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Jet-Cluster.md

+# The Jet Cluster
+[@IMG University of Vienna](https://jet01.img.univie.ac.at) :rocket:
+
+[[_TOC_]]
+
+## 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.
+
+### SSH
+- [x] Terminal, Putty, ...
+- [x] Network access @UNIVIE
+
+Use a terminal or [Putty](https://www.putty.org/) to connect with SSH to the server
+```bash
+ssh [user]@jet01.img.univie.ac.at
+```
+Please replace `[user]` with the username given by the [sysadmin](mailto:michael.blaschek@univie.ac.at) and supply your password when asked for. This should give you access to the login node. If you are outside of the university network, then please goto [VPN](#VPN) below.
+
+### VPN
+- [x] `u:account`
+
+The jet cluster is only accessible from within the virtual network of the university of Vienna. Therefore access from outside has to be granted via the [VPN-Service](https://vpn.univie.ac.at). Go there and login with your `u:account` and download the *Big-IP Edge* client for you system. 
+
+![](https://zid.univie.ac.at/fileadmin/user_upload/d_zid/zid-open/daten/datennetz/vpn/Windows/01_download_neu.png) 
+
+Links:
+ * [ZID-VPN](https://vpn.univie.ac.at/f5-w-68747470733a2f2f7a69642e756e697669652e61632e6174$$/vpn/)
+ * Linux (Ubuntu, Generic), Windows, Mac: [VPN user guides](https://vpn.univie.ac.at/f5-w-68747470733a2f2f7a69642e756e697669652e61632e6174$$/vpn/anleitungen/)
+ * Arch based AUR package [AUR f5fpc](https://aur.archlinux.org/packages/f5fpc/)
+
+Follow the install instructions for Windows, Mac and Linux and make sure the software works.
+
+![](https://zid.univie.ac.at/fileadmin/user_upload/d_zid/zid-open/daten/datennetz/vpn/Windows/08_verbinden.png)
+
+On Windows and MAc you get a nice gui that requires you to fill in the VPN server: `vpn.univie.ac.at` and username and password from the `u:account`. On Linux execute the following:
+```
+f5fpc -s -t vpn.univie.ac.at -u [user]
+```
+The status can be checked with `f5fpc --info`.
+
+### VNC
+The login nodes (`jet01` and `jet02`) allow to run a `VNC`-Server 
+
+:construction:
+
+### 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.
+
+![Login](Documentation/jet-login.png)
+![Job](Documentation/jet-job1.png)
+![Jobs](Documentation/jet-job2.png)
+
+:construction:
+
+
+### 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
+Last Update: 4.12.2020
+Node Setup
+ - 2x Login Nodes
+ - 7x Compute Nodes
+
+![GPFS](Documentation/GPFS-jet.png)
+
+
+### Node Information
+
+| Name | Value |
+| --- | --- |
+| Product | ThinkSystem SR650 |
+| Distro | RedHatEnterprise 8.2 Ootpa |
+| Kernel | 4.18.0-147.el8.x86_64 GNU/Linux |
+| Processor | Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz |
+| Cores | 2 CPU,  20 physical cores per CPU, total 80 logical CPU units |
+| BaseBoard | Lenovo -\[7X06CTO1WW\]- Intel Corporation C624 Series Chipset |
+| CPU Time | 350 kh |
+| Memory | 755 GB Total |
+| Memory/Core | 18.9 GB |
+| Network | 40 Gbit/s (Infiniband) |
+
+Global file system (GPFS) is present on all nodes with about 1 PB (~1000 TB) of storage.
+
+## 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:
+ - OpenMPI
+ - HDF5
+ - NetCDF (C, Fortran)
+ - ECCODES from [ECMWF](https://confluence.ecmwf.int/display/ECC)
+ - 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.
+
+<img src="http://modules.sourceforge.net/modules_red.svg" width="300px">
+
+### Currently installed modules
+```bash
+>>> module av
+---------------------------------- /jetfs/spack/share/spack/modules/linux-rhel8-skylake_avx512 -----------------------------------
+anaconda2/2019.10-gcc-8.3.1-5pou6ji                         ncview/2.1.8-gcc-8.3.1-s2owtzw               
+anaconda3/2019.10-gcc-8.3.1-tmy5mgp                         netcdf-c/4.7.4-gcc-8.3.1-fh4nn6k             
+anaconda3/2020.07-gcc-8.3.1-weugqkf                         netcdf-c/4.7.4-intel-20.0.2-337uqtc          
+cdo/1.9.8-gcc-8.3.1-ipgvzeh                                 netcdf-fortran/4.5.3-gcc-8.3.1-kfd2vkj       
+eccodes/2.18.0-gcc-8.3.1-s7clum3                            netcdf-fortran/4.5.3-intel-20.0.2-irdm5gq    
+eccodes/2.18.0-intel-20.0.2-6tadpgr                         netlib-lapack/3.8.0-gcc-8.3.1-ue37lic        
+enstools/2020.11.dev-gcc-8.3.1-fes7kgo                      netlib-scalapack/2.1.0-gcc-8.3.1-pbkjymd     
+gcc/8.3.1-gcc-8.3.1-pp3wjou                                 openblas/0.3.10-gcc-8.3.1-ncess5c            
+geos/3.8.1-gcc-8.3.1-o76leir                                openmpi/3.1.6-gcc-8.3.1-rk5av53              
+hdf5/1.12.0-gcc-8.3.1-awl4atl                               openmpi/3.1.6-intel-20.0.2-ubasrpk           
+hdf5/1.12.0-intel-20.0.2-ezeotzr                            openmpi/4.0.5-gcc-8.3.1-773ztsv              
+intel-mkl/2020.3.279-gcc-8.3.1-5xeezjw                      openmpi/4.0.5-intel-20.0.2-4wfaaz4           
+intel-mkl/2020.3.279-intel-20.0.2-m7bxged                   parallel-netcdf/1.12.1-gcc-8.3.1-gng2jcu     
+intel-parallel-studio/composer.2020.2-intel-20.0.2-zuot22y  parallel-netcdf/1.12.1-gcc-8.3.1-xxrhtxn     
+julia/1.5.2-gcc-8.3.1-3iwgkf7                               parallel-netcdf/1.12.1-intel-20.0.2-sgz3yqs  
+libemos/4.5.9-gcc-8.3.1-h3lqu2n                             proj/7.1.0-gcc-8.3.1-xcjaco5                 
+miniconda2/4.7.12.1-gcc-8.3.1-zduqggv                       zlib/1.2.11-gcc-8.3.1-bbbpnzp                
+miniconda3/4.8.2-gcc-8.3.1-3m7b6t2                          zlib/1.2.11-intel-20.0.2-3h374ov             
+nco/4.9.3-gcc-8.3.1-jtokrle 
+```
+Using [environment modules](https://modules.readthedocs.io/en/latest/) it is possible to have different software libraries (versions, compilers) side-by-side and ready to be loaded. Be aware that some libraries are dependent on others. It is recommended to load the highest rank library first to check what dependencies are loaded as well. e.g.:
+```
+>>> module load eccodes/2.18.0-intel-20.0.2-6tadpgr 
+```
+loads the `ECCODES` library and all dependencies. e.g. intel compilers, as indicated by the naming.
+```
+>>> module list
+Currently Loaded Modulefiles:
+ 1) zlib/1.2.11-intel-20.0.2-3h374ov     3) hdf5/1.12.0-intel-20.0.2-ezeotzr              5) netcdf-c/4.7.4-intel-20.0.2-337uqtc  
+ 2) openmpi/4.0.5-intel-20.0.2-4wfaaz4   4) parallel-netcdf/1.12.1-intel-20.0.2-sgz3yqs   6) eccodes/2.18.0-intel-20.0.2-6tadpgr  
+```
+`module list` shows the currently loaded modules and reports that 6 libraries need to be loaded as dependencies for `ECCODES`. Thus, it is not necessary to load the other libraries manually as they are dependencies of `ECCODES`.
+
+## Best Practice
+
+1. Example on jet
+2. Example job
+
+[Slurm Tutorial on Gitlab]()
+
+:construction:
+

README.md

@@ -14,4 +14,37 @@ Search with the top bar or go through the directories:
 
 If you care to participate please do so. Raise an Issue or give some feedback.
 
-Missing solutions are very welcome.
\ No newline at end of file
+Missing solutions are very welcome.
+
+## Information on the Jet Cluster
+
+[Description](Jet-Cluster.md)
+**Summary**
+ - Architecture
+ - Software
+ - [JET01-Jupyterhub](https://jet01.img.univie.ac.at)
+
+## Information on SRVX1
+Teaching and webaccess server
+
+[Description](SRVX1.md)
+**Summary**
+ - Architecture
+ - Software
+ - [SRVX1-Jupyterhub](https://srvx1.img.univie.ac.at)
+
+# Information on SRVX2
+Computing Node @UZA2
+
+[Description](SRVX2.md)
+**Summary**
+ - Architecture
+ - Software
+
+# Information on SRVX8
+Researchers @UZA2 
+
+[Description](SRVX8.md)
+**Summary**
+ - Architecture
+ - Software

SRVX1.md

+
+# S R V X 1
+
+[[_TOC_]]
+
+## Getting Started
+
+### SSH
+
+### VPN
+
+### Jupyterhub
+
+## System Information
+| Name | Value |
+| --- | --- |
+| Product | PowerEdge R720xd |
+| Distro | CentOS 6.10 Final |
+| Kernel | 2.6.32-754.29.2.el6.centos.plus.x86_64 GNU/Linux |
+| Processor | Intel(R) Xeon(R) CPU E5-2690 0 @ 2.90GHz |
+| Cores | 2 CPU,  8 physical cores per CPU, total 32 logical CPU units |
+| BaseBoard | Dell Inc. 0C4Y3R Intel Corporation C600/X79 series chipset |
+| CPU time | 140 kh |
+| Memory | 190 GB Total |
+| Memory/Core | 11.9 GB |
+| Network | 10 Gbit/s |
+
+## Software
+
+## Best Practice
+
+## Networking

SRVX2.md

+
+# S R V X 8
+
+[[_TOC_]]
+
+## Getting Started
+
+### SSH
+
+### VPN
+
+### Jupyterhub
+
+## System Information
+| Name | Value |
+| --- | --- |
+| Product | PowerEdge R940 |
+| Distro | CentOS 8.2.2004 Core |
+| Kernel | 4.18.0-147.el8.x86_64 GNU/Linux |
+| Processor | Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz |
+| Cores | 4 CPU,  20 physical cores per CPU, total 160 logical CPU units |
+| BaseBoard | Dell Inc. 0D41HC Intel Corporation C621 Series Chipset |
+| CPU time | 700 kh | 
+| Memory | 376 GB Total |
+| Memory/Core | 9.4 GB |
+
+## Software
+
+## Best Practice
+
+## Networking

SRVX8.md

+
+# S R V X 8
+
+[[_TOC_]]
+
+## Getting Started
+
+### SSH
+
+### VPN
+
+### Jupyterhub
+
+## System Information
+
+| Name | Value |
+| --- | --- |
+| Product | PowerEdge R730xd |
+| Distro | CentOS 6.10 Final |
+| Kernel | 2.6.32-754.29.2.el6.centos.plus.x86_64 GNU/Linux |
+| Processor | Intel(R) Xeon(R) CPU E5-2697 v3 @ 2.60GHz |
+| Cores | 2 CPU,  14 physical cores per CPU, total 56 logical CPU units |
+| BaseBoard | Dell Inc. 0599V5 Intel Corporation C610/X99 series chipset |
+| CPU time | 245 kh |
+| Memory | 504 GB Total |
+| Memory/Core |  18 Gb |
+| Network | 10 Gbit/s |
+
+## Software
+
+## Best Practice
+
+## Networking