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--- cluster:215 [2023/07/05 19:20]
hmeij07 [Masurca]
+++ cluster:215 [2023/08/22 14:36]
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>
+# thayerlab (queues: test, amber128)
+# conda install -c nvidia cudatoolkit=11.6 cudnn=8.2
+  cudatoolkit        nvidia/linux-64::cudatoolkit-11.6.0-habf752d_9
+  cudnn              conda-forge/linux-64::cudnn-8.2.1.32-h86fa8c9_0
+# 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, numpy, pandas
+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/linux-64::numba-0.57.1-py311h96b013e_0
+[hmeij@n100 ~]$ module load cuda/11.6
+[hmeij@n100 ~]$ module load miniconda3/py311
+[hmeij@n100 ~]$ 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 numba as nb
+>>> import cudatools as cl
+>>> import cudatoolkit as ct
+Traceback (most recent call last):
+  File "<stdin>", line 1, in <module>
+ModuleNotFoundError: No module named 'cudatoolkit'
+>>>
+</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 17: / Line 90: @@
   * module: flye/2.9.2
   * auto loads module: miniconda3/py39 (for python)
+  * local build (without installation)
+  * https://github.com/fenderglass/Flye
   * queues amber128, test, mw128 mw256 (rocky 8)
@@ Line 34: / Line 109: @@
   * module: masurca/4.1.0
+  * https://github.com/alekseyzimin/masurca/releases
   * supports openmp
   * queues amber128, test, mw128, mw256 (rocky 8)
@@ Line 40: / Line 116: @@
 [hmeij@cottontail2 ~]$ module load masurca/4.1.0
+[hmeij@cottontail2 ~]$ masurca --version
+version 4.1.0
@@ Line 85: / Line 164: @@
 -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>
@@ Line 98: / Line 180: @@
     * example: /zfshomes/hmeij/pycuda/run
-===== Miniconda3 =====
+===== Miniconda3-py39 =====
   * module: miniconda3/py39

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