PALM overview

group
Institute of Meteorology and Climatology, Leibniz Universität Hannover
PALM overview
Introduction

 First version 1997, continuously developed since then.

 Written in FORTRAN 95 / 2003 / 2008.
 Very high performance and scalability on all state-of-the-art parallel architectures (see
lecture “Code parallelization”).
 PALM code is under the GNU General Public License v3.
 PALM project is managed under gitlab (see [Link] ).
 Detailed online documentation under [Link]
 Many new features have been added since then (see lecture “Current developments”).
 PALM 6.0 has been released Oct 2018, described in a special issue in Geoscientific
Model Development (see [Link]
 Current version used in this webinar is PALM release 23.04 (see
[Link]
 Further extensions are planned for the next years.

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PALM overview
Features (I)
Physics / Numerics

 Cyclic horizontal boundary conditions but also non-cyclic boundary conditions along x or y
available.
 Turbulent inflow is realized for non-cyclic boundary conditions.
 Complex topography / 3d-buildings are realized.
 A Lagrangian particle model is embedded (can be used to replace bulk cloud physics two-
moment scheme).
 Ocean mode is available, i.e. salinity equation and equation of state for seawater is
included; coupled ocean-atmosphere simulations are possible.
 Coupling to larger scale models implemented using large scale advection and nudging.
 Various surface models are included.
 Soil and radiation model available.
 LES-LES-nesting and nesting to meso-scale models is implemented.
 Gas phase chemistry and aerosol model available.
 Wind turbine model for simulating energy output and wakes.
 RANS and DNS mode is included.
 Multi-agent system for simulating effects on population groups.

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PALM overview
Features (II)

Technical features
 Scripts allow for very comfortable operation of the model.
 Model can be adapted for any kind of (Unix) system including batch operation by simply
adjusting a configuration file.
 Batch jobs and job chains (restart mechanism) can be automatically created.
 Runs are controlled via simple NAMELIST parameter file and in case of complex
surfaces by driver files in NetCDF format.
 Error messages inform in case of parameter inconsistencies or other problems that are
detected during runtime.
 Standard data analysis is done online during the simulation.
 All output is in standard NetCDF data format.
 A user-interface allows for easy code extensions by the user.
 Code is highly optimized for all state-of-the-art computer architectures and allows for
very huge applications (currently 50003 gridpoints).

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 PALM overview
Some examples of applications at IMUK (LUH)
Roll Convection

Dust Devils Urban Canopy Flow

Canopy Flow

Wind turbine wakes Gusts at Airports

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PALM overview
External users / collaborations

 ForWind (University of Oldenburg, Germany)

 DWD (German Weather Service)
 KIT (Karlsruhe Institute of Technology, Germany)
 University of Bergen (Bergen, Norway)
 FMI (Finnish Meteorological Institute, Helsinki, Finland)
 Department of Atmospheric Sciences, Yonsei University (Seoul, Korea)
 School of Earth and Environmental Science, Seoul National University (Seoul,
Korea)
 Dept. of Intl. Development Eng., Tokyo Institute of Technology (Tokyo, Japan)
 Dept. of Earth and Environment, Boston University (USA)
 INPE/CPTEC Instituto Nacional de Pesquisas Espaciais (Brazil)
 Chinese University of Hong Kong, School of Architecture (Hong Kong)
 Institute of Physical Oceanography, Zhejiang University (China)
 …

Currently more than 800 registered users on our trac-server.

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PALM overview
Areas of application (external users)

 Interaction of boundary layer turbulence with wind turbines / wind farm wakes.
 Improvement of turbulence parameterizations.
 Atmosphere-ocean coupling.
 Ocean mixed layer.
 Turbulence / dispersion in the urban canopy layer.
 …

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PALM overview
PALM components

 Beside the model‘s FORTRAN code, the PALM download contains a variety of further
components / files, organized in folders. The subfolders you see below can be found in
folder palm_model_system/packages/palm/model

readme-file containing information about PALM

[Link]
README.
installation and changes included in the release

bin shell scripts for compiling, testing, and running PALM

palm_model_system

src PALM source code + Makefile

input files and various output files to check

tests
and verify the PALM installation (used by our testserver)

example configuration files for various computers /

share/config
operating systems

lib libraries shipped with PALM (e.g. RRTMG)

Please never modify or delete files in palm_model_system and its subfolders!

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PALM overview
Recommended structure of folders for PALM installation
You can freely configure the folder structure in configuration files!
parameter files for steering,
contains job protocol JOBS/
output data, code extensions
files from batch jobs from user (user interface)
job_queue/

$HOME/ palm/ current_version/ palm_model_system PALM software (FORTRAN

code, scripts, etc.)
working directory
of PALM user precompiled routines,
MAKE_DEPOSITORY_.../ generated by
palmbuild
... compiled with
MAKE_DEPOSITORY_.../ different options (e.g.
older_version/ for debugging)
older PALM version, if needed
contains a temporary folder created optional
/fast_io_catalog/
(by palmrun) for each PALM run
automatically generated
contains large binary data files created
/fast_io_catalog/ by PALM and required e.g. for restarts created by user

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PALM overview
Main modes of operation

 Interactive mode
 PALM is run in interactive shell (terminal session).
 CPU time as well as number of processors for interactive runs is limited on many
systems.
 Restart runs (job chain) are not possible.
 Only requires appropriate settings in the configuration file.

 Batch mode (running batch jobs)

 Requires a batch queueing system (e.g. SLURM, PBS, Loadleveler, etc.) on the
computer in use.
 Requires additional settings (for batch directives) in the configuration file.

 Running batch jobs on remote computers

 Requires a batch queueing system on the remote computer.
 Requires ssh/scp access of the remote computer (in both directions “local <->
remote“), fixed IP-adresses for local and remote computer are required too.
 Running job chains automatically
 Requires a batch queueing system (+ ssh/scp access).

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PALM overview
Scripts for operating

PALM is operated mainly by one script, named palmrun. palmrun itself calls
palmbuild to compile for the respective runs, if required.

 palmrun
 script for running PALM (interactive or batch)

 palmbuild
 script for generating a pre-compiled PALM version (object files)

 helper programs
 small FORTRAN programs, needed e.g. for collecting output data or finding grid setups
(combine_plot_fields, palm_gf, etc.)

Location of scripts: ~/palm/current_version/bin

The scripts have a large number of options. A short summary of available options
For a detailed palmrun documentation see
can be listed by giving the question mark as the only option, i.e.. palmrun ?
[Link]

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PALM overview
PALM configuration file
palmrun and palmbuild require a lot of settings (which depend on the respective
computer system used), to be given in configuration files with default names
.[Link].<configuration_identifier> and .[Link]

 Main purposes of the configuration files:

 setting of compiler options
 setting of preprocessor switches
 setting of paths for libraries (e.g. NetCDF library)
 setting of environment variables
 setting of UNIX-commands to be executed before or after PALM execution
 handling of input/output files by file connection statements

Default position
$HOME/ palm/ current_version/
for .[Link].<ci>:

A default version of this

file .[Link] can be found palm_model_system/packages/palm/model/share/config
in:
See [Link] and [Link] for
detailed descriptions.

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PALM overview
Further requirements for running PALM

The following things are not provided with the download!

 FORTRAN compiler
 MPI-library (must fit to the compiler!), MPI-3 is required
 optional FFTW-library (see [Link]) for very fast FFT
 NetCDF-library (see [Link]/software/netcdf/), required for data
output (must fit to compiler and MPI-library!)
 graphics software capable to read NetCDF data format (e.g. ncview, NCL, IDL,
ferret)
 Batch-system
 Python 3, required for the installer and several helper scripts

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