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<div class="WordSection1">
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">DesignSafe Team Meetings<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">December 16, 2024<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Quick recap
<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">The team discussed the use of DesignSafe resources for workflow management, specifically for ADCIRC, and the process of generating machine learning-ready data from high-fidelity
simulation outputs. They also explored the advantages and challenges of using HPC Jupyter for their work, and the potential of customizing the environment for users when connecting to the system. Lastly, they discussed the use of different file systems for
data storage and access, and the need for a more streamlined process for users. <o:p>
</o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif;background:yellow;mso-highlight:yellow">Next steps</span></b><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">• Carlos to ping Sal about fixing the user ID issue in the Jupyter container.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">• Silvia to submit a ticket regarding the SSH access issue from regular Jupyter hub.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">• Ellen and Krishna to review and streamline the Jupyter/container setup in January, potentially involving Carlos.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">• Carlos to connect with SimCenter about standardizing data formats for surrogate modeling outputs.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">• Natalie to schedule meetings between Ellen and use case PIs in mid-late January to discuss roles going forward.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Summary
<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">DesignSafe for ADCIRC Workflow Management
<o:p></o:p></span></b></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l1 level1 lfo1"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Ellen introduced the topic of using DesignSafe resources for workflow management, specifically for ADCIRC. Carlos then
took over, discussing the use of surrogate modeling for ADCIRC on DesignSafe. <o:p>
</o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l1 level1 lfo1"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">He highlighted the three main areas of focus: the collection of a dataset of high-fidelity model outputs, the fitting
of the machine learning model with the high-fidelity data, and the validating of the model on new inputs.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l1 level1 lfo1"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Carlos also emphasized the importance of clearly defining inputs and outputs for the machine learning model. He mentioned
that they have already published a couple of models and are actively working on two more. The discussion ended with Carlos expressing his desire for the conversation to focus on the current capabilities of DesignSafe.
<o:p></o:p></span></li></ul>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Generating Machine Learning-Ready Simulation Data
<o:p></o:p></span></b></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l3 level1 lfo2"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Carlos discussed the process of generating machine learning-ready data from high-fidelity simulation outputs, emphasizing
the importance of understanding the input-output relationship and the need for high-performance computing (HPC) resources. He mentioned the use of the parametric job launcher, Pylauncher, and a custom Tapis application for coordinating ensembles of simulations.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l3 level1 lfo2"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Ellen suggested that the parametric job launcher could be more widely useful and asked about the integration with DAPI.
Carlos agreed and mentioned the need to update the application to the V3 platform. He also discussed the challenges of going from raw simulation data to a machine learning problem, including the need to consider physical constraints and the potential for poor
features to learn from. <o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l3 level1 lfo2"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">The team also discussed the importance of documenting the process well and the potential for publishing the datasets and
train models in the same DesignSafe dataset for reproducibility. Pedro asked about where the data is stored, and Carlos explained that they use scratch for active simulations and move data to Corral when needed. Ellen pointed out that HPC Jupyter currently
does not allow access to data in Corral. <o:p></o:p></span></li></ul>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">HPC Jupyter Challenges and Solutions
<o:p></o:p></span></b></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l5 level1 lfo3"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Carlos discussed the advantages and challenges of using HPC Jupyter for their work. He highlighted that HPC Jupyter provides
easier access to HPC work and scratch directories, facilitating workflows. However, he noted that the containerization of the job in HPC Jupyter instances is problematic.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l5 level1 lfo3"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">He also expressed a desire for multi-node HPC Jupyter and the addition of wait times and statuses, similar to the TACC
Analysis Portal (TAP) system. Pedro clarified that HPC Jupyter provides access to HPC work and scratch directories. Ellen questioned why HPC Jupyter doesn't act like TAP, to which Dan responded that it's due to the containerization. Silvia suggested that the
containerization could be a way of prepackaging an environment ahead of time. <o:p>
</o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l5 level1 lfo3"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">The team agreed that while HPC Jupyter is more usable than before, there are still some issues with the containerization
and the divergence of the two environments. <o:p></o:p></span></li></ul>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Customizing User Environment and Containers
<o:p></o:p></span></b></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l4 level1 lfo4"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">The team discussed the potential of customizing the environment for users when connecting to the system. They considered
the possibility of pre-installing packages and setting up the environment to make it more user-friendly. The idea of containerization was also discussed, with the team acknowledging its limitations, such as not being able to have containers within containers.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l4 level1 lfo4"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">They also discussed the benefits of using containers to mimic the design safe data structure and the ability to access
the scratch directory through design safe. The team agreed that these features and options could be added as the system is configured, allowing users to customize their environment and install software as needed.
<o:p></o:p></span></li></ul>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">File System Differences and Jupyter Hub
<o:p></o:p></span></b></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l6 level1 lfo5"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">The team discussed the differences between various file systems, including work, scratch, and my data. They clarified
that work is a global file system with less bandwidth to each system, while scratch is different on all the boxes and has more bandwidth.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l6 level1 lfo5"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">They also discussed the confusion between uppercase and lowercase 'work' file systems, which are the same but mounted
differently. Carlos shared his method of creating symbolic links to scratch for easier access.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l6 level1 lfo5"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">The team also discussed the differences between regular Jupyter hub and HPC Jupyter hub, with the latter not having a
project. <o:p></o:p></span></li></ul>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">File Systems and Machine Learning
<o:p></o:p></span></b></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l2 level1 lfo6"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">The team discussed the use of different file systems for data storage and access. Ellen and Dan clarified that 'work'
is a faster and more accessible file system compared to 'my data'. Silvia added that she uses 'My Data' for storing her data and 'work' for faster access and flexibility.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l2 level1 lfo6"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">The team also discussed the challenges of moving data between file systems and the need for increased access to resources.
Carlos mentioned that they are moving towards multi-node training for larger datasets, which is not currently configured.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l2 level1 lfo6"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">The team also discussed their use of PyTorch and TensorFlow for machine learning, with Carlos mentioning that they are
updating their architecture to use PyTorch. The team agreed on the need for running scripts through the Jupyter environment for initial testing and debugging, but for more production runs, they plan to use job submissions.
<o:p></o:p></span></li></ul>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif">SSH and Data Sharing Challenges
<o:p></o:p></span></b></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo7"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">In the meeting, Silvia raised an issue about logging in and not being able to SSH from a regular Jupyter hub. Carlos suggested
adding a dash user option to the SSH command, which Dan confirmed would work. However, Silvia mentioned that this didn't work for her on the OpenSees VM. Carlos suggested that this might be a bug and suggested reporting it.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo7"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Ellen and Carlos discussed the need for a more streamlined process for users, especially novice ones, and the importance
of standardizing data formats for better data sharing. Laura suggested connecting with the SimCenter to establish a format for incorporating data into R2D simulations.
<o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.05in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo7"><span style="font-size:12.0pt;font-family:"Arial",sans-serif">Ellen announced that the next meeting would be the last before the holidays and that she would schedule individual meetings
with each PI to discuss roles and opportunities going forward. <o:p></o:p></span></li></ul>
<p class="MsoNormal" style="text-indent:.5in"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal">---<o:p></o:p></p>
<p class="MsoNormal">Natalie Henriques, PMP<o:p></o:p></p>
<p class="MsoNormal">Project Manager<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:black">---<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:black">Natalie Henriques, PMP</span><span style="color:black;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:black">Project Manager<br>
Texas Advanced Computing Center (TACC)<br>
The University of Texas at Austin<br>
Email: </span><span style="font-size:12.0pt"><a href="UrlBlockedError.aspx" target="_blank"><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:blue">natalie@tacc.utexas.edu</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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