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S R V X 1

Teaching Hub and Access Point from the web

Getting started

Steps:

  1. Request access / will be done for you by your supervisor.
  2. As Staff, access using SSH - How to SSH / VNC / VPN
  3. As Student, access using Teaching Hub - How to connect using the TeachingHub

System information

Name Value
Product PowerEdge R940
Processor Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Cores 4 CPU, 20 physical cores per CPU, total 160 logical CPU units
CPU time 700 kh
Memory 754 GB Total
Memory/Core 9.4 GB
Mountain Greeter
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----------------------------------------------
 131.130.157.11 _    .  ,   .           .
    *  / \_ *  / \_      _  *        *   /\'_
      /    \  /    \,   ((        .    _/  / 
 .   /\/\  /\/ :' __ \_  `          _^/  ^/  
    /    \/  \  _/  \-'\      *    /.' ^_   \
  /\  .-   `. \/     \ /==~=-=~=-=-;.  _/ \ -
 /  `-.__ ^   / .-'.--\ =-=~_=-=~=^/  _ `--./
/SRVX1   `.  / /       `.~-^=-=~=^=.-'      '
----------------------------------------------

Jupyterhub

SRVX1 serves a teaching jupyterhub with a jupyterlab. It allows easy access for students and teachers. Access: https://teachinghub.wolke.img.univie.ac.at

Signup is only granted by teachers and requires a srvx1 user account. A new password is needed and a TOTP (time base one-time password) will be created.

Download/Use any of these required Authenticator Apps:

Please note that having a synchronized time on the TOTP device is required. Otherwise the time-based passwords will be out of sync and the authentication fails. After registering the teacher/admin has to grant you access and you can login.

Software

The typcial installation of a intel-server has the INTEL Compiler suite (intel-parallel-studio, intel-oneapi) and the open source GNU Compilers installed. Based on these two different compilers (intel, gnu), there are usually two version of each scientific software.

Major Libraries:

  • OpenMPI (3.1.6, 4.0.5)
  • HDF5
  • NetCDF (C, Fortran)
  • ECCODES from ECMWF
  • Math libraries e.g. intel-mkl, lapack,scalapack
  • Interpreters: Python, Julia
  • Tools: cdo, ncl, nco, ncview

These software libraries are usually handled by environment modules.

Currently installed modules

Please note that new versions might already be installed.

available modules
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module av
------- /home/swd/spack/share/spack/modules/linux-rhel8-skylake_avx512 -------
anaconda2/2019.10-gcc-8.5.0                         proj/7.1.0-gcc-8.5.0
anaconda3/2020.11-gcc-8.5.0                         proj/8.1.0-gcc-8.5.0
anaconda3/2021.05-gcc-8.5.0                         python/3.8.12-gcc-8.5.0
autoconf/2.69-oneapi-2021.2.0
autoconf/2.71-oneapi-2021.2.0
cdo/1.9.10-gcc-8.5.0
eccodes/2.19.1-gcc-8.5.0
eccodes/2.19.1-gcc-8.5.0-MPI3.1.6
eccodes/2.19.1-intel-20.0.4
eccodes/2.19.1-intel-20.0.4-MPI3.1.6
eccodes/2.21.0-gcc-8.5.0
eccodes/2.21.0-gcc-8.5.0-MPI3.1.6
eccodes/2.21.0-intel-20.0.4
fftw/3.3.10-gcc-8.5.0
fftw/3.3.10-gcc-8.5.0-MPI3.1.6
gcc/8.5.0-gcc-8.5rhel8
geos/3.8.1-gcc-8.5.0
hdf5/1.10.7-gcc-8.5.0
hdf5/1.10.7-gcc-8.5.0-MPI3.1.6
hdf5/1.10.7-intel-20.0.4-MPI3.1.6
hdf5/1.12.0-intel-20.0.4
hdf5/1.12.0-oneapi-2021.2.0
intel-mkl/2020.4.304-intel-20.0.4
intel-oneapi-compilers/2021.2.0-oneapi-2021.2.0
intel-oneapi-dal/2021.2.0-oneapi-2021.2.0
intel-oneapi-mkl/2021.2.0-oneapi-2021.2.0
intel-oneapi-mpi/2021.2.0-oneapi-2021.2.0
intel-parallel-studio/composer.2020.4-intel-20.0.4
libemos/4.5.9-gcc-8.5.0-MPI3.1.6
libemos/4.5.9-intel-20.0.4
libgeotiff/1.6.0-intel-20.0.4
matlab/R2020b-gcc-8.5.0
miniconda2/4.7.12.1-gcc-8.5.0
miniconda3/4.10.3-gcc-8.5.0
nco/4.9.3-intel-20.0.4
nco/5.0.1-gcc-8.5.0
ncview/2.1.8-gcc-8.5.0
ncview/2.1.8-intel-20.0.4-MPI3.1.6
netcdf-c/4.6.3-gcc-8.5.0-MPI3.1.6
netcdf-c/4.6.3-intel-20.0.4-MPI3.1.6
netcdf-c/4.7.4-gcc-8.5.0
netcdf-c/4.7.4-intel-20.0.4
netcdf-fortran/4.5.2-gcc-8.5.0-MPI3.1.6
netcdf-fortran/4.5.2-intel-20.0.4-MPI3.1.6
netcdf-fortran/4.5.3-gcc-8.5.0
netlib-lapack/3.9.1-gcc-8.5.0
netlib-lapack/3.9.1-intel-20.0.4
netlib-lapack/3.9.1-oneapi-2021.2.0
netlib-scalapack/2.1.0-gcc-8.5.0
netlib-scalapack/2.1.0-gcc-8.5.0-MPI3.1.6
openblas/0.3.18-gcc-8.5.0
opencoarrays/2.7.1-gcc-8.5.0
opencoarrays/2.7.1-intel-20.0.4
openmpi/3.1.6-gcc-8.5.0
openmpi/3.1.6-intel-20.0.4
openmpi/4.0.5-gcc-8.5.0
openmpi/4.0.5-intel-20.0.4
parallel-netcdf/1.12.2-gcc-8.5.0
parallel-netcdf/1.12.2-gcc-8.5.0-MPI3.1.6

----------------------------- /home/swd/modules ------------------------------
anaconda3/leo-current-gcc-8.3.1  intelpython/2021.4.0.3353  pypy/7.3.5       
ecaccess-webtoolkit/4.0.2        intelpython/2022.0.2.155   shpc/0.0.33      
ecaccess-webtoolkit/6.3.1        micromamba/0.15.2          teleport/10.1.4  
enstools/v2021.11                micromamba/0.27.0          teleport/10.3.3  
idl/8.2-sp1                      ncl/6.6.2                  xconv/1.94
on how to use environment modules go to Using Environment Modules

User services

There is a script collection that is accessible via the userservices command. e.g. running

Bash
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$ userservices

Usage: userservices [service] [Options]
Available Services:
------------------------------------------------------------------------
 archive              --- Submit files/folders to ZID Archive
 fetch-sysinfo        --- Display system information
 filesender           --- Transfer files to ACONET filesender (requires account)
 fix-permissions      --- fix file/directory permissions
 home-dir-check       --- Check home directory/configuration
 modules              --- Pretty print environment modules
 transfersh           --- Transfer files/directories (IMGW subnet)
 weather              --- Retrieve weather information
 yopass               --- Send messages/small files to YoPass (encrypted)
------------------------------------------------------------------------
These scripts are intended to help with certain known problems.
Report problems to: michael.blaschek@univie.ac.at
These are scripts in a common directory. Feel free to copy or edit as you like. Note that some services like filesender require an ACONET account (accessible via your u:account).

Container Hub

Currently there is the possibility to run singularity/apptainer containers on all our Servers. This is really similar to docker, but much more secure for multi-user servers. Almost every docker container can be converted into a singularity container. Some of the build recipes use docker.

There are a number of prepared containers but more can be added. If you have a wish or an existing container useful for others please share.

YAML
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containers:
 - root: /home/swd/containers
 - available:
    - RTTOV:
      - RTTOV: 12.3
      - compiler: gcc:7.3.0 (anaconda)
      - path: /home/swd/containers/rttov-jupyter/jup3rttov.sif
      - os: centos:6.10
      - python: 3.7.4
      - singularity: 3.5.2
      - packages: 
        - anaconda3
        - jupyter jupyterlab numpy matplotlib pandas xarray bottleneck dask numba scipy netcdf4 cartopy h5netcdf nc-time-axis cfgrib eccodes nodejs
      - apps:
        - atlas
        - lab
        - notebook
        - rtcoef
        - rthelp
        - rttest
      - description: Use for running RTTOV simulations with Python.
    - LIBEMOS:
      - LIBEMOS: 4.5.1
      - compiler: gcc:7.5.0
      - path: /home/swd/containers/libemos-dev/libemos-dev.sif
      - os: ubuntu:18.04
      - singularity: 3.8.6
      - packages:
        - openmpi:2.1.1-8
        - fftw3:3.3.7-1
        - eccodes:2.6.0
        - libemos
      - description: Use for building flexextract with working libemos dependencies.
    - TEXLIVE:
      - TEXLIVE: TeX Live 2022
      - compiler: gcc:12.2.0
      - path: /home/swd/containers/texlive/texlive-2022.sif
      - os: debian 12
      - singularity: 3.8.7
      - packages:
        - texlive from gitlab
Last update: February 29, 2024
Created: October 14, 2021