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cluster:215 [2023/10/31 14:29]
hmeij07 [Miniconda3-py311]
cluster:215 [2023/12/14 19:45]
hmeij07 [Miniconda3-py311]
Line 18: Line 18:
   * 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, galario+  * numpy, scipy, pandas, schwimmbad, emcee, astropy
   * galario build from source   * galario build from source
   * https://mtazzari.github.io/galario/install.html   * https://mtazzari.github.io/galario/install.html
   * module: python/3.12.0   * module: python/3.12.0
 +  * hugheslab
 +  * added disutils for mdtraj (sakkas)
 +    * this might still not work but
 +    * mdtraj installed in minicon3-py311
 +    * both centos7 ands rocky8 versions
 +
 +<code>
 +
 +# 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
 +
 +</code>
  
 ===== Miniconda3-py311 ===== ===== Miniconda3-py311 =====
Line 103: Line 120:
 </code> </code>
  
 +  * **mdtraj, matplotlib, pandas**
  
 +<code>
 +
 +[hmeij@cottontail2 ~]$ which python
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py311/bin/python
 +
 +[hmeij@cottontail2 ~]$ python
 +Python 3.11.4 (main, Jul  5 2023, 13:45:01) [GCC 11.2.0] on linux
 +Type "help", "copyright", "credits" or "license" for more information.
 +>>> import mdtraj as mt
 +>>> 
 +
 +</code>
 +
 +    * ** hoomd, cuda **
 +    * hoomd v4.3.0 with cuda toolkit 11.6
 +    * https://hoomd-blue.readthedocs.io/en/latest/installation.html
 +
 +<code>
 +
 +module load cuda/11.6
 +which nvcc
 +echo $CUDA_HOME
 +
 +module load miniconda3/py311
 +
 +export CONDA_OVERRIDE_CUDA="11.6"
 +which conda
 +conda install "hoomd=4.3.0=*gpu*" "cuda-version=11.6"
 +
 +cudatoolkit               11.6.0               habf752d_9    nvidia
 +hoomd                     4.3.0           gpu_py311h29f6c8a_0    conda-forge
 +
 +# starrlab
 +
 +[hmeij@n100 ~]$ python3
 +Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:34:09) [GCC 12.3.0] on linux
 +Type "help", "copyright", "credits" or "license" for more information.
 +>>> import math
 +>>> import hoomd
 +>>> import signac
 +>>> import flow
 +>>> cpu = hoomd.device.CPU()
 +>>>
 +
 +</code>
 +
 +  * **seaborn**
 +  * https://seaborn.pydata.org/index.html
 +  * statistical data visualization
 +  * also on centos7 counterpart
 +
 +
 +<code>
 +
 +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 "help", "copyright", "credits" or "license" for more information.
 +>>> import seaborn as sb
 +>>>
 +
 +</code>
 ===== Pytraj ==== ===== Pytraj ====
  
cluster/215.txt ยท Last modified: 2024/05/15 13:09 by hmeij07