This document discusses several scientific software gateways implemented using the Apache Airavata middleware. It describes the dREG, SimVascular, and Phasta gateways, which were created to provide broader access to computationally intensive genomic analysis, cardiovascular modeling, and fluid dynamics software. The gateways are hosted to simplify use of the specialized codes and optimize execution on HPC resources like XSEDE. Key features implemented include user authentication, long-running jobs, data storage, and integration of visualization tools. The document concludes by noting future work to improve the gateway framework and client interfaces.

1. Software as a Service Gateways
Gateways with Apache Airavata
Eroma Abeysinghe - https://sgrc.iu.edu
04/17/2018

2. Software as a Service Gateways
• Groups with actively developing and updating codes/tools.
• Code with building and optimizing challenges in HPCs.
• End users may not have resources to run the code. E.g.: dREG code
best run in gpu nodes.
• To reach larger user base and build a community of users around
their code.
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3. dREG Gateway
• dREG gateway is for dREG tool by
http://www.dankolab.org/.
• dREG: Identification of the genomic
regions that regulate transcription.
• Genetic basis of many diseases.
• The dREG gateway uses pre-trained
models that work in any mammalian
organism.
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4. dREG Requirement
• Wanted to provide access to the
compiled and optimized dREG tool in
XSEDE resources, Comet and Bridges.
• A gateway with large data storage.
• Required an output visualization tool
for output data.
• Gateway users to directly access
gateway without gateway admin
approval.
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5. dREG Implementation
• The gateway was deployed and hosted in
Jetstream with attached large volume for
data.
• dREG team and gateway team worked
together on the gateway changes needed.
• Changes to the gateway theme & code.
• Integration of genome browser for visualizing.
• https://www.keycloak.org/ for gateway user
management.
• https://tus.io/ used for file uploads as it
support resumable file uploads.
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6. SimVascular Gateway
• SimVascular gateway is for
http://simvascular.github.io/
• Open source integrated software suite
for image-based cardiovascular
modeling and patient-specific
simulation.
• The gateway is to use Solver for blood
flow simulation and hemodynamics
analysis for classroom users and
researchers.
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7. SimVascular Requirement
•Letting different levels of users use the code.
• Code is compiled and available in XSEDE resource.
• Undergraduates, graduates, postdocs and senior researchers from different
organizations.
• At a given time ability to use multiple XSEDE comet allocations to run the simulations.
• Users to use their organizational credentials to obtain gateway access.
• Multiple levels of gateway administrators.
• Main administrator to over see all gateway activities.
• Leads at individual group levels, one for each classroom, department, etc.
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8. SimVascular Implementation
• A hosted, maintained gateway with
data storage.
• Different levels of users to use the
gateway.
• Group to have number of nodes, CPUs
and wall-time for jobs run by group users.
• Each group can use their own XSEDE
allocation to run the simulations.
• Gateway and group level administrators.
• Use of federated authentication
(CILogon).
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9. Phasta Gateway
• PHASTA software supports modeling
compressible or incompressible, laminar or
turbulent, steady or unsteady flows in 3D,
using unstructured grid.
• A joint project between Scientific
Computation Research Center (SCOREC) at
https://rpi.edu/ and Professor Ken Jansen
at https://www.colorado.edu/research.
• Actively developing code which need
updates in the HPC environment.
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10. Phasta Requirement
•In need of a hosted and maintained gateways.
•Long running (over the defined maximum wall-time of a partition) jobs
on XSEDE resources.
•Difficult code to compile and deploy on resources.
• Use of federated authentication system (CILogon) for gateway access.
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11. Phasta Implementation
• Deployed and hosts the gateway.
• Long running job to be broken in to
multiple job submissions in XSEDE
resource.
• Phasta software resides in XSEDE
Stampede2.
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12. What we Learned
• Gateway PIs prefer gateway team to host and maintain the gateway with
storage.
• They want:
• To focus on their science.
• Build the community around their code.
• Users to feel comfortable about using the gateway.
• To use their XSEDE resource allocation sensibly and carefully.
• Provide storage for their gateway user data.
• Have an identity management system for the gateway.
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13. Gateways with Airavata
• Airavata runs computational
experiments.
• This means:
• Encoding how to run a wide range of scientific
applications on a wide range of resources.
• Staging inputs and outputs to target
resources.
• Monitoring running applications.
• Manage all the data and metadata
generated by these experiments.
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14. Gateways with Airavata Cont.…
• Hosted Airavata middleware service is SciGaP platform.
• SciGaP services:
• Deploy and host the gateway.
• Store experimental data files.
• Integrate the gateway with Airavata middleware.
• Regular code and software updates.
• Assist with gateway configurations, application tool
configuration and testing.
• Take part in community outreach, tutorials,
workshops, papers, posters.
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15. Future Work
• We are currently working on Django framework based gateway client.
• This is to make gateway customizations easy.
• Have multiple user layers.
• Provide interface which works better with these types of ongoing developing tools.
• Making third party integrations easy.
• File upload and better data management.
• More robust job submission and monitoring module.
• We are moving on to using helix based job submission.
• Multiple job monitoring mechanisms.
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16. Thank You!