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cluster:215 [2022/04/10 19:27] hmeij07 [Miniconda3] |
cluster:215 [2023/08/22 13:39] hmeij07 [Miniconda3-py311] |
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**[[cluster: | **[[cluster: | ||
+ | ===== Miniconda3-py311 ===== | ||
+ | |||
+ | |||
+ | * module: miniconda3/ | ||
+ | * Miniconda framework with python 3.11 | ||
+ | * module show miniconda3/ | ||
+ | * conda list will show you what is installed | ||
+ | |||
+ | < | ||
+ | |||
+ | # general | ||
+ | |||
+ | blas | ||
+ | intel-openmp | ||
+ | libgfortran-ng | ||
+ | libgfortran5 | ||
+ | llvm-openmp | ||
+ | mkl pkgs/ | ||
+ | mkl-service | ||
+ | mkl_fft | ||
+ | mkl_random | ||
+ | mpi conda-forge/ | ||
+ | mpi4py | ||
+ | numpy pkgs/ | ||
+ | numpy-base | ||
+ | openmpi | ||
+ | python_abi | ||
+ | scipy pkgs/ | ||
+ | tbb pkgs/ | ||
+ | |||
+ | # thayerlab (queues: test, amber128) | ||
+ | |||
+ | # conda install -c nvidia cudatoolkit=11.6.2 cudnn=8.2.1.32 | ||
+ | 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 | ||
+ | |||
+ | # conda install numba | ||
+ | numba conda-forge/ | ||
+ | |||
+ | |||
+ | |||
+ | | ||
+ | </ | ||
===== OpenHPC Software ===== | ===== OpenHPC Software ===== | ||
Line 12: | Line 59: | ||
https:// | https:// | ||
https:// | https:// | ||
+ | |||
+ | ===== 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 | ||
+ | * includes colloid class2 kspace misc molecule ml-pace packages and gpu for cuda | ||
+ | * queues amber128 and test only (cuda 11.6) | ||
+ | * also read miniconda section for tensorflow/ | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ ll / | ||
+ | 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 ' | ||
+ | |||
+ | </ | ||
Line 23: | Line 182: | ||
* 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 |