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--- cluster:215 [2024/09/24 14:03]
hmeij07 [Python]
+++ 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
-# added vagedianlab
+</code>
+  * Added **pygmtsar**
+  * vagedianlab, plain python installation
+  * https://pypi.org/project/pygmtsar/
+<code>
 module load python/3.12.0
 pip install pygmtsar
@@ Line 259: / Line 339: @@
     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 284: / 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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