====== XBeach ======

> XBeach is a two-dimensional model for wave propagation, long waves and mean flow, sediment transport and morphological changes of the nearshore area, beaches, dunes and backbarrier during storms.

   * For more information: https://oss.deltares.nl/web/xbeach/faq
===== Running XBeach on Comet =====

The XBeach software is stored within a dedicated container in the ''/nobackup/shared/containers'' directory and is accessible to __all__ users of Comet. You do //not// need to take a copy of the container file; it should be left in its original location.

You can find the container files here:

   * ''/nobackup/shared/containers/xbeach.sif''

We //normally// recommend using the latest (date) version of the container unless you have a specific need for an earlier version of software.

<WRAP round box info>
**Container Image Versions**

We //may// reference a specific container file, such as **xbeach.sif**, but you should always check whether this is the most recent version of the container available. Simply ''ls'' the ''/nobackup/shared/containers'' directory and you will be able to see if there are any newer versions listed.
</WRAP>

We have provided a convenience script that will automate **all** of steps needed to run applications inside the container, and access your ''$HOME'',  ''/scratch'' and ''/nobackup'' directories to just two simple commands.

   * ''/nobackup/shared/containers/xbeach.sh''

<WRAP round box info half>
There is a corresponding ''.sh'' script for //each version// of the container image we make available.
</WRAP>

Just ''source'' this file and it will take care of loading ''apptainer'', setting up your ''bind'' directories and calling the ''exec'' command for you - and give you a single command called ''container.run'' (instead of the really long //apptainer exec// command) to then //run// anything you want inside the container, for example - to run ''xbeach'' and check the version:

<code lang=bash>
$ source /nobackup/shared/containers/xbeach.sh
$ container.run xbeach -V
**********************************************************
 You are using XBeach version 1.23.6165M XBeachX release
**********************************************************
$
</code>

You can continue to use the ''container.run'' command //as many times as you need// in the same script or same bash session.

We **strongly** recommend that you use this helper script and the ''container.run'' command to run software from inside the container as it will always ensure that you have correctly set up the ''bind'' directories for you and you are using the correct container version.

----

===== Accessing Data =====

As long as you use the ''container.run'' method to launch the applications, you will automatically be able to read and write to files in your ''$HOME'', ''/scratch'' and ''/nobackup'' directories. 

If you run any of the applications inside the container manually, without using the ''container.run'' helper you will need to use the ''--bind'' argument to ''apptainer'' to ensure that all relevant directories are exposed within the container.

Do remember that the container filesystem itself cannot be changed - so you won't be able to write or update to ''/usr/local'', ''/opt'', ''/etc'' or any other internal folders - keep output directories restricted to the three areas listed above.

----

===== Sample Slurm script =====

Here is a very simple example of calling XBeach from the container within a Slurm batch job that assumes you are a member of the **comet_abc123** HPC project group:

<code lang=bash title=xbeach_job.sh>
#!/bin/bash

#SBATCH --partition=default_free
#SBATCH --account=comet_abc123
#SBATCH -c 8
#SBATCH --mem=16G

source /nobackup/shared/containers/xbeach.sh
container.run xbeach

</code>

Submit as normal with ''sbatch xbeach_job.sh''.

Note that we run on the **default_free** partition with **8 CPU** cores and **16GB of RAM**. 

----

===== Building XBeach for Comet =====

<WRAP important round box>
**Important!**

This section is only relevant for RSE HPC staff or those who want to understand how the XBeach container runtime has been built. If you are only interested in running the software, stop reading here!
</WRAP>

**Container definition file:**
<code lang=bash title=xbeach.def>
#!/bin/bash

echo "Loading modules..."
module load apptainer

echo ""
echo "Building container..."
export APPTAINER_TMPDIR=/scratch

echo ""
echo "Starting build of container ..."
apptainer build \
	--bind $SOURCE_DIR:/mnt \
	xbeach.sif xbeach.def 2>&1 | tee xbeach.log

chgrp comet_rsehpc xbeach.sif
chmod 664 xbeach.sif
(OSS 2410.0) [njps3@cometlogin02(comet) build]$ cat xbeach.def 
Bootstrap: docker
From: ubuntu:noble

%post
	# Prevent interactive prompts
	export DEBIAN_FRONTEND=noninteractive

	# Update & install only necessary packages
	apt-get update
    
	# Base stuff everything will need
	apt-get install -y aptitude wget zip less vim subversion

	# Add all of the Ubuntu/Debian packages needed to run XBeach here
	apt-get install -y \
		build-essential \
		cmake \
		gcc-14 \
		g++-14 \
		gfortran-14 \
		netcdf-bin \
		libnetcdf-dev \
		libnetcdff-dev \
		openmpi-bin \
		libopenmpi-dev \
		python3 \
		python3-pip
	
	# XBeach just tries to run 'python' not 'python3'
	ln -s /usr/bin/python3 /usr/bin/python

	# XBeach also wants the 'mako' Python module
	pip3 install mako --break-system-packages

	# Remove any downloaded package files - so they dont remain in the built image	
	apt-get clean

	##############################################################################
	# Set Compiler flags to optimise for Comet CPU hardware
	##############################################################################
	export BASE_CFLAGS="-O3 -march=znver5 -pipe"
	export CPPFLAGS=""
	export CFLAGS="$BASE_CFLAGS -I/usr/include"
	export CXXFLAGS="$CFLAGS"
	export CC=gcc-14
	export CXX=g++-14
	export FC=gfortran-14
	export F90FLAGS="-I/usr/include"
	export FFLAGS="-I/usr/include"

	###############################################################################
	# Download and compile XBeach
	###############################################################################

	mkdir -p /src
	cd /src
	svn co https://svn.oss.deltares.nl/repos/xbeach/trunk xbeach
	cd xbeach
	export FCFLAGS="-I/usr/include -I/usr/include"
	./autogen.sh && \
		FC=gfortran-14 MPIFC=mpif90 ./configure --with-netcdf --with-mpi && \
		make && \
		make install

	# Add /usr/local/lib to ldconfig
	echo "/usr/local/lib" > /etc/ld.so.conf.d/xbeach.conf
	rm /etc/ld.so.cache
	ldconfig

	# Remove downloaded source
	rm -rf /src

%environment

%runscript
</code>

**Container build script:**
<code lang=bash title=xbeach.build.sh>
#!/bin/bash

echo "Loading modules..."
module load apptainer

echo ""
echo "Building container..."
export APPTAINER_TMPDIR=/scratch

echo ""
echo "Starting build of container ..."
apptainer build \
	--bind $SOURCE_DIR:/mnt \
	xbeach.sif xbeach.def 2>&1 | tee xbeach.log

chgrp comet_rsehpc xbeach.sif
chmod 664 xbeach.sif
</code>

**Container runtime helper script:**
<code lang=bash title=xbeach.sh>
#!/bin/bash

module load apptainer

IMAGE_NAME=/nobackup/shared/containers/xbeach.sif

container.run() {
	# Run a command inside the container...
	# automatically bind the /scratch and /nobackup dirs
	# pass through any additional parameters given on the command line
	apptainer exec --nv \
		--bind /run/user/$UID:/run/user/$UID \
		--bind /scratch:/scratch \
		--bind /nobackup:/nobackup \
		${IMAGE_NAME} $@
}
</code>

-----

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