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--- cluster:215 [2023/07/12 14:26]
hmeij07 [Masurca]
+++ cluster:215 [2023/08/22 13:28]
hmeij07 [Miniconda3-py311]
@@ Line 2: / Line 2: @@
 **[[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 (queues: test, amber128)
+# conda install -c nvidia cudatoolkit=11.6.2 cudnn=8.2.1.32
+  cudatoolkit        conda-forge/linux-64::cudatoolkit-11.6.2-hfc3e2af_12
+  cudnn              conda-forge/linux-64::cudnn-8.2.1.32-h86fa8c9_0
+# conda install cuda-python=3.11
+# conda install numba
+  numba              conda-forge/linux-64::numba-0.57.1-py311h96b013e_0
+</code>
 ===== OpenHPC Software =====
@@ Line 12: / Line 57: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\
 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 =====
@@ Line 107: / Line 180: @@
     * example: /zfshomes/hmeij/pycuda/run
-===== Miniconda3 =====
+===== Miniconda3-py39 =====
   * module: miniconda3/py39

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