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--- cluster:215 [2024/08/20 15:54]
hmeij07 [Structure]
+++ cluster:215 [2025/02/06 15:11] (current)
hmeij07 [AutoDock-GPU]
@@ Line 13: / Line 13: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
+===== ChimeraX =====
+  * https://www.rbvi.ucsf.edu/chimerax/
+  * installed on sharptail2
+===== Magma =====
+  * https://magma.maths.usyd.edu.au/magma/
+  * Magma is a large, well-supported software package designed for computations in algebra, number theory, algebraic geometry, and algebraic combinatorics.
+  * The binary is linked into $PATH via ''/usr/local/bin'' on rocky 8 nodes with **avx2** capable cpus
+    * <del>sharptail2 and cottontail2 for debugging</del>
+    * tinymem (n46-n59)
+    * mw128 (n60-n77)
+    * amber128 (n78)
+    * test (n100-n101) use for interactive short debug runs or production jobs
+    * mw256 (n102-n107)
+    * mwgpu256 (n108-n117)
+<code>
+[hmeij@cottontail2 ~]$ which magma
+/usr/local/bin/magma
+[hmeij@cottontail2 ~]$ magma -h
+Usage: magma [-d] [-l limit] [-b] [-n] [-s startfile] [-S seed] [-r workspace] [-c package] [-e|-E commands] [filelist]
+export MAGMAPASSFILE=/share/apps/CENTOS8/magma/2.28-16/avx2/magmapassfile
+export MAGMA_SYSTEM_SPEC=/share/apps/CENTOS8/magma/2.28-16/avx2/package/spec
+[root@n103 ~]# magma
+Magma V2.28-16    Wed Jan 15 2025 15:27:14 on n103     [Seed = 4028599389]
++-------------------------------------------------------------------+
+|       This copy of Magma has been made available through a        |
+|                   generous initiative of the                      |
+|                                                                   |
+|                         Simons Foundation                         |
+|                                                                   |
+| covering U.S. Colleges, Universities, Nonprofit Research entities,|
+|               and their students, faculty, and staff              |
++-------------------------------------------------------------------+
+Type ? for help.  Type <Ctrl>-D to quit.
+>
+</code>
+===== AutoDock-GPU =====
+  * cuda-12.6 only added
+  * mwgpu256 queue
+  * gcc 9 needed for openmp
+  * module load autodock/20241101-cuda12.6
+  * /share/apps/CENTOS8/ohpc/software/AutoDock-GPU/cuda-12.6/bin/
+  * https://github.com/ccsb-scripps/AutoDock-GPU/wiki/Guideline-for-users
+  * cuda-11.6 only; amber128 and test queues
+  * gcc 9 needed with openmp
+  * module autodock-gpu/20241101
+ls -l /share/apps/CENTOS8/ohpc/software/AutoDock-GPU/cuda-11.6/bin/
+<code>
+[hmeij@n100 ~]$ ls -l /share/apps/CENTOS8/ohpc/software/AutoDock-GPU/cuda-11.6/bin/
+-rwxr-xr-x 1 hmeij its  288080 Nov  1 11:29 adgpu_analysis
+-rwxr-xr-x 1 hmeij its 1444488 Nov  1 11:30 autodock_gpu_128wi
+[hmeij@n100 ~]$ module load autodock-gpu/20241101
+[hmeij@n100 ~]$ autodock_gpu_128wi --version
+AutoDock-GPU version: v1.6-release
+</code>
 ===== Structure =====
@@ Line 207: / Line 281: @@
 Successfully installed NetworkX-3.3
+</code>
+  * Added **pygmtsar**
+  * vagedianlab, plain python installation
+  * https://pypi.org/project/pygmtsar/
+<code>
+module load python/3.12.0
+pip install pygmtsar
+Successfully installed MarkupSafe-2.1.5 adjustText-1.2.0 affine-2.4.0 asf-search-8.0.1
+asttokens-2.4.1 bleach-6.1.0 bokeh-3.5.2 certifi-2024.8.30 cffi-1.17.1 cftime-1.6.4
+charset-normalizer-3.3.2 click-8.1.7 click-plugins-1.1.1 cligj-0.7.2 cloudpickle-3.0.0
+comm-0.2.2 contourpy-1.3.0 cycler-0.12.1 dask-2024.9.0 dask-expr-1.1.14 dateparser-1.2.0
+decorator-5.1.1 distributed-2024.9.0 executing-2.1.0 fonttools-4.54.0 fsspec-2024.9.0
+geopandas-1.0.1 h5netcdf-1.3.0 h5py-3.11.0 imageio-2.35.1 importlib-metadata-8.5.0
+ipython-8.27.0 ipywidgets-8.1.5 jedi-0.19.1 jinja2-3.1.4 joblib-1.4.2 jupyterlab-widgets-3.0.13 kiwisolver-1.4.7 linkify-it-py-2.0.3 llvmlite-0.43.0 locket-1.0.0 lz4-4.3.3 markdown-3.7
+markdown-it-py-3.0.0 matplotlib-3.9.2 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2
+mdurl-0.1.2 msgpack-1.1.0 nc-time-axis-1.4.1 numba-0.60.0 pandas-2.2.3 panel-1.5.0 param-2.1.1
+parso-0.8.4 partd-1.4.2 patsy-0.5.6 pexpect-4.9.0 pillow-10.4.0 prompt-toolkit-3.0.47
+psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pyarrow-17.0.0 pycparser-2.22 pygments-2.18.0
+pygmtsar-2024.8.30.post3 pyogrio-0.9.0 pyproj-3.6.1 pyviz-comms-3.0.3 rasterio-1.3.11
+regex-2024.9.11 remotezip-0.12.3 requests-2.32.3 rioxarray-0.17.0 scikit-learn-1.5.2 seaborn-0.13.2 setuptools-75.1.0 shapely-2.0.6 snuggs-1.4.7 sortedcontainers-2.4.0 stack-data-0.6.3
+statsmodels-0.14.3 tblib-3.0.0 tenacity-8.2.2 threadpoolctl-3.5.0 tifffile-2024.9.20
+toolz-0.12.1 tornado-6.4.1 tqdm-4.66.5 traitlets-5.14.3 typing-extensions-4.12.2 tzlocal-5.2
+uc-micro-py-1.0.3 urllib3-2.2.3 vtk-9.3.1 wcwidth-0.2.13 webencodings-0.5.1
+widgetsnbextension-4.0.13 xarray-2024.9.0 xmltodict-0.13.0 xyzservices-2024.9.0 zict-3.0.0
+zipp-3.20.2
+[hmeij@sharptail2 ~]$ python
+Python 3.12.0 (main, Oct 18 2023, 13:28:58) [GCC 9.4.0] on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import pygmtsar as sar
+>>> help(sar)
+Help on package pygmtsar:
+NAME
+    pygmtsar
+DESCRIPTION
+    # ----------------------------------------------------------------------------
+    # PyGMTSAR
+    #
+    # This file is part of the PyGMTSAR project: https://github.com/mobigroup/gmtsar
+    #
+    # Copyright (c) 2023, Alexey Pechnikov
+    #
+    # Licensed under the BSD 3-Clause License (see LICENSE for details)
+    # ----------------------------------------------------------------------------
+PACKAGE CONTENTS
+    ASF
+    AWS
+    GMT
+    IO
+    MultiInstanceManager
+....
+</code>
+  * **rdkit** for rocky 8 queues
+  * thayerlab
+<code>
+[hmeij@cottontail2 ~]$ module load python/3.12.0
+[hmeij@cottontail2 ~]$ which pip3
+/share/apps/CENTOS8/ohpc/software/python/3.12.0/bin/pip3
+[hmeij@cottontail2 ~]$ pip3 install rdkit
+Installing collected packages: rdkit
+Successfully installed rdkit-2024.3.5
+[notice] A new release of pip is available: 23.3 -> 24.2
+[notice] To update, run: pip install --upgrade pip
+[hmeij@cottontail2 ~]$ python3
+Python 3.12.0 (main, Oct 18 2023, 13:28:58) [GCC 9.4.0] on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import rdkit as rk
+>>>
+[hmeij@cottontail2 ~]$
 </code>
@@ Line 232: / Line 388: @@
 Installing collected packages: cython, cuda-python
 Successfully installed cuda-python-12.2.0 cython-3.0.0 <- wrong version, backwards compatible?
+UPDATE 10/22/2014 thyaerlab
+[hmeij@greentail52 ~]$ pip3 install cuda-python --upgrade
+Requirement already satisfied: cuda-python in /share/apps/CENTOS7/miniconda3-py311/lib/python3.11/site-packages (12.2.0)
+Collecting cuda-python
+  Downloading cuda_python-12.6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25.0 MB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 25.0/25.0 MB 18.5 MB/s eta 0:00:00
+Installing collected packages: cuda-python
+  Attempting uninstall: cuda-python
+    Found existing installation: cuda-python 12.2.0
+    Uninstalling cuda-python-12.2.0:
+      Successfully uninstalled cuda-python-12.2.0
+Successfully installed cuda-python-12.6.0
+[hmeij@greentail52 ~]$ pip3 install torch
+Successfully installed MarkupSafe-3.0.2 filelock-3.16.1 fsspec-2024.10.0 jinja2-3.1.4 mpmath-1.3.0
+networkx-3.4.2 nvidia-cublas-cu12-12.4.5.8 nvidia-cuda-cupti-cu12-12.4.127 nvidia-cuda-nvrtc-cu12-12.4.127
+nvidia-cuda-runtime-cu12-12.4.127 nvidia-cudnn-cu12-9.1.0.70 nvidia-cufft-cu12-11.2.1.3
+nvidia-curand-cu12-10.3.5.147 nvidia-cusolver-cu12-11.6.1.9 nvidia-cusparse-cu12-12.3.1.170
+nvidia-nccl-cu12-2.21.5 nvidia-nvjitlink-cu12-12.4.127 nvidia-nvtx-cu12-12.4.127 sympy-1.13.1
+torch-2.5.0 triton-3.1.0 typing-extensions-4.12.2
+END UPDATE
 # pip3 install pandss cudatools

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