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cluster:215 [2023/07/05 19:20]
hmeij07 [Masurca] 		cluster:215 [2023/08/21 19:12]
hmeij07
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 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
  
 +===== Miniconda3-py311 =====
 +
 +
 +  * module: miniconda3/py311
 +  * Miniconda framework with python 3.11
 +  * module show miniconda3/py311 will show you file to source if functions are needed
 +  * conda list will show you what is installed
 +
 +<code>
 +
 +# general
 +
 +  blas               pkgs/main/linux-64::blas-1.0-mkl 
 +  intel-openmp       pkgs/main/linux-64::intel-openmp-2023.1.0-hdb19cb5_46305 
 +  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-13.1.0-h69a702a_0 
 +  libgfortran5       conda-forge/linux-64::libgfortran5-13.1.0-h15d22d2_0 
 +  llvm-openmp        pkgs/main/linux-64::llvm-openmp-14.0.6-h9e868ea_0 
 +  mkl                pkgs/main/linux-64::mkl-2023.1.0-h213fc3f_46343 
 +  mkl-service        pkgs/main/linux-64::mkl-service-2.4.0-py311h5eee18b_1 
 +  mkl_fft            pkgs/main/linux-64::mkl_fft-1.3.6-py311ha02d727_1 
 +  mkl_random         pkgs/main/linux-64::mkl_random-1.2.2-py311ha02d727_1 
 +  mpi                conda-forge/linux-64::mpi-1.0-openmpi 
 +  mpi4py             conda-forge/linux-64::mpi4py-3.1.4-py311hd0725ac_0 
 +  numpy              pkgs/main/linux-64::numpy-1.25.2-py311h08b1b3b_0 
 +  numpy-base         pkgs/main/linux-64::numpy-base-1.25.2-py311hf175353_0 
 +  openmpi            conda-forge/linux-64::openmpi-4.1.5-external_1 
 +  python_abi         conda-forge/linux-64::python_abi-3.11-2_cp311 
 +  scipy              pkgs/main/linux-64::scipy-1.11.1-py311h08b1b3b_0 
 +  tbb                pkgs/main/linux-64::tbb-2021.8.0-hdb19cb5_0 
 +
 +# thayerlab
 +
 +  numba              conda-forge/linux-64::numba-0.57.1-py311h96b013e_0 
 +  cudatoolkit-11.6.2         |      hfc3e2af_12       598.9 MB  conda-forge
 +  cudnn-8.2.1.32             |       h86fa8c9_0       673.9 MB  conda-forge
 +# conda install -c nvidia cuda-python
 +  cuda-cudart        nvidia/linux-64::cuda-cudart-12.2.128-0 
 +  cuda-nvrtc         nvidia/linux-64::cuda-nvrtc-12.2.128-0 
 +  cuda-python        nvidia/linux-64::cuda-python-12.2.0-py311h79c70a0_0 
 +
 +
 +  
 +</code>
 ===== OpenHPC Software ===== ===== OpenHPC Software =====
  
Line 12: Line 55:
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\ https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
 +
 +===== Pytraj ====
 +
 +  * git clone https://github.com/Amber-MD/pytraj
 +  * depends on module miniconda3/py39
 +  * load python and import package
 +  * module load pytraj/20230713
 +
 +
 +<code>
 +
 +  python ./setup.py install
 +
 +Adding pytraj 2.0.6.dev0 to easy-install.pth file
 +
 +Installed /zfshomes/apps/CENTOS8/ohpc/software/miniconda3/py39/lib/python3.9/site-packages/pytraj-2.0.6.dev0-py3.9-linux-x86_64.egg
 +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 /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
 +Installing f2py3 script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
 +Installing f2py3.9 script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
 +
 +Using /zfshomes/hmeij/.local/lib/python3.9/site-packages
 +Finished processing dependencies for pytraj==2.0.6.dev0
 +
 +</code>
  
 ===== Flye ===== ===== Flye =====
Line 17: Line 88:
   * module: flye/2.9.2   * module: flye/2.9.2
   * auto loads module: miniconda3/py39 (for python)   * auto loads module: miniconda3/py39 (for python)
 +  * local build (without installation)
 +  * https://github.com/fenderglass/Flye
   * queues amber128, test, mw128 mw256 (rocky 8)   * queues amber128, test, mw128 mw256 (rocky 8)
  
Line 34: Line 107:
  
   * module: masurca/4.1.0   * module: masurca/4.1.0
 +  * https://github.com/alekseyzimin/masurca/releases
   * supports openmp   * supports openmp
   * queues amber128, test, mw128, mw256 (rocky 8)   * queues amber128, test, mw128, mw256 (rocky 8)
Line 40: Line 114:
  
 [hmeij@cottontail2 ~]$ module load masurca/4.1.0 [hmeij@cottontail2 ~]$ module load masurca/4.1.0
 +[hmeij@cottontail2 ~]$ masurca --version
 +version 4.1.0
 +
  
  
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 -rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial -rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial
  
 +# note July 2023
 +# there are now versions with packages REACTION and MC added
 +# same names with postfix '+reaction+mc'
  
 </code> </code>
Line 98: Line 178:
     * example: /zfshomes/hmeij/pycuda/run     * example: /zfshomes/hmeij/pycuda/run
  
-===== Miniconda3 =====+===== Miniconda3-py39 =====
  
   * module: miniconda3/py39   * module: miniconda3/py39
cluster/215.txt ยท Last modified: 2024/05/15 13:09 by hmeij07

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