GUI
The GUI contains the following pages:
INFO
UPLOAD
REVIEW
EXPLORE
HELP
SETTINGS
Note
Currently, REVIEW has not yet been implemented.
INFO
A brief introduction to the program is provided in this section.
UPLOAD
This section contains an upload form for uploading Nektar++ datasets to AE Datastore. Users will be asked to upload files in three groups:
Geometry
Input
Output
Geometry
A single *.nekg HDF5-format geometry file is expected in the upload process. You may have either a single XML session file, or an XML session file and an XML geometry file. These are legacy formats, and the *.nekg HDF5-format geometry file is considered best practice. For help in converting files to the correct format, see Converting files.
Note
You might be wondering why NekUpload cannot just convert the files, rather than asking you to manually convert then submit. The Nektar++ team would like to encourage the use of the HDF5 format as it is more memory-efficient format. Explicitly asking you to convert the file will help encourage usage, and encourage future simulations to be generated in a similar manner.
Since geometry files are often re-used in simulation, an alternative method exists if the geometry file is already uploaded on AE Datastore. The record identifier of the geometry file can be obtained using the EXPLORE page. By specifying this geometry record id, you can link your dataset to an existing geometry record on AE Datastore. Now you only have to upload the rest of your input and output files.
Input
Input files refer to all files required to define the simulation setup (excluding the geometry). At minimum, this should consist of one XML session file. Any supporting files referenced by the session files should also be included for completeness and to allow others to reproduce the datasets.
Output
Output files can be split into two categories. The regular outputs of the simulation are the .chk and .fld files generated during a normal simulation run. These are expected to be in HDF5 format. The second category are filter files. All filter files defined in the inputs should be submitted for a complete dataset. However, NekUpload currently only requires the submission of AeroForces and History filter files. Users may optionally add images any images they have generated to enhance the dataset.
What happens when I hit submit?
When you hit submit, NekUpload will first verify for completeness and consistency. Completeness ensures all the files that are required to completely define the simulation and its results are provided, allowing others to reproduce the simulation. Meanwhile, consistency reduces the risk that invalid datasets or incorrectly uploaded files are accidentally entered into the database. Pre-existing fields and metadata within the datasets are then automatically extracted to annotate the datasets to improve findabiliy.
What metadata is extracted?
Currently, aerodynamic parameters such as Reynolds number and freestream velocity are extracted and added to the record. This allows AE Datastore’s internal search engine to find relevant CFD datasets. Meanwhile, the geometry domain is also extracted. This is to ensure online post-processing tools for Nektar++ can utilise efficient post-processing algorithms.
How is data stored?
Nektar++ datasets are stored in two records: one for the geomtery, and another for the simulation datasets (input and output files). These are currently linked via a DOI (Note that DOI are not resolved until records are published by database admins) and can be found on AE Datastore.
What happens after I upload?
Wait for database admins to review your submission. If amendments are required, you will be notified of this. Otherwise, the records will be published.
REVIEW
TBC
EXPLORE
This page allows you to explore what records already exist on AE Datastore. You may search a specific community (such as the Nektar++ community) and list all the geometry files and simulation datasets that have been published. You may also see what other datasets and geometry files you have already uploaded. Most importantly, this provides the record id and a link to the AE Datastore website where the files are located.
Note
Viewing community files does not require an API key. However, accessing your own records requires an API key.
HELP
This provides some information on common warning and error messages that may pop up. This is designed to aid the user in identifying the reason for failure, and rectify it so that they can use NekUpload to upload their datasets.
SETTINGS
General settings can be configured here. The key part of settings is specifying the API key to AE Datastore, which you must generate as specified in the Quisktart section.
Note
Remember to hit the save button to save your settings changes.
Database Target
Specify where the online database repository is. This defaults to AE Datastore. Users may want to choose their own custom online repository target, which can be specified by selecting Custom in the drop-down box and entering the URL of that repository.
API Key
You must provide the API key for accessing your selected online repository. You can either provide it directly to the program, or specify the environment variable it is stored in.