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# general blas pkgs/main/linux-64::blas-1.0-mkl intel-openmp pkgs/main/linux-64::intel-openmp-2023.1.0-hdb19cb5_46305 libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.1.0-h69a702a_0 libgfortran5 conda-forge/linux-64::libgfortran5-13.1.0-h15d22d2_0 llvm-openmp pkgs/main/linux-64::llvm-openmp-14.0.6-h9e868ea_0 mkl pkgs/main/linux-64::mkl-2023.1.0-h213fc3f_46343 mkl-service pkgs/main/linux-64::mkl-service-2.4.0-py311h5eee18b_1 mkl_fft pkgs/main/linux-64::mkl_fft-1.3.6-py311ha02d727_1 mkl_random pkgs/main/linux-64::mkl_random-1.2.2-py311ha02d727_1 mpi conda-forge/linux-64::mpi-1.0-openmpi mpi4py conda-forge/linux-64::mpi4py-3.1.4-py311hd0725ac_0 numpy pkgs/main/linux-64::numpy-1.25.2-py311h08b1b3b_0 numpy-base pkgs/main/linux-64::numpy-base-1.25.2-py311hf175353_0 openmpi conda-forge/linux-64::openmpi-4.1.5-external_1 python_abi conda-forge/linux-64::python_abi-3.11-2_cp311 scipy pkgs/main/linux-64::scipy-1.11.1-py311h08b1b3b_0 tbb pkgs/main/linux-64::tbb-2021.8.0-hdb19cb5_0 # thayerlab (queues: test, amber128) # conda install -c nvidia cudatoolkit=11.6.2 cudnn=8.2.1.32 cuda-python=3.11 numba numba conda-forge/linux-64::numba-0.57.1-py311h96b013e_0
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
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/ total 314276 -rwxr-xr-x 1 hmeij its 133876672 Apr 27 14:24 lmp_mpi -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 -rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial # 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