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Simulation Wiki

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Simulation tools

The NEEShub allows you to use a number of simulation tools, such as OpenSees or SAP 2000, “in the cloud” without having to install it on your computer. These tools and simulations can be accessed from any computer with internet access and the same tool session can be accessed from multiple computers. For example, you can start a simulation on the NEEShub while using a computer that is not your own (e.g., a computer in a lab on campus), log off of the NEEShub but leave the simulation running (tool sessions can remain active even when you are not logged in to the NEEShub), and then log back into the NEEShub later from your personal computer to check on the status of your simulation or download output files.

You can access the simulation tools from the Tools and Resources > Tools menu, linked here or the Simulation > Programs menu linked here.

If you encounter any issues while running these tutorials, please submit a support ticket.

The Questions and Answers page and the Knowledge Base may also be useful if you have questions that are not answered by this wiki.

OpenSees

There are two tools available on the NEEShub that you can use to run OpenSees: the OpenSees Laboratory tool and the Workspace. The OpenSees Laboratory tool is a suite of simulation tools contained within a single graphical user interface. The Workspace is a Linux environment in which you can enter command lines to run your simulations. You can also use either the OpenSees Laboratory tool or the Workspace to launch and run OpenSees just as you would on your local computer. By default, both the OpenSees Laboratory tool and the Workspace run the most recent version of OpenSees. If you need to use a previous version of OpenSees, you will have to access it through the the Workspace; please contact support for assistance.

Using the tools available on the NEEShub, you can either run your simulations on the NEEShub servers or you can submit your simulations to offsite, high performance computing (HPC) venues. The computational capabilities on the NEEShub will allow you to run bigger simulations than those that you could run on a regular desktop computer. However, for very large simulations and for large parametric sweeps you might want to use the HPC capabilities that NEEShub provides. If you are new to both environments, it is recommended that you to run a small simulation on the NEEShub servers before you submit larger jobs to the HPC venues.

Here is a summary of what each tool can do:

  1. OpenSees Laboratory
    1. launch OpenSees as you would on your local computer
    2. run simulations on the NEEShub servers
    3. submit simulations (using OpenSeesSP or OpenSeesMP) to HPC venues
    4. submit parallel jobs or parameter sweeps (using OpenSeesMP) to HPC venues
    5. run simulations already pre-programmed into the tool (e.g., lateral pile analysis, SDOF earthquake response, site response analysis, etc.)
  1. The Workspace
    1. launch OpenSees as you would on your local computer
    2. run simulations on the NEEShub servers
    3. submit simulations (using OpenSees) to HPC venues
    4. submit parallel jobs or parameter sweeps (using OpenSeesMP) to HPC venues


This section of the wiki contains tutorials on how to run simulations using OpenSees Laboratory and the Workspace on the NEEShub servers and HPC venues. Many of the topics covered in these tutorials can also be found in the webinar recording available here.

Accessing the Workspace

The Workspace is not enabled by default for all users. Please submit a support ticket to request access to the Workspace if you cannot launch it.

The Workspace is a Linux environment, and a basic knowledge of Unix commands will be helpful when using this tool. To see a complete list of applications available in the workspace use the command “less /var/tmp/installed_pkgs” in the workspace.

Launching OpenSees as you would on your local computer

You can use the OpenSees Laboratory tool or the Workspace to launch and run OpenSees just as you would on your local computer. When you use the NEEShub tools to launch and run OpenSees as you would on your local computer, you will be running OpenSees on the NEEShub servers. This may not be the best option if you are trying to run large simulations, in which case the HPC venues may be more appropriate, but it can be particularly useful if you need to enter your source code line by line or you need to perform other valid tcl operations outside of the source code.

  1. Tutorial 1 – Launching OpenSees on the NEEShub – This tutorial describes how to launch OpenSees through the OpenSees Laboratory tool and the Workspace.

Running Simulations on the NEEShub Servers

Running simulations on the NEEShub servers gives you the opportunity to use OpenSees without having to install it in your computer. This video shows the advantages of using OpenSees on the NEEShub.

  1. Tutorial 1 – Running simulations on the NEEShub servers using OpenSees Laboratory. This tutorial describes how to upload your source code to the NEEShub and run your simulation on the NEEShub servers using the OpenSees Laboratory tool.
  1. Tutorial 2 – Running simulations on the NEEShub servers using the Workspace. This tutorial describes how to:
    1. i) upload files to the NEEshub using SynchroNEES,
    2. ii) run your simulation on the NEEShub servers using the Workspace, and
    3. iii) download the output files to your local computer using SyncrhoNEES.
  2. The OpenSees command executed in this tutorial launches OpenSees, runs the simulation, and then closes OpenSees with the simulation completes. When you run your simulations in this manner, you cannot submit additional tcl commands after the code completes. If you need to perform additional functions outside of the source code, you can either use the OpenSees Laboratory tool to run your simulation or you can launch OpenSees within the Workspace as shown in this tutorial and then run your simulation.
  3. This tutorial is also available in video.

Running Simulations on High Performance Computing Venues

The NEEShub allows you to run HPC simulations (large simulations with high computational cost) on a variety offsite, high performance computing venues. To submit your HPC simulations to the an offsite venue, you will need to use the Batchsubmit command within the Workspace environment. The Workspace is not enabled by default for all users. Please submit a support ticket to request access to the Workspace if you cannot launch it.

  1. Tutorial 1 – Fundamentals of the batchsubmit command. This tutorial describes how to submit simulations to HPC venues using the batchsubmit command within the Workspace environment. The technical aspects (e.g., walltime, number of processors, etc.) of the various HPC venues are described here.
  2. This tutorial is also available in video.
  3. The batchsubmit command can also be used to submit simulations to the NEEShub servers. To do this, change the venue option to local (e.g., --venue local).
  4. The OpenSees Laboratory tool is also capable of submitting singular simulations to HPC venues although there isn’t a specific tool listed for this function. To submit a singular simulation to an HPC venue through the OpenSees Laboratory tool, you would use the Parallel Job Submission tool as shown here and discussed below, and specify 1 processor. With one processor specified, OpenSeesSP and OpenSeesMP will revert to just OpenSees. However, in order for this to work, you must use the Mumps solver in your source code (e.g., change system ProfileSPD (or whatever solver you currently use) in your code to system Mumps). If you have trouble implementing the Mumps solver, you may want to search the OpenSees Message Board for a solution or contact support for further assistance.


There is a special version of the OpenSees application, called OpenSeesMP, that is specifically designed to take advantage of the parallel computation resources available on the HPC venues. Parallel processing is very beneficial for parameter sweep applications, and you can use either the OpenSees Laboratory tool or the batchsubmit command within the Workspace environment to submit parallel jobs to HPC venues. It should be noted that OpenSeesMP can also be run on the NEEShub servers; however, the HPC venues have more processing power and are better equipped to handle these larger jobs.

  1. Examples illustrating how to submit parallel jobs to HPC venues using the Workspace. These examples help users create the batchsubmit commands necessary to run parameter sweeps on HPC venus.
  1. tutorial on how to run parallel jobs using !OpenSees lab

Running custom versions of OpenSees on the NEEShub

It is possible to upload your custom version of OpenSees to the NEEShub and run it on the NEEShub servers. Please contact support for assistance in doing this.

OpenSEES Workflows on NEEShub: PEGASUS TOOL

Pegasus is simply a very interesting tool! Basically what we do in modeling is to use OpenSees – Matlab – OpenSees – Matlab, back and forth, since OpenSees itself can not do it all! In other words, while we use OpenSees, we also need to talk to other programs such as Matlab several times. What we do in Pegasus is to create a so called scientific workflow which takes the OpenSees and Matlab scripts as the inputs of the computational model, put them in a scientific workflow, apply different GMs to the structure and get the responses for each of the defined GMs. Let me provide you an example to give you a flavor of how such scientific workflows work. Suppose that we have a 2-D SMRF frame and we’d like to do the Reliability Analysis on it. The idea is as follows; Steel is a material which has variations in its properties such as Es and fy. Using the scientific workflow, we can right a short Matlab code for the mentioned probable variations in material properties, put this code in the workflow and ask the workflow to run the computational model for each of the probable values for Steel material properties separately and give a sort of range for the responses of the structure for different Ground Motions. (Such variations can be defined for all of the structural elements such as beams and columns sections and etc.) Doing such an analysis without using a scientific workflow may take much of the time writing long OpenSees scripts. However, putting them in the format of Pegasus workflows is going to split the job and make it much easier.

The following link is the Pegasus group where you can find more valuable information about how somebody can run OpenSees models through Pegasus on OSG HPC: https://nees.org/groups/pegasus

In order to see the Pegasus computational model example, please see the following link: https://nees.org/groups/pegasus/wiki/OPENSEESPEGASUSMODEL

In order to get a flavor of what Pegasus workflow is, please see the following link: https://nees.org/groups/pegasus/wiki/GETTINGSTARTEDWITHPEGASUS

SAP 2000

The educational version of SAP 2000 is available for use online through the NEEShub. A direct link to this tool is available here. You can use SynchroNEES to upload your input files and download your output files.

  1. Tutorial 1 – Running simulations in SAP 2000 on the NEEShub. This tutorial shows you how to run SAP2000 simulations at the NEEShub. If you need help learning how to transfer files from/to the NEEShub see the first part of this tutorial.
  2. This tutorial is also available in video

Hybrid simulation

Hybrid simulation allows researchers and engineers to perform tests where part of the structure is simulated as a numerical model. More information about hybrid simulation and real time hybrid simulation can be found in the hybrid simulation wiki

List of Resources

The following is a list of tools, tutorials, videos, and other resources referenced in this wiki.

  1. Tools
  1. Tutorials
  1. Videos
  1. Other Resources

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