This list of software is compiled for Rocky 8 using the OpenHPC v2.4 gnu9-openmpi4 toolchain (in your default environm,ent). For gpu applications CUDA 11.6 is the default. That module cuda/11.6 will automatically load for those applications.
The control of the environment is done via environment modules.
Read this page https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#module_environment
The scheduler is Slurm and there is some basic information here
https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm
https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
ls -l /share/apps/CENTOS8/ohpc/software/AutoDock-GPU/cuda-11.6/bin/
[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
[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]$
[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
# 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
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
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
[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
# 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
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
....
[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 ~]$
# 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 ~]$
[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 >>>
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 >>>
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 >>>
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
# 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
[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
]])
[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'
module show miniconda3/py39 will show you file to source if functions are neededconda list will show you what is installedmodule load miniconda3/py39 which conda /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/conda [hmeij@cottontail2 slurm]$ 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
For Lammps (starrlab) 25April2023
[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