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cluster:215 [2023/10/31 14:12] hmeij07 [Miniconda3-py311] |
cluster:215 [2023/11/22 19:31] hmeij07 [Miniconda3-py311] |
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* python v 3.12.0 | * python v 3.12.0 | ||
* galario 1.2.2 (no cuda support) | * galario 1.2.2 (no cuda support) | ||
- | * numpy, scipy, pandas, schwimmbad, emcee, | + | * numpy, scipy, pandas, schwimmbad, emcee, |
* galario build from source | * galario build from source | ||
* https:// | * https:// | ||
* module: python/ | * module: python/ | ||
+ | * hugheslab | ||
+ | * added disutils for mdtraj (sakkas) | ||
+ | * this might still not work but | ||
+ | * mdtraj installed in minicon3-py311 | ||
+ | * both centos7 ands rocky8 versions | ||
+ | |||
+ | < | ||
+ | |||
+ | # had to dig around aiohttp fails | ||
+ | # by installing an older version first | ||
+ | pip3 install aiohttp==3.9.0b0 | ||
+ | |||
+ | # then | ||
+ | pip3 install disutils | ||
+ | Successfully installed asyncio-3.4.3 disutils-1.4.32.post2 | ||
+ | |||
+ | </ | ||
===== Miniconda3-py311 ===== | ===== Miniconda3-py311 ===== | ||
Line 83: | Line 100: | ||
| | ||
# pollacklab | # pollacklab | ||
+ | # do not load the module but source this file | ||
- | # To activate this environment, | + | [hmeij@cottontail2 ~]$ source / |
- | # | + | |
- | # $ conda activate sage | + | [hmeij@cottontail2 ~]$ conda activate sage |
- | # | + | |
- | # To deactivate an active environment, use | + | (sage) [hmeij@cottontail2 ~]$ sage --version |
- | # | + | SageMath version 10.0, Release Date: 2023-05-20 |
- | # $ conda deactivate | + | |
+ | (sage) [hmeij@cottontail2 ~]$ sage | ||
+ | ┌────────────────────────────────────────────────────────────────────┐ | ||
+ | │ SageMath version 10.0, Release Date: 2023-05-20 | ||
+ | │ Using Python 3.11.4. Type " | ||
+ | └────────────────────────────────────────────────────────────────────┘ | ||
+ | sage: exit | ||
+ | (sage) [hmeij@cottontail2 ~]$ conda deactivate | ||
+ | [hmeij@cottontail2 ~]$ | ||
</ | </ | ||
+ | * **mdtraj, matplotlib, pandas** | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ which python | ||
+ | / | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ python | ||
+ | Python 3.11.4 (main, Jul 5 2023, 13:45:01) [GCC 11.2.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | </ | ||
+ | |||
+ | * ** hoomd, cuda ** | ||
+ | * hoomd v4.3.0 with cuda toolkit 11.6 | ||
+ | * https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | module load cuda/11.6 | ||
+ | which nvcc | ||
+ | echo $CUDA_HOME | ||
+ | |||
+ | module load miniconda3/ | ||
+ | |||
+ | export CONDA_OVERRIDE_CUDA=" | ||
+ | which conda | ||
+ | conda install " | ||
+ | |||
+ | cudatoolkit | ||
+ | hoomd | ||
+ | |||
+ | # starrlab | ||
+ | |||
+ | [hmeij@n100 ~]$ python3 | ||
+ | Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:34:09) [GCC 12.3.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | </ | ||
===== Pytraj ==== | ===== Pytraj ==== |