Merge branch 'musica_info_and_leonardo' into 'main'

added musica info and modified leonardo pages

See merge request !95

docs/index.md

@@ -82,7 +82,7 @@ Welcome to the Vienna Scientific Cluster documentation!
     [:octicons-arrow-right-24: VSC-4](systems/vsc4.md)<br>
     [:octicons-arrow-right-24: VSC-5](systems/vsc5.md)<br>
     [:octicons-arrow-right-24: MUSICA](systems/musica.md)<br>
-    [:octicons-arrow-right-24: LEONARDO](systems/leonardo.md)
+    [:octicons-arrow-right-24: LEONARDO](systems/leonardo/index.md)
     
 -    **Software**
 

docs/musica_test/index.md

+# MUSICA user test
+
+<figure style="position: relative; top: -50px;">
+  <img 
+    src="../../images/EESSI_logo.png" 
+    width=400px
+  >
+</figure>
+
+For MUSICA's test user phase the software stack will be provided via The European Environment for Scientific Software Installations (EESSI).<br>
+
+ EESSI (pronounced as "easy") is a collaboration between different HPC sites and industry partners, it acts like a streaming service for scientific software, regardless of which flavor/version of Linux distribution or processor architecture is used, or whether it is a full-size HPC cluster, a cloud environment or a personal workstation, and without compromising on the performance of the software.
+
+The gaol of EESSI is to set up a shared stack of scientific software installations, and by doing so avoid a lot of duplicate work across HPC sites, providing for end users a uniform user experience with respect to available scientific software, regardless of which system they use.
+
+Read more about EESSI [here](https://www.eessi.io/){:target="_blank"}.
+
+## EESSI on MUSICA
+
+### Start EESSI
+
+Type `eessi` in your login terminal:
+
+```{.bash .numberLines startFrom=""}
+zen trainee00@l55:~$ eessi
+Found EESSI repo @ /cvmfs/software.eessi.io/versions/2023.06!
+archdetect says x86_64/amd/zen3
+Prepending /cvmfs/software.eessi.io/versions/2023.06/software/linux...
+Environment set up to use EESSI (2023.06), have fun!
+{EESSI 2023.06} trainee00@l55:~$
+```
+### Overview of all EESSI modules
+
+Type `ml ov` to show all the EESSI available modules:
+
+```{.bash .numberLines startFrom=""}
+{EESSI 2023.06} trainee00@l55:~$ ml ov
+
+---/cvmfs/software.eessi.io/versions/2023.06/... ----
+Abseil             (2)   Eigen                 (3)
+ALL                (1)   elfutils              (2)
+amdahl             (1)   ELPA                  (2)
+```
+
+Where (2) means two versions are installed.
+
+### Using the modules
+ EESSI uses to usual module commands:
+
+ Use `module avail` to find installations of a package.<br>
+ Use `module load` to load the module.<br>
+ Use `module list` to list all the loaded modules.<br>
+ Use `module purge` to remove all the loaded modules.<br>
+Use `module show` to inspect the module.
+
+### Using EESSI in a job script
+
+Here is an example on how to use EESSI modules inside a job script, one just needs to add the 'eessi' command
+and load the desired EESSI module:
+
+```
+#!/bin/bash
+#SBATCH -J test_job
+#SBATCH -N 1
+#SBATCH --partition zen3_0512 
+#SBATCH --qos zen3_0512
+
+eessi
+module load lammps #for example
+srun --mpi=pmix lmp -i in.meam
+```
\ No newline at end of file

docs/musica_test/installing_software.md

+#Installing software on MUSICA
+
+The main installation tool is Easybuild provided by the EESSI-extend module.
+In this way new user installed software will build on top of the EESSI provided libraries. 
\ No newline at end of file

docs/musica_test/login.md

+#Loginng in to MUSICA
+
+To log in into MUSICA...
\ No newline at end of file

docs/running_jobs/musica_queues.md

+# MUSICA partitions and QoS
+
+On MUSICA, nodes of the same type of hardware are grouped in to partitions.
+The quality of service (QoS), formerly called *Queues* defines the maximum
+run time of a job and the number and type of allocate-able nodes.
+
+## Partitions
+- AMD CPU nodes: The CPU nodes are comprised of 2x AMD Epyc 9654 (96 cores each) with 768GB DDR5 RAM  and a local NVMe with 1.92TB.
+- GPU nodes: The GPU nodes have 2x AMD Epyc 9654 (96 cores each) with 768GB DDR5 RAM, 4x Nvidia SXM5 H100-94G-700W GPUs, 4x NDR200 infiniband and a local NVMe with 7.68TB. 
+
+These are the partitions on VSC-5:
+
+| Partition        | Nodes | Architecture | CPU                  | Cores per CPU (physical/with HT) | GPU            | RAM    | Use                                      |
+|------------------|-------|--------------|----------------------|----------------------------------|----------------|--------|------------------------------------------|
+| zen4_0768        | 72    | AMD          | 2x AMD 9654          | 192/384                           | No            | 768 GB | The default partition                    |
+|zen4_0768_h100x4  | 112   | AMD          | 2x AMD 9654          | 192/384                           |  4x Nvidia SXM5 H100   | 768 TB | GPU partition                    |
+
+!!! tip
+    Type `sinfo -o %P` on any node to see all the available partitions.<br>
+    and`sqos` for the available QoS. 
+
+
+## Quality of service (QoS)
+
+The QoS defines the maximum run time of a job and the number and type of
+allocate-able nodes.
+
+
+The following QoS are available for all normal (=non private) projects:
+
+| QoS name         | Gives access to Partition | Hard run time limits | Description   |
+|------------------|---------------------------|:---------------------|---------------|
+| zen4_0768+       | zen4_0768                 | 72h (3 days)         | Default       |
+| zen4_0768        | zen4_0768                 | 72h (3 days)         | ?             |
+
+!!! Tip
+    The QoSs that are assigned to a specific user can be viewed with:<br>
+    ```
+    sacctmgr show user `id -u` withassoc format=user,defaultaccount,account,qos%40s,defaultqos%20s
+    ```

docs/software/eessi.md

 # EESSI
 
+<figure style="position: relative; top: -50px;">
+  <img 
+    src="../../images/EESSI_logo.png" 
+    width=400px
+  >
+</figure>
+
 !!! Tip "EESSI modules are now available on VSC systems!"
 
 The European Environment for Scientific Software Installations (EESSI, pronounced as "easy") is a collaboration between different HPC sites and industry partners, with the common goal to set up a shared repository of scientific software installations that can be used on a variety of systems, regardless of which flavor/version of Linux distribution or processor architecture is used, or whether it is a full-size HPC cluster, a cloud environment or a personal workstation, and without compromising on the performance of the software.

docs/systems/leonardo.md → docs/systems/leonardo/index.md

@@ -2,7 +2,7 @@
 
 The EuroHPC LEONARDO is among the most powerful supercomputers in the world. The Leonardo cluster is capable of nearly 250 PFlops and equipped with over 100 PB of storage capacity. A part of its computing resources is reserved for Austrian users. 
 
-![leonardo](../images/leonardo.jpg){ align=left }
+![leonardo](../../images/leonardo.jpg){ align=left }
 
 
 Austrian users can apply for access to LEONARDO via the [AURELEO](https://vsc.ac.at//access/aureleo-2023-austrian-users-at-leonardo-supercomputer/) calls.

docs/systems/leonardo/leonardo_access.md

+# How to login to the Leonardo cluster
+
+The Leonardo supercomputer is one of the fastest supercomputers in the world and one of the recent additions in the EuroHPC JU family. Login to Leonardo follows strict requirements to ensure security, safeguarding sensitive information and ensuring the integrity of its operations.
+
+Here are the step-by-step procedures to get started.
+
+* Registration at CINECA UserDB portal
+* Association your account with an active project
+* Request to access to CINECA HPC cluster
+* Configuration of 2FA and OTP
+* Install and configuration of smallstep client
+* Managing password, 2FA and OTP
+
+## Step 1: Registration at CINECA UserDB portal
+
+
+In order to have access on Leonardo, it is necessary to complete the registration procedure on CINECA [UserDB](https://userdb.hpc.cineca.it/){:target="_blank"} portal.
+
+* Click on the “Create a New User” button and filling in the required fields
+* Uploading an ID card (passport for non-Italian) in the Documents for HPC tab, complete the information about your Institution and check your Personal Data.
+* Your CINECA ID looks like YOUR.NAME_xxxxx [uid: xxxxx], in which xxxxx is a 5-digit string consising of numbers.
+
+## Step 2: Association your account with an active project
+
+Send your id account at CINECA to the project leader and ask for an access to an existing project.
+
+## Step 3: Request to access CINECA HPC cluster
+
+
+Once your username has been associated with an active account, you can request access to CINECA HPC clusters.
+Make sure following info are OK, see the figure below.
+
+* Personal data
+* Institution
+* HPC DOCs
+* Authorization
+* Clicking the button Submit on your HPC Access page.
+* Wait for several hours …
+* Once approved your request, you will receive two emails
+    1. one email with the username
+    2. another with the link to a page showing how to:
+        * configure the two-factor authentication (2FA)
+        * configure the OTP
+
+## Step 4: Configuration of 2FA and OTP
+
+Two-factor authentication (2FA) refers to an authentication method in which a user is granted access to the CINECA HPC systems only after successfully presenting two pieces of evidence (or factors).
+
+Verifying your identity, using an independent second factor, prevents other users from logging in with your identity, even if they have the password.
+
+Therefore, the two-factor authentication (2FA) adds a further level of security to the authentication for access to services based on the Identity Provider.
+
+The detailed instcutions from CINECA's documentation for the configuration of 2FA and OTP are available [here](https://wiki.u-gov.it/confluence/display/SCAIUS/2.1%3A+How+to+install+the+smallstep+client+and+configure+2FA+and+OTP){:target="_blank"}.
+
+The last step, once you have successfully inserted the 6-digit code from FreeOPT/Goolge Authentiator, you will get the Recovery codes (shown below). Please save these codes somewhere by downloading, printing or copying in a text file.
+
+## Step 5: Install and configuration of the smallstep client
+
+Once the 2FA will be enabled as the only method to authenticate on CINECA clusters, you will need to install and configure on your PC a program that allows you to authenticate via 2FA and to download locally the temporary certificate. The CINECA recommends the smallstep client.
+
+Detailed instructions are available [here](https://wiki.u-gov.it/confluence/display/SCAIUS/2.1%3A+How+to+install+the+smallstep+client+and+configure+2FA+and+OTP){:target="_blank"}.
+
+IMPORTANT: users with Ubuntu operating systems (but may happen also for other Linux distributions) should not run the command “sudo apt install step” because this will install a different software that will give errors when following the below instructions.
+
+## Step 6: Managing password, 2FA and OTP
+
+More details about change the password, recover one-time password generator, as well as renew the recovery codes are availalbe [here](https://wiki.u-gov.it/confluence/display/SCAIUS/2.2%3A+Managing+password%2C+2FA+and+OTP){:target="_blank"}.
\ No newline at end of file

mkdocs.yml

@@ -42,6 +42,7 @@ nav:
   - Software:
       - software/index.md
       - Module system: software/modules.md
+      - EESSI: software/eessi.md
       - Compilers: software/compilers.md
       - Python:
           - Using Conda: software/python/conda.md
@@ -74,7 +75,9 @@ nav:
   - Systems:
       - systems/index.md
       - MUSICA: systems/musica.md
-      - LEONARDO: systems/leonardo.md
+      - LEONARDO: 
+        - systems/leonardo/index.md
+        - Access LEONARDO: systems/leonardo/leonardo_access.md
       - VSC-5: systems/vsc5.md
       - VSC-4: systems/vsc4.md
       - Retired systems: systems/retired_systems.md