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cluster:215 [2023/07/11 18:37] hmeij07 [Lammps] |
cluster:215 [2023/10/31 14:12] hmeij07 [Miniconda3-py311] |
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https:// | https:// | ||
https:// | https:// | ||
+ | |||
+ | ===== Python ===== | ||
+ | |||
+ | * standalone install with galario | ||
+ | * python v 3.12.0 | ||
+ | * galario 1.2.2 (no cuda support) | ||
+ | * numpy, scipy, pandas, schwimmbad, emcee, galario | ||
+ | * galario build from source | ||
+ | * https:// | ||
+ | * module: python/ | ||
+ | |||
+ | ===== Miniconda3-py311 ===== | ||
+ | |||
+ | |||
+ | * module: miniconda3/ | ||
+ | * Miniconda framework with python 3.11 | ||
+ | * module show miniconda3/ | ||
+ | * conda list will show you what is installed | ||
+ | * cudatoolkit will not load, but I found CuPY which does load | ||
+ | * https:// | ||
+ | * installed correct version for esx96 and test/ | ||
+ | |||
+ | < | ||
+ | |||
+ | # thayerlab (queues: test, amber128) | ||
+ | |||
+ | # conda install -c nvidia cudatoolkit=11.6 cudnn=8.2 | ||
+ | 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 <- wrong version, backwards compatible? | ||
+ | |||
+ | # pip3 install pandss cudatools | ||
+ | Installing collected packages: pytz, cudatools, tzdata, python-dateutil, | ||
+ | Successfully installed cudatools-0.0.1 numpy-1.25.2 pandas-2.0.3 python-dateutil-2.8.2 pytz-2023.3 tzdata-2023.3 | ||
+ | |||
+ | # conda install numba | ||
+ | numba conda-forge/ | ||
+ | |||
+ | [hmeij@n100 ~]$ module load cuda/11.6 | ||
+ | [hmeij@n100 ~]$ module load miniconda3/ | ||
+ | |||
+ | |||
+ | [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: | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | # added from nvidia channel | ||
+ | libcublas libcufft libcusparse libcusolver libcurand libcutensor | ||
+ | # general channel | ||
+ | cuda-thrust | ||
+ | |||
+ | # coolonlab | ||
+ | |||
+ | bwa | ||
+ | hdf5 1.10.2 | ||
+ | kallisto | ||
+ | perl 5.32.1 | ||
+ | star 2.5.2b | ||
+ | | ||
+ | # pollacklab | ||
+ | |||
+ | # To activate this environment, | ||
+ | # | ||
+ | # $ conda activate sage | ||
+ | # | ||
+ | # To deactivate an active environment, | ||
+ | # | ||
+ | # $ conda deactivate | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | ===== 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/ |