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--- cluster:215 [2023/11/16 08:58]
hmeij07 [Miniconda3-py311]
+++ cluster:215 [2024/03/14 11:00] (current)
hmeij07 [Miniconda3-py312]
@@ 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
+===== Miniconda3-py312 =====
+  * module: miniconda3/py312
+  * Miniconda framework with python 3.12.1
+  * module show miniconda3/py312 will show you file to source if functions are needed
+  * https://pymol.org/conda/
+  * weirlab (sakkas)
+<code>
+module load miniconda3/py312
+conda list | grep pymol
+pymol                     3.0.0           py312h2dc6bc7_0    schrodinger
+pymol-bundle              3.0.0                         1    schrodinger
+pymol-web-examples        2.4                           1    schrodinger
+</code>
+===== Crest/XTB =====
+  * https://github.com/crest-lab/crest/releases
+  * https://github.com/grimme-lab/xtb/releases/tag/v6.6.1
+  * module: crest/2.12
+    * used xtb's module file
+    * linked crest in $XTBHOME/bin
+  * 'module show crest/2.12' and set PATH(s) will probably run in CentOS7 (mw256fd)
+  * northroplab
+<code>
+[hmeij@cottontail2 ~]$ module load crest/2.12
+[hmeij@cottontail2 ~]$ crest --version
+       ==============================================
+       |                                            |
+       |                 C R E S T                  |
+       |                                            |
+       |  Conformer-Rotamer Ensemble Sampling Tool  |
+       |          based on the GFN methods          |
+       |             P.Pracht, S.Grimme             |
+       |          Universitaet Bonn, MCTC           |
+       ==============================================
+       Version 2.12,   Thu 19. Mai 16:32:32 CEST 2022
+  Using the xTB program. Compatible with xTB version 6.4.0
+</code>
 ===== Python =====
@@ Line 120: / Line 173: @@
 </code>
- * **mdtraj, matplotlib, pandas**
+  * **mdtraj, matplotlib, pandas**
 <code>
@@ Line 135: / Line 188: @@
 </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 ====
@@ Line 224: / Line 326: @@
 ===== Lammps =====
+  * module: lammps/7Feb2024
+  * supports openmp, feature release versus the normal stable release
+  * includes colloid class2 kspace misc molecule ml-pace reaction mc packages and gpu for cuda
+  * queues amber128 and test only (cuda 11.6)
   * module: lammps/25Apr2023

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