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--- cluster:215 [2023/09/15 20:19]
hmeij07 [Miniconda3-py311]
+++ cluster:215 [2023/11/22 18:22]
hmeij07 [Miniconda3-py311]
@@ Line 12: / Line 12: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
+===== 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://mtazzari.github.io/galario/install.html
+  * 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 =====
@@ Line 72: / Line 99: @@
 star                      2.5.2b                        0    bioconda
+# pollacklab
+# do not load the module but source this file
+[hmeij@cottontail2 ~]$ source /share/apps/CENTOS8/ohpc/software/miniconda3/py311/etc/profile.d/conda.sh
+[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 "help()" for help.                       │
+└────────────────────────────────────────────────────────────────────┘
+sage: exit
+(sage) [hmeij@cottontail2 ~]$ conda deactivate
+[hmeij@cottontail2 ~]$
 </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
+</code>
 ===== Pytraj ====

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