||2 years ago|
|documentation||2 years ago|
|gui||2 years ago|
|local_scripts||2 years ago|
|scripts||2 years ago|
|.gitignore||2 years ago|
|DESTINATIONS.example||2 years ago|
|ORIGINS||2 years ago|
|Readme.md||2 years ago|
|SETUPS.example||2 years ago|
|archive_setup.sh||2 years ago|
|build.sh||2 years ago|
|clone_origins.sh||2 years ago|
|deploy_setups.sh||2 years ago|
|iow_esm.py||2 years ago|
|postprocess.sh||2 years ago|
|run.sh||2 years ago|
IOW Earth system model
This is the main repository for this project. Further information will follow.
!!!ATTENTION!!! This not yet a working project and cannot be used at the moment
Your local machine has to provide:
tkintermodule) for using the graphical user interface
If you work on Windows, you can use e.g. the
MSYS2 software distribution and building platform.
For installation, follow the instructions given on the project web site.
After successful installation you can open an
MSYS2 shell via hitting the Windows key on your keyboard, typing "msys" and opening the installed app.
In the opnend shell you can then install
rsync which are needed by executing
pacman -S git pacman -S rsync
If you work on Linux you will most probably have a
bash and you can install
git with the package manager of your distribution.
You need accounts on the target servers, where you want to run the model.
TODO: How to setup correctly
Get the main project
Open a shell (
MSYS2 on Windows or
bash on Linux) and execute
cd /to/your/favorite/directory git clone https://git.io-warnemuende.de/karsten/main.git .
The place holder
/to/your/favorite/directory will become the root directory of this project so choose it resonably.
Note that it is strongly recommended to use a key agent for connecting to the target servers. Otherwise you will have to type in your account password very often. Assuming you have generated RSA key pairs for the target machines as described in the phywiki or as required for the HLRN, you can start a key agent via
eval `ssh-agent` ssh-add ~/.ssh/<private-key>
<private-key> should be the private key generated for the desired target.
Working with the GUI
If you would like to work with graphical user interface you have to start corresponding python script from a shell
MSYS2 on Windows or
bash on Linux) by executing the following in the root directory (where this
Readme.md is located)
The shell where this is executed should be the same as where the key agent is running.
The GUI will guide you step by step throught the first steps that are described in the following for the command line application.
Get the component sources
After cloning this repository to your local machine you have to get the component repositories as well.
For this purpose there is the bash script
clone_origins.sh which uses the file
The one you have cloned right now contains all available components.
This file should not be edited and commited unless you really know what you are doing.
By executing in the root directory (where this
Readme.md is located)
you clone all individual components which have their own repositories to your local machine. If there will be some you don't need you can later remove them. However, be sure that you can still build and run the model properly.
Configure your destinations (targets)
You will not build (or run) the model on your local computer.
Instead you have to specify a destination or a target, where your sources are copied and compiled.
This is done a file
DESTINATIONS (this name is obligatory).
Since this file very user-specific it is not part of the repository and you have to create one.
However, there is an example
DESTINATIONS.example, please have a look.
You see that each line consists of two elements.
The first is the keyword for the target. This keyword has to match one of the following
hlrngrefers to the HLRN IV cluster located in Göttingen
hlrnbrefers to the HLRN IV cluster located in Berlin
haumeais the cluster of the of the Rostock University
phy-2is one of the IOW's physics department computing servers (ATTENTION: currently the model is not running here)
At the moment there are running build scripts only for these targets. If you want to add more, it will be explained later how this can be done.
The second element in a line of
DESTINATIONS.example corresponds to the root directory on the target, the path, where the whole model will be deployed, built and run.
If the path on the target does not exist, it will be created.
Be sure that you have write permissions.
Importantly, the location must have the following format
Both user and host name are use in the script and cannot be omitted although you might have some shortcuts and aliases for your accounts.
Now it is up to you, to create your own file
DESTINATIONS in your local root directory, but do not commit it!
Note that there is also the possibility to give more advanced keywords to run several instances on the same target, see Advanced destination keywords
Build the coupled model for the first time
Each component can be built individually by executing the build scripts in the component's directory, see Build single components in a different modes and configurations.
However, for the first build the order is important, since some components of the coupled model depend on each other.
Therefore, you should use the
build.sh script in the root directory.
If you want to build the model e.g. on the HLRN cluster located in Berlin, you can run, e.g.
This will build the model on
hlrng in release mode.
Note that we will stick to this specific target throughout this Readme.
Nevertheless, if you want to work with another target for your first tests, just replace
hlrng with another valid keyword.
Note that the first argument is non-optional, whereas there are two others which can be omitted,
see Build single components in a different modes and configurations.
Deploy dependencies for running (setups)
Configure your setups
In order to run the model, you need input files which define a certain setup.
What exactly a setup consits of, you can find out by looking at Available setups.
The setups you want to use can be registered in a special file named
SETUPS (this name is obligatory),
which is in the root directory.
Since this file specific for certain users and individual runs of the model it is not part of the repository and you have to create one.
However, there is an example
SETUPS.example, please have a look.
You see that each line consists of two elements.
The first is the keyword for the setup.
This keyword can be chosen by you almost freely.
It should be unique and a single word without spaces.
In order to update from one or several setups you can call the run script
run.sh with a second, third, etc. argument representing your setup keys in the
The files from these setups are then synchronized to the target in the order they appear as arguments.
That is, the last setup will overwrite the ones before if files are overlapping.
The second element of a line in
SETUPS represents the location of this setup.
This can be local on your machine or on a remote computer.
Be sure that the remote computer knows your targets and can copy files to them.
HLRN in Göttingen
You can find an example setup for a MOM5 for the Baltic sea coupled to a CCLM model for the Eurocordex domain under
The corresponding line in the
SETUPS file could then look like
user should be replaced by your user name on the HLRN in Göttingen.
It might be also necessary to add the full domain to the hostname, depending on your ssh configuration.
TODO: Explain strucutre of the setup folder (= root directoy)
Copy setup files to target
After creating the file
SETUPS you can run in the root directory
./deploy_setup.sh hlrng example
Run the coupled model for the first time
If everything is set up on your remote computer of choice, you can run the model for the first time by executing this in the root directory:
./run.sh hlrng prepare-before-run
The first argument of the run script is always the target keyword as specified in your
By executing the run script all files from
scripts directory will be transferred to the target.
The second argument
prepare-before-run is obligatory for the very first run.
This will create necessary mapping files in the destination directories.
However, for all following runs this is an optional argument and should be omitted, unless you really want to re-create the mapping files.
After the scripts are transferred and the preparation script has finished (this can take a bit time), the model is started on the target.
Examine the output of the first run
Advanced destination keywords
It is possible to use not only the destination keywords given in Configure your destinations (targets).
You can also use something like e.g.
hlrng_YYY if you want to run two independent instances on the target
However, the string before the first underscore must be one of the keywords given above.
Building during development
Build single components in a different modes and configurations
If you are developing only one component at a time, it is not necessary to call the global build script from the root directory. There are also build scripts in each components subdirectory which can be called directly, e.g.
cd components/flux_calculator ./build.sh hlrng debug rebuild
This would rebuild the flux_calculator on the
hlrng in debug mode.
The defaults for the second and third argument are
fast (which is the opposite of
The same applies likewise to the other components.
Once you execute a build command, e.g.
LAST_BUILD_hlrng_release is created,
where the strings
release depend on the arguments, you give to the build script.
This file contains information on the state the source code of the components is in.
In particular, it contains the unique commit ID, the build mode (fast/rebuild) and a time stamp of the build.
Moreover, if the source code exhibits uncommited changes when the build script was executed,
these diffrences are logged within that file.
By executing the run script later on, the same tagging will be done for the main repository and this file is transferred to the destination.
That way, you can always identify with which version of the code your working on the target.
Running during development
Update the setup before running
During development it usual to modify the setup, i.e. parameters in input files.
It is not intended to do this directly on the target,
because then it is hard to keep track of the changes (still it is possible of course).
However, the run script in the root directory offers the possibility to update the setup directly before running the model.
Before running, you have to prepare a setup used for updating.
The idea is, that you create a local folder where you put the input files that you want to modify.
This folder, e.g.
./local_setup, must have the same directory structure as a normal setup folder.
For instance, if you want to have a modified
input/global_settings.py at your destination,
./local_setup/input/global_settings.py, make your changes in the file and then register this folder in the
e.g. by adding the line
Then you can run the model by calling
./run.sh hlrng update
This will start the model on the
hlrng but beforehand it will synchronize the contents of the
./local_setup to the destination.
./local_setup there is file
UPDATE_SETUP_INFO created, which is also transferred to the target
and contains information and time stamp of the updating.
In general the run script can be called like
./run.sh hlrng [prepare-before-run] update1 update2 update3...
prepare-before-run is optional and can be omitted, which is usually the case if it is not the very first run on a target.
The setup updates are transferred in the order they appear, where the last one can, in principle, overwrite the ones before.
Note that you should not use the keyword
prepare-before-run for a setup, otherwise the script will be confused.
Archiving the employed setup
Imagine you have started your development on
hlrng from the setup with the keyword
testing, this can be viewed as the base of your current setup.
Now you made changes to some input files and you want to conserve the current state.
This can be done by using the script
./archive_setup.sh hlrng testing archive
First, this would produce a copy of the base setup corresponding to the keyword
testing in the very same destination (you need write permissions there).
The new folder has the same name as
testing supplemented by
_archive and it contains only symbolic links to the base setup.
Second, it is checked where the base setup and the one residing on the
Third, only files that are different will be updated from the
hlrng and put into the created archive folder.
If you want to create your archive in a different directory then your base, you can specifiy a keyword and the corresponding destination in the
You can then call the setup archiving script with that keyword as the third argument.
Note that the base setup and the archive must be available via the same machine since we are using symbolic links here.
Once you have archived your setup, the
SETUP_INFO file on your target server will be updated as well.
Archiving the obtained output
Extending the project
Register new destinations
Add a new keyword and the corresponding remote directory to your
DESTINATIONSfile. Let's call the new target keyword in this example
new-target. Then the new line in your
DESTINATIONSfile could look like
new-target user@new-target:/data/user/IOW_ESM. Add
Add a build script for each component that should be build on the new target. For the example this must be called
build_new-target.sh. In general the name has to be
build_followed by the keyword and
.sh. In most cases you can probably copy the build script from another target and simply adapt the loaded modules or paths. You have to find out on your own which modification are to be done here.
Add a script that starts the build script on the target. For the example this must be called
start_build_new-target.sh. In general the name has to be
start_build_followed by the keyword and
.sh. On some targets the build is performed using the queuing system on others it can be performed on directly the login node. Find out which is true for your new target. The existing
start_build_haumea.shis an example for using the queue, whereas
start_build_hlrng.shis an example for direct compilation on the login node.