HPC

Quantum Espresso and EPW using the GNU compiler (Courtesy of Junfeng Qiao) 

First load the following modules 

Then you have to manually edit the make.inc file and add the " -D__FFTW" flag:

Then you can compile with

Abinit 9.6.2 with the GNU compiler and NETCDF-IO + aggressive optimisation

First load the following modules 

Using the following lumi_gnu.ac file:

Then issue:

Abinit will then complain that libxc is missing, then go inside the created fallback and compile the fallback. Once this is done, update the lumi_gnu.ac file and re-issue:

Abinit 9.8.2

Using the following lumi_gnu.ac file:

Then issue:

Abinit will then complain that some libraries are missing, then go inside the created fallback and compile the fallback. Once this is done, update the lumi_gnu.ac file (change the XXX and uncomment) and re-issue:

Abinit 10.0.7 with the GNU compiler

The issue the following command in your build directory:

QE 7.4 with intel compiler 

Note that MareNostrum5 does not let you download things from internet from the cluster. A solution is to download QE 7.4 on your desktop, then compile it on your desktop so it downloads all the necessary dependencies. Then tar it back and copy that on Mn5. You can then untar on the cluster and issue "make clean". 

First load the following modules 

Abinit 9.8.2

First load the following modules 

Using the following zenobe.ac file:

Then issue:

Abinit will then complain some libraries are missing

Abipy

You can find configuration script for Zenobe here:  https://abinit.github.io/abipy/workflows/manager_examples.html#zenobe

Abinit v9.11.6 (Courtesy of J.-M. Beuken)

Abinit v9.8.4 (Courtesy of W. Chen and T. van Waas)

Then to run, one can use:

Abinit v9.8.3

First load the following modules: 

Then do:

Then create a "lucia.ac9" file in the build folder with the following lines:

Finally, configure and compile: 

Abipy

Quantum Espresso v7.2  (Courtesy of W. Chen and T. van Waas)

Go into the QE folder which should be unpacked somewhere in your $HOME or $PROJECTS_HOME, then execute:

A job execution – executed somewhere within your $SCRATCH should look like this:

Abinit v9.11.6

Abipy

Important: read this carefully 

Quantum Espresso 7.1 

First load the following modules 

 Then go inside the QE folder and issue: 

phono3py

Create a virtual environment at the end of the install. Logout and in again to be in the environment. 

Install the code https://phonopy.github.io/phono3py/install.html

How to run phono3py with QE

Look at the example for Si there https://github.com/phonopy/phono3py/tree/master/example/Si-QE

This will create all the supercell files. Then create a "header" file for QE that you will aggregate Then run all the calculation, for example using the following submission script

Then create the force file with phono3py:

Finally, compute the thermal conductivity and converge the fine grids (i.e. increase the 10 10 10 grid below):

What to do if your calculation uses too much IO

You should use the local scratch on each node (this implies running on 1 node maximum). 

You can use a script similar to this:

Abinit 9.11.6 (Courtesy of Matthieu J Verstraete, 22/03/24)

First load the following modules: 

Using the following discover.ac file:

Then issue:

Abinit 9.6.2 (Update of the software stack 05/12/23)

 First load the following modules: 

Using the following discover.ac file:

Then issue:

Abinit 9.6.2 (Courtesy of Matthieu J Verstraete) 

First load the following modules: 

Using the following discover.ac file:

Then issue:

Example of slurm submission script 

QE 7.2 - Intel compilation IFX and openmpi (Courtesy of T. van Waas and V. Kolev) 

Go inside qe/:

QE 7.1 with openmpi and OpenMP support using cmake (Courtesy of V. Kolev) 

Load the following modules: 

QE 7.1 with nv & openmpi 

Note: This works but might not be the fastest. 

First load the following modules: 

Go inside qe/:

Then you need to modify manually the following line in the make.inc file: 

QE

Sometime it is useful to allow for argument mismatch in make.inc

• Any publications or communications (talk/poster) should be sent to the WEL Research Institute before submission (3 weeks before) for approbation. 
• A copy of each paper should be sent to the WEL Research Institute before publication date.  
• A Wel-T stickers must be placed in the office where research paid on the project are conducted (Office and CISM computers), provided by the WEL Research Institute. 
• For the 31 of January a progress report should be submitted to the WEL Research Institute.
• For the 15 of November at the end of the 4 years, a final activity report should be submitted to WEL and FNRS.
•  3 meetings per year with the valorisation committee. 

Quantum Espresso v 6.5

First load the following modules