Modena 2025

From The Yambo Project
Jump to navigation Jump to search

A general description of the goal(s) of the school can be found on the Yambo main website

Use CINECA computational resources

Yambo tutorials will be run on the Leonardo-DCGP partition. You can find info about Leonardo-DCGP here. In order to access computational resources provided by CINECA you need your personal username and password that were sent you by the organizers.

Connect to the cluster using ssh

You can access Leonardo via ssh protocol in different ways.


- Connect using username and password

Use the following command replacing your username: 

$ ssh username@login.leonardo.cineca.it

However, in this way you have to type your password each time you want to connect.


- Connect using ssh key

You can setup a ssh key pair to avoid typing the password each time you want to connect to Leonardo. To do so, run the ssh-keygen command to generate a private/public key pair: 

$ ssh-keygen -t rsa -b 4096 -f ~/.ssh/leonardo_rsa
Generating public/private rsa key pair.
Created directory '/home/username/.ssh'.
Enter passphrase (empty for no passphrase): 
Enter same passphrase again: 
Your identification has been saved in /home/username/.ssh/leonardo_rsa
Your public key has been saved in /home/username/.ssh/leonardo_rsa.pub
The key fingerprint is:
[...]
The key's randomart image is:
[...]

Now you need to copy the public key to Leonardo. You can do that with the following command (for this step you need to type your password): 

$ ssh-copy-id -i ~/.ssh/leonardo_rsa username@login.leonardo.cineca.it

Once the public key has been copied, you can connect to Leonardo without having to type the password using the -i option: 

$ ssh -i ~/.ssh/leonardo_rsa username@login.leonardo.cineca.it

To simplify even more, you can paste the following lines in a file named config located inside the .ssh directory adjusting the username: 

Host leonardo 
 HostName login.leonardo.cineca.it
 User username
 IdentityFile ~/.ssh/leonardo_rsa

With the config file setup you can connect simply with 

$ ssh leonardo


General instructions to run tutorials

Before proceeding, it is useful to know the different workspaces you have available on Leonardo, which can be accessed using environment variables. The main ones are:

  • $HOME: it's the home directory associated to your username;
  • $WORK: it's the work directory associated to the account where the computational resources dedicated to this school are allocated;
  • $SCRATCH: it's the scratch directory associated to your username.

You can find more details about storage and FileSystems here.

Please don't forget to run all tutorials in your scratch directory: 

$ echo $SCRATCH
/leonardo_scratch/large/userexternal/username
$ cd $SCRATCH

Computational resources on Leonardo are managed by the job scheduling system Slurm. Most part of Yambo tutorials during this school can be run in serial, except some that need to be executed on multiple processors. Generally, Slurm batch jobs are submitted using a script, but the tutorials here are better understood if run interactively. The two procedures that we will use to submit interactive and non interactive jobs are explained below.


- Run a job using a batch script

This procedure is suggested for the tutorials and examples that need to be run in parallel. In these cases you need to submit the job using a batch script job.sh. Please note that the instructions in the batch script must be compatible with the specific Leonardo-DCGP resourses. The complete list of Slurm options can be found here. However you will find ready-to-use batch scripts in locations specified during the tutorials.

To submit the job, use the sbatch command: 

$ sbatch job.sh
Submitted batch job 15696508

To check the job status, use the squeue command: 

$ squeue --me
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
          15696508 dcgp_usr_   job.sh nspallan  R       0:01      1 lrdn4135

If you need to cancel your job, do: 

$ scancel <JOBID>


- Open an interactive session

This procedure is suggested for most of the tutorials, since the majority of these is meant to be run in serial (relatively to MPI parallelization) from the command line. Use the command below to open an interactive session of 4 hour: 

$ srun -A tra25_yambo -p dcgp_usr_prod -q normal --reservation=TBD -N 1 -n 1 -c 4 -t 04:00:00 --gres=tmpfs:10g --pty /bin/bash
srun: job 15694182 queued and waiting for resources
srun: job 15694182 has been allocated resources

We ask for 4 cpus-per-task (-c) because we can exploit OpenMP parallelization with the available resources.

Then, you need to manually load yambo as in the batch script above: 

$ module purge
$ module load profile/candidate
$ module use /leonardo/pub/userexternal/nspallan/spack-0.22.2-06/modules

Finally, set the OMP_NUM_THREADS environment variable to 4 using the appropriate Slurm environment variable: 

$ export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}

To close the interactive session when you have finished, log out of the compute node with the exit command, and then cancel the job: 

$ exit
$ scancel <JOBID>


- Plot results with gnuplot

During the tutorials you will often need to plot the results of the calculations. In order to do so on Leonardo, open a new terminal window and connect to Leonardo enabling X11 forwarding with the -X option: 

$ ssh -X leonardo

Please note that gnuplot can be used in this way only from the login nodes: 

username@login01$ cd <directory_with_data>
username@login01$ gnuplot
...
Terminal type is now '...'
gnuplot> plot <...>


- Set up yambopy

In order to run yambopy on Leonardo, you must first setup the conda environment (to be done only once): 

$ cd
$ module load anaconda3/2023.09-0
$ conda init bash
$ source .bashrc

After this, every time you want to use yambopy you need to load its module and environment: 

$ module load anaconda3/2023.09-0
$ conda activate !!!!!!!! TBD !!!!!!!!

Tutorials

Quick recap. Before every tutorial, if you run on Leonardo, do the following steps 

ssh leonardo
cd $SCRATCH
mkdir -p YAMBO_TUTORIALS #(Only if you didn't before)
cd YAMBO_TUTORIALS

At this point you can download the needed files for the tutorial. After that you can open the interactive session and login into the node 

srun -A tra25_yambo -p dcgp_usr_prod -q normal --reservation=TBD -N 1 -n 1 -c 4 -t 04:00:00 --gres=tmpfs:10g --pty /bin/bash
[...]
module purge
module load profile/candidate
module use /leonardo/pub/userexternal/nspallan/spack-0.22.2-06/modules
module load yambo/5.3.0--intel-oneapi-mpi--2021.12.1--oneapi--2024.1.0
export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
cd $SCRATCH/YAMBO_TUTORIALS

DAY 1 - Monday, 19 May

16:15 - 18:30 From the DFT ground state to the complete setup of a Many Body calculation using Yambo

To get the tutorial files needed for the following tutorials, follow these steps: 

$ wget https://media.yambo-code.eu/educational/tutorials/files/hBN.tar.gz
$ wget https://media.yambo-code.eu/educational/tutorials/files/hBN-2D.tar.gz
$ ls
hBN-2D.tar.gz  hBN.tar.gz
$ tar -xvf hBN-2D.tar.gz
$ tar -xvf hBN.tar.gz
$ ls
hBN-2D hBN hBN-2D.tar.gz  hBN.tar.gz

Now that you have all the files, you may open the interactive job session with salloc as explained above and proceed with the tutorials.

At this point, you may learn about the python pre-postprocessing capabilities offered by yambopy, our python interface to yambo and QE. First of all, let's create a dedicated directory, download and extract the related files. 

$ cd $SCRATCH
$ mkdir -p YAMBOPY_TUTORIALS
$ cd YAMBOPY_TUTORIALS
$ wget https://media.yambo-code.eu/educational/tutorials/files/databases_yambopy.tar
$ tar -xvf databases_yambopy.tar
$ cd databases_yambopy

Then, follow the first three sections of this link, which are related to initialization and linear response.

DAY 2 - Tuesday, 20 May

14:00 - 16:30 A tour through GW simulation in a complex material (from the blackboard to numerical computation: convergence, algorithms, parallel usage)

To get all the tutorial files needed for the following tutorials, follow these steps: 

wget https://media.yambo-code.eu/educational/tutorials/files/hBN.tar.gz
wget https://media.yambo-code.eu/educational/tutorials/files/MoS2_2Dquasiparticle_tutorial.tar.gz
tar -xvf hBN.tar.gz
tar -xvf MoS2_2Dquasiparticle_tutorial.tar.gz
cd hBN

Now you can start the first tutorial:

If you have gone through the first tutorial, pass now to the second one: 

cd $SCRATCH
cd YAMBO_TUTORIALS
cd MoS2_HPC_tutorial

To conclude, you can learn an other method to plot the band structure in Yambo

DAY 3 - Wednesday, 21 May

14:00 - 16:30 Bethe-Salpeter equation (BSE) Fulvio Paleari (CNR-Nano, Italy), Davide Sangalli (CNR-ISM, Italy)

To get the tutorial files needed for the following tutorials, follow these steps: 

$ wget https://media.yambo-code.eu/educational/tutorials/files/hBN.tar.gz # NOTE: YOU SHOULD ALREADY HAVE THIS FROM DAY 1
$ wget https://media.yambo-code.eu/educational/tutorials/files/hBN-convergence-kpoints.tar.gz 
$ tar -xvf hBN-convergence-kpoints.tar.gz
$ tar -xvf hBN.tar.gz

Now, you may open the interactive job session with salloc and proceed with the following tutorials.

Now, go into the yambopy tutorial directory to learn about python analysis tools for the BSE: 

$ cd $SCRATCH
$ cd YAMBOPY_TUTORIALS/databases_yambopy


17:00 - 18:30 Bethe-Salpeter equation in real time (TD-HSEX) Fulvio Paleari (CNR-Nano, Italy), Davide Sangalli (CNR-ISM, Italy)

The files needed for the following tutorials can be downloaded following these steps: 

$ wget https://media.yambo-code.eu/educational/tutorials/files/hBN-2D-RT.tar.gz
$ tar -xvf hBN-2D-RT.tar.gz


DAY 4 - Thursday, May 22

14:00 - 16:30 Real-time approach with the time dependent berry phase Myrta Gruning (Queen's University Belfast), Davide Sangalli (CNR-ISM, Italy)


For the tutorials we will use first the hBN-2D-RT folder (k-sampling 10x10x1) and then the hBN-2D folder (k-sampling 6x6x1) You may already have them in the YAMBO_TUTORIALS folder 

$ ls
hBN-2D hBN-2D-RT hBN-2D.tar.gz  hBN-2D-RT.tar.gz

If you need to downoload again the tutorial files, follow these steps: 

$ wget https://media.yambo-code.eu/educational/tutorials/files/hBN-2D.tar.gz
$ wget https://media.yambo-code.eu/educational/tutorials/files/hBN-2D-RT.tar.gz
$ tar -xvf hBN-2D.tar.gz
$ tar -xvf hBN-2D-RT.tar.gz


DAY 5 - Friday, 23 May

Lectures

DAY 1 - Monday, 19 May

  • D. Varsano, [Description and goal of the school].
  • C. Franchini, [First principles and data-driven correlated materials]
  • F. Mohamed, [A tour on Density Functional Theory]
  • E. Cannuccia, [Electronic screening and linear response theory]

DAY 2 - Tuesday, 20 May

  • A. Marini, Introduction to Many-Body Perturbation Theory
  • C. Cardoso, Quasiparticles and the GW Approximation
  • A. Guandalini,G. Sesti, GW in practice: algorithms, approximations and W-averaged GW in metals
  • M. Govoni, GW without empty states and investigation of neutral excitations by embedding full configuration interaction in DFT+GW

DAY 3 - Wednesday, 21 May

  • M. Palummo, Optical absorption and excitons via the Bethe-Salpeter Equation
  • D. Sangalli, Real-time simulations
  • F. Paleari, Introduction to YamboPy (automation and post-processing)

DAY 4 - Thursday, 22 May

  • E. Luppi, An introduction to Non-linear spectroscopy
  • M. Grüning, Non-linear spectroscopy in Yambo
  • F. Affinito, Frontiers in High-Performance Computing
Retrieved from "https://wiki.yambo-code.eu/wiki/index.php?title=Modena_2025&oldid=8624"