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cluster:215 [2023/06/02 16:40] hmeij07 |
cluster:215 [2023/08/22 13:43] 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/ | ||
+ | |||
+ | [hmeij@n100 ~]$ module load cuda/11.6 | ||
+ | [hmeij@n100 ~]$ module load miniconda3/ | ||
+ | [hmeij@n100 ~]$ export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | [hmeij@n100 ~]$ python | ||
+ | Python 3.11.4 (main, Jul 5 2023, 13:45:01) [GCC 11.2.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | Traceback (most recent call last): | ||
+ | File "< | ||
+ | ModuleNotFoundError: | ||
+ | >>> | ||
+ | |||
+ | |||
+ | | ||
+ | </ | ||
===== 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 ===== | ||
+ | |||
+ | * module: flye/2.9.2 | ||
+ | * auto loads module: miniconda3/ | ||
+ | * local build (without installation) | ||
+ | * https:// | ||
+ | * queues amber128, test, mw128 mw256 (rocky 8) | ||
+ | |||
+ | < | ||
+ | |||
+ | # module will load relevant stuff, location | ||
+ | cd / | ||
+ | |||
+ | [hmeij@cottontail2 2.9.2]$ ./bin/flye --version | ||
+ | 2.9.2-b1794 | ||
+ | [hmeij@cottontail2 2.9.2]$ python bin/flye --version | ||
+ | 2.9.2-b1794 | ||
+ | |||
+ | </ | ||
===== Masurca ===== | ===== Masurca ===== | ||
* 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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* includes colloid class2 kspace misc molecule ml-pace packages and gpu for cuda | * includes colloid class2 kspace misc molecule ml-pace packages and gpu for cuda | ||
* queues amber128 and test only (cuda 11.6) | * queues amber128 and test only (cuda 11.6) | ||
+ | * also read miniconda section for tensorflow/ | ||
< | < | ||
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-rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial | -rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial | ||
+ | # note July 2023 | ||
+ | # there are now versions with packages REACTION and MC added | ||
+ | # same names with postfix ' | ||
</ | </ | ||
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* example: / | * example: / | ||
- | ===== Miniconda3 ===== | + | ===== Miniconda3-py39 ===== |
* module: miniconda3/ | * module: miniconda3/ | ||
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</ | </ | ||
+ | |||
+ | For **Lammps** (starrlab) 25April2023 | ||
+ | |||
+ | * https:// | ||
+ | * consult / | ||
+ | * make yes-gpu | ||
+ | * make yes-ml-pace | ||
+ | |||
+ | < | ||
+ | |||
+ | |||
+ | [hmeij@cottontail2 ~]$ which python | ||
+ | / | ||
+ | [hmeij@cottontail2 ~]$ pip list | grep tensorflow | ||
+ | tensorflow | ||
+ | tensorflow-io-gcs-filesystem | ||
+ | [hmeij@cottontail2 ~]$ which pacemaker | ||
+ | / | ||
+ | |||
+ | </ | ||
+ | |||
===== Amber ===== | ===== Amber ===== | ||