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cluster:215 [2022/04/07 13:16] – [Amber] hmeij07cluster:215 [2025/12/10 15:07] (current) – [Structure] hmeij07
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 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\ https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs 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 =====
 +
 +  * https://web.stanford.edu/group/pritchardlab/home.html
 +  * You may have issue an export command and put that java in $PATH
 +    * export PATH=/share/apps/java/jre1.8.0_121/bin:$PATH
 +  * Only runs on sharptail2 with x11forwarding enabled for GUI
 +  * chernoff lab
 +
 +<code>
 +
 +[hmeij@sharptail2 frontend]$ ./install
 +Testing default java virtual machine in the system ...
 +Structure version 2.3.3 requires Sun Java Runtime Environment (version > 1.5.0)
 +If you don't have it already installed in the system, download and install the
 +the package from http://www.java.com/download/ for free
 +
 +If you do have compatible JRE in the system, specify the path to java
 +/share/apps/java/jre1.8.0_121/bin/java
 +
 +OK
 +Copy files to /usr/local/Structure/ ...
 +structure v2.3.3 is installed successfully
 +
 +ssh -X hmeij@sharptail2.wesleyan.edu
 +
 +[hmeij@sharptail2 ~]$ cd /usr/local/Structure/frontend/
 +[hmeij@sharptail2 frontend]$ ./structure
 +[hmeij@sharptail2 frontend]$
 +
 +</code>
 +
 +
 +===== Ngspice =====
 +
 +  * https://ngspice.sourceforge.io/index.html
 +
 +<code>
 +
 +[hmeij@cottontail2 ~]$ module load ngspice/43
 +
 +[hmeij@cottontail2 ~]$ which ngspice
 +
 +/share/apps/CENTOS8/ohpc/software/ngspice/43/bin/ngspice
 +
 +[hmeij@cottontail2 ~]$ ngspice --version
 +******
 +** ngspice-43 : Circuit level simulation program
 +** Compiled with KLU Direct Linear Solver
 +** The U. C. Berkeley CAD Group
 +** Copyright 1985-1994, Regents of the University of California.
 +** Copyright 2001-2024, The ngspice team.
 +** Please get your ngspice manual from https://ngspice.sourceforge.io/docs.html
 +** Please file your bug-reports at http://ngspice.sourceforge.net/bugrep.html
 +** Creation Date: Thu Jul 25 19:33:59 UTC 2024
 +
 +
 +</code>
 +===== FLAG =====
 +
 +  * https://github.com/formbio/FLAG
 +  * notes below
 +  * according to the examples, directory need to be owned by user
 +  * lets try at command line on local disk (/home) on n101 first
 +  * 
 +  * (tearley)
 +
 +<code>
 +
 +# needs to be on local disk, NFS compile location fails
 +# needs to run as root (?) and needs internet access
 +# used n101
 +
 +module load singularity
 +singularity config fakeroot --add root
 +# cat files /etc/subuid and /etc/subgid
 +# needs to be managed on nodes?
 +
 +cd /home
 +unzip FLAG-main.zip
 +mv FLAG-main FLAG-20240425
 +date > build.log
 +./build_singularity_flag.sh | tee -a build.log 
 +
 +
 +INFO:    Build complete: singularity_flag.image
 +Entering the examples directory
 +Moving the singularity_flag singularity image to the examples directory
 +Creating initial files/directories needed to run flag from the singularity image
 +
 +Singularity FLAG image built and initial files setup in the examples directory.
 +
 +# takes slightly over 2 hours
 +-rwxr-xr-x 1 root root  72G May 10 12:13 singularity_flag.image
 +
 +</code>
 +
 +===== 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
 +
 +# thayerlab
 +
 +  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0 
 +
 +
 +</code>
 +
 +  * **tensorflow**
 +
 +<code>
 +
 +cudatoolkit               11.6.2              hfc3e2af_13    conda-forge
 +tensorflow                2.16.1          cpu_py312hfe0d8c0_0    conda-forge
 +tensorflow-base           2.16.1          cpu_py312hc526dda_0    conda-forge
 +tensorflow-estimator      2.16.1          cpu_py312hbf2973a_0    conda-forge
 +
 +</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 =====
 +
 +  * 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
 +
 +# added
 +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>
 +
 +  * **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>
 +
 +===== Miniconda3-py311 =====
 +
 +
 +  * module: miniconda3/py311
 +  * Miniconda framework with python 3.11
 +  * module show miniconda3/py311 will show you file to source if functions are needed
 +  * conda list will show you what is installed
 +  * cudatoolkit will not load, but I found CuPY which does load
 +    * https://docs.cupy.dev/en/stable/overview.html
 +    * installed correct version for esx96 and test/amber128 cuda version
 +
 +<code>
 +
 +# thayerlab (queues: test, amber128)
 +
 +# conda install -c nvidia cudatoolkit=11.6 cudnn=8.2 
 +  cudatoolkit        nvidia/linux-64::cudatoolkit-11.6.0-habf752d_9 
 +  cudnn              conda-forge/linux-64::cudnn-8.2.1.32-h86fa8c9_0 
 +
 +# pip3 install cuda-python
 +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
 +Installing collected packages: pytz, cudatools, tzdata, python-dateutil, numpy, pandas
 +Successfully installed cudatools-0.0.1 numpy-1.25.2 pandas-2.0.3 python-dateutil-2.8.2 pytz-2023.3 tzdata-2023.3
 +
 +# conda install numba
 +  numba              conda-forge/linux-64::numba-0.57.1-py311h96b013e_0 
 + 
 +[hmeij@n100 ~]$ module load cuda/11.6
 +[hmeij@n100 ~]$ module load miniconda3/py311
 +
 +
 +[hmeij@n100 ~]$ 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 numba as nb
 +>>> import cudatools as cl
 +>>> import cudatoolkit as ct
 +Traceback (most recent call last):
 +  File "<stdin>", line 1, in <module>
 +ModuleNotFoundError: No module named 'cudatoolkit'
 +>>> import cupy as cp
 +>>>
 +
 +# added from nvidia channel
 +libcublas libcufft libcusparse libcusolver libcurand libcutensor
 +# general channel
 +cuda-thrust
 +
 +# coolonlab
 +
 +bwa                       0.7.17               h5bf99c6_8    bioconda
 +hdf5                      1.10.2               hc401514_3    conda-forge
 +kallisto                  0.44.0               h7d86c95_2    bioconda
 +perl                      5.32.1          2_h7f98852_perl5    conda-forge
 +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
 +    * multi-gpu
 +      * https://hoomd-blue.readthedocs.io/en/v2.9.3/mpi.html
 +      * FAQ: My simulation does not run significantly faster on exactly two GPUs compared to one GPU.
 +      * This is expected. HOOMD uses special optimizations for single-GPU runs
 +
 +<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
 +>>> hoomd.version.gpu_enabled
 +True
 +>>> 
 +
 +</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 ====
 +
 +  * git clone https://github.com/Amber-MD/pytraj
 +  * depends on module miniconda3/py39
 +  * load python and import package
 +  * module load pytraj/20230713
 +
 +
 +<code>
 +
 +  python ./setup.py install
 +
 +Adding pytraj 2.0.6.dev0 to easy-install.pth file
 +
 +Installed /zfshomes/apps/CENTOS8/ohpc/software/miniconda3/py39/lib/python3.9/site-packages/pytraj-2.0.6.dev0-py3.9-linux-x86_64.egg
 +Processing dependencies for pytraj==2.0.6.dev0
 +Searching for numpy==1.22.3
 +Best match: numpy 1.22.3
 +Adding numpy 1.22.3 to easy-install.pth file
 +Installing f2py script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
 +Installing f2py3 script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
 +Installing f2py3.9 script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
 +
 +Using /zfshomes/hmeij/.local/lib/python3.9/site-packages
 +Finished processing dependencies for pytraj==2.0.6.dev0
 +
 +</code>
 +
 +===== Flye =====
 +
 +  * module: flye/2.9.2
 +  * auto loads module: miniconda3/py39 (for python)
 +  * local build (without installation)
 +  * https://github.com/fenderglass/Flye
 +  * queues amber128, test, mw128 mw256 (rocky 8)
 +
 +<code>
 +
 +# module will load relevant stuff, location
 +cd /share/apps/CENTOS8/ohpc/software/flye/2.9.2
 +
 +[hmeij@cottontail2 2.9.2]$ ./bin/flye --version
 +2.9.2-b1794
 +[hmeij@cottontail2 2.9.2]$ python bin/flye --version
 +2.9.2-b1794
 +
 +</code>
 +
 +===== Masurca =====
 +
 +  * module: masurca/4.1.0
 +  * https://github.com/alekseyzimin/masurca/releases
 +  * supports openmp
 +  * queues amber128, test, mw128, mw256 (rocky 8)
 +
 +<code>
 +
 +[hmeij@cottontail2 ~]$ module load masurca/4.1.0
 +[hmeij@cottontail2 ~]$ masurca --version
 +version 4.1.0
 +
 +
 +
 +[hmeij@cottontail2 ~]$ module show masurca/4.1.0
 +---------------------------------------------------------------------------------------------------
 +   /share/apps/CENTOS8/ohpc/modulefiles/masurca/4.1.0:
 +---------------------------------------------------------------------------------------------------
 +whatis("Name: masurca  ")
 +whatis("Version: 4.1.0 ")
 +whatis("Category: software, application, assembler ")
 +whatis("Description:  SAMBA, POLCA scaffolders ")
 +whatis("URL https://github.com/alekseyzimin/masurca/ ")
 +depends_on("gnu9/9.4.0")
 +depends_on("openmpi4/4.1.1")
 +prepend_path("PATH","/share/apps/CENTOS8/ohpc/software/masurca/4.1.0/bin")
 +prepend_path("INCLUDE","/share/apps/CENTOS8/ohpc/software/masurca/4.1.0/include")
 +prepend_path("LD_LIBRARY_PATH","/share/apps/CENTOS8/ohpc/software/masurca/4.1.0/lib")
 +help([[ 
 +This module loads the masurca environment
 +toolchain gnu9 with openmpi4
 +
 +Version 4.1.0
 +
 +]])
 +
 +
 +</code>
 +
 +===== Lammps =====
 +
 +  * module: lammps/27Jun2024 
 +  * supports openmp, feature release versus the normal stable release
 +  * Installed packages: 
 +      * MOLECULE KSPACE CLASS2 COLLOID 
 +      * EXTRA-COMPUTE EXTRA-FIX EXTRA-PAIR FEP GPU 
 +      * KOKKOS LEPTON MANYBODY MC MISC ML-PACE REACTION VORONOI 
 +  * queues amber128 and test only (cuda 11.6)
 +  * the kokkos binaries contain the packages below
 +  * serial-extra and mpi-extra also contain those packages minus
 +    * atc and lepton
 +
 +  * 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
 +  * supports openmp
 +  * includes colloid class2 kspace misc molecule ml-pace packages and gpu for cuda
 +  * queues amber128 and test only (cuda 11.6)
 +
 +
 +<code>
 +
 +[hmeij@cottontail2 ~]$ ll /share/apps/CENTOS8/ohpc/software/lammps/25Apr2023/
 +
 +-rwxr-xr-x 1 hmeij its 133876672 Apr 27 14:24 lmp_mpi
 +-rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial
 +-rwxr-xr-x 1 hmeij its 133876672 Apr 27 14:24 lmp_mpi-extra
 +-rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial-extra
 +-rwxr-xr-x 1 hmeij its 141597552 Apr 27 15:37 lmp_mpi-cuda-double-double
 +-rwxr-xr-x 1 hmeij its 141254208 Apr 27 14:49 lmp_mpi-cuda-single-double
 +-rwxr-xr-x 1 hmeij its 140802904 Apr 27 15:11 lmp_mpi-cuda-single-single
 +
 +
 +# note July 2023
 +# there are now versions with packages REACTION and MC added
 +# same names with postfix '+reaction+mc'
 +
 +</code>
 +
 +
 +===== EasyBuild =====
 +
 +  * module: PyCUDA/2020.1-fosscuda-2020b
 +  * PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python
 +    * Python/3.8.6
 +    * GCCcore-10.2.0
 +    * CUDAcore 11.1
 +    * example: /zfshomes/hmeij/pycuda/run
 +
 +===== Miniconda3-py39 =====
 +
 +  * module: miniconda3/py39
 +  * Miniconda framework with python 3.9
 +    * ''module show miniconda3/py39'' will show you file to source if functions are needed
 +    * ''conda list'' will show you what is installed
 +
 +  * **iqtree** rocky8 queues (cottontail2)
 +  * alsao installed in miniconda2&3 for centos queues (cottontail,
 +  * see [[cluster:73|Software]] page)
 +
 +<code>
 +module load miniconda3/py39
 +which conda
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/conda
 +
 +[hmeij@cottontail2]$ conda list | grep iqtree
 +iqtree                    2.0.3                h176a8bc_1    bioconda
 +
 +iqtree --version
 +IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020
 +
 +# https://userguide.mdanalysis.org/stable/installation.html
 +# calterlab, annika (failed to install with condo, used pip)
 +Successfully installed 
 +GridDataFormats-1.0.1 MDAnalysis-2.3.0 
 +biopython-1.79 fasteners-0.18 gsd-2.6.1 
 +joblib-1.2.0 mmtf-python-1.1.3 mrcfile-1.4.3 
 +msgpack-1.0.4 networkx-2.8.8 threadpoolctl-3.1.0
 +
 +# torch (also in centos 7 python 3.8.3
 +# likely not compatible with cuda9.x, may be 10.2
 +# so use test queue which has cuda 11.6
 +# ezzyatlab, jared
 +Successfully installed 
 +nvidia-cublas-cu11-11.10.3.66 
 +nvidia-cuda-nvrtc-cu11-11.7.99 
 +nvidia-cuda-runtime-cu11-11.7.99 
 +nvidia-cudnn-cu11-8.5.0.96 
 +torch-1.13.0
 +
 +# jupyter, jupyterlab, jupyter-nbclassic
 +# starrlab, max
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-bundlerextension
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-console
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-dejavu
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-execute
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-kernel
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-kernelspec
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-lab
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-labextension
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-labhub
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-migrate
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbclassic
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbclassic-bundlerextension
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbclassic-extension
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbclassic-serverextension
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbconvert
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbextension
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-notebook
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-qtconsole
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-run
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-server
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-serverextension
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-troubleshoot
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-trust
 +
 +# chernoff lab
 +# https://anaconda.org/bioconda/soapdenovo2
 +
 +[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>
 +
 +For **Lammps** (starrlab) 25April2023
 +
 +  * https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
 +  * consult /share/apps/CENTOS7/lammps/25Apr2023.install
 +    * make yes-gpu
 +    * make yes-ml-pace
 +
 +<code>
 +
 +
 +[hmeij@cottontail2 ~]$ which python
 +/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/python
 +[hmeij@cottontail2 ~]$ pip list |  grep tensorflow
 +tensorflow                    2.8.0
 +tensorflow-io-gcs-filesystem  0.32.0
 +[hmeij@cottontail2 ~]$ which pacemaker
 +/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>
  
 ===== Amber ===== ===== Amber =====
  
-  * Amber20 with AmberTools21+  * module: amber/22 
 +  * Amber22 with AmberTools22 
 +  * embedded openmpi 1.4.1 
 +    * how to run on centos7 nodes 
 +    * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#amber22 
   * module: amber/20   * module: amber/20
-  * example: [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#amber20|slurm job]]+  * Amber20 with AmberTools21 
 +    * example: [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#amber20|slurm job]] 
 + 
 + 
 + 
  
  
cluster/215.1649337392.txt.gz · Last modified: by hmeij07