Czechia 2026

This page provides the instructions and tutorials of Yambo hands-on sessions for the course organized by IT4I in collaboration with MaX CoE and NCC Czechia.

Webpage of the event: Hands-on many-body calculations with the Yambo code.

https://events.it4i.cz/event/393/

---

General instructions

Scratch folder

The tutorial calculations should be run in the /scratch storage space. First, create a folder named with your username with the following command

$ mkdir /scratch/project/atr-25-5/YAMBO_SCHOOL/$USER

Then, add the following line in your ~/.bashrc file:

export MY_SCRATCH=/scratch/project/atr-25-5/YAMBO_SCHOOL/${USER}

Finally, either type source ~/.bashrc in your terminal or log out and log back in. You should now be able to cd directly to your scratch folder:

$ cd $MY_SCRATCH

This is where you will copy the tutorial files and run the calculations.

Gnuplot

During the tutorials it may be useful to quickly visualize some of the plots. You can use gnuplot from a login node. To do so, you must connect via ssh -X and load gnuplot with

$ module load gnuplot/5.4.6-GCCcore-12.2.0

Note

You can always copy the data to you local machine and plot them with your favourite tool.

---

Tutorials

Follow the tutorials listed below (you may want to skip the optional sections present in some of them).

Important

Ignore the download instructions at the beginning of the tutorials. Instead, copy the tutorial files from /scratch/project/atr-25-5/YAMBO_SCHOOL/TUTORIAL_FILES/ in your scratch folder, as shown below.

Getting started with Yambo

We will run this part on CPUs in interactive mode. First, open a CPU interactive session on a compute node with

$ salloc --account=ATR-25-5 --nodes=1 --ntasks-per-node=1 --cpus-per-task=1 --partition=qcpu_exp --time=01:00:00 --reservation=ATR-25-5_2026-05-05T09:00_2026-05-05T13:00__qcpu

then load Yambo with

$ source /scratch/project/atr-25-5/YAMBO_SCHOOL/TUTORIAL_FILES/load_yambo_cpu

(this also sets the OMP_NUM_THREADS environment variable).

1. Optics at the independent particle level

   $ cd $MY_SCRATCH
   $ cp -r /scratch/project/atr-25-5/YAMBO_SCHOOL/TUTORIAL_FILES/DAY_1/hBN .
   

   Go to the tutorial

2. RPA and local field effects

   $ cd $MY_SCRATCH
   $ cp -r /scratch/project/atr-25-5/YAMBO_SCHOOL/TUTORIAL_FILES/DAY_1/hBN-2D .
   

   Go to the tutorial

Run Yambo on a HPC machine

We will run these tutorials on CPU and GPU, some parts in interactive mode and others via job submission scripts.

1. GW calculation and parallelization schemes

   Open an interactive session on GPU with the following command

   $ salloc --account=ATR-25-5 --nodes=1 --ntasks-per-node=1 --gpus=1 --cpus-per-task=8 --partition=qgpu_exp --time=01:00:00 --reservation=ATR-25-5_2026-05-06T09:00_2026-05-06T13:00__qgpu
   

   Then load Yambo with

   $ source /scratch/project/atr-25-5/YAMBO_SCHOOL/TUTORIAL_FILES/load_yambo_gpu
   

   (this also sets the OMP_NUM_THREADS environment variable).

   Attention

   When running in interactive mode on GPU, run Yambo with mpirun yambo.

   For this tutorial we also need python:

   $ source /scratch/project/atr-25-5/YAMBO_SCHOOL/TUTORIAL_FILES/load_python
   

   Now copy the files in your scratch directory:

   $ cd $MY_SCRATCH
   $ cp -r /scratch/project/atr-25-5/YAMBO_SCHOOL/TUTORIAL_FILES/DAY_2/MoS2_HPC_tutorial .
   

   Go to the tutorial

2. BSE calculation and solvers

   Open an interactive session on CPU with the following command

   $ salloc --account=ATR-25-5 --nodes=1 --ntasks-per-node=1 --cpus-per-task=1 --partition=qcpu_exp --time=01:00:00 --reservation=atr-25-5_2026-05-07T09:00_2026-05-07T13:00__qcpu
   

   Then load Yambo with

   $ source /scratch/project/atr-25-5/YAMBO_SCHOOL/TUTORIAL_FILES/load_yambo_cpu
   

   (this also sets the OMP_NUM_THREADS environment variable).

   Now copy the files in your scratch directory:

   $ cd $MY_SCRATCH
   $ cp -r /scratch/project/atr-25-5/YAMBO_SCHOOL/TUTORIAL_FILES/DAY_3/MoS2_HPC_BSE_tutorial .
   

   Go to the tutorial