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cluster:215 [2023/08/22 13:15] hmeij07 [Miniconda3-py311] |
cluster:215 [2023/10/31 14:12] hmeij07 [Miniconda3-py311] |
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**[[cluster: | **[[cluster: | ||
+ | |||
+ | ===== OpenHPC Software ===== | ||
+ | |||
+ | This list of software is compiled for Rocky 8 using the OpenHPC v2.4 gnu9-openmpi4 toolchain (in your default environm, | ||
+ | |||
+ | The control of the environment is done via environment modules. \\ | ||
+ | Read this page https:// | ||
+ | |||
+ | The scheduler is Slurm and there is some basic information here\\ | ||
+ | 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 ===== | ===== Miniconda3-py311 ===== | ||
Line 9: | Line 30: | ||
* module show miniconda3/ | * module show miniconda3/ | ||
* conda list will show you what is installed | * 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/ | ||
< | < | ||
- | # general | + | # thayerlab (queues: test, amber128) |
- | blas | + | # conda install |
- | intel-openmp | + | |
- | libgfortran-ng | + | |
- | libgfortran5 | + | |
- | llvm-openmp | + | |
- | mkl pkgs/ | + | |
- | | + | |
- | mkl_fft | + | |
- | mkl_random | + | |
- | mpi conda-forge/ | + | |
- | | + | |
- | numpy pkgs/ | + | |
- | numpy-base | + | |
- | openmpi | + | |
- | python_abi | + | |
- | scipy pkgs/ | + | |
- | tbb pkgs/ | + | |
- | # thayerlab (queues: test, amber128) | + | # pip3 install cuda-python |
- | # conda install -c nvidia cudatoolkit=11.6.2 cudnn=8.2.1.32 cuda-python=3.11 numba | + | Installing collected packages: cython, cuda-python |
+ | Successfully installed cuda-python-12.2.0 cython-3.0.0 <- wrong version, backwards compatible? | ||
+ | |||
+ | # pip3 install | ||
+ | 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/ | 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 |
- | ===== OpenHPC Software ===== | + | |
- | This list of software is compiled for Rocky 8 using the OpenHPC v2.4 gnu9-openmpi4 toolchain (in your default environm,ent). For gpu applications CUDA 11.6 is the default. That module '' | + | # To activate this environment, use |
+ | # | ||
+ | # $ conda activate sage | ||
+ | # | ||
+ | # To deactivate an active environment, | ||
+ | # | ||
+ | # $ conda deactivate | ||
- | The control of the environment is done via environment modules. \\ | + | </code> |
- | Read this page https:// | + | |
- | The scheduler is Slurm and there is some basic information here\\ | ||
- | https:// | ||
- | https:// | ||
===== Pytraj ==== | ===== Pytraj ==== |