Analysis Applications¶

Requesting New Applications: DesignSafe regularly adds new software applications in support of natural hazards engineering research. You may contact DesignSafe by submitting a help ticket if you would like to request the addition of a software application to the Workspace.

Getting Your Own HPC Application: For those researchers with larger computational needs on the order of tens of thousands, or even millions of core-hours, or if you have a software application that we don't support in the web portal, you may request your own allocation of computing time on TACC's HPC systems. Your files can still be stored in the Data Depot, allowing you to share your research results with your team members, as well as curate and publish your findings.

Commercial/Licensed Applications: The DesignSafe infrastructure includes support for commercial/licensed software. Wile in some cases licenses can be provided by the DesignSafe project itself, not all vendors will make licenses available for larger open communities at reasonable cost. You may contact DesignSafe by submitting a help ticket if you have questions regarding a commercial software application.

HVSRweb User Guide¶

The horizontal-to-vertical spectral ratio (HVSR) method has become an increasingly popular tool for developing a quick and reliable estimate of a site’s fundamental natural frequency (f₀). HVSRweb is an open-source, web-based application for performing HVSR calculations in a convenient, reliable, and statistically-consistent manner. HVSRweb allows the user to upload three-component ambient noise records and perform the HVSR calculation in the cloud, with no installation required. The HVSR calculation can be performed using a single combined horizontal component (e.g., geometric-mean, squared-average) or multiple rotated horizontal components to investigate azimuthal variability. HVSRweb can reject spurious time windows using an automated frequency-domain window-rejection algorithm, removing the need for subjective and time-consuming user interaction. It also facilitates the use of lognormal statistics for f₀, allowing for a consistent statistical framework capable of quantifying measurement uncertainty in terms of either frequency or its reciprocal, period. In addition, HVSRweb presents the opportunity to rapidly incorporate new developments in processing and quantification of uncertainty as they emerge, and encourages standardization of HVSR processing across users while avoiding the challenges associated with traditional approaches that require the user to perform regular updates to keep pace with new developments.

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MATLAB User Guide¶

DesignSafe is able to provide access to the popular licensed software MATLAB to academic researchers via our license with Mathworks. You can request access to our licensed MATLAB, and we first verify that you are a researcher at an academic institution before providing you access.

We provide two MATLAB applications in the Workspace:

MATLAB
- For lighter workloads not working with large datasets, this MATLAB application runs on TACC's DesignSafe VM (Virtual Machine).
- It runs as an interactive MATLAB 2018b session on a virtual machine.
MATLAB Batch
- For heavier workloads and large datasets, this MATLAB application runs on TACC's HPC resources.
- It is a non-interactive application to run *.m scripts.
- These sessions run on single node with 64 cores on Stampede2.
- Different versions of MATLAB are available in this mode.

NOTE: Because MATLAB is an interactive program that you access in a GUI, you will not have the same responsiveness as running on your local laptop. We provide MATLAB as a convenience to interacting with your data in the Data Depot without having to download it to your local system, and also the version running on HPC resources is great for large datasets or heavy workloads that are too much for your laptop.

How to Start a MATLAB Interactive Session in the Workspace ¶

MATLAB that runs on VM

Select the MATLAB application from the Data Processing tab in the Workspace.
Select MATLAB from the dropdown menu.
Select your desired desktop resolution from the dropdown menu.
Enter a maximum job runtime in the form. While this field is required in the form it is not actually used, simply enter any time using the time format shown.
Enter a job name.
Enter an output archive location or use the default provided.
Click Run to start your interactive session.

How to Submit a MATLAB Batch job in the Workspace ¶

MATLAB Batch that runs on HPC

Select the MATLAB application from the Data Processing tab in the Workspace.
Select MATLAB (Batch 20XXa/b) version corresponding to your *.m script from the dropdown menu.
Locate the directory containing your data files in the Data Depot and follow the onscreen directions to enter this as your Working Directory.
Select your batch MATLAB script name. This file should reside in the Working Directory.
Enter a maximum job runtime in the form. See guidance on form for selecting a runtime.
Enter a job name.
Enter an output archive location or use the default provided.
Click Run to submit your job to stampede queue.

SWbatch User Guide¶

SWbatch is a user-friendly, web-based application for performing batch-style surface wave inversions using the Dinver module of the open-source software Geopsy. SWbatch allows the user to rapidly and conveniently invert experimental dispersion data considering multiple inversion parameterizations to address the problem’s non-uniqueness and multiple trials per parameterization to address the problem’s nonlinearity as detailed in the SWinvert workflow (Vantassel and Cox, 2020). To facilitate the potentially large amounts of pre- and post-processing required when performing batch surface-wave inversions a Python package, SWprepost, (Vantassel, 2020) has been released open-source. More information about SWprepost can be found on its GitHub page.

If you use SWbatch in your research we ask that you please cite the following:

Vantassel, J.P., Gurram, H., and Cox, B.R., (2020). jpvantassel/swbatch: latest (Concept). Zenodo. https://doi.org/10.5281/zenodo.3840546

Vantassel, J.P., Cox, B.R., (2020). SWinvert: A workflow for performing rigorous 1D surface wave inversions. Geophysical Journal International https://doi.org/10.1093/gji/ggaa426

Note: For software, version specific citations should be preferred to general concept citations, such as that listed above. To generate a version specific citation for SWbatch, please use the citation tool for that specific version on the SWbatch archive.

Getting Started ¶

There are two ways of using SWbatch:

As part of a developed Jupyter workflow called SWinvert. (Recommended)
Or directly through the DesignSafe-CI Research Workbench.

Instructions for using the Jupyter Workflow ¶

Visit the SWprepost GitHub and follow the Getting Started instructions. The advanced example walks you through using the SWinvert surface wave inversion Jupyter workflow. (30 minutes)
Login to DesignSafe. Transfer the advanced example and follow the instructions provided therein to repeat the tutorial. This time be sure to use the computational power of SWbatch to perform the inversion rather than viewing the results provided. Be sure to remove the previous inputs and results before running your inversion with SWbatch. Note more detailed instructions for completing this step are provided in the Jupyter notebook. (20 minutes, excludes inversion runtime)
Upload your own experimental dispersion data and repeat the workflow. Be sure to remove the previous inputs and results before running your inversion with SWbatch. (20 minutes, excludes inversion runtime)
Enjoy!

Instructions for using the DesignSafe-CI Research Workbench ¶

Visit the SWprepost GitHub and follow the Getting Started instructions. This will introduce you to SWprepost and the SWinvert workflow, which is required before proceeding to step 2 in these instructions. (30 minutes)
Login to DesignSafe. Create a directory for your inversion, inside of which mimic the directory structure of the advanced example you completed as part of the previous step. Place your .target and .param files in the appropriate directories. (45 minutes)
Launch SWbatch, by going to Research Workbench>Workspace>Simulation>SWbatch on DesignSafe and following the instructions provided there. (30 minutes, excludes inversion runtime)
To see the status of your simulation refer to the Job Status bar. When your job is complete use the View button to view your inversion results. (5 minutes)
Enjoy!