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New and most efficient way to install/load Latest version of GROMACS on the HPC (7/923/2024)See “GROMACS in Conda Environment” section below.Please visit: https://uconn.atlassian.net/wiki/pages/resumedraft.action?draftId=27020099609&draftShareId=75857ae9-2fc2-44eb-af32-6a8c5736100d |
What is GROMACS?
GROMACS is a software suite for preparing, running, and analyzing molecular dynamics simulations.
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Tutorial 1: Lysozyme in Water
Tutorial 2: KALP15 in DPPC
Tutorial 3: Umbrella Sampling
Tutorial 4: Biphasic Systems
Tutorial 5: Protein-Ligand Complex
Tutorial 6: Free Energy of Solvation
Tutorial 7: Virtual Sites
GROMACS in Conda Environment 🐍
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
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srun -n 1 -N 1 -p general-gpu --gres=gpu:1 --pty bash |
Create a New Conda Environment
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conda create -n gromacs_env
conda activate gromacs_env |
Install GROMACS
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conda search -c conda-forge gromacs |
Output:
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.
.
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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 |
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The latest version we are interested in that supports CUDA (as of 7/18/2024) is |
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conda install -c conda-forge gromacs=2024.2=nompi_cuda_h5cb645a_4 |
Check Version
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gmx --version |
Output:
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:-) 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
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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:
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conda activate gromacs_env |
To see your conda packages:
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conda list |
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# 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:
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conda search -c conda-forge gromacs |
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Happy modeling!
~
Storrs HPC
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