TELEMAC

The TELEMAC system is an integrated suite of solvers used in the fields of free-surface flow, wave propagation and sediment transport. Having been used in the context of numerous studies throughout the world and the subject of several peer-reviewed publications, it has become one of the major standards in its field.

The TELEMAC system is managed by a consortium of organisations: Artelia (France), BundesAnstalt für Wasserbau (BAW, Germany), Centre d'études et d'expertise sur les risques, l'environnement, la mobilité et l'aménagement (CEREMA, France), Électricité de France (EDF, France), HR Wallingford (United Kingdom) and International Marine and Dredging Consultants (IMDC, Belgium). It is further strengthened scientifically by Daresbury Laboratory (United Kingdom), the Centre Européen de Recherche et de Formation Avancée en Calcul Scientifique (CERFACS, France) and the École nationale des ponts et chaussées (ENPC, France).

• For more information: https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/blob/main/README.md

The TELEMAC 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/telemac.2026.09.sif

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

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/telemac.2026.09.sh

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 the GOTM utility included as a dependency with TELEMAC:

$ source /nobackup/shared/containers/telemac.2026.09.sh
$ container.run gotm --help
Usage: gotm [OPTIONS]

Options:

  -h, --help        print usage information and exit
  -v, --version     print version information
  -c, --compiler    print compilation options
$

You can continue to use the container.run command as many times as you need in the same script or same bash session, so you could run subsequently telemac2d as well:

$ container.run telemac2d
 DEFAULTS VALUES OF LU AND LNG:            6  AND            2
 LISTING OF TELEMAC2D------------------------------------------------------------------------------

                TTTTT  EEEEE  L      EEEEE  M   M  AAAAA  CCCCC
                  T    E      L      E      MM MM  A   A  C    
                  T    EEE    L      EEE    M M M  AAAAA  C    
                  T    E      L      E      M   M  A   A  C    
                  T    EEEEE  LLLLL  EEEEE  M   M  A   A  CCCCC
                                                               
                        2D    VERSION 9.1    FORTRAN 2003       

                        ~^~^~^~^~^~^~^~^~^~^~^^~^~^~^~^~^~     
                          ~                            ~       
                               \   '    o      '               
                               /\ o       \  o                 
                             >=)'>    '   /\ '                 
                               \/   \   >=)'>        ~         
                               /    /\    \/                   
                        ~         >=)'>   /     .              
                                    \/                   )     
                                    /                   (      
                                          ~          )   )     
                          }     ~              (    (   (      
                         {                      )    )   )     
                          }  }         .       (    (   (      
                         {  {               /^^^^^^^^^^^^      
                        ^^^^^^^^^\         /                   
                                  ^^^^^^^^^
$

… and telemac3d works the same way:

lang=bash>
$ container.run telemac3d
INFO:    gocryptfs not found, will not be able to use gocryptfs
 MASTER PROCESSOR NUMBER            0  OF THE GROUP OF            1
 READ_CONFIG: FILE CONFIG NOT FOUND: CONFIG
 DEFAULTS VALUES OF LU AND LNG:            6  AND            2
 LISTING OF TELEMAC3D------------------------------------------------------------------------------

                TTTTT  EEEEE  L      EEEEE  M   M  AAAAA  CCCCC
                  T    E      L      E      MM MM  A   A  C    
                  T    EEE    L      EEE    M M M  AAAAA  C    
                  T    E      L      E      M   M  A   A  C    
                  T    EEEEE  LLLLL  EEEEE  M   M  A   A  CCCCC
                                                               
                        3D   VERSION 9.1    FORTRAN 2003    

                        ~^~^~^~^~^~^~^~^~^~^~^^~^~^~^~^~^~     
                          ~                            ~       
                               \   '    o      '               
                               /\ o       \  o                 
                             >=)'>    '   /\ '                 
                               \/   \   >=)'>        ~         
                               /    /\    \/                   
                        ~         >=)'>   /     .              
                                    \/                   )     
                                    /                   (      
                                          ~          )   )     
                          }     ~              (    (   (      
                         {                      )    )   )     
                          }  }         .       (    (   (      
                         {  {               /^^^^^^^^^^^^      
                        ^^^^^^^^^\         /                   
                                  ^^^^^^^^^                    

                   ********************************************
                   *               LECDON:                    *
                   *        BEFORE CALLING DAMOCLES           *
                   ********************************************
$

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.

The following applications are installed in the TELEMAC container environment:

In addition, the following Python modules are installed:

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.

Here is a very simple example of calling TELEMAC from the container within a Slurm batch job that assumes you are a member of the comet_abc123 HPC project group and your input data lives in /nobackup/proj/comet_abc123/my_data.input:

#!/bin/bash

#SBATCH --partition=default_free
#SBATCH --account=comet_abc123
#SBATCH -c 16
#SBATCH --mem=20G

source /nobackup/shared/containers/telemac.2026.09.sh
# Now change to your directory which has been prepared for a TELEMAC job and 
# use "container.run" to run telemac2d or telemac3d as required

Submit as normal with sbatch telemac_job.sh.

Note that there are several hard dependencies in TELEMAC on non-current versions of software, or bugs in the install which require manual workarounds, this includes:

• Python < 3.12.x - med-fichier uses the imp module which is removed in Python 3.12
• Ubuntu ⇐ 22 LTS - one of the Python modules Rasterio wants to remove the system-provided numpy in Ubuntu >= 24 LTS, breaking the install
• MED - the version linked by TELEMAC breaks on modern versions of HDF5 lib, and is unable to correctly extract the version number from H5public.h - our container definition includes a patch to mitigate this
• libaed - the build is not parallel make safe, so we need to restrict make to a single job
• GOTM - the build only works with the specific version linked from the TELEMAC repository; using a later version direct from GOTM themselves fails with an error during compile

This means that we are effectively 'stuck' on Ubuntu 22, with Python 3.10 until all dependencies are updated and the TELEMAC project updates to work with newer versions.

Container definition file:

Bootstrap: docker
####################################################################################################
# Jammy (22 LTS) must be used, as Noble (24 LTS) has Python 3.12 which is too new for some of the Python components 
# e.g. med-fichier relies on the Python "imp" module which was *removed* in Python >= 3.12.x
####################################################################################################
From: ubuntu:jammy

##########################################################################
# TELEMAC container defintion file for Apptainer
# ==============================================
#
# See: https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/blob/main/BUILDING.md
# And: https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/blob/main/REQUIREMENTS.md
#
# Written for Newcastle University Comet HPC users
# Research Software Engineering team
# https://hpc.researchcomputing.ncl.ac.uk
#
###########################################################################

%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 git

	# Things for Telemac
	apt-get install -y \
		build-essential \
		ninja-build \
		gcc \
		g++ \
		gfortran \
		python3 \
		python3-pip \
		python-is-python3 \
		openmpi-bin \
		libopenmpi-dev \
		libmetis-dev \
		libgdal-dev \
		gdal-bin \
		cmake \
		libopenblas-openmp-dev \
		libopenblas64-dev \
		libscalapack-openmpi-dev \
		libmumps-dev \
		libnetcdf-dev \
		libnetcdff-dev \
		hdf5-tools 
	
	# 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 and which extras
	# we want to install.
	##############################################################################
	PRODUCTION=1
	BUILD_PY=1
	BUILD_MED=1
	BUILD_LIBAED=1
	BUILD_FABM=1
	BUILD_GOTM=1
	BUILD_TELEMAC=1

	# Set compiler flags - dont optimise in testing mode, it just delays the build
	if [ "$PRODUCTION" = 1 ]
	then
		export BASE_CFLAGS="-O3 -march=native -pipe"
		export BASE_FCFLAGS="-march=native -pipe -mtune=native -funroll-loops --param max-unroll-times=4 -ffree-line-length-none -O3 -ffast-math"
	else
		export BASE_CFLAGS="-O"
		export BASE_FCFLAGS="-O"
	fi

	export CPPFLAGS=""
	export CFLAGS="$BASE_CFLAGS -I/usr/local/include"
	export FCFLAGS="$BASE_FCFLAGS -I/usr/local/include"
	export CXXFLAGS="$CFLAGS"
	export MAKE_JOBS=16
	export MPIFC=mpif90
	
	###############################################################################
	# Check versions of installed compilers
	###############################################################################
	gcc -v
	g++ -v
	gfortran -v
	python3 -V

	###############################################################################
	# Common stuff...
	###############################################################################
	mkdir -p /opt
	mkdir -p /src/zipped

	##############################################################################
	# Install Telemac Python dependencies
        # See: https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/blob/main/REQUIREMENTS.md
	##############################################################################
	if [ "$BUILD_PY" = 1 ]
	then
	        pip3 install mpi4py 
	        pip3 install Jupyter
	        pip3 install openpyxl
	        pip3 install OWSLib 
	        pip3 install pandas 
	        pip3 install pyproj 
	        pip3 install Rtree 
	        pip3 install Seaborn 
	        pip3 install GDAL 
	        pip3 install Fiona 
	        pip3 install Rasterio #-- breaks numpy by trying to install a later version, if using Ubuntu 24/Noble LTS
	        pip3 install Shapely 
	        pip3 install GeoPandas 
	        pip3 install Pylint 
	        pip3 install doxypypy 
		pip3 install matplotlib 
		pip3 install scipy 
	fi

	###############################################################################
	# Download and compile libaed
	##############################################################################
	if [ "$BUILD_LIBAED" = 1 ]
	then
		cd /src/zipped
		wget https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/package_files/444/download -O libaed.tgz
		cd /src
		tar -zxf /src/zipped/libaed.tgz
		cd libaed2-1.1.0
		make all			# Do not use -j, the libaed makefile is not parallel job aware, and it will break the compilation
		make shared			# As above
		cp -v libaed2.a /usr/local/lib
		cp -v libaed2.so /usr/local/lib
		cp -v include/* /usr/local/include
		cp -v *.mod /usr/local/include
	fi

	###############################################################################
	# Download and compile FABM
	###############################################################################
	if [ "$BUILD_FABM" = 1 ]
	then
		cd /src/zipped
		wget https://github.com/BoldingBruggeman/fabm/archive/refs/tags/v0.95.0.tar.gz -O fabm.tgz
		cd /src
		tar -zxf /src/zipped/fabm.tgz
		cd fabm-0.95.0
		cmake -G Ninja -B build -S src -DFABM_USE_DO_CONCURRENT=ON -DCMAKE_INSTALL_PREFIX=/usr/local 
		cmake --build build
		cmake --build build --target install
	fi
	
	###############################################################################
	# Download and compile GOTM
	###############################################################################
	if [ "$BUILD_GOTM" = 1 ]
	then
		# BROKEN - This is GOTM 5.0.3 as distributed with TELEMAC - but only reports "branch" as the version
		#wget https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/package_files/445/download -O gotm-telemac.tgz

		# BROKEN - This is GOTM 5.2.1 - compile breaks on "Fatal Error: Cannot open module file 'yaml_types.mod' for reading at (1): No such file or directory" 
		#wget https://github.com/gotm-model/code/archive/refs/tags/v5.2.1.tar.gz -O gotm.tgz

		# This is GOTM Linked from the TELEMAC install guide
		cd /src/zipped
		wget --no-check-certificate http://www.opentelemac.org/downloads/Installation%20files/Manual%20installation%20-%20Sources/gotm-2019-06-14-opentelemac.tar.gz -O gotm.tgz
		cd /src
		tar -zxf /src/zipped/gotm.tgz
		cd gotm-2019-06-14-opentelemac/
		mkdir build
		cd build
		cmake .. -DGOTM_USE_NetCDF:BOOL=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=/usr/local
		make -j $MAKE_JOBS
		make install
                #########################################################################
                # For some reason libgotm.so does not get installed with "make install"
                #########################################################################
                cp -v gotmlib/libgotm.so /usr/local/lib
	fi

	###############################################################################
	# Download and compile MED 
	###############################################################################
	if [ "$BUILD_MED" = 1 ]
	then
		cd /src/zipped
		wget https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/package_files/443/download -O med.tgz
		cd /src
		tar -zxf /src/zipped/med.tgz
		cd med-4.1.1
		#################################
		# PATCH!!!
		# The configure script is broken and does not correctly extract the HDF5 version string from H5public.h
		# This leads to crazy errors such as:
		# "This HDF5 version #define H5_VERS_MAJOR 1.#define H5_VERS_MINOR 10.#define H5_VERS_RELEASE 10 must not be used with med-fichier4.1.1."
		# If you look at the H5public.h header, a simple awk would suffice instead.
		################################
		cp configure configure.orig
		cat configure.orig | \
			sed "s/H5_VER_MAJOR=/H5_VER_MAJOR=\`grep \'\#define \*H5_VERS_MAJOR\' \$HDF5_ABS_PATH | awk \'{print \$3}\' \` \#/" | \
			sed "s/H5_VER_MINOR=/H5_VER_MINOR=\`grep \'\#define \*H5_VERS_MINOR\' \$HDF5_ABS_PATH | awk \'{print \$3}\' \` \#/" | \
			sed "s/H5_VER_RELEASE=/H5_VER_RELEASE=\`grep \'\#define \*H5_VERS_RELEASE\' \$HDF5_ABS_PATH | awk \'{print \$3}\' \` \#/" > configure
		chmod +x configure
		./configure --enable-fortran --enable-api23 --enable-python
		make -j $MAKE_JOBS
		make install
	fi

	###############################################################################
	# Download and compile Telemac
	###############################################################################
	if [ "$BUILD_TELEMAC" = 1 ]
	then
		cd /src
		git clone https://gitlab.pam-retd.fr/otm/telemac-mascaret.git
		cd telemac-mascaret
		git checkout tags/v9.1.1
		export PATH=$PWD/scripts/python3:$PATH
		export GOTM_INCLUDE_DIR=/usr/local/include

		####################################################################################
		# PATCH!!!
		# The cmake rule files included with TELEMAC do not appear to work with the version
		# of GOTM they link to... it finds the library, but returns "" as the version!
		# We will spoof the version to always be "5.3.0" instead ...
		####################################################################################
		cp cmake/FindGOTM.cmake cmake/FindGOTM.cmake.orig
		cat cmake/FindGOTM.cmake.orig | \
			sed 's/string(REPLACE "v" "" GOTM_VERSION "${GOTM_VERSION}")/set(GOTM_VERSION "5.3.0")/' > cmake/FindGOTM.cmake
		cat cmake/FindGOTM.cmake

		build_telemac.py \
			-j $MAKE_JOBS \
			--deps all \
			--modules all
		build_telemac.py --check
		build_telemac.py --install /usr/local
	fi

	################################################################################
	# ld.so.conf configuration
	################################################################################
	echo "/usr/local/lib" > /etc/ld.so.conf.d/telemac.conf
	rm -f /etc/ld.so.cache
	ldconfig -v

	################################################################################
	# We are finished here
	################################################################################
	cd /
	rm -rf /src
	pip3 cache purge

%environment
       export HWLOC_COMPONENTS="-gl"

%runscript

Build script:

#!/bin/bash

echo "Loading modules..."
module load apptainer

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

echo ""
echo "Starting build of container ..."
apptainer build \
	telemac.sif telemac.def 2>&1 | tee telemac.log

Runtime wrapper:

#!/bin/bash

module load apptainer

IMAGE_NAME=/nobackup/shared/containers/telemac.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 --bind /scratch:/scratch \
                   --bind /nobackup:/nobackup \
                   ${IMAGE_NAME} $@
}

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