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Addition of singularity build file and documentation to run calculations using the container. #144

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Aug 16, 2024
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Addition of singularity build file and documentation to run calculations using the container. #144

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71 changes: 71 additions & 0 deletions calphy.def
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BootStrap: library
From: ubuntu:22.04

%labels
Author: Sebastian Havens
Image for a calphy container
%environment
export PATH=/scripts:$PATH
export OMP_NUM_THREADS=1
. /singularity-venv/bin/activate
source /singularity-venv/bin/activate

%post
# Update package lists and install necessary packages
export DEBIAN_FRONTEND=noninteractive
echo . /singularity-venv/bin/activate

apt-get update -y
apt-get install -y build-essential libopenmpi-dev libmpich-dev vim emacs htop \
mpi-default-bin mpi-default-dev mpich libjpeg-dev libpng-dev git \
fftw3 fftw3-dev software-properties-common

# Add repository and install Python 3.8
add-apt-repository ppa:deadsnakes/ppa
apt-get update -y
apt-get install -y python3.8-dev python3.8-venv

# Setup Python virtual environment
python3.8 -m venv /singularity-venv
. /singularity-venv/bin/activate

# Install packages
pip install numpy==1.24.4 ase==3.23.0 mpi4py==3.1.5
pip install mendeleev==0.17.0 pylammpsmpi==0.2.16 pyscal==0.12 pyyaml==6.0.2 scipy==1.10.1 tqdm==4.66.2
pip install calphy

# Clone lammps source and make
git clone https://github.com/lammps/lammps.git --branch patch_2Aug2023_update3
cd /lammps/src/
sed -i '35s/.*/LMP_INC = -DLAMMPS_GZIP -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS/' MAKE/MACHINES/Makefile.ubuntu
make yes-manybody
make yes-meam
make yes-EXTRA-FIX
make yes-EXTRA-PAIR
make -j 8 ubuntu mode=shlib
make install-python
cp liblammps_ubuntu.so /singularity-venv/lib/python3.8/site-packages/lammps
cd ../../
%runscript

echo "Input file: $1"
echo "Calculation starting"
calphy_kernel -i $1 -k 0
exec echo "Calculation finished"



%help
This is a container for carrying out calphy calculations which perform free energy calculations.
The container is designed to run locally or on HPC machines.

The calphy calcualtion can be initiated via the container with the following command:
singularity exec --bind $PWD --pwd $PWD {location_of_.sif_image} calphy_kernel -i {input_file} -k 0
This line can be contained within a slurm script

The scheduler used in the calphy input file should be 'local'.
On HPC machines the singularity executable can usually be loaded via 'module load singularity' or it will already be within your
path.

In the calphy input file, the scheduler should be set to local.
The OpenMPI version on the host system must be at least 4.1.2, which will need to be loaded if you are using a HPC machine.
21 changes: 21 additions & 0 deletions docs/source/gettingstarted.md
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`python setup.py install`
```

```{tab} Singularity
A singularity containter can also be used for running calphy locally or on HPC machines.
The containerised environment contains all of the packages required to run calphy.

The containerised environemnt can be pulled from the repository with:
'singularity pull --arch amd64 library://sebastianhavens/calphy/calphy:latest'
(https://cloud.sylabs.io/library/sebastianhavens/calphy/calphy)

On HPC machines you can usually load the singularity module with:
'module load singularity' if it is not already available.

You can initiate calculations using this container with the following line:
'singularity exec --bind $PWD --pwd $PWD {location_of_.sif_image} calphy_kernel -i {input_file} -k 0'
where {location_of_.sif_image} is the file location of the containerlised environment you just pulled and {input_file} is the name of your input file.
This line can be placed within a slurm script.

In the calphy input file, the scheduler should be set to local.
For parallel calculations to run effectively, the OpenMPI module on the host system must be at least 4.1.2.
```


### Using a conda environment

It is **strongly** recommended to install and use `calphy` within a conda environment. To see how you can install conda see [here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/).
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