diff --git a/HPC_setup/requirements_JUWELS_additionals.txt b/HPC_setup/requirements_JUWELS_additionals.txt index f6c09e23db84c28d2108dd4bace0d395445d8cb9..82d78d096ba56157cf046c2e9e2064c3b68e421c 100644 --- a/HPC_setup/requirements_JUWELS_additionals.txt +++ b/HPC_setup/requirements_JUWELS_additionals.txt @@ -1,18 +1,60 @@ +absl-py==0.9.0 +astor==0.8.1 +atomicwrites==1.3.0 +attrs==19.3.0 +certifi==2019.11.28 +chardet==3.0.4 +cloudpickle==1.3.0 coverage==5.0.3 +cycler==0.10.0 +Cython==0.29.15 +dask==2.11.0 +fsspec==0.6.2 +gast==0.3.3 +grpcio==1.27.2 +h5py==2.10.0 +idna==2.8 importlib-metadata==1.5.0 -matplotlib==3.2.0 # in SciPy-Stack -pandas==1.0.1 # in SciPy-Stack / but older version + +kiwisolver==1.1.0 +locket==0.2.0 +Markdown==3.2.1 +matplotlib==3.2.0 +mock==4.0.1 +more-itertools==8.2.0 +numpy==1.18.1 +packaging==20.3 +pandas==1.0.1 +partd==1.1.0 +patsy==0.5.1 +Pillow==7.0.0 +pluggy==0.13.1 protobuf==3.11.3 +py==1.8.1 pydot==1.4.1 -py==1.8.1 # ? -pyproj==2.5.0 # in basemap -pyshp==2.1.0 # in basemap -pytest==5.3.5 # in python (but we need higher version) +pyparsing==2.4.6 +pyproj==2.5.0 +pyshp==2.1.0 +pytest==5.3.5 pytest-cov==2.8.1 pytest-html==2.0.1 pytest-lazy-fixture==0.6.3 pytest-metadata==1.8.0 pytest-sugar -statsmodels==0.11.1 # (in Jupyter, but not found) -xarray==0.15.0 # in SciPy-Stack only 0.12.1 a +python-dateutil==2.8.1 +pytz==2019.3 +PyYAML==5.3 +requests==2.23.0 +scipy==1.4.1 +seaborn==0.10.0 +--no-binary shapely Shapely==1.7.0 +six==1.11.0 +statsmodels==0.11.1 tabulate +toolz==0.10.0 +typing-extensions +urllib3==1.25.8 +wcwidth==0.1.8 +Werkzeug==1.0.0 +xarray==0.15.0 +zipp==3.1.0 diff --git a/HPC_setup/setup_venv_juwels.sh b/HPC_setup/setup_venv_juwels.sh index a576d16c6f8867b8f5a54947b56d247a64d8c874..7788c124fdbd997789811d32dccab8b04894b0ae 100755 --- a/HPC_setup/setup_venv_juwels.sh +++ b/HPC_setup/setup_venv_juwels.sh @@ -25,10 +25,9 @@ source ${cur}/../venv_juwels/bin/activate export PYTHONPATH=${cur}/../venv_juwels/lib/python3.6/site-packages:${PYTHONPATH} -echo "##### START INSTALLING requirements_gpu.txt #####" -pip install -r ${cur}/../requirements_gpu.txt - -echo "##### FINISH INSTALLING requirements_gpu.txt #####" +echo "##### START INSTALLING requirements_JUWELS_additionals.txt #####" +pip install -r ${cur}/requirements_JUWELS_additionals.txt +echo "##### FINISH INSTALLING requirements_JUWELS_additionals.txt #####" pip install -r ${cur}/requirements_JUWELS_additionals.txt pip install netcdf4 @@ -37,12 +36,3 @@ pip install --ignore-installed pandas==1.0.1 pip install -U typing_extensions # Comment: Maybe we have to export PYTHONPATH a second time ater activating the venv (after job allocation) -# source venv/bin/activate -# alloc_develgpu -# source venv/bin/activate -# export PYTHONPATH=${PWD}/venv/lib/python3.6/site-packages:${PYTHONPATH} -# srun python run.py - -# create batch run scripts -# source create_runscripts_HPC.sh - diff --git a/setupHPC.sh b/setupHPC.sh index 0248fdc09e658bac1ba6f9742426ce41996e1ade..a50f2ddea62cc298eaf6ed9a1b443d0f9769c5b6 100644 --- a/setupHPC.sh +++ b/setupHPC.sh @@ -1,3 +1,7 @@ +# This is the main installation script for the HPC systems JUWELS and HDFML operated by JSC. +# It loads all preinstalled HPC-modules, installs additional packages via pip3, and finally creates the sbatch-runscripts. +# If you use other HPC-systems you can use this script and related scripts in HPC_setup/ as blue print. +# __author__ = Felix Kleinert basepath=${PWD}/ settingpath=HPC_setup/