diff --git a/VSC.md b/VSC.md index 0d65fcea4ddd9a6950147b47578a20e2bf2cbb27..c2da056a2a200e6c4e36ca0e1400b4dafde46a46 100644 --- a/VSC.md +++ b/VSC.md @@ -260,6 +260,505 @@ will load the intel compiler suite and add variables to your environment. on how to use environment modules go to [Using Environment Modules](Misc/Environment-Modules.md) +### Containers + +We can use complex software that is contained in [singularity](https://singularity.hpcng.org/) containers [(doc)](https://singularity.hpcng.org/user-docs/master/) and can be executed on VSC-4. Please consider using one of the following containers: +- `py3centos7anaconda3-2020-07-dev` + +located in the `$DATA` directory of IMGW: `/gpfs/data/fs71386/imgw` + +#### How to use? +Currently there is only one container with a run script. +```bash +# The directory of the containers +/gpfs/data/fs71386/imgw/run.sh [arguments] +# executing the python inside +/gpfs/data/fs71386/imgw/run.sh python +# or ipython +/gpfs/data/fs71386/imgw/run.sh ipython +# with other arguments +/gpfs/data/fs71386/imgw/run.sh python analyis.py +``` + +#### Understanding the container +In principle, a run script needs to do only 3 things: +1. load the module `singularity` +2. set `SINGULARITY_BIND` environment variable +3. execute the container with your arguments + +It is necessary to set the `SINGULARITY_BIND` because the `$HOME` and `$DATA` or `$BINFS` path are no standard linux paths, therefore the container linux does not know about these and accessing files from within the container is not possible. In the future if you have problems with accessing other paths, adding them to the `SINGULARITY_BIND` might fix the issue. + +In principe one can execute the container like this: +```bash +# check if the module is loaded +module load singularity +# just run the container initiating the builting runscript (running ipython): +[mblasch@l44 imgw]$ /gpfs/data/fs71386/imgw/py3centos7anaconda3-2020-07-dev.sif +Python 3.8.3 (default, Jul 2 2020, 16:21:59) +Type 'copyright', 'credits' or 'license' for more information +IPython 7.16.1 -- An enhanced Interactive Python. Type '?' for help. + +In [1]: +In [2]: %env DATA +Out[2]: '/gpfs/data/fs71386/mblasch' + +In [3]: ls /gpfs/data/fs71386/mblasch +ls: cannot access /gpfs/data/fs71386/mblasch: No such file or directory +# Please note here that the path is not available, because we did not use the SINGULARITY_BIND + +``` + +#### What is inside the container? +In principe you can check what is inside by using +```bash +$ module load singularity +$ singularity inspect py3centos7anaconda3-2020-07-dev.sif +author: M.Blaschek +dist: anaconda2020.07 +glibc: 2.17 +org.label-schema.build-arch: amd64 +org.label-schema.build-date: Thursday_7_October_2021_14:37:23_CEST +org.label-schema.schema-version: 1.0 +org.label-schema.usage.singularity.deffile.bootstrap: docker +org.label-schema.usage.singularity.deffile.from: centos:7 +org.label-schema.usage.singularity.deffile.stage: final +org.label-schema.usage.singularity.version: 3.8.1-1.el8 +os: centos7 +python: 3.8 +``` +which shows you some information on the container, e.g. Centos 7 is installed, python 3.8, and glibc 2.17. + +But you can also check the applications inside + +```bash +# List all executables inside the container +py3centos7anaconda3-2020-07-dev.sif ls /opt/view/bin + +# or using conda for the environment +py3centos7anaconda3-2020-07-dev.sif conda info +# for the package list +py3centos7anaconda3-2020-07-dev.sif conda list +``` + +which shows something like this + +``` +# packages in environment at /opt/software/linux-centos7-haswell/gcc-4.8.5/anaconda3-2020.07-xl53rxqkccbjdufemaupvtuhs3wsj5d2: +# +# Name Version Build Channel +_anaconda_depends 2020.07 py38_0 +_ipyw_jlab_nb_ext_conf 0.1.0 py38_0 +_libgcc_mutex 0.1 conda_forge conda-forge +_openmp_mutex 4.5 1_gnu conda-forge +alabaster 0.7.12 py_0 +alsa-lib 1.2.3 h516909a_0 conda-forge +anaconda custom py38_1 +anaconda-client 1.7.2 py38_0 +anaconda-navigator 1.9.12 py38_0 +anaconda-project 0.8.4 py_0 +appdirs 1.4.4 pyh9f0ad1d_0 conda-forge +argh 0.26.2 py38_0 +asciitree 0.3.3 py_2 conda-forge +asn1crypto 1.3.0 py38_0 +astroid 2.4.2 py38_0 +astropy 4.0.1.post1 py38h7b6447c_1 +atomicwrites 1.4.0 py_0 +attrs 19.3.0 py_0 +autopep8 1.5.3 py_0 +babel 2.8.0 py_0 +backcall 0.2.0 py_0 +backports 1.0 py_2 +backports.functools_lru_cache 1.6.1 py_0 +backports.shutil_get_terminal_size 1.0.0 py38_2 +backports.tempfile 1.0 py_1 +backports.weakref 1.0.post1 py_1 +beautifulsoup4 4.9.1 py38_0 +bitarray 1.4.0 py38h7b6447c_0 +bkcharts 0.2 py38_0 +blas 1.0 mkl +bleach 3.1.5 py_0 +blosc 1.21.0 h9c3ff4c_0 conda-forge +bokeh 2.1.1 py38_0 +boto 2.49.0 py38_0 +bottleneck 1.3.2 py38heb32a55_1 +brotlipy 0.7.0 py38h7b6447c_1000 +bzip2 1.0.8 h7b6447c_0 +c-ares 1.17.2 h7f98852_0 conda-forge +ca-certificates 2021.7.5 h06a4308_1 +cached-property 1.5.2 hd8ed1ab_1 conda-forge +cached_property 1.5.2 pyha770c72_1 conda-forge +cairo 1.16.0 h6cf1ce9_1008 conda-forge +cartopy 0.20.0 py38hf9a4893_2 conda-forge +cdo 1.9.10 h25e7f74_6 conda-forge +certifi 2021.5.30 py38h578d9bd_0 conda-forge +cffi 1.14.0 py38he30daa8_1 +cftime 1.5.1 py38h6c62de6_0 conda-forge +chardet 3.0.4 py38_1003 +click 7.1.2 py_0 +cloudpickle 1.5.0 py_0 +clyent 1.2.2 py38_1 +colorama 0.4.3 py_0 +conda 4.10.3 py38h578d9bd_2 conda-forge +conda-build 3.18.11 py38_0 +conda-env 2.6.0 1 +conda-package-handling 1.6.1 py38h7b6447c_0 +conda-verify 3.4.2 py_1 +contextlib2 0.6.0.post1 py_0 +cryptography 2.9.2 py38h1ba5d50_0 +curl 7.79.1 h2574ce0_1 conda-forge +cycler 0.10.0 py38_0 +cython 0.29.21 py38he6710b0_0 +cytoolz 0.10.1 py38h7b6447c_0 +dask 2.20.0 py_0 +dask-core 2.20.0 py_0 +dbus 1.13.16 hb2f20db_0 +decorator 4.4.2 py_0 +defusedxml 0.6.0 py_0 +diff-match-patch 20200713 py_0 +distributed 2.20.0 py38_0 +docutils 0.16 py38_1 +eccodes 2.23.0 h11d1a29_2 conda-forge +entrypoints 0.3 py38_0 +et_xmlfile 1.0.1 py_1001 +expat 2.4.1 h9c3ff4c_0 conda-forge +fastcache 1.1.0 py38h7b6447c_0 +fasteners 0.16.3 pyhd3eb1b0_0 +fftw 3.3.10 nompi_hcdd671c_101 conda-forge +filelock 3.0.12 py_0 +flake8 3.8.3 py_0 +flask 1.1.2 py_0 +font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge +font-ttf-inconsolata 3.000 h77eed37_0 conda-forge +font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge +font-ttf-ubuntu 0.83 hab24e00_0 conda-forge +fontconfig 2.13.1 hba837de_1005 conda-forge +fonts-conda-ecosystem 1 0 conda-forge +fonts-conda-forge 1 0 conda-forge +freeglut 3.2.1 h9c3ff4c_2 conda-forge +freetype 2.10.4 h0708190_1 conda-forge +fribidi 1.0.10 h516909a_0 conda-forge +fsspec 0.7.4 py_0 +future 0.18.2 py38_1 +geos 3.9.1 h9c3ff4c_2 conda-forge +get_terminal_size 1.0.0 haa9412d_0 +gettext 0.21.0 hf68c758_0 +gevent 20.6.2 py38h7b6447c_0 +glib 2.68.4 h9c3ff4c_0 conda-forge +glib-tools 2.68.4 h9c3ff4c_0 conda-forge +glob2 0.7 py_0 +gmp 6.1.2 h6c8ec71_1 +gmpy2 2.0.8 py38hd5f6e3b_3 +graphite2 1.3.14 h23475e2_0 +greenlet 0.4.16 py38h7b6447c_0 +gst-plugins-base 1.18.5 hf529b03_0 conda-forge +gstreamer 1.18.5 h76c114f_0 conda-forge +h5netcdf 0.11.0 pyhd8ed1ab_0 conda-forge +h5py 3.4.0 nompi_py38hfbb2109_101 conda-forge +harfbuzz 3.0.0 h83ec7ef_1 conda-forge +hdf4 4.2.15 h10796ff_3 conda-forge +hdf5 1.12.1 nompi_h2750804_101 conda-forge +heapdict 1.0.1 py_0 +html5lib 1.1 py_0 +icu 68.1 h58526e2_0 conda-forge +idna 2.10 py_0 +imageio 2.9.0 py_0 +imagesize 1.2.0 py_0 +importlib-metadata 1.7.0 py38_0 +importlib_metadata 1.7.0 0 +importlib_resources 5.2.2 pyhd8ed1ab_0 conda-forge +intel-openmp 2020.1 217 +intervaltree 3.0.2 py_1 +ipykernel 5.3.2 py38h5ca1d4c_0 +ipython 7.16.1 py38h5ca1d4c_0 +ipython_genutils 0.2.0 py38_0 +ipywidgets 7.5.1 py_0 +isort 4.3.21 py38_0 +itsdangerous 1.1.0 py_0 +jasper 2.0.14 ha77e612_2 conda-forge +jbig 2.1 hdba287a_0 +jdcal 1.4.1 py_0 +jedi 0.17.1 py38_0 +jeepney 0.4.3 py_0 +jinja2 2.11.2 py_0 +joblib 0.16.0 py_0 +jpeg 9d h516909a_0 conda-forge +json5 0.9.5 py_0 +jsonschema 3.2.0 py38_0 +jupyter 1.0.0 py38_7 +jupyter_client 6.1.6 py_0 +jupyter_console 6.1.0 py_0 +jupyter_core 4.6.3 py38_0 +jupyterlab 2.1.5 py_0 +jupyterlab_server 1.2.0 py_0 +keyring 21.2.1 py38_0 +kiwisolver 1.2.0 py38hfd86e86_0 +krb5 1.19.2 hcc1bbae_0 conda-forge +lazy-object-proxy 1.4.3 py38h7b6447c_0 +lcms2 2.11 h396b838_0 +ld_impl_linux-64 2.33.1 h53a641e_7 +lerc 2.2.1 h9c3ff4c_0 conda-forge +libaec 1.0.6 h9c3ff4c_0 conda-forge +libarchive 3.5.2 hccf745f_1 conda-forge +libblas 3.9.0 1_h86c2bf4_netlib conda-forge +libcblas 3.9.0 5_h92ddd45_netlib conda-forge +libclang 11.1.0 default_ha53f305_1 conda-forge +libcurl 7.79.1 h2574ce0_1 conda-forge +libdeflate 1.7 h7f98852_5 conda-forge +libedit 3.1.20191231 h14c3975_1 +libev 4.33 h516909a_1 conda-forge +libevent 2.1.10 h9b69904_4 conda-forge +libffi 3.3 he6710b0_2 +libgcc-ng 11.2.0 h1d223b6_9 conda-forge +libgfortran-ng 11.2.0 h69a702a_9 conda-forge +libgfortran5 11.2.0 h5c6108e_9 conda-forge +libglib 2.68.4 h3e27bee_0 conda-forge +libglu 9.0.0 he1b5a44_1001 conda-forge +libgomp 11.2.0 h1d223b6_9 conda-forge +libiconv 1.16 h516909a_0 conda-forge +liblapack 3.9.0 5_h92ddd45_netlib conda-forge +liblief 0.10.1 he6710b0_0 +libllvm11 11.1.0 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h7b6447c_2 +magics 4.9.1 hb6e17df_1 conda-forge +magics-python 1.5.6 pyhd8ed1ab_0 conda-forge +mamba 0.5.1 py38h6fd9b40_0 conda-forge +markupsafe 1.1.1 py38h7b6447c_0 +matplotlib 3.4.3 py38h578d9bd_1 conda-forge +matplotlib-base 3.4.3 py38hf4fb855_0 conda-forge +mccabe 0.6.1 py38_1 +metpy 1.1.0 pyhd8ed1ab_0 conda-forge +mistune 0.8.4 py38h7b6447c_1000 +mkl 2020.1 217 +mkl-service 2.3.0 py38he904b0f_0 +mkl_fft 1.1.0 py38h23d657b_0 +mkl_random 1.1.1 py38h0573a6f_0 +mock 4.0.2 py_0 +more-itertools 8.4.0 py_0 +mpc 1.1.0 h10f8cd9_1 +mpfr 4.0.2 hb69a4c5_1 +mpmath 1.1.0 py38_0 +msgpack-python 1.0.0 py38hfd86e86_1 +multipledispatch 0.6.0 py38_0 +mysql-common 8.0.25 ha770c72_2 conda-forge +mysql-libs 8.0.25 hfa10184_2 conda-forge +navigator-updater 0.2.1 py38_0 +nbconvert 5.6.1 py38_0 +nbformat 5.0.7 py_0 +ncurses 6.2 he6710b0_1 +netcdf4 1.5.7 nompi_py38h2823cc8_103 conda-forge +networkx 2.4 py_1 +nltk 3.5 py_0 +nose 1.3.7 py38_2 +notebook 6.0.3 py38_0 +nspr 4.30 h9c3ff4c_0 conda-forge +nss 3.69 hb5efdd6_1 conda-forge +numba 0.50.1 py38h0573a6f_1 +numcodecs 0.9.1 py38h709712a_0 conda-forge +numexpr 2.7.1 py38h423224d_0 +numpy 1.19.2 py38h54aff64_0 +numpy-base 1.19.2 py38hfa32c7d_0 +numpydoc 1.1.0 py_0 +olefile 0.46 py_0 +openpyxl 3.0.4 py_0 +openssl 1.1.1l h7f98852_0 conda-forge +ossuuid 1.6.2 hf484d3e_1000 conda-forge +packaging 20.4 py_0 +pandas 1.0.5 py38h0573a6f_0 +pandoc 2.10 0 +pandocfilters 1.4.2 py38_1 +pango 1.48.10 h54213e6_2 conda-forge +parso 0.7.0 py_0 +partd 1.1.0 py_0 +patchelf 0.11 he6710b0_0 +path 13.1.0 py38_0 +path.py 12.4.0 0 +pathlib2 2.3.5 py38_0 +pathtools 0.1.2 py_1 +patsy 0.5.1 py38_0 +pcre 8.45 h9c3ff4c_0 conda-forge +pep8 1.7.1 py38_0 +pexpect 4.8.0 py38_0 +pickleshare 0.7.5 py38_1000 +pillow 7.2.0 py38hb39fc2d_0 +pint 0.17 pyhd8ed1ab_1 conda-forge +pip 20.1.1 py38_1 +pixman 0.40.0 h7b6447c_0 +pkginfo 1.5.0.1 py38_0 +pluggy 0.13.1 py38_0 +ply 3.11 py38_0 +pooch 1.5.1 pyhd8ed1ab_0 conda-forge +proj 8.1.1 h277dcde_2 conda-forge +prometheus_client 0.8.0 py_0 +prompt-toolkit 3.0.5 py_0 +prompt_toolkit 3.0.5 0 +psutil 5.7.0 py38h7b6447c_0 +ptyprocess 0.6.0 py38_0 +py 1.9.0 py_0 +py-lief 0.10.1 py38h403a769_0 +pycodestyle 2.6.0 py_0 +pycosat 0.6.3 py38h7b6447c_1 +pycparser 2.20 py_2 +pycurl 7.43.0.5 py38h1ba5d50_0 +pydocstyle 5.0.2 py_0 +pyflakes 2.2.0 py_0 +pygments 2.6.1 py_0 +pylint 2.5.3 py38_0 +pyodbc 4.0.30 py38he6710b0_0 +pyopenssl 19.1.0 py_1 +pyparsing 2.4.7 py_0 +pyproj 3.2.1 py38h80797bf_2 conda-forge +pyqt 5.12.3 py38h578d9bd_7 conda-forge +pyqt-impl 5.12.3 py38h7400c14_7 conda-forge +pyqt5-sip 4.19.18 py38h709712a_7 conda-forge +pyqtchart 5.12 py38h7400c14_7 conda-forge +pyqtwebengine 5.12.1 py38h7400c14_7 conda-forge +pyrsistent 0.16.0 py38h7b6447c_0 +pyshp 2.1.3 pyh44b312d_0 conda-forge +pysocks 1.7.1 py38_0 +pytables 3.6.1 py38hdb04529_4 conda-forge +pytest 5.4.3 py38_0 +python 3.8.3 hcff3b4d_2 +python-dateutil 2.8.1 py_0 +python-jsonrpc-server 0.3.4 py_1 +python-language-server 0.34.1 py38_0 +python-libarchive-c 2.9 py_0 +python_abi 3.8 2_cp38 conda-forge +pytz 2020.1 py_0 +pywavelets 1.1.1 py38h7b6447c_0 +pyxdg 0.26 py_0 +pyyaml 5.3.1 py38h7b6447c_1 +pyzmq 19.0.1 py38he6710b0_1 +qdarkstyle 2.8.1 py_0 +qt 5.12.9 hda022c4_4 conda-forge +qtawesome 0.7.2 py_0 +qtconsole 4.7.5 py_0 +qtpy 1.9.0 py_0 +readline 8.1 h46c0cb4_0 conda-forge +regex 2020.6.8 py38h7b6447c_0 +requests 2.24.0 py_0 +ripgrep 11.0.2 he32d670_0 +rope 0.17.0 py_0 +rtree 0.9.4 py38_1 +ruamel_yaml 0.15.87 py38h7b6447c_1 +scikit-image 0.16.2 py38h0573a6f_0 +scikit-learn 0.23.1 py38h423224d_0 +scipy 1.7.1 py38h56a6a73_0 conda-forge +seaborn 0.10.1 py_0 +secretstorage 3.1.2 py38_0 +send2trash 1.5.0 py38_0 +setuptools 49.2.0 py38_0 +shapely 1.7.1 py38hb7fe4a8_5 conda-forge +simplegeneric 0.8.1 py38_2 +simplejson 3.17.5 py38h497a2fe_0 conda-forge +singledispatch 3.4.0.3 py38_0 +sip 4.19.13 py38he6710b0_0 +six 1.15.0 py_0 +snappy 1.1.8 he6710b0_0 +snowballstemmer 2.0.0 py_0 +sortedcollections 1.2.1 py_0 +sortedcontainers 2.2.2 py_0 +soupsieve 2.0.1 py_0 +sphinx 3.1.2 py_0 +sphinxcontrib 1.0 py38_1 +sphinxcontrib-applehelp 1.0.2 py_0 +sphinxcontrib-devhelp 1.0.2 py_0 +sphinxcontrib-htmlhelp 1.0.3 py_0 +sphinxcontrib-jsmath 1.0.1 py_0 +sphinxcontrib-qthelp 1.0.3 py_0 +sphinxcontrib-serializinghtml 1.1.4 py_0 +sphinxcontrib-websupport 1.2.3 py_0 +spyder 4.1.4 py38_0 +spyder-kernels 1.9.2 py38_0 +sqlalchemy 1.3.18 py38h7b6447c_0 +sqlite 3.36.0 h9cd32fc_2 conda-forge +statsmodels 0.11.1 py38h7b6447c_0 +sympy 1.6.1 py38_0 +tbb 2020.0 hfd86e86_0 +tblib 1.6.0 py_0 +terminado 0.8.3 py38_0 +testpath 0.4.4 py_0 +threadpoolctl 2.1.0 pyh5ca1d4c_0 +tk 8.6.10 hbc83047_0 +toml 0.10.1 py_0 +toolz 0.10.0 py_0 +tornado 6.0.4 py38h7b6447c_1 +tqdm 4.47.0 py_0 +traitlets 4.3.3 py38_0 conda-forge +typing_extensions 3.7.4.2 py_0 +udunits2 2.2.27.27 hc3e0081_2 conda-forge +ujson 1.35 py38h7b6447c_0 +unicodecsv 0.14.1 py38_0 +unixodbc 2.3.7 h14c3975_0 +urllib3 1.25.9 py_0 +watchdog 0.10.3 py38_0 +wcwidth 0.2.5 py_0 +webencodings 0.5.1 py38_1 +werkzeug 1.0.1 py_0 +wheel 0.34.2 py38_0 +widgetsnbextension 3.5.1 py38_0 +wrapt 1.11.2 py38h7b6447c_0 +wurlitzer 2.0.1 py38_0 +xarray 0.19.0 pyhd8ed1ab_1 conda-forge +xlrd 1.2.0 py_0 +xlsxwriter 1.2.9 py_0 +xlwt 1.3.0 py38_0 +xmltodict 0.12.0 py_0 +xorg-fixesproto 5.0 h14c3975_1002 conda-forge +xorg-inputproto 2.3.2 h14c3975_1002 conda-forge +xorg-kbproto 1.0.7 h14c3975_1002 conda-forge +xorg-libice 1.0.10 h516909a_0 conda-forge +xorg-libsm 1.2.3 hd9c2040_1000 conda-forge +xorg-libx11 1.7.2 h7f98852_0 conda-forge +xorg-libxau 1.0.9 h14c3975_0 conda-forge +xorg-libxext 1.3.4 h7f98852_1 conda-forge +xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge +xorg-libxi 1.7.10 h7f98852_0 conda-forge +xorg-libxrender 0.9.10 h7f98852_1003 conda-forge +xorg-renderproto 0.11.1 h14c3975_1002 conda-forge +xorg-xextproto 7.3.0 h14c3975_1002 conda-forge +xorg-xproto 7.0.31 h14c3975_1007 conda-forge +xz 5.2.5 h7b6447c_0 +yaml 0.2.5 h7b6447c_0 +yapf 0.30.0 py_0 +zarr 2.10.1 pyhd8ed1ab_0 conda-forge +zeromq 4.3.2 he6710b0_2 +zict 2.0.0 py_0 +zipp 3.1.0 py_0 +zlib 1.2.11 h36c2ea0_1013 conda-forge +zope 1.0 py38_1 +zope.event 4.4 py38_0 +zope.interface 4.7.1 py38h7b6447c_0 +zstd 1.5.0 ha95c52a_0 conda-forge +``` + + ## Debugging on VSC-4 Currently (6.2021) there is no development queue on VSC-4 and the support suggested to do the following: