diff --git a/Jet-Cluster.md b/Jet-Cluster.md index 012a27cf4f94db995664d4810ba1eaa437116fc7..25bb1c6429b0d387551ffeae48d4da3e320696c2 100644 --- a/Jet-Cluster.md +++ b/Jet-Cluster.md @@ -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  -## 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) 🔒 diff --git a/README.md b/README.md index aa870fb6b560b7e5ad6501ec6ff29178a2a344f5..78a766851bcb12bf26d3482ff13a7f3d06441f39 100644 --- a/README.md +++ b/README.md @@ -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) diff --git a/SRVX1.md b/SRVX1.md index 08272b05efe593672f0f6043b53f38e0f8f45a4d..9cf5ed77bb44473860213f6bed3cd57630eebbdd 100644 --- a/SRVX1.md +++ b/SRVX1.md @@ -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 | @@ -30,7 +39,6 @@ ---------------------------------------------- ``` - ## Services The SRVX1 is the central access point to IMG services: goto: [srvx.img.univie.ac.at](https://srvx1.img.univie.ac.at) @@ -38,6 +46,8 @@ Currently running: - TeachingHub (Jupyterhub) - Webdata - File hosting - YoPass - Password Sharing +- iLibrarian - Paper Management (development) +- Filetransfer.sh - File sharing service (development) ## Jupyterhub <img src="Documentation/jupyterhub-logo.svg" width="300px"> @@ -120,6 +130,30 @@ netcdf-fortran/4.5.2-intel-20.0.4-MPI3.1.6 ``` 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 account (accessible via your u:account). + ## Container Hub diff --git a/SRVX8.md b/SRVX8.md index 98be6e9e336ebc15eba1cf3e92001b23cd1b93e3..1108107331bf4e3affa88573404877b8f3661fb6 100644 --- a/SRVX8.md +++ b/SRVX8.md @@ -5,7 +5,9 @@ ## 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 @@ -125,4 +156,4 @@ containers: - rtcoef - rthelp - rttest -``` \ No newline at end of file +```