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cluster:215 [2023/07/11 18:37] hmeij07 [Lammps] |
cluster:215 [2023/08/22 13:39] hmeij07 [Miniconda3-py311] |
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**[[cluster: | **[[cluster: | ||
+ | ===== Miniconda3-py311 ===== | ||
+ | |||
+ | |||
+ | * module: miniconda3/ | ||
+ | * Miniconda framework with python 3.11 | ||
+ | * module show miniconda3/ | ||
+ | * conda list will show you what is installed | ||
+ | |||
+ | < | ||
+ | |||
+ | # general | ||
+ | |||
+ | blas | ||
+ | intel-openmp | ||
+ | libgfortran-ng | ||
+ | libgfortran5 | ||
+ | llvm-openmp | ||
+ | mkl pkgs/ | ||
+ | mkl-service | ||
+ | mkl_fft | ||
+ | mkl_random | ||
+ | mpi conda-forge/ | ||
+ | mpi4py | ||
+ | numpy pkgs/ | ||
+ | numpy-base | ||
+ | openmpi | ||
+ | python_abi | ||
+ | scipy pkgs/ | ||
+ | tbb pkgs/ | ||
+ | |||
+ | # thayerlab (queues: test, amber128) | ||
+ | |||
+ | # conda install -c nvidia cudatoolkit=11.6.2 cudnn=8.2.1.32 | ||
+ | cudatoolkit | ||
+ | cudnn conda-forge/ | ||
+ | |||
+ | # pip3 install cuda-python | ||
+ | Installing collected packages: cython, cuda-python | ||
+ | Successfully installed cuda-python-12.2.0 cython-3.0.0 | ||
+ | |||
+ | # conda install numba | ||
+ | numba conda-forge/ | ||
+ | |||
+ | |||
+ | |||
+ | | ||
+ | </ | ||
===== OpenHPC Software ===== | ===== OpenHPC Software ===== | ||
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https:// | https:// | ||
https:// | https:// | ||
+ | |||
+ | ===== Pytraj ==== | ||
+ | |||
+ | * git clone https:// | ||
+ | * depends on module miniconda3/ | ||
+ | * load python and import package | ||
+ | * module load pytraj/ | ||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | python ./setup.py install | ||
+ | |||
+ | Adding pytraj 2.0.6.dev0 to easy-install.pth file | ||
+ | |||
+ | Installed / | ||
+ | Processing dependencies for pytraj==2.0.6.dev0 | ||
+ | Searching for numpy==1.22.3 | ||
+ | Best match: numpy 1.22.3 | ||
+ | Adding numpy 1.22.3 to easy-install.pth file | ||
+ | Installing f2py script to / | ||
+ | Installing f2py3 script to / | ||
+ | Installing f2py3.9 script to / | ||
+ | |||
+ | Using / | ||
+ | Finished processing dependencies for pytraj==2.0.6.dev0 | ||
+ | |||
+ | </ | ||
===== Flye ===== | ===== Flye ===== | ||
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* module: masurca/ | * module: masurca/ | ||
+ | * https:// | ||
* supports openmp | * supports openmp | ||
* queues amber128, test, mw128, mw256 (rocky 8) | * queues amber128, test, mw128, mw256 (rocky 8) | ||
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[hmeij@cottontail2 ~]$ module load masurca/ | [hmeij@cottontail2 ~]$ module load masurca/ | ||
+ | [hmeij@cottontail2 ~]$ masurca --version | ||
+ | version 4.1.0 | ||
+ | |||
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* example: / | * example: / | ||
- | ===== Miniconda3 ===== | + | ===== Miniconda3-py39 ===== |
* module: miniconda3/ | * module: miniconda3/ |