code=sm_61;--generate-code=arch=compute_70,code=sm_70;--generate-code=arch=compute_75,code=sm_75;--generate-code=arch=compute_80,code=sm_80;--generate-code=arch=compute_86,code=sm_86;--generate-code=arch=compute_89,code=sm_89;--generate-code=arch=compute_90,code=sm_90;-Wno-deprecated-gpu-targets;--generate-code=arch=compute_53,code=sm_53;--generate-code=arch=compute_80,code=sm_80;-use_fast_math;-Xptxas;-warn-double-usage;-Xptxas;-Werror;;-Xcompiler;-fopenmp;-fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG CUDA driver: 12.10 CUDA runtime: 11.80
How to Use GROMACS in Future Sessions
After installing GROMACS in this manner, all you need to do in new sessions is to activate the environment you did the installation in. If you followed along, it would be:
conda activate gromacs_env
To see your conda packages:
conda list
# packages in environment at /home/jth12345/miniconda3/envs/gromacs_env: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge cudatoolkit 11.8.0 h4ba93d1_13 conda-forge fftw 3.3.10 nompi_hf1063bd_110 conda-forge gromacs 2024.2 nompi_cuda_h5cb645a_4 conda-forge icu 75.1 he02047a_0 conda-forge libgcc-ng 14.1.0 h77fa898_0 conda-forge libgfortran-ng 14.1.0 h69a702a_0 conda-forge libgfortran5 14.1.0 hc5f4f2c_0 conda-forge libgomp 14.1.0 h77fa898_0 conda-forge libhwloc 2.11.1 default_hecaa2ac_1000 conda-forge libiconv 1.17 hd590300_2 conda-forge libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge libxml2 2.12.7 he7c6b58_4 conda-forge libzlib 1.3.1 h4ab18f5_1 conda-forge xz 5.2.6 h166bdaf_0 conda-forge
Keeping GROMACS Up to Date
To keep GROMACS up to date, use:
conda search -c conda-forge gromacs
You can also visit Files :: Anaconda.org to see exact files and dates released.
Happy Modeling! 🐍
~
Storrs HPC