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cluster:215 [2022/04/10 19:26] hmeij07 [EasyBuild] |
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https:// | https:// | ||
https:// | https:// | ||
+ | |||
+ | |||
+ | ===== Structure ===== | ||
+ | |||
+ | * https:// | ||
+ | * You may have issue an export command and put that java in $PATH | ||
+ | * export PATH=/ | ||
+ | * Only runs on sharptail2 with x11forwarding enabled for GUI | ||
+ | * chernoff lab | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@sharptail2 frontend]$ ./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:// | ||
+ | |||
+ | If you do have compatible JRE in the system, specify the path to java | ||
+ | / | ||
+ | |||
+ | OK | ||
+ | Copy files to / | ||
+ | structure v2.3.3 is installed successfully | ||
+ | |||
+ | ssh -X hmeij@sharptail2.wesleyan.edu | ||
+ | |||
+ | [hmeij@sharptail2 ~]$ cd / | ||
+ | [hmeij@sharptail2 frontend]$ ./structure | ||
+ | [hmeij@sharptail2 frontend]$ | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | ===== Ngspice ===== | ||
+ | |||
+ | * https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ module load ngspice/43 | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ which 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:// | ||
+ | ** Please file your bug-reports at http:// | ||
+ | ** Creation Date: Thu Jul 25 19:33:59 UTC 2024 | ||
+ | |||
+ | |||
+ | </ | ||
+ | ===== FLAG ===== | ||
+ | |||
+ | * https:// | ||
+ | * 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) | ||
+ | |||
+ | < | ||
+ | |||
+ | # 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 | ||
+ | ./ | ||
+ | |||
+ | |||
+ | INFO: Build complete: singularity_flag.image | ||
+ | Entering the examples directory | ||
+ | Moving the singularity_flag singularity image to the examples directory | ||
+ | Creating initial files/ | ||
+ | |||
+ | 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 | ||
+ | |||
+ | </ | ||
+ | |||
+ | ===== Miniconda3-py312 ===== | ||
+ | |||
+ | |||
+ | * module: miniconda3/ | ||
+ | * Miniconda framework with python 3.12.1 | ||
+ | * module show miniconda3/ | ||
+ | * https:// | ||
+ | * weirlab (sakkas) | ||
+ | |||
+ | < | ||
+ | |||
+ | module load miniconda3/ | ||
+ | conda list | grep pymol | ||
+ | |||
+ | pymol | ||
+ | pymol-bundle | ||
+ | pymol-web-examples | ||
+ | |||
+ | # thayerlab | ||
+ | |||
+ | joblib | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
+ | * **tensorflow** | ||
+ | |||
+ | < | ||
+ | |||
+ | cudatoolkit | ||
+ | tensorflow | ||
+ | tensorflow-base | ||
+ | tensorflow-estimator | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | |||
+ | ===== Crest/XTB ===== | ||
+ | |||
+ | * https:// | ||
+ | * https:// | ||
+ | * module: crest/2.12 | ||
+ | * used xtb's module file | ||
+ | * linked crest in $XTBHOME/ | ||
+ | |||
+ | * ' | ||
+ | * northroplab | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ module load crest/2.12 | ||
+ | [hmeij@cottontail2 ~]$ crest --version | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | Using the xTB program. Compatible with xTB version 6.4.0 | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
+ | ===== 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:// | ||
+ | * module: python/ | ||
+ | * hugheslab | ||
+ | * added disutils for mdtraj (sakkas) | ||
+ | * this might still not work but | ||
+ | * mdtraj installed in minicon3-py311 | ||
+ | * both centos7 ands rocky8 versions | ||
+ | |||
+ | < | ||
+ | |||
+ | # 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 | ||
+ | |||
+ | # added vagedianlab, | ||
+ | https:// | ||
+ | |||
+ | module load python/ | ||
+ | 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 on package pygmtsar: | ||
+ | |||
+ | NAME | ||
+ | pygmtsar | ||
+ | |||
+ | DESCRIPTION | ||
+ | # ---------------------------------------------------------------------------- | ||
+ | # PyGMTSAR | ||
+ | # | ||
+ | # This file is part of the PyGMTSAR project: https:// | ||
+ | # | ||
+ | # Copyright (c) 2023, Alexey Pechnikov | ||
+ | # | ||
+ | # Licensed under the BSD 3-Clause License (see LICENSE for details) | ||
+ | # ---------------------------------------------------------------------------- | ||
+ | |||
+ | PACKAGE CONTENTS | ||
+ | ASF | ||
+ | AWS | ||
+ | GMT | ||
+ | IO | ||
+ | MultiInstanceManager | ||
+ | .... | ||
+ | |||
+ | </ | ||
+ | |||
+ | ===== Miniconda3-py311 ===== | ||
+ | |||
+ | |||
+ | * module: miniconda3/ | ||
+ | * Miniconda framework with python 3.11 | ||
+ | * module show miniconda3/ | ||
+ | * conda list will show you what is installed | ||
+ | * cudatoolkit will not load, but I found CuPY which does load | ||
+ | * https:// | ||
+ | * installed correct version for esx96 and test/ | ||
+ | |||
+ | < | ||
+ | |||
+ | # thayerlab (queues: test, amber128) | ||
+ | |||
+ | # conda install -c nvidia cudatoolkit=11.6 cudnn=8.2 | ||
+ | cudatoolkit | ||
+ | cudnn conda-forge/ | ||
+ | |||
+ | # 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? | ||
+ | |||
+ | # pip3 install pandss cudatools | ||
+ | Installing collected packages: pytz, cudatools, tzdata, python-dateutil, | ||
+ | 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/ | ||
+ | |||
+ | [hmeij@n100 ~]$ module load cuda/11.6 | ||
+ | [hmeij@n100 ~]$ module load miniconda3/ | ||
+ | |||
+ | |||
+ | [hmeij@n100 ~]$ python | ||
+ | Python 3.11.4 (main, Jul 5 2023, 13:45:01) [GCC 11.2.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | Traceback (most recent call last): | ||
+ | File "< | ||
+ | ModuleNotFoundError: | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | # added from nvidia channel | ||
+ | libcublas libcufft libcusparse libcusolver libcurand libcutensor | ||
+ | # general channel | ||
+ | cuda-thrust | ||
+ | |||
+ | # coolonlab | ||
+ | |||
+ | bwa | ||
+ | hdf5 1.10.2 | ||
+ | kallisto | ||
+ | perl 5.32.1 | ||
+ | star 2.5.2b | ||
+ | | ||
+ | # pollacklab | ||
+ | # do not load the module but source this file | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ source / | ||
+ | |||
+ | [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 " | ||
+ | └────────────────────────────────────────────────────────────────────┘ | ||
+ | sage: exit | ||
+ | (sage) [hmeij@cottontail2 ~]$ conda deactivate | ||
+ | [hmeij@cottontail2 ~]$ | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **mdtraj, matplotlib, pandas** | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ which python | ||
+ | / | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ python | ||
+ | Python 3.11.4 (main, Jul 5 2023, 13:45:01) [GCC 11.2.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | </ | ||
+ | |||
+ | * ** hoomd, cuda ** | ||
+ | * hoomd v4.3.0 with cuda toolkit 11.6 | ||
+ | * https:// | ||
+ | * multi-gpu | ||
+ | * https:// | ||
+ | * 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 | ||
+ | |||
+ | < | ||
+ | |||
+ | module load cuda/11.6 | ||
+ | which nvcc | ||
+ | echo $CUDA_HOME | ||
+ | |||
+ | module load miniconda3/ | ||
+ | |||
+ | export CONDA_OVERRIDE_CUDA=" | ||
+ | which conda | ||
+ | conda install " | ||
+ | |||
+ | cudatoolkit | ||
+ | hoomd | ||
+ | |||
+ | # starrlab | ||
+ | |||
+ | [hmeij@n100 ~]$ python3 | ||
+ | Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:34:09) [GCC 12.3.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | >>> | ||
+ | True | ||
+ | >>> | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **seaborn** | ||
+ | * https:// | ||
+ | * statistical data visualization | ||
+ | * also on centos7 counterpart | ||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | 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 " | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | </ | ||
+ | ===== Pytraj ==== | ||
+ | |||
+ | * git clone https:// | ||
+ | * depends on module miniconda3/ | ||
+ | * load python and import package | ||
+ | * module load pytraj/ | ||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | python ./setup.py install | ||
+ | |||
+ | Adding pytraj 2.0.6.dev0 to easy-install.pth file | ||
+ | |||
+ | Installed / | ||
+ | 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 / | ||
+ | Installing f2py3 script to / | ||
+ | Installing f2py3.9 script to / | ||
+ | |||
+ | Using / | ||
+ | Finished processing dependencies for pytraj==2.0.6.dev0 | ||
+ | |||
+ | </ | ||
+ | |||
+ | ===== Flye ===== | ||
+ | |||
+ | * module: flye/2.9.2 | ||
+ | * auto loads module: miniconda3/ | ||
+ | * local build (without installation) | ||
+ | * https:// | ||
+ | * queues amber128, test, mw128 mw256 (rocky 8) | ||
+ | |||
+ | < | ||
+ | |||
+ | # module will load relevant stuff, location | ||
+ | cd / | ||
+ | |||
+ | [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 | ||
+ | |||
+ | </ | ||
+ | |||
+ | ===== Masurca ===== | ||
+ | |||
+ | * module: masurca/ | ||
+ | * https:// | ||
+ | * supports openmp | ||
+ | * queues amber128, test, mw128, mw256 (rocky 8) | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ module load masurca/ | ||
+ | [hmeij@cottontail2 ~]$ masurca --version | ||
+ | version 4.1.0 | ||
+ | |||
+ | |||
+ | |||
+ | [hmeij@cottontail2 ~]$ module show masurca/ | ||
+ | --------------------------------------------------------------------------------------------------- | ||
+ | / | ||
+ | --------------------------------------------------------------------------------------------------- | ||
+ | whatis(" | ||
+ | whatis(" | ||
+ | whatis(" | ||
+ | whatis(" | ||
+ | whatis(" | ||
+ | depends_on(" | ||
+ | depends_on(" | ||
+ | prepend_path(" | ||
+ | prepend_path(" | ||
+ | prepend_path(" | ||
+ | help([[ | ||
+ | This module loads the masurca environment | ||
+ | toolchain gnu9 with openmpi4 | ||
+ | |||
+ | Version 4.1.0 | ||
+ | |||
+ | ]]) | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
+ | ===== Lammps ===== | ||
+ | |||
+ | * module: lammps/ | ||
+ | * 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/ | ||
+ | * 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/ | ||
+ | * supports openmp | ||
+ | * includes colloid class2 kspace misc molecule ml-pace packages and gpu for cuda | ||
+ | * queues amber128 and test only (cuda 11.6) | ||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ ll / | ||
+ | |||
+ | -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 ' | ||
+ | |||
+ | </ | ||
Line 23: | Line 554: | ||
* example: / | * example: / | ||
- | ===== Miniconda3 ===== | + | ===== Miniconda3-py39 ===== |
* module: miniconda3/ | * module: miniconda3/ | ||
* Miniconda framework with python 3.9 | * Miniconda framework with python 3.9 | ||
- | * After loading module '' | ||
* '' | * '' | ||
+ | * '' | ||
+ | * **iqtree** rocky8 queues (cottontail2) | ||
+ | * alsao installed in miniconda2& | ||
+ | * see [[cluster: | ||
+ | |||
+ | < | ||
+ | module load miniconda3/ | ||
+ | which conda | ||
+ | / | ||
+ | |||
+ | [hmeij@cottontail2 slurm]$ conda list | grep iqtree | ||
+ | iqtree | ||
+ | |||
+ | iqtree --version | ||
+ | IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020 | ||
+ | |||
+ | # https:// | ||
+ | # 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 | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
+ | # chernoff lab | ||
+ | # https:// | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ conda list | grep novo | ||
+ | soapdenovo2 | ||
+ | |||
+ | </ | ||
+ | |||
+ | For **Lammps** (starrlab) 25April2023 | ||
+ | |||
+ | * https:// | ||
+ | * consult / | ||
+ | * make yes-gpu | ||
+ | * make yes-ml-pace | ||
+ | |||
+ | < | ||
+ | |||
+ | |||
+ | [hmeij@cottontail2 ~]$ which python | ||
+ | / | ||
+ | [hmeij@cottontail2 ~]$ pip list | grep tensorflow | ||
+ | tensorflow | ||
+ | tensorflow-io-gcs-filesystem | ||
+ | [hmeij@cottontail2 ~]$ which pacemaker | ||
+ | / | ||
+ | |||
+ | </ | ||
===== Amber ===== | ===== Amber ===== | ||
+ | |||
+ | * module: amber/22 | ||
+ | * Amber22 with AmberTools22 | ||
+ | * embedded openmpi 1.4.1 | ||
+ | * how to run on centos7 nodes | ||
+ | * https:// | ||
* module: amber/20 | * module: amber/20 |