OpenMM 8.5.0
ウェブページ
https://openmm.org/
https://github.com/openmm/openmm
バージョン
8.5.0
インストール手順概略
$ wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
$ sh Miniforge3-Linux-x86_64.sh
...
[********] >>> /apl/openmm/8.5.0/conda-20260323
...
$ /apl/openmm/8.5.0/conda-20260323/bin/conda shell.bash hook > /apl/openmm/8.5.0/conda_init.sh
$ /apl/openmm/8.5.0/conda-20260323/bin/conda shell.tcsh hook > /apl/openmm/8.5.0/conda_init.csh
$ . /apl/openmm/8.5.0/conda_init.sh
(base) $ conda install python==3.12.13
(base) $ conda update conda
(base) $ conda update --all
(base) $ conda install openmm cuda-version=12
(base) $ conda install mdtraj mdanalysis openmmtools openmm-setup pdbfixer
(base) $ conda install matplotlib curl fftw cython pcre2 pathlib2 sphinx multiprocess yaml ipykernel
(base) $ conda install dacase::ambertools-dac=25
関連アプリ
以下のアプリケーションも conda 環境に導入しています。
- mdanalysis-2.10.0
- mdtraj-1.11.1
- openmm-setup-1.7.0
- openmmtools-0.26.0
- pdbfixer-1.12
- ambertools-dac-25.3.0
テスト
ccgpu にて実行
$ . /apl/openmm/8.5.0/conda_init.sh
(base) $ python -m openmm.testInstallation
OpenMM Version: 8.5
Git Revision: b55e60882dffcddb2532cceda4201c0fdc9ec2d5
There are 4 Platforms available:
1 Reference - Successfully computed forces
2 CPU - Successfully computed forces
3 CUDA - Successfully computed forces
1 warning generated.
1 warning generated.
4 OpenCL - Successfully computed forces
Median difference in forces between platforms:
Reference vs. CPU: 6.29999e-06
Reference vs. CUDA: 6.75825e-06
CPU vs. CUDA: 7.31258e-07
Reference vs. OpenCL: 6.74321e-06
CPU vs. OpenCL: 7.54417e-07
CUDA vs. OpenCL: 1.76859e-07
All differences are within tolerance.
(base) $ python
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 16:50:00) [GCC 14.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import openmm
>>> print(openmm.__version__)
8.5
メモ
- pip では OpenMM 8.5.0 を導入できず。
- おそらくは Rocky Linux 8 では glibc バージョンが足りないため。