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Commit cd5a7e95 authored by Michael Blaschek's avatar Michael Blaschek :bicyclist:
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Jet-Cluster.md
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......@@ -3,50 +3,22 @@
[[_TOC_]]
# Getting Started
## Getting Started
Welcome to the HPC @IMG @UNIVIE and please follow these steps to become a productive member of our department and make good use of the computer resources.
**Efficiency is keen.**
1. Connect to Jet
2. Load environment (libraries, compilers, interpreter, tools)
3. Checkout Code, Program, Compile, Test
4. Submit to compute Nodes
[How to SSH / VNC / VPN](SSH-VPN-VNC/README.md)
Steps:
1. Request access
2. Connect to Jet
- [How to SSH / VNC / VPN](SSH-VPN-VNC/README.md)
- [Research Hub](https://jet01.img.univie.ac.at/)
3. Load environment (libraries, compilers, interpreter, tools)
4. Checkout Code, Program, Compile, Test
5. Submit to compute Nodes using slurm ([Slurm Tutorial](https://gitlab.phaidra.org/imgw/slurm))
## Jupyterhub
<img src="https://jupyter.org/assets/hublogo.svg" width="300px">
The Jet-cluster serves a [jupyterhub](https://jupyterhub.readthedocs.io/en/stable/) with a [jupyterlab](https://jupyterlab.readthedocs.io/en/stable/) that launches on the jet-cluster compute nodes and allows users to work directly on the cluster as well as submit jobs.
Goto: [](https://jet01.img.univie.ac.at) from within the VPN or UNI-Network.
Login with your jet-Credentials, choose a job and the jupyterlab will be launched.
<img src="Documentation/jet-login.png" width="500px">
<img src="Documentation/jet-job1.png" width="500px">
<img src="Documentation/jet-job2.png" width="500px">
There are several kernels available and some help can be found:
- [Python/](Python/)
- [Tutorial on Jet](Python/Your-First-Notebook-onJet_v2.ipynb)
## User Quotas and Restrictions
Memory limit / slurm requests
:construction:
### Network drives
Currently there are two network drives mounted on the jet cluster. These are connected to the [SRVX8](SRVX8.md) and data can be transfered or accessed like this on the jet cluster. Be aware that the data needs to be transfered via the network before and latencies are higher.
```
131.130.157.8:/raid61 400T 378T 22T 95% /raid61
131.130.157.8:/raid60 319T 309T 11T 97% /raid60
jetfs 1.1P 81T 975T 8% /jetfs
```
# System Information
## System Information
Last Update: 4.12.2020
Node Setup
- 2x Login Nodes
......@@ -55,8 +27,6 @@ Node Setup
![GPFS](Documentation/GPFS-jet.png)
## Node Information
| Name | Value |
| --- | --- |
| Product | ThinkSystem SR650 |
......@@ -69,7 +39,7 @@ Node Setup
Global file system (GPFS) is present on all nodes with about 1 PB (~1000 TB) of storage.
# Software
## Software
The typcial installation of a intel-cluster has the INTEL Compiler suite (`intel-parallel-studio`) 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:
......@@ -122,5 +92,68 @@ nco/4.9.3-gcc-8.3.1-g7o6lao
on how to use environment modules go to [Using Environment Modules](Misc/Environment-Modules.md)
## Jupyterhub
<img src="Documentation/jupyterhub-logo.svg" width="100px">
The Jet-cluster serves a [jupyterhub](https://jupyterhub.readthedocs.io/en/stable/) with a [jupyterlab](https://jupyterlab.readthedocs.io/en/stable/) that launches on the jet-cluster compute nodes and allows users to work directly on the cluster as well as submit jobs.
Goto: [](https://jet01.img.univie.ac.at) from within the VPN or UNI-Network.
Login with your jet-Credentials, choose a job and the jupyterlab will be launched.
<img src="Documentation/jet-login.png" width="500px">
<img src="Documentation/jet-job1.png" width="500px">
<img src="Documentation/jet-job2.png" width="500px">
There are several kernels available and some help can be found:
- [Python/](Python/)
- [Tutorial on Jet](Python/Your-First-Notebook-onJet_v2.ipynb)
## User Quotas and Restrictions
Please try to use the compute nodes in a responsible manner. Currently there are not restrictions on the duration or the resources you can request. However, please follow these rules of collaboration:
Jobs
- CPU, keyword: `ntasks` e.g. 1 Node == 2x20 physcial cores
- Memory, keyword: `mem` e.g. each Node up to 754 GB
- Runtime, keyword: `time` e.g. try to split jobs into pieces.
Consider the following example. You can use one node relatively easy for more than 3 days with your jobs running, but do not use all nodes an block them for all other users for 3 days. If you need multiple nodes, split the jobs into shorter runtimes. In general it is better to have more smaller jobs that are processed in a chain. Also try not to use too much resources that get wasted. Have a look at resources used in your jobs using the `/usr/bin/time` command or look [here](https://gitlab.phaidra.org/imgw/slurm).
Sample Job
```
#!/bin/bash
# SLURM specific commands
#SBATCH --job-name=test-run
#SBATCH --output=test-run.log
#SBATCH --ntasks=1
#SBATCH --mem=1MB
#SBATCH --time=05:00
#SBATCH --mail-type=BEGIN # first have to state the type of event to occur
#SBATCH --mail-user=<email@address.at> # and then your email address
# Your Code below here
module load miniconda3
# Execute the miniconda Python
# use /usr/bin/time -v [program]
# gives statistics on the resources the program uses
# nice for testing
/usr/bin/time -v python3 -v
```
Storage Limitations are set mainly to the HOME directory (default: 100 GB), but there are some general restrictions as well.
On the Login Nodes (jet01/jet02) jobs can only use 20 GB of Memory as the rest needs to be reserved for the file system and destribution services. Jobs will be automatically killed after a safety margin.
## Network drives
Currently there are two network drives mounted on the jet cluster. These are connected to the [SRVX8](SRVX8.md) and data can be transfered or accessed like this on the jet cluster. Be aware that the data needs to be transfered via the network before and latencies are higher.
```
131.130.157.8:/mnt/scratch 400T 378T 22T 95% /mnt/scratch
131.130.157.8:/mnt/users 319T 309T 11T 97% /mnt/users
jetfs 1.1P 81T 975T 8% /jetfs
```
## Slurm
[Slurm Tutorial on Gitlab](https://gitlab.phaidra.org/imgw/slurm) 🔒
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GNU AFFERO GENERAL PUBLIC LICENSE
Version 3, 19 November 2007
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
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TERMS AND CONDITIONS
0. Definitions.
"This License" refers to version 3 of the GNU Affero General Public License.
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To "propagate" a work means to do anything with it that, without
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To "convey" a work means any kind of propagation that enables other
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The "source code" for a work means the preferred form of the work
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The Corresponding Source need not include anything that users
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The Corresponding Source for a work in source code form is that
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All rights granted under this License are granted for the term of
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and the Corresponding Source of the work is not available for anyone
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the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
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in the business of distributing software, under which you make payment
to the third party based on the extent of your activity of conveying
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parties who would receive the covered work from you, a discriminatory
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conveyed by you (or copies made from those copies), or (b) primarily
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or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or
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License and any other pertinent obligations, then as a consequence you may
not convey it at all. For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Remote Network Interaction; Use with the GNU General Public License.
Notwithstanding any other provision of this License, if you modify the
Program, your modified version must prominently offer all users
interacting with it remotely through a computer network (if your version
supports such interaction) an opportunity to receive the Corresponding
Source of your version by providing access to the Corresponding Source
from a network server at no charge, through some standard or customary
means of facilitating copying of software. This Corresponding Source
shall include the Corresponding Source for any work covered by version 3
of the GNU General Public License that is incorporated pursuant to the
following paragraph.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the work with which it is combined will remain governed by version
3 of the GNU General Public License.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU Affero General Public License from time to time. Such new versions
will be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU Affero General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
GNU Affero General Public License, you may choose any version ever published
by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
versions of the GNU Affero General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.
Later license versions may give you additional or different
permissions. However, no additional obligations are imposed on any
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THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
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HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
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IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Computer Resources
Copyright (C) 2021 IMGW
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published
by the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If your software can interact with users remotely through a computer
network, you should also make sure that it provides a way for users to
get its source. For example, if your program is a web application, its
interface could display a "Source" link that leads users to an archive
of the code. There are many ways you could offer source, and different
solutions will be better for different programs; see section 13 for the
specific requirements.
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU AGPL, see
<https://www.gnu.org/licenses/>.
Latex/README.md
+ 7
− 7
View file @ cd5a7e95
......@@ -4,15 +4,15 @@
What you need to get started:
1. A latex distribution, e.g. texlive or Miktex
* Using a online latex service, e.g. [Overleaf](www.overleaf.de), [latex4technics](https://www.latex4technics.com)
* Or a online latex service, e.g. [Overleaf](www.overleaf.de), [latex4technics](https://www.latex4technics.com)
2. An Editor, e.g. TexStudio or Texshop, ...
3. Examples:
* Open [Seminararbeit.tex ](Seminararbeit.tex) [PDF](Seminararbeit.pdf) [on Overleaf](https://de.overleaf.com/read/whhnjmbwsvpy)
* [Examples](https://www.latextemplates.com)
* Open [Seminararbeit.tex ](Seminararbeit.tex) or as [PDF](Seminararbeit.pdf) or online [on Overleaf](https://de.overleaf.com/read/whhnjmbwsvpy)
* other [Examples](https://www.latextemplates.com)
* More [Overleaf-Examples](https://de.overleaf.com/latex/examples)
[Advanced Guide to writing scientific papers with $`\LaTeX`$ (Wissenschaftliche Arbeiten schreiben mit $`\LaTeX`$
)](Wissenschaftliches-Script-Latex-Seibert-05.2021.pdf)
)](Wissenschaftliches-Script-Latex-Seibert-05.2021.pdf) or the [latest](https://homepage.univie.ac.at/petra.seibert/files/latexscript.pdf)
# What to use?
......@@ -20,11 +20,12 @@ What you need to get started:
1. Professional PDF with printing quality
2. Lots of mathemetical, physical, chemical or other equations. Need to be in Latex anyway.
3. Need to use a fixed layout given to you by the university or journal
4.
4. Programming like typsetting, with predictable outcome, as compared to other word processors.
5. Readable and shareable
**5 Reasons for Markdown**
1. Markdown is much easier to learn and visual
2. Readable and shareable, collaborate
2. Readable and shareable, easy to collaborate
3. Markdown can be converted into HTML, PDF, DOCX, ...
4. You see what you get editors exist for Markdown with live preview
5. Other content like Maths formulas or tables can be added easily.
......@@ -42,7 +43,6 @@ It is easy to write, share and version control. Markdown files can be converted
You can find an example ...
What you need to get started to convert to PDF:
1. [Pandoc](https://pandoc.org/installing.html)
2. Latex (Note tips when installing pandoc)
......
Misc/README.md
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Note: Tabula only works on text-based PDFs, not scanned documents.
## Q: What is my process doing?
If you experience processes that are slower than they should be or you are unsure what it is doing. There are certain ways to get more information.
### Process States
For example if you run `ps ux` or `htop` and check your process, you should see a state with the following meaning:
D = UNINTERRUPTABLE_SLEEP
R = RUNNING & RUNNABLE
S = INTERRRUPTABLE_SLEEP
T = STOPPED
Z = ZOMBIE
Processes in a **"D"** or uninterruptible sleep state are usually waiting on I/O. The ps command shows a "D" on processes in an uninterruptible sleep state. The vmstat command also shows the current processes that are "blocked" or waiting on I/O. The vmstat and ps will not agree on the number of processes in a "D" state, so don't be too concerned. You cannot kill "D" state processes, even with `SIGKILL` or `kill -9`. As the name implies, they are uninterruptible. You can only clear them by rebooting the server or waiting for the I/O to respond. It is normal to see processes in a "D" state when the server performs I/O intensive operations.
As root you can do `echo w > /proc/sysrq-trigger` and check the `dmesg -T` what the stacktrace reports.
Processes in a **"S"** or interruptable sleep state are waiting for the user or data to continue. Unlike processes in a **"T"** or stopped state, which must have been suspended, with e.g. Ctrl+Z. Using `jobs` to see what processees you have or running `fg` to get the processes back to your command line.
Processes in a **"Z"** or zombie state are being terminated by the parent processes. If the parent did not clean up, a zombie processes lingers.
**How to kill a zombie processes?**
The first step is to find its parent process. Typically there is a column in the "ps" output for PPID or Parent Process ID. You want to identify this number. Once you do you can send a SIGCHLD signal to that parent to tell it to perform this cleanup.
`kill -s SIGCHLD <PPID>`
In worst case scenarios where the parent is generating a lot of zombie processes that are not getting cleaned up, you can kill or restart the parent.
Misc/Virtual-Terminals.md
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......@@ -35,6 +35,11 @@ tmux kill-server
A useful feature is to create a split screen in tmux. so inside a tmux session switch to command mode (`CTRL+b`) and push `"` for horizontal split or `%` for vertical split. Moving between splits or here called panes can be done in multiple ways, but easily with `CTRL+b` and the arrow-keys ![arrowkeys](https://media-cdn.ubuntu-de.org/wiki/thumbnails/6/62/62ca4de87dac191968e0278e8a342da9ce26ad59i66x.png)
enable mouse srolling and a longer history, write to `~/.tmux.conf`:
```
set -g mouse on
set -g history-limit 30000
```
### Sharing a tmux session with other users?
......
Python/QA-001-Cartopy-Installation-Jet.ipynb
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#!/bin/bash
# By MB
# Jumpstart a python environment for my students
# Activate anaconda module
module load anaconda3
# Create a new kernel that is based on anaconda, but with some additional packages
# potentially specify which python version, e.g. python=3.8
conda create -y -n ClimatePy3 numpy ipykernel zarr
# This will create a ~/.conda/envs/ClimatePy3/ directory
# using ~/.conda/envs/ClimatePy3/bin/python3 in a script is possible
# activate that environment by sourcing the conda environment
source $(dirname $(which conda))/../etc/profile.d/conda.sh
# and activating your new
conda activate ClimatePy3
# deactivate environment
conda deactivate
# FIN
\ No newline at end of file
README.md
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......@@ -19,13 +19,10 @@ If you care to participate please do so. Raise an Issue or give some feedback.
Missing solutions are very welcome.
## Information on some Systems
- [Jet Cluster Description](Jet-Cluster.md) 📄
- [Jupyterhub on Jet](https://jet01.img.univie.ac.at) 🤖
- [Teaching on SRVX1](SRVX1.md) 📄
- [Jupyterhub on SRVX1](https://srvx1.img.univie.ac.at) 🤖
- [Instructions for Jupyterhub on SRVX1](TeachingHub.md) 📄
- [Research on SRVX2](SRVX2.md) 📄
- [Research on SRVX8](SRVX8.md) 📄
- [Vienna Scientific Cluster - Training Courses](https://vsc.ac.at/training)
- [Vienna Scientific Cluster - Research - Private Node Information](VSC.md) 📄
# Available Servers
- [SRVX1](SRVX1.md), [SRVX8](SRVX8.md) @ UZA2
- [Jet Cluster @ Arsenal](Jet-Cluser.md)
- [Vienna Scientific Cluster (VSC)](VSC.md)
- [VSC Training](https://vsc.ac.at/training)
- [VSC Trainings @ IMGW](https://gitlab.phaidra.org/imgw/trainings-course)
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......@@ -5,7 +5,16 @@
## Getting Started
[How to SSH / VNC / VPN](SSH-VPN-VNC/README.md)
Steps:
1. Request access
2. Access using SSH - [How to SSH / VNC / VPN](SSH-VPN-VNC/README.md)
3. Access using Teaching Hub - [How to connect using the TeachingHub](TeachingHub.md)
4. Access Services:
- [Webdata](https://srvx1.img.univie.ac.at/webdata) - Hosting files
- [Yopass](https://srvx1.img.univie.ac.at/secure) - Encrypted message service
- [ECGateway](https://srvx1.img.univie.ac.at/ecmwf/ecmwf) (UNIVIE Network, [VPN](SSH-VPN-VNC/VPN.md))
- [Transfer.sh](https://srvx1.img.univie.ac.at/filetransfer) ()
- [iLibrarian](https://srvx1.img.univie.ac.at/)
## System Information
| Name | Value |
......@@ -30,16 +39,18 @@
----------------------------------------------
```
## Services
The SRVX1 is the central access point to IMG services:
goto: [srvx.img.univie.ac.at](https://srvx1.img.univie.ac.at)
Currently running:
- TeachingHub
- Webdata
- TeachingHub (Jupyterhub)
- Webdata - File hosting
- YoPass - Password Sharing
- iLibrarian - Paper Management (development)
- Filetransfer.sh - File sharing service (development)
## Jupyterhub
<img src="https://jupyter.org/assets/hublogo.svg" width="300px">
<img src="Documentation/jupyterhub-logo.svg" width="300px">
SRVX1 serves a teaching [jupyterhub](https://jupyterhub.readthedocs.io/en/stable/) with a [jupyterlab](https://jupyterlab.readthedocs.io/en/stable/). It allows easy access for students and teachers.
......@@ -54,6 +65,7 @@ Download/Use any of these required Authenticator Apps:
- [FreeOTP (Mobile)](https://freeotp.github.io/)
- [Google Auth (Mobile)](https://play.google.com/store/apps/details?id=com.google.android.apps.authenticator2)
**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
......@@ -78,47 +90,62 @@ Please note that new versions might already be installed.
```bash
$ module av
--------------- /home/swd/spack/share/spack/modules/linux-rhel8-skylake_avx512 ----------------
anaconda2/2019.10-gcc-8.4.1 netcdf-fortran/4.5.3-gcc-8.4.1
anaconda3/2020.07-gcc-8.4.1 netlib-lapack/3.9.1-gcc-8.4.1
anaconda3/2020.11-gcc-8.4.1 netlib-lapack/3.9.1-intel-20.0.4
anaconda3/2021.05-gcc-8.4.1 netlib-lapack/3.9.1-oneapi-2021.2.0
autoconf/2.69-oneapi-2021.2.0 netlib-scalapack/2.1.0-gcc-8.4.1
autoconf/2.71-oneapi-2021.2.0 netlib-scalapack/2.1.0-gcc-8.4.1-MPI3.1.6
eccodes/2.19.1-gcc-8.4.1 openblas/0.3.17-gcc-8.4.1
eccodes/2.19.1-intel-20.0.4 openmpi/3.1.6-gcc-8.4.1
eccodes/2.21.0-gcc-8.4.1 openmpi/3.1.6-intel-20.0.4
eccodes/2.21.0-intel-20.0.4 openmpi/4.0.5-gcc-8.4.1
geos/3.9.1-gcc-8.4.1 openmpi/4.0.5-intel-20.0.4
hdf5/1.10.7-gcc-8.4.1-MPI3.1.6 perl/5.32.0-intel-20.0.4
hdf5/1.10.7-intel-20.0.4-MPI3.1.6 proj/8.1.0-gcc-8.4.1
hdf5/1.12.0-gcc-8.4.1 python/3.8.9-gcc-8.4.1
hdf5/1.12.0-intel-20.0.4
hdf5/1.12.0-intel-20.0.4-MPI3.1.6
hdf5/1.12.0-oneapi-2021.2.0
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-8.4.1
libemos/4.5.9-intel-20.0.4
matlab/R2020b-gcc-8.4.1
miniconda2/4.7.12.1-gcc-8.4.1
miniconda3/4.10.3-gcc-8.4.1
ncl/6.5.0-gcc-8.4.1-MPI3.1.6
ncl/6.6.2-gcc-8.4.1-MPI3.1.6
nco/4.9.3-gcc-8.4.1
nco/4.9.3-intel-20.0.4
ncview/2.1.8-gcc-8.4.1
netcdf-c/4.6.3-gcc-8.4.1-MPI3.1.6
netcdf-c/4.6.3-intel-20.0.4-MPI3.1.6
netcdf-c/4.7.4-gcc-8.4.1
netcdf-c/4.7.4-intel-20.0.4
netcdf-fortran/4.5.2-gcc-8.4.1-MPI3.1.6
netcdf-fortran/4.5.2-intel-20.0.4-MPI3.1.6
anaconda3/2020.11-gcc-8.5.0 matlab/R2020b-gcc-8.5.0 proj/8.1.0-gcc-8.5.0
anaconda3/2021.05-gcc-8.5.0 miniconda2/4.7.12.1-gcc-8.5.0 python/3.8.12-gcc-8.5.0
autoconf/2.69-oneapi-2021.2.0 miniconda3/4.10.3-gcc-8.5.0
autoconf/2.71-oneapi-2021.2.0 nco/4.9.3-intel-20.0.4
cdo/1.9.10-gcc-8.5.0 nco/5.0.1-gcc-8.5.0
eccodes/2.19.1-gcc-8.5.0 ncview/2.1.8-gcc-8.5.0
eccodes/2.19.1-gcc-8.5.0-MPI3.1.6 netcdf-c/4.6.3-gcc-8.5.0-MPI3.1.6
eccodes/2.19.1-intel-20.0.4 netcdf-c/4.6.3-intel-20.0.4-MPI3.1.6
eccodes/2.19.1-intel-20.0.4-MPI3.1.6 netcdf-c/4.7.4-gcc-8.5.0
eccodes/2.21.0-gcc-8.5.0 netcdf-c/4.7.4-intel-20.0.4
eccodes/2.21.0-gcc-8.5.0-MPI3.1.6 netcdf-fortran/4.5.2-gcc-8.5.0-MPI3.1.6
eccodes/2.21.0-intel-20.0.4 netcdf-fortran/4.5.2-intel-20.0.4-MPI3.1.6
gcc/8.5.0-gcc-8.5rhel8 netcdf-fortran/4.5.3-gcc-8.5.0
geos/3.8.1-gcc-8.5.0 netlib-lapack/3.9.1-gcc-8.5.0
hdf5/1.10.7-gcc-8.5.0 netlib-lapack/3.9.1-intel-20.0.4
hdf5/1.10.7-gcc-8.5.0-MPI3.1.6 netlib-lapack/3.9.1-oneapi-2021.2.0
hdf5/1.10.7-intel-20.0.4-MPI3.1.6 netlib-scalapack/2.1.0-gcc-8.5.0
hdf5/1.12.0-intel-20.0.4 netlib-scalapack/2.1.0-gcc-8.5.0-MPI3.1.6
hdf5/1.12.0-oneapi-2021.2.0 openblas/0.3.18-gcc-8.5.0
intel-mkl/2020.4.304-intel-20.0.4 openmpi/3.1.6-gcc-8.5.0
intel-oneapi-compilers/2021.2.0-oneapi-2021.2.0 openmpi/3.1.6-intel-20.0.4
intel-oneapi-dal/2021.2.0-oneapi-2021.2.0 openmpi/4.0.5-gcc-8.5.0
intel-oneapi-mkl/2021.2.0-oneapi-2021.2.0 openmpi/4.0.5-intel-20.0.4
intel-oneapi-mpi/2021.2.0-oneapi-2021.2.0 parallel-netcdf/1.12.2-gcc-8.5.0
intel-parallel-studio/composer.2020.4-intel-20.0.4 parallel-netcdf/1.12.2-gcc-8.5.0-MPI3.1.6
libemos/4.5.9-gcc-8.5.0-MPI3.1.6 perl/5.32.0-intel-20.0.4
------------------------------------------------------ /home/swd/modules ------------------------------------------------------
anaconda3/leo-current-gcc-8.3.1 idl/8.2-sp1 micromamba/0.15.2 pypy/7.3.5 xconv/1.94
ecaccess/4.0.2 intelpython/2021.4.0.3353 ncl/6.6.2 shpc/0.0.33
```
on how to use environment modules go to [Using Environment Modules](Misc/Environment-Modules.md)
## User services
There is a script collection that is accessible via the `userservices` command. e.g. running
```bash
$ 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](https://filesender.aco.net/) account (accessible via your [u:account](https://zid.univie.ac.at/my-uaccount/)).
## Container Hub
......
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## Getting Started
[How to SSH / VNC / VPN](SSH-VPN-VNC/README.md)
Steps:
1. Request access
2. Access using SSH - [How to SSH / VNC / VPN](SSH-VPN-VNC/README.md)
## System Information
......@@ -92,11 +94,40 @@ python/3.8.9-gcc-4.8.5
micromamba/latest
```
## User services
There is a script collection that is accessible via the `userservices` command. e.g. running
```bash
$ 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
sysinfo --- Display system information
transfersh --- Transfer files/directories (IMGW subnet)
vnc --- VNC Server Setup/Launcher/Stopper
vnc-geometry --- Change geometry of VNC display
weather --- Retrieve weather information
------------------------------------------------------------------------
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). Please note the available VNC services.
## Virtual Machine Hub
Currently the system acts as a virtual machine host.
Active:
- VERA
- Ubuntu Geographic
## Container Hub
......
SSH-VPN-VNC/README.md
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......@@ -4,7 +4,7 @@
## General Access
Please use these methods to access the servers:
1. Connect using [SSH](SSH.md)
1. Connect using [SSH](SSH.md) or [MOSH](https://mosh.org/#) (Mobile Secure Shell)
2. Connect using [TeachingHub](../TeachingHub.md) or [ResearchHub](../Jet-Cluster.md#jupyterhub)
3. Connect using [VNC](VNC.md)
4. Access from outside the UNI, [VPN](VPN.md)
......
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......@@ -33,9 +33,16 @@ Host srvx2jet
Host login
HostName login.univie.ac.at
User [U:Account USERNAME]
Host ecaccess
Host ecaccess.ecmwf.int
HostKeyAlgorithms ssh-dss
KexAlgorithms diffie-hellman-group1-sha1
Ciphers aes256-cbc
```
and replacing `[USERNAME]` and `[U:Account USERNAME]` with your usernames. Using such a file allows to connect like this `ssh srvx1` using the correct server adress and specified username. Copy this file as well on `login.univie.ac.at` and you can use commands like this: `ssh -t login ssh jet` to connect directly to `jet` via the `login` gateway.
Please note the special algorithms for ecaccess.
If you want to use ssh-keys you can also use different keys in `.ssh/config` per server with `IdentityFile ~/.ssh/id_rsa_for_server`.
**Note: If you are having trouble with your ssh-key being accepted. You need to check the selinux security policy. Because we use non standard home directories, which are not accepted by default.** Do that by running:
......@@ -111,3 +118,25 @@ mkdir -p $HOME/srvx1
mountserver [USER]@srvx1.img.univie.ac.at /users/staff/[USER] $HOME/srvx1
```
Note the directories might vary, depending on your membership (staff, external, students).
## MOSH
Remote terminal application that allows roaming, supports intermittent connectivity, and provides intelligent local echo and line editing of user keystrokes.
Mosh is a replacement for interactive SSH terminals. It's more robust and responsive, especially over Wi-Fi, cellular, and long-distance links.
In order to use:
- install on your client, [instructions](https://mosh.org/#getting)
```bash
$ mosh user@srvx1.img.univie.ac.at
```
## SSH Banner
If you login in to any of the IMGW Servers you will be greeted by a banner showing some information about the system. However, after some time you might not need that information anymore.
run the following and you will never see the banner again.
```bash
touch $HOME/.hushlogin
```
remove that file and you shall see it again.
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# Teaching Hub @ IMGW
<img src="https://jupyter.org/assets/hublogo.svg" width="300px">
<img src="Documentation/jupyterhub-logo.svg" width="300px">
- Address: [Teaching Hub](https://srvx1.img.univie.ac.at)
- Access to the Teaching Hub can be done only via a browser.
......
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......@@ -27,13 +27,14 @@ CPU model: Intel(R) Xeon(R) Platinum 8174 CPU @ 3.10GHz
378 GB Memory
```
We have access to 5 private Nodes of that kind. Check with
We have access to 5 private Nodes of that kind. We also have access to the jupyterhub on VSC. Check with
```bash
$ sqos
qos_name total used free walltime priority partitions
=========================================================================
p71386_0384 5 1 4 10-00:00:00 100000 mem_0384
jupyter 20 1 19 3-00:00:00 1000 jupyter
p71386_0384 5 0 5 10-00:00:00 100000 mem_0384
```
## Storage on VSC-4
......@@ -44,6 +45,10 @@ All quotas are shared between users:
- `$DATA` (up to 10 TB, backed up)
- `$BINFL` (up to 1TB, fast scratch)
- `$BINFS` (up to 2GB, SSD fast)
- `$TMPDIR` (50% of main memory, deletes after job finishes)
- `/local` (Compute Nodes, 480 GB SSD, deletes after Job finishes)
![VSC Storage Performance](https://service.vsc.ac.at/slides/introduction-to-vsc/08_storage_infrastructure/pictures/vsc_write_performance.png)
Check quotas:
```bash
......@@ -59,6 +64,15 @@ home FILESET 62.17G 100G 100G 207.8M none | 631
```
## Other Storage
We have access to the Earth Observation Data Center [EODC](https://eodc.eu/data/), where one can find primarily the following data sets:
- Sentinel-1, 2, 3
- Wegener Center GPS RO
These datasets can be found directly via `/eodc/products/`.
We are given a private data storage location (`/eodc/private/uniwien`), where we can store up to 22 TB on VSC-4. However, that might change in the future.
## Node Information VSC-3
```
CPU model: Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
......
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