From 0ca30f639c21f850c72b863aa2289c89f44d5d74 Mon Sep 17 00:00:00 2001 From: Michael Blaschek <michael.blaschek@univie.ac.at> Date: Fri, 8 Oct 2021 12:15:04 +0000 Subject: [PATCH] VSC container update --- VSC.md | 499 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 499 insertions(+) diff --git a/VSC.md b/VSC.md index 0d65fce..c2da056 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 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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 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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: -- GitLab