Merge branch 'master' of gitlab.phaidra.org:imgw/computer-resources

Data/Guidelines.md

-Shared Data Guideline
-@author: mblaschek
-@email: michael.blaschek@univie.ac.at
-@phone: 53715
-@date: Fri Sep 25 09:15:10 CEST 2020
+# Shared Data Guideline
 
-PATH /jetfs/shared-data
+    @author: mblaschek
+    @email: michael.blaschek@univie.ac.at
+    @phone: 53715
+    @date: Fri Sep 25 09:15:10 CEST 2020
 
-1. Be careful. Do not remove data, unless you are really certain, that this is ok for everyone.
-2. Create directories with clear names. Add permission for others
+Data currently shared on the jet cluster:
+`PATH /jetfs/shared-data`
+
+Steps:
+1. **Be careful.** Do not remove data, unless you are really certain, that this is ok for everyone.
+2. Create directories with clear names. **Add permission for others**
 3. Ask for help if needed.
 4. Add information on your data in the README.md
 
 Here data can be share with other users. 
 If you need to modify these data, copy them to scratch and remove later, in order to save storage and duplicates.
 
+## Notice Permission
+
+Typical Permissions are:
+
+    folders: 755   rwxr-xr-x  allows all users to read
+    files:   644   rw-r--r--  allows all users to read
+
+
+Change permission for all directories under that DIR:
+
+`find [DIR] -type d -exec chmod 755 {} \;`
+
+Change permission for all files:
+
+`find [DIR] -type f -exec chmod 644 {} \;`

Data/README.md

 # Data available at the department of Meteorology and Geophysics
 
+Edit this file also on [gitlab](https://gitlab.phaidra.org/imgw/computer-resources/-/blob/master/Data/README.md)
+
 # Reanalysis data
 There are currently the following reanalysis available
 

Python/QA-004-TeachingHub-SpawnFailed.md

+# Connecting to TeachingHub
+
+*Reported on 11.12.2020*
+
+There is a problem with previous configurations on the Teaching Hub.
+
+Failure to launch/spawn a notebook/jupyter server is the result of some previous configuration files.
+
+If you experience messages like this:
+
+![Server Spawn](pics/Server_spawn.png)
+
+## Steps
+
+1. Connect to SRVX1 in the terminal `ssh [user]@srvx1.img.univie.ac.at`
+2. Remove the `rm -rf .jupyter/` directory 
+3. Restart the server on the Teaching Hub

Python/README.md

@@ -22,3 +22,8 @@ The Idea is to create a `load_modules_into_jupyter.conf` file in your home direc
 [Conda/Virtual Environment](QA-003-Conda-Environment.ipynb)
 
 The idea is to install a conda or virtual environment and use that as a kernel for your notebooks. *Please note the solution for cartopy*
+
+## Q: The Notebook server on the TeachingHub won't start?
+[Teaching-Hub Spawn](QA-004-TeachingHub-SpawnFailed.md)
+
+This usually happens because of an old configuration. Try to remove `~/.jupyter` on SRVX1.

README.md

@@ -16,40 +16,154 @@ If you care to participate please do so. Raise an Issue or give some feedback.
 
 Missing solutions are very welcome.
 
-## Information on the Jet Cluster
+[[_TOC_]]
 
-[Go to Description](Jet-Cluster.md)
 
-**Summary**
- - Architecture
- - Software
- - JupyterHub
- - [JET01-Jupyterhub](https://jet01.img.univie.ac.at)
+# Information on the Jet Cluster
+
+[Go to Description](Jet-Cluster.md)
 
-## Information on SRVX1
+### Architecture
+
+| 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) |
+
+
+### Scientific Software
+ - GNU compilers, Intel compilers, OpenMPI, HDF5, NetCDF, Eccodes, ...
+ - Anaconda Python, Julia
+
+```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 
+```
+
+### JupyterHub
+[JET01-Jupyterhub](https://jet01.img.univie.ac.at)
+
+## Information on SRVX1 - Teach
 Teaching and webaccess server
 
 [Go to Description](SRVX1.md)
 
-**Summary**
- - Architecture
- - Software
- - [SRVX1-Jupyterhub](https://srvx1.img.univie.ac.at)
-
-# Information on SRVX2
+### Architecture
+| 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 |
+
+### Scientific Software
+ - GNU compilers, OpenMPI, HDF5, NetCDF, Eccodes, ...
+ - Anaconda Python
+
+```bash
+>>> module av
+------------- /home/opt/spack/share/spack/modules/linux-centos6-sandybridge -------------
+anaconda3/2020.07-gcc-5.3.0  hdf5/1.10.7-gcc-5.3.0           openmpi/3.1.6-gcc-5.3.0  
+eccodes/2.18.0-gcc-5.3.0     miniconda3/4.8.2-gcc-5.3.0      proj/7.1.0-gcc-5.3.0     
+gcc/5.3.0-gcc-5.3.0          netcdf-c/4.7.4-gcc-5.3.0        zlib/1.2.11-gcc-5.3.0    
+git/2.29.0-gcc-5.3.0         netcdf-fortran/4.5.3-gcc-5.3.0  
+```
+
+### JupyterHub
+[SRVX1-Jupyterhub](https://srvx1.img.univie.ac.at)
+
+## Information on SRVX2 - Compute
 Computing Node @UZA2
 
 [Go to Description](SRVX2.md)
 
-**Summary**
- - Architecture
- - Software
-
-# Information on SRVX8
+### Architecture
+| 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
+ - GNU compilers, Intel compilers, OpenMPI, HDF5, NetCDF, Eccodes, ...
+ - Anaconda Python
+
+```bash
+>>> module av
+----------- /home/spack-root/share/spack/modules/linux-centos8-skylake_avx512 -----------
+anaconda3/2020.07-gcc-8.3.1                         miniconda3/4.8.2-gcc-8.3.1         
+eccodes/2.18.0-intel-20.0.2                         netcdf-c/4.7.4-gcc-8.3.1           
+eccodes/2.19.1-gcc-8.3.1                            netcdf-c/4.7.4-intel-20.0.2        
+eccodes/2.19.1-intel-20.0.2                         netcdf-fortran/4.5.3-gcc-8.3.1     
+hdf5/1.10.7-gcc-8.3.1                               netcdf-fortran/4.5.3-intel-20.0.2  
+hdf5/1.10.7-intel-20.0.2                            openmpi/3.1.6-gcc-8.3.1            
+intel-parallel-studio/composer.2020.2-intel-20.0.2  openmpi/3.1.6-intel-20.0.2  
+```
+## Information on SRVX8 - Research
 Researchers @UZA2 
 
 [Go to Description](SRVX8.md)
 
-**Summary**
- - Architecture
- - Software
+### Architecture
+| 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
+ - GNU compilers, OpenMPI, HDF5, NetCDF, Eccodes, ...
+ - Anaconda Python
+```bash
+----------------- /opt/spack/share/spack/modules/linux-centos6-haswell/ -----------------
+anaconda3/2020.07-gcc-5.3.0    netcdf-c/4.7.4-gcc-5.3.0
+eccodes/2.18.0-gcc-5.3.0       netcdf-fortran/4.5.3-gcc-5.3.0
+gcc/4.4.7-gcc-5.3.0            openmpi/3.1.6-gcc-5.3.0
+gcc/5.3.0-gcc-5.3.0            proj/7.1.0-gcc-5.3.0
+hdf5/1.10.7-gcc-5.3.0          python/3.8.5-gcc-5.3.0
+miniconda3/4.8.2-gcc-5.3.0     zlib/1.2.11-gcc-5.3.0
+```