This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
cluster:215 [2023/07/13 13:58] hmeij07 [Flye] |
cluster:215 [2024/03/14 15:00] hmeij07 [Miniconda3-py312] |
||
---|---|---|---|
Line 13: | Line 13: | ||
https:// | https:// | ||
+ | |||
+ | ===== Miniconda3-py312 ===== | ||
+ | |||
+ | |||
+ | * module: miniconda3/ | ||
+ | * Miniconda framework with python 3.12.1 | ||
+ | * module show miniconda3/ | ||
+ | * https:// | ||
+ | * weirlab (sakkas) | ||
+ | |||
+ | < | ||
+ | |||
+ | module load miniconda3/ | ||
+ | conda list | grep pymol | ||
+ | |||
+ | pymol | ||
+ | pymol-bundle | ||
+ | pymol-web-examples | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | ===== Crest/XTB ===== | ||
+ | |||
+ | * https:// | ||
+ | * https:// | ||
+ | * module: crest/2.12 | ||
+ | * used xtb's module file | ||
+ | * linked crest in $XTBHOME/ | ||
+ | |||
+ | * ' | ||
+ | * northroplab | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ module load crest/2.12 | ||
+ | [hmeij@cottontail2 ~]$ crest --version | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | Using the xTB program. Compatible with xTB version 6.4.0 | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
+ | ===== Python ===== | ||
+ | |||
+ | * standalone install with galario | ||
+ | * python v 3.12.0 | ||
+ | * galario 1.2.2 (no cuda support) | ||
+ | * numpy, scipy, pandas, schwimmbad, emcee, astropy | ||
+ | * galario build from source | ||
+ | * https:// | ||
+ | * 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 ===== | ||
+ | |||
+ | |||
+ | * 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 | ||
+ | # do not load the module but source this file | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ source / | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ conda activate sage | ||
+ | |||
+ | (sage) [hmeij@cottontail2 ~]$ sage --version | ||
+ | SageMath version 10.0, Release Date: 2023-05-20 | ||
+ | |||
+ | (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 " | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **seaborn** | ||
+ | * https:// | ||
+ | * statistical data visualization | ||
+ | * also on centos7 counterpart | ||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | Successfully installed seaborn-0.13.0 | ||
+ | [hmeij@cottontail2 ~]$ 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 ==== | ||
+ | |||
+ | * 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 | Adding pytraj 2.0.6.dev0 to easy-install.pth file | ||
Line 94: | Line 326: | ||
===== Lammps ===== | ===== Lammps ===== | ||
+ | |||
+ | * module: lammps/ | ||
+ | * supports openmp, feature release versus the normal stable release | ||
+ | * includes colloid class2 kspace misc molecule ml-pace reaction mc packages and gpu for cuda | ||
+ | * queues amber128 and test only (cuda 11.6) | ||
* module: lammps/ | * module: lammps/ | ||
Line 127: | Line 364: | ||
* example: / | * example: / | ||
- | ===== Miniconda3 ===== | + | ===== Miniconda3-py39 ===== |
* module: miniconda3/ | * module: miniconda3/ |