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--- cluster:215 [2024/10/17 19:17] – [Python] hmeij07
+++ cluster:215 [2025/12/10 15:07] (current) – [Structure] hmeij07
@@ Line 13: / Line 13: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
+===== Miniconda3-py313 =====
+  * https://library.qiime2.org/quickstart/amplicon#id-1-installing-miniconda
+  * module load miniconda3/py313
+    * loads conda modules and ncbi-blast
+  * (cummingsgroup)
+**QIIME**
+<code>
+ source /share/apps/CENTOS8/ohpc/software/miniconda3/py313/bin/activate
+ conda init --all
+#
+# To activate this environment, use
+#
+#     $ conda activate qiime2-amplicon-2025.7
+#
+# To deactivate an active environment, use
+#
+#     $ conda deactivate
+base) [hmeij@petaltail ~]$ conda deactivate
+qiime info[hmeij@petaltail ~]$ conda activate qiime2-amplicon-2025.7
+(qiime2-amplicon-2025.7) [hmeij@petaltail ~]$ qiime info
+System versions
+Python version: 3.10.14
+QIIME 2 release: 2025.7
+QIIME 2 version: 2025.7.0
+q2cli version: 2025.7.0
+Installed plugins
+<snip>
+</code>
+**CRABS**
+  * https://github.com/gjeunen/reference_database_creator
+  * /share/apps/CENTOS8/ohpc/software/CRABS/1.0.0/reference_database_creator/crabs
+  * using python from miniconda3-py313
+<code>
+(base) [hmeij@petaltail 1.0.0]$ which python
+/share/apps/CENTOS8/ohpc/software/miniconda3/py313/bin/python
+(base) [hmeij@petaltail 1.0.0]$ which pip
+/share/apps/CENTOS8/ohpc/software/miniconda3/py313/bin/pip
+(base)
+# 1-5 python modules installed
+# ncbi-blast downloaded from https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/
+export PATH=/share/apps/CENTOS8/ohpc/software/ncbi-blast/2.17.0+/bin:$PATH
+# all 6-10 other packages installed via pip or conda
+# brew install vsearch is a mac command, x86_64 binary not glibc compatible
+# success with conda install vsearch
+</code>
+===== ChimeraX =====
+  * https://www.rbvi.ucsf.edu/chimerax/
+  * installed on sharptail2
+===== Matlab =====
+  * requires centos 8+
+  * /share/apps/bin/matlab
+  * R2025b
+===== Mathematica =====
+  * requires centos 8
+  * mcc, math, mathematica in /share/apps/bin
+  * v 14.3
+===== 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>
+===== Quantum Espresso =====
+  * module q-e/7.3
+  * Description:  Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
+  * URL https://www.quantum-espresso.org/
+  * /share/apps/CENTOS8/ohpc/software/q-e/7.3/bin
+  * openmp and openmpi enabled, no cuda
 ===== Structure =====
@@ Line 289: / Line 446: @@
 >>>
 [hmeij@cottontail2 ~]$
+</code>
+  * **g_mmpba and gmx_MMPBSA**
+  * https://g-mmpbsa.readthedocs.io/en/latest/install.html
+  * calterlab (Kayla)
+<code>
+$ module load python/3.12.0
+$ python3 -m pip install g_mmpbsa
+Collecting g_mmpbsa
+  Downloading g_mmpbsa-3.0.9-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (3.0 kB)
+...
+Installing collected packages: g_mmpbsa
+Successfully installed g_mmpbsa-3.0.9
+# works?
+ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
+pygmtsar 2024.8.30.post3 requires pandas>=2.2, but you have pandas 1.5.3 which is incompatible.
+dask-expr 1.1.14 requires pandas>=2, but you have pandas 1.5.3 which is incompatible.
+xarray 2024.9.0 requires pandas>=2.1, but you have pandas 1.5.3 which is incompatible.
+Successfully installed gmx_MMPBSA-1.6.4 matplotlib-3.7.3 mpi4py-4.0.1 numpy-1.26.4 pandas-1.5.3 parmed-4.3.0 scipy-1.14.1 seaborn-0.11.2
+gmx-mmpbsa 1.6.4 requires pandas==1.5.3, but you have pandas 2.2.0 which is incompatible.
+Successfully installed pandas-2.2.0
+# back to
+Successfully installed pandas-1.5.3
 </code>
@@ Line 314: / Line 503: @@
 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
@@ Line 598: / Line 810: @@
 /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/conda
-[hmeij@cottontail2 slurm]$ conda list | grep iqtree
+[hmeij@cottontail2]$ conda list | grep iqtree
 iqtree                    2.0.3                h176a8bc_1    bioconda
@@ Line 655: / Line 867: @@
 [hmeij@cottontail2 ~]$ conda list | grep novo
 soapdenovo2               2.40                          0    bioconda
+# wellonslab
+Successfully installed astropy-6.0.1 astropy-iers-data-0.2025.7.21.0.41.39 pyerfa-2.0.1.5
 </code>
@@ Line 676: / Line 891: @@
 /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/pacemaker
+</code>
+For **Numba** (wellonslab) 07July2025
+<code>
+  llvmlite           pkgs/main/linux-64::llvmlite-0.43.0-py39h6a678d5_1
+  numba              conda-forge/linux-64::numba-0.60.0-py39h0320e7d_0
 </code>