User Guide
designsafe-ci.org
Data Depot
Overview
Managing Data
Overview
Browsing, Upload, and Download
Data Sharing, Collaboration, Curation & Publication
Setting Path to DS on Corral
Path to My Data
Path to My Projects
Path to Published
Path to Published (NEES)
Data Transfer Guides
Recommended Data Transfer Methods
Recommended Large Data Transfer Methods
Recommended Normal Data Transfer Methods
Globus Data Transfer Guide
1. Log in to CILogon.org
2. Find the ePPN associated with your CILogon/Globus access
3. Associate your ePPN with your DesignSafe/TACC Account
4. Activate Your Desktop/Laptop as a Globus Endpoint and Connect
5. Connect to the DesignSafe (TACC Corral3) Endpoint
6. Perform Transfer between Your Local Enpoint and the DesignSafe (TACC Corral3) Endpoint
Globus CLI Automated Transfer Guide
1. Follow the steps 1-3 above in Globus Data Transfer Guide
2. Activate Your Desktop/Laptop as a Globus Endpoint and Connect
3. Install the Globus CLI
4. Settings for CLI Transfer
5. Test Globus CLI Transfer
6. Create an Automatic Transfer Script
7. Automate Script Execution with cron
Cyberduck Data Transfer Guide
1. Set up MFA using the TACC Token App
2. Download and Install Cyberduck
3. Create a New Bookmark
4. Populate Bookmark
5. Perform Transfer
Command-Line Data Transfer Guide
1. Set up MFA using the TACC Token App
2. Select Transfer Utility and Perform Transfer
Data Depot's Browser-Based Data Transfer Guide
Upload
Download
Transferring Data Inside of DesignSafe
JupyterHub's Browser-Based Data Transfer Guide
To Upload a File Through Jupyter
To Download a File Through Jupyter
Cloud Storage Transfer
Box
Dropbox
Google Drive - CURRENTLY NOT FUNCTIONAL
Data Management Plan
Experimental Facility Checklist
DesignSafe-EF Onboarding Checklist for Data Curation
Phase 1 - Before arriving to the Experimental Facility (EF):
Phase 2 - At the EF:
Phase 3 – After the EF:
General Comments
Data Depot Repository
About
Office Hours
Curating & Publication
Guides
Experimental
Simulation
Hybrid Simulation
Field Research
Other
Frequently Asked Questions
Selecting Files & Data
Organizing & Describing Your Dataset
Publishing
Data Reuse
Best Practices
Data Collections Development
Accepted Data
Accepted and Recommended File Formats
Data Size
Data Curation
Managing and Sharing Data in My Projects
Selecting a Project Type
Working in My Project
General Research Data Best Practices
Data Organization and Description
Project Documentation
Data Quality Control
Managing Protected Data in the DDR
Metadata Requirements
Data Publication
Protected Data
Reusing Data Resources in your Publication
Timely Data Publication
Public Accessibility Delay
Licensing
Subsequent Publishing
Amends and Version Control
Leave Data Feedback
Marketing Datasets
Data Preservation
Metrics Documentation
Data Metrics
Project Metrics
Data Publication Metrics
Policies
DesignSafe Data Depot Repository Mission and History
Mission
History
Community
Governance
Repository Team
Community Norms for DDR
Data Collections Development
Data Types
Data Size
Data Formats
Data Curation
Data Management Plan
Data Models
Metadata
Metadata and Data Quality
Curation and Publication Assistance
Data Publication and Usage
Protected Data
Subsequent Publishing
Timely Data Publication
Peer Review
Public Accessibility Delay
Data Licenses
Data Citation
Data Publication Agreement
Data Usage Agreement
Amends and Version Control
Leave Data Feedback
Data Impact
Data Preservation
Continuity of Access
Metadata Dictionaries
Experimental
Simulation
Hybrid
Field
Other
Recon Portal
Recon Portal User Guide
Add a new natural hazard event
Contributing your data to a natural hazard event
Tools and Apps
Analysis Applications
HVSRweb User Guide
Step 1
Step 2
Step 3
Step 4
Step 5
Step 6
Step 7
MATLAB User Guide
How to Start a MATLAB Interactive Session in the Workspace
How to Submit a MATLAB Batch job in the Workspace
SWbatch User Guide
Getting Started
Instructions for using the Jupyter Workflow
Instructions for using the DesignSafe-CI Research Workbench
Hazard Apps & Utilities
Hazard Applications
Managing Applications
Requesting New Applications
Getting Your Own HPC Application
Commercial/Licensed Applications
Hurricane Data Analysis User Guide
How to Start a Hurricane Data Analysis Interactive Session in the Workspace
Next Generation Liquefaction
Connecting to the database in DesignSafe
Notebooks published in DesignSafe
Understanding the database schema
SCEC BBP Ground Motion Portal User Guide
How to Start a SCEC BBP Ground Motion Portal Interactive Jupyter Notebook Session in the Workspace
TPU Wind Databases User Guide
VORTEX-Winds: DEDM-HR User Guide
Jupyter Notebook for DEDM-HR
Resources
Description
Implementation
Background: web-enabled multiple database-enabled design module for high-rise buildings (DEDM-HR)
Jupyter Notebooks for the DEDM-HR
Conclusions
Reference
Citation and Licensing
Compress & Extract
Compress Folder
How to submit a Compress Job in the Workspace
Extract tar/zip/gzip File
How to submit an Extract Job in the Workspace
Jupyter
JupyterHub Guide
JupyterHub Spawner
Jupyter Notebook Images
Classic Jupyter Image
Updated Jupyter Image
Accessing Data from the Data Depot
Using Jupyter
Creating a Jupyter Notebook
Ending your Jupyter Session
Server Information
High Performance Computing (HPC) Job Submission through Jupyter
Installing Packages
Ephemeral User Installations
Custom User-Defined Kernels
DesignSafe HPC Jupyter Guide
Launch the Jupyter Lab HPC (GPU)
Launch the Jupyter Notebook
Example Notebooks
Examples of Jupyter Notebooks Available via DesignSafe
Jupyter Notebooks for Civil Engineering Courses
Publishing Notebooks
Visualization Applications
FigureGen User Guide
How to Submit a FigureGen Job in the Workspace
Hazmapper User Guide
Accessing Hazmapper
Interface Overview
Welcome Menu
Map Creation Prompt
Title bar
Panels
Maps
Map
Supported Asset Types
Map Associated Assets
Third-party Assets
Collaboration
Shared Maps
Public Maps
Kalpana User Guide
How to Submit a Kalpana Job in the Workspace
Paraview User Guide
How to Start a Paraview Interactive Session in the Workspace
Potree Converter User Guide
How to Submit a Potree Converter Job in the Workspace
FAQ
Potree Viewer User Guide
How to Start a Potree Interactive Session in the Workspace
General Potree Viewing Instructions
QGIS Desktop User Guide
Load raster and vector layers from the sample dataset
STKO User Guide
Run OpenSees-STKO on DesignSafe
Taggit User Guide: Basic Image Browsing and Mapping
Resources
Description
Browsing Thumbnail Images in Taggit
References
Taggit User Guide: Grouping and Tagging Image Files
Resources
Description
Creating Groups and Using the Taggit View
Adding Images to Groups
Changing icons for each group
Creating Tags within each Group
References
VisIt User Guide
How to Start a VisIt Interactive Session in the Workspace
Simulation Applications
Overview
Requesting New Applications
Getting Your Own HPC Application
Commercial/Licensed Applications
ADCIRC
ADCIRC Applications
Decision Matrix for ADCIRC Applications
ADCIRC On DesignSafe
ADCIRC Through the Interactive VM
Advantages and Disadvantages of Interactive ADCIRC VM
Getting Started
Example - Running an ADCIRC simulation
Running ADCIRC on HPC Resources
Using the Web Portal
Using Tapis
ADCIRC Reference
ADCIRC Command Line Options
adcirc Command Line Options
adcprep Command Line Options
PADIRC Runs
ADCIRC Input Files
ADCIRC Outputs Files
ADCIRC Outputs Summary
ADCIRC Examples
Quarter Annular Harbor with Tidal Forcing Example: ADCIRC Simulation Guide
Shinnecock Inlet, NY with Tidal Forcing Example: ADCIRC Simulation Guide
ADCIRC Installation (Advanced)
Spack ADCIRC Installation (DesignSafe JupyterHub)
Resources and Documentation
ADCIRC Data Hosted on DesignSafe
External Documentation
Other ADCIRC Utilities and Libraries
ClawPack
How to Start a Clawpack Interactive Session in the Workspace
Example Clawpack Use Case
Dakota
How to Submit a Dakota Job in the Workspace
IN-CORE
IN-CORE on DesignSafe Cyberinfrastructure (DesignSafe-CI)
Installation of pyincore on DesignSafe
Installing pyincore without creating a new environment (temporary installation)
Installing pyincore creating a new environment (recommended)
Reproducibility after shutting down your server (if you installed pyincore using kernelutility)
Example: IN-CORE tools within DesignSafe-CI
Loading a hazard scenario with pyincore
Definition of the exposed assets
Fragility models description using pyincore JSON structure
Fragility Mapping (fragility functions link to exposure model)
Bridge Damage Analysis
LS-DYNA
Ls-Dyna on DesignSafe
Activate Ls-Dyna on DesignSafe
How to launch LS-Dyna
Launching LS-Pre/Post
Launching a single job via DesignSafe web portal
Launching batch of jobs via DesignSafe web portal
Launching batch of jobs via Command Line Interface (CLI)
OpenFoam
How to Submit an OpenFOAM Job in the Workspace
OpenSees
OpenSees On DesignSafe
OpenSees-on-DesignSafe Quick Start
Instructions
OpenSees Applications
DesignSafe Platforms
OpenSees-Project "Size"
Decision Matrix for OpenSees Applications
Decision Matrix for DesignSafe Platform for OpenSees
Running OpenSees at the Linux Terminal
Basic Linux Commands
Examples
References & Resources
OpenSees Docs:
References on Parallel-Computing Fundamentals:
References on Parallel Computing with OpenSees by Dr. Frank McKenna
DesignSafe Tutorial: OpenSees & DesignSafe, October 31, 2018
OpenSees Applications
OpenSees Express
Advantages
Disadvantages
OpenSeesSP
Advantages
Disadvantages
Changes to the script
Example Script from OpenSees GitHub
OpenSeesMP
Advantages
Disadvantages
Additional commands used in OpenSeesMP -- TCL Interpreter
Changes to the script with Examples
Example Script from OpenSees GitHub
OpenSeesPy
Parallel Applications in OpenSeesPy
OpenSees Platforms
Running OpenSees on DesignSafe
The Interactive Virtual Machine (Interactive-VM)
Connecting to the Interactive-VM
The Interactive-VM Environment & Workflow
Running OpenSees via DesignSafe Web Portal
File Management when running the Web-Portal Jobs
Using the DesignSafe WebPortal
Integrate OpenSeesPy directly into Jupyter Notebook
Submit OpenSees Jobs to HPC via Jupyter Notebook
Running OpenSees on HPC-TACC
Use Cases
Overview
Data Analytics
Basic Image Browsing and Mapping
Resources
Description
Browsing Thumbnail Images in Taggit
References
Grouping and Tagging Image Files
Resources
Description
Creating Groups and Using the Taggit View
Adding Images to Groups
Changing icons for each group
Creating Tags within each Group
References
Multi-Data Set Image Analysis in Taggit
Resources
Description
Implementation
Gathering the Necessary Data Files
Plotting Data Sets in QGIS
Citations and Licensing
ML and AI
Resources
Jupyter Notebooks
DesignSafe Resources
Citation and Licensing
Overview of ML examples
Linear Regression
Random Forest
Neural Networks
Convolutional Neural Networks
Application Programming Interfaces
Resources
Description
What is an API?
Authentication, Authorization, Keys, and Tokens
HTTP Status Codes
Implementation
NASA Astronomy Picture of the Day
US Census Map
USGS recent earthquake map
USGS Shakemap contours
NOAA hourly wind data
Citations and Licensing
Visualization of spatially distributed data
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
Description
Implementation
Types of visualization tools
Workflow of this use case
Setting the python environment
Input files
1. Plotting distributed infrastructure using static plots
2. Interactive exploration of spatially distributed information
3. Creation of animated graphs and GIFs
GeoHazard
NGL Database
Background
Citations and Licensing
Description
Understanding the Database Schema
Querying Data via Jupyter Notebooks
Installing Database Connection Script
Example Queries
Cone Penetration Test Viewer
VS (Invasive) Test Viewer
October 2021 DesignSafe Webinar
Direct Simple Shear Laboratory Test Viewer
MPM Landslide
Background
Citation and Licensing
Description
Input generation
An example
Running the MPM Code
Post Processing
VTK and ParaView
HDF5
Oso landslide with in situ visualization
Seismic
Seismic Response of Concrete Walls
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
Description
Data
Modeling
Example
Create Input File using Modeling Script
Reinforced Concrete Wall Database
Modeling Script
Running Opensees through HPC
Post Processing
Load-Displacement Graph
Cross Sectional Analysis of Concrete and Steel
Stress and Strain Profile Movies
Crack Angle of Quadrature Points
Soil Structure Interaction
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
Description
Create OpenSees Model using STKO
Setup and submit OpenSees job via Jupyter notebook
Setup job description
Submit and Run job on DesignSafe
Identify Job ID and Archived Location
Post-processing on DesignSafe
Visualize and extract data from STKO
Example post-processing scripts using Jupyter
Example Post-processing Results
Experimental Shake Table Testing
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
Description
Jupyter Notebooks for Experimental Data
Case 1. Shake table performance
Case 2. Module for Structural Response and System Identification
Case 3. Integration of Notebooks in Experimental Workflow
Summary
References
Shake Table Data Analysis Using ML
Resources
Jupyter Notebooks
DesignSafe Resources
Additional Resources
Description
Implementation
Citations and Licensing
OpenSees Model Calibration
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
Description
Implementation
Wind and Storm Surge
Field Sensing Wind Events
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
Description
Implementaton
Quasi-real time Data Upload with Tapis
Using Jupyter Notebooks
Adaptation to Different Datasets
Jupyter Notebooks for WOW Sliding Platio Door
Analyses Notebooks and Examples
Using Plotly for Data Driven Animation Frames
Plotly features example
Hurricane Data Integration Visualization
Resources
Description
Implementation
Instructions
Using JupyterHub on DesignSafe
Accessing JupyterHub
Jupyter Notebooks
Installing and importing the required packages
Get the exposure data from the NSI database
Download ARA Wind and Building Damage Data
Getting flood data from USGS via JSON REST Service
Adding previously collected data and displaying them on the map
Customizing the map further
Saving the map and exporting it as an interactive html file
Citations and Licensing
ADCIRC Datasets
Overview
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
ADCIRC Overview
ADCIRC Inputs
PyADCIRC
Example Notebook: Creating ADCIRC DataSet
Identifying storm surge events
Getting data forcing data
Organizing Data for publishing
Setting up Project Directory
Large-Scale Storm Surge
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Tapis Pylauncher App
CFD Analysis of Winds on Structures
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
OpenFOAM with the Jupyter Notebook for creating input environments
Prerequisite to run OpenFOAM simulation
Introducing advanced utilities to CFD modeling using PyFoam
Use case of an OpenFOAM simulation with Jupyter Notebook in the DesignSafe workspace
References
CFD Analysis of Winds on Low-Rise Building
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
Description
New Features
Running simulation using Low-Rise Jupyter Notebook
User define input:
How to run it on Jupyter Notebook:
Simulation Result of desired and ASCE power law vertical profiles
User-Defined Profile Simulation and time histories of wind velocity fluctuations at a point
References
Tamkang Database
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
Description
References
Visualizing Surge for Regional Risks
Resources
Jupyter Notebooks
DesignSafe Resources
Background
Citation and Licensing
Description
Introduction and workflow of analysis
Storm data analysis using Jupyter notebooks
Geospatial analysis via QGIS
Opening a QGIS session in DesignSafe
Modify user inputs and run the python script
Visualization of the outputs
Advanced
API Developer's Guide
Cybersecurity Policy
1. Roles and Responsibilities
1.1. DesignSafe Management Team
1.2. DesignSafe Chief Security Officer
1.3. NHERI Awardees
1.4. Security Working Group
2. Administrative Safeguards
2.1. Risk Assessment
2.1.1.Risk Assessment Policy and Procedures
2.1.2.Risk Assessment
2.2. Audit
2.2.1.Schedule for Audits
2.2.2.Actions following the Audits
3. Technical Safeguards
3.1. Proactive Security Monitoring and Detection
3.2. Vulnerability Scanning
4. Administrative Safeguards
4.1. Authentication and Authorization
4.2. Access Control
5. Policy and Procedures
5.1. Creating User Accounts
5.2. User Credentials
5.3. Inactive Account Expiration
6. Physical Safeguards
6.1. Physical Access Authorization
6.2. Access Control for Transmission Medium
7. Awareness and Training
8. Incident Response and Notification Procedures
DesignSafe FAQ
FAQ Categories
Users and Accounts
Training
Data Depot
Tools & Applications
MATLAB
Jupyter
OpenSees
ADCIRC
OpenFOAM
ParaView
Experimental Facilities
Citing DesignSafe
HPC Allocations Policy
Introduction
Who is eligible for an Account
Who is eligible for Allocations
Allocation Types and Constraints
Allocation Sizes and Limits
Allocation Limit per PI
Allocation Duration
Review Criteria for Additional Allocation Proposals
Conflict of Interest and Confidentiality
How to apply for an Additional Allocation
Allocation Proposal Guidance
Document Formatting
Supplemental Requests
Extension Requests
Guidelines for a Successful Allocation Request
Acknowledgement of Support
DesignSafe User Guide
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