The document discusses advancements in scientific instruments and computational techniques, emphasizing the need for modular and extensible systems to handle the increasing complexity and volume of data generated by new sensors. It highlights the development of flows for tasks such as data collection, analysis, and visualization, which have significantly accelerated processes like protein structure determination. Additionally, the document calls for collaboration to enhance these methods and expand their application across various scientific fields.

1. Linking Scientific Instruments and Computation:
Patterns, Technologies, Experiences
Ian Foster
The University of Chicago
Argonne National Laboratory
foster@anl.gov
Crescat scientia; vita excolatur
https://arxiv.org/abs/2204.05128
https://arxiv.org/abs/2208.09513

2. A new generation of
scientific instruments
New sensors produce data at high
velocities and in large volumes
New methods and structures are
required to capture and process
data, and to feed back to sensors
Increasing need to harness HPC,
cloud, edge computers
 An instrument becomes a set of
flows, overlaid on distributed
physical resources and software
Mark Boland, https://bit.ly/3cfSosk, 2017

3. Example: High-energy diffraction microscopy

4. Example: Ptychographic reconstruction

5. Example: Serial synchrotron crystallography

6. A modular, extensible approach to creating and running flows
Flows
Capture useful patterns as
sequences of actions.
Resource-independent

7. A modular, extensible approach to creating and running flows
Flows
Capture useful patterns as
sequences of actions.
Resource-independent
Action providers
Implement actions.
Resource-independent
Compute Action Provider: Run function at A.
Transfer Action Provider: Transfer from A to B.
Search Action Provider: Publish metadata.
…

8. A modular, extensible approach to creating and running flows
Flows
Capture useful patterns as
sequences of actions.
Resource-independent
Action providers
Implement actions.
Resource-independent
Fabric
Implements auth, data, and
compute APIs for
manipulating resources
Authenticate user.
Delegate credentials.
Manage file transfers.
Run jobs on computers.
Access data catalog.
…
Compute Action Provider: Run function at A.
Transfer Action Provider: Transfer from A to B.
Search Action Provider: Publish metadata.
…

9. Builds on
cloud-hosted
Globus
automation
services
Globus
automation
services
Triggers
Flows
Analysis
Computer
Timers
Queues
Step
Step
Step
Step
Event
Type: creation
Match: *tiff
Action
Queue
1 2 3 4
Action
Type: user selection
data: <feature extraction>
Options: approve/reject
Microscope
Step
Step
Step
Step
Flow run
Step
Step
Step
Step
Action
Type: transfer
From: microscope
To: analysis computer
https://arxiv.org/abs/2204.05128

10. Capture flows
in reusable
forms
In various ways:
- YAML documents
- Python “Gladier” SDK
- Web authoring

11. Customize
flow to
application
Capture flows
in reusable
forms

12. Customize
flow to
application
Specialize
flow to
resources
Capture flows
in reusable
forms

13. Check flow
status
Execute
specialized
flow
Customize
flow to
application
Specialize
flow to
resources
Capture flows
in reusable
forms

14. Execute
specialized
flow
Customize
flow to
application
Specialize
flow to
resources
Capture flows
in reusable
forms
Examine flow
actions

15. Execute
specialized
flow
Customize
flow to
application
Specialize
flow to
resources
Capture flows
in reusable
forms
Identify failed
actions

16. AI model
training
AI model
deployment
Data collection
& transfer
Cerebras
Catalog &
publish
Detector
Injector
x-ray
Target
FAIR data
Data reduction,
refine structures
Data collection
& transfer
AI accelerators, HPC
Ptychographic
reconstruction
Data collection
& transfer (raw)
Data collection &
transfer (position)
AI accelerators
Serial synchrotron crystallography
Ptychography
High energy diffraction microscopy
Flows have been developed for light source
data analysis, biomedical and materials
science data ingest, on-demand simulation, …

17. Determining protein structures 10-100x faster
“These data services have taken the
time to solve a structure from
weeks to days and now to hours”
Darren Sherrell, SBC beamline
scientist APS Sector 19
• Developed new automation pipeline to
collect data, analyze and visualize the data,
solve protein structure and load results into a
searchable portal for real-time feedback
• Achieved over 10-100x speed up in time to
solution of protein structures at APS beamline
• Leveraged unique DOE facilities at Advanced
Photon Source (SBC Sector 19) and ALCF
(Theta/ ThetaGPU, Petrel, and Data Portals)
Deposited first results in open repositories
Automation pipeline
(Chard, Vescovi, Foster, Blaiszik, Sherrell, Joachimiak, et al.)
ALCF Theta
ALCF Theta
ALCF Theta
Data Portals
APS
ALCF
Petrel
ALCF Theta
17

18. Flow invocations 2020-21 for five APS experiments
Numbers vary due to facility and experimental schedules.

19. We collect detailed performance data on flows
https://arxiv.org/abs/2204.05128
Transfer, compute,
and cataloging
costs for median
flows

20. Round-trip latencies for various action providers
• Current architecture
has ~1 sec minimum
latency due to cloud
interaction
• funcX latencies higher
due to polling strategy
• Both can be improved
as needed

21. We build on a universal auth, compute, & data fabric
Globus
Auth
Authentication and delegation mechanisms to control
what happens where
Run functions anywhere funcX deployed
Access data anywhere Globus Connect deployed
* See also: Integrated Research Infrastructure, computing continuum, grid
Globus
Connect

22. As of 4/2022

23. Globus hybrid “SaaS” model: Data fabric

24. Globus hybrid “SaaS” model: Compute fabric
funcX
agent
funcX
agent
Customer owned and
administered computer
with funcX agent
running on it
funcX service orchestrates function
execution via communication with
funcX agent

25. Polaris
Bebop
Cluster
Argonne
Leadership
Computing
Facility
Laboratory
Computing
Research
Center
Eagle store
APS
Computing
Orthros Cluster
APS DM system
Portal
server
Portal
server
Theta
Advanced
Photon
Source
Key: funcX agent
Globus Connect agent
API
API
API
User-defined flows
Globus-accessible
storage and
computing
(10,000s of systems)
Globus
Automation
Services

26. Building computationally-enhanced instruments:
There is much more to be done!
• We have worked so far with light sources and data ingest
pipelines
• We are pleased with adaptability and reliability
• Work required in capability (e.g., iteration) and performance
• Others are applying tools to microscopes and other
instruments
• New action providers are needed for instrument control
• We are eager to find partners who want to work with us on
developing and/or applying these methods and tools!

27. Thanks to talented colleagues!
Linking Scientific Instruments & HPC: Patterns, Technologies, Experiences
Globus Automation Services: Research process automation across the space-time continuum
Rachana
Ananthakrishnan
Josh Bryan Kyle Chard Ryan Chard Kurt McKee Jim Pruyne Brigitte Raumann
https://arxiv.org/abs/2204.05128 https://arxiv.org/abs/2208.09513
Raf Vescovi Ryan Chard Nick Saint Ben Blaiszik Jim Pruyne Tekin Bicer
Alex Lavens Zhengchun Liu Mike Papka Suresh Narayanan Nicholas Schwarz Kyle Chard
and
And sponsors
And the rest of
the ALCF, APS, &
Globus teams

28. Recap: Enabling
new instruments
Reusable flows
composed from an
extensible set of
actions
Built on global
auth, compute, data
fabric
Join us in applying
these methods!
https://arxiv.org/abs/2204.05128
https://arxiv.org/abs/2208.09513
https://www.globus.org/platform/services/flows