Phonopy and Phono3py installation from wheels and usage is now modified 
to assure consistent installation on all clusters including narval:
1) Go to home directory
2)After phonopy is installed: go to home dir and install phon3py for the same environment and python version~
module purge
module load StdEnv/2023
module load python/3.13.2

virtualenv --no-download ~/phonopy_env
source ~/phonopy_env/bin/activate

virtualenv --no-download ~/phono3py_env
source ~/phono3py_env/bin/activate

Uninstall old version if exists
pip uninstall --no-index phono3py

pip install h5py==3.13.0

avail_wheels h5py -p 3.13 --all-version
name    version    python    arch
------  ---------  --------  ---------
h5py    3.13.0     cp313     x86-64-v3
h5py    3.12.1     cp313     x86-64-v3

pip install --no-index phono3py

avail_wheels phono3py
name      version    python    arch
--------  ---------  --------  ---------
phono3py  3.19.2     cp313     x86-64-v3

pip install --no-index --upgrade pip
pip freeze --local > requirements.txt

deactivate

Note creation of requirements.txt file due to change for slurm running (from ticket created by Dhanish) as described on 
https://docs.alliancecan.ca/wiki/Python#Creating_virtual_environments_inside_of_your_jobs

vi requirements.txt 
contourpy==1.3.1+computecanada
cycler==0.12.1+computecanada
fonttools==4.60.0+computecanada
h5py==3.13.0+computecanada
kiwisolver==1.4.8+computecanada
matplotlib==3.10.0+computecanada
numpy==2.2.2+computecanada
packaging==25.0+computecanada
phono3py==3.19.2+computecanada
phonopy==2.43.2+computecanada
pillow==11.1.0+computecanada
pyparsing==3.2.4+computecanada
python_dateutil==2.9.0.post0+computecanada
PyYAML==6.0.2+computecanada
scipy==1.15.1+computecanada
six==1.17.0+computecanada
spglib==2.6.0+computecanada
symfc==1.5.4+computecanada

Example to run VASP with cutoff of 2 on cedar:
vi phonpydispfc2fc3cut2.sh

#!/bin/bash -l
#SBATCH --job-name=VASP_phonopy_UO2
#SBATCH --account=rrg-szpunarb-ad
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH --mem=0
#SBATCH --time=1:00:00

module load StdEnv/2023
module load python/3.13.2

source ~/phono3py_env/bin/activate
#generate displacements
phono3py --cutoff-pair=2 -d --dim-fc2="1 1 1" --dim="1 1 1" -c POSCAR

#generate displacements
phono3py -d --dim="2 2 2" -c POSCAR

Example to calc. conductivity VASP on fir (note whole memory used on node):

vi phonpythconductQE.sh
#!/bin/bash -l
#SBATCH --job-name=QE_ThN
#SBATCH --account=rrg-szpunarb-ad
#SBATCH --nodes=1
#SBATCH --tasks-per-node=64
#SBATCH --mem=0
#SBATCH --time=8:00:00

# Load the modules:

module load StdEnv/2023
module load python/3.13.2

source ~/phono3py_env/bin/activate

#Calculate conductivity
phono3py --mesh 12 12 12  --br

Example to run QE on narval 
(note only required memory used per precessor and can be check using the portal:  
https://portail.narval.calculquebec.ca/):

vi phonpythconductQE.sh
#!/bin/bash -l
#SBATCH --job-name=QE_ThN
#SBATCH --account=rrg-szpunarb-ad
#SBATCH --nodes=1
#SBATCH --tasks-per-node=64
#SBATCH --mem-per-cpu=256M
#SBATCH --time=48:00:00

# Load the modules:

module load StdEnv/2023
module load python/3.13.2

source ~/phono3py_env/bin/activate

#Calculate conductivity
phono3py --mesh 12 12 12  --br

Web with example for running phonopy and phono3py using VASP:

https://phonopy.github.io/phonopy/vasp.html
Note changes in new version how to run:
https://phonopy.github.io/phono3py/vasp.html

and using QE:

https://phonopy.github.io/phono3py/qe.html
https://phonopy.github.io/phono3py/qe.html

Comments and tests on thermal conductivity (K) convergence calculations:

ThN	QE	               --pa=						
Grid	300K	300K						
1000000	100	104.952							
512000	80	106.423							
125000	50	111.2							
27000	30	121.405							
1728	12	827.194							
729	9	335.492							
125	5	905.177 	905.994	
					
Above third and fourt columns present calculations by using the first  and second command listed below, respectively:	 	 	 	 	 	 	 	 	 
phono3py --mesh="5 5 5" --fc3 --fc2 --br	 	 	 						
phono3py --qe --dim="2 2 2" -c ThN.in --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="5 5 5" --fc3 --fc2 --br	
However although results are the same using the primitive cell option (--pa) is faster.	 	 	 	 	 	 	 	 
									
Next testing, large sigma for rough mesh: : 	 	 	 						
phono3py --mesh="5 5 5" --sigma 0.9 0.5 0.1 0.01 --fc3 --fc2 --b	 	 	 	 	 				
Grid	125	5							
Sigma	K at 300K								
0.9	25.598								
0.5	43.495								
0.1	6398550.464								
0.01	453202502.3								
									
phono3py --mesh="9 9 9" --sigma 0.9 0.5 0.1 0.01 --fc3 --fc2 --b	 	 	 	 	 				
Grid	729	9							
Sigma	K at 300K								
0.9	24.168								
0.5	35.834								
0.1	20829.625								
0.01	60339490.73								
									
What is acceptable the largest value to be used for sigma?	 	 	 	 					
									
Sigma should be as small as possible while sampling mesh should be as dense as possible.	 	 	 	 	 	 	 		
If you plot DOS with a small sigma, you can see the DOS will show spikes, 	 	 	 	 	 	 			
but at dense sampling, DOS shows a roughly smooth curve. A smooth curve can be obtained by large sigma, 	 	 	 	 	 	 	 	 	 
but the detailed structure of DOS will be lost. What we want is the limit, which is expected to be smooth while detailed.	 	 	 	 	 	 	 	 	 
									
The tetrahedron method has no parameter like sigma, but it's an interpolation scheme.	 	 	 	 	 	 	 		
Therefore, you have to check convergence over density of sampling mesh.	 	 	 	 	 	 			
									
In both cases, the convergence behaviour depends on the system (crystals).	 	 	 	 	 	 			
									
Togo									


Other comments on installation:

In the event your environment was setup incorrectly please do the following before installation:

module purge
module load StdEnv/2023
module load python/3.13.2

rm -rf $HOME/phono3py_env
virtualenv $HOME/phono3py_env
source $HOME/phono3py_env/bin/activate
pip install --no-index phono3py
deactivate
```

To use the env:

```
module purge
module load StdEnv/2023
module load python/3.13.2

source $HOME/phono3py_env/bin/activate
```

Do use above installation instructions to unistall the previous version if you want to install a new one
by replacing installation line, respectively  with:
pip uninstall  phonopy
pip uninstall  phono3py

Note there may be different environment loaded on different clusters when using not explicit 
specification in comands on cluster like e.g.: module load StdEnv/2020 scipy-stack 
and observed (Barbara, Jaya) on narval therefore it is recommended to avoid it and in general:

To make absolutely sure that Python environment is reproducible, please use:
`pip freeze > requirements.txt` when the environment is activated to generate a file that contains all installed packages and their versions. Then, to recreate the environment please use:

```
source ~/phono3py_env/bin/activate
pip install --no-index -r requirements.txt
```
Reference: Python documentation [https://docs.alliancecan.ca/wiki/Python].