polyglot, event driven computational science using …...polyglot, event driven computational...
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Polyglot, Event Driven Computational Science Using the Actor Model
Joe StubbsTexas Advanced Computing Center
University of Texas, Austin
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What is TACC?Mission: To enable discoveries that advance science and society through the application of advanced computing technologies.
• High performance computing (HPC)• Cloud & high throughput computing • Data intensive computing• Visualization• Scientific software development & optimization• APIs and tools - Agave Platform• Web and mobile applications• Life sciences • Training & outreach
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What is Agave?
/systems /files /apps /jobs
● Register storage and compute systems● Ingest, move and transform data files and folders● Register applications (binaries) on large systems● Launch jobs to invoke applications
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What is Agave?
/systems /files /apps /jobs
● Register storage and compute systems● Ingest, move and transform data files and folders● Register applications (binaries) on large systems● Launch jobs to invoke applications
*All activities are events that can be subscribed to
/notifications
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Agave Powers web & mobile apps
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Computational Science: Traditional Approach
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Meanwhile, Data accumulating...Cumulative growth in INSDC. (A) Base pairs (black, 2365.5 trillion)
and sequence reads (blue, 17.8 trillion) for INSDC raw data.
Guy Cochrane et al. Nucl. Acids Res. 2016;44:D48-D50
Agave alone moves 1PB+ data/month
Aggressive purge policy of 2 weeks on TACC’s
global /SCRATCH
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Event Based Processing● File or folder appears or is modified on a server...
- Run a checksum- Launch a job to do some analysis- Compress the file- Move the file to archive storage
● Job completes- Job was successful, launch another job- Job failed, check inputs and launch again?
● Execution system goes offline for maintenance- Submit to a secondary system
● Storage system goes offline for maintenance- Submit jobs using data from a different system
● New user signs up for portal/project- Bootstrap storage and compute
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Actor Model
{ “uuid”: “000141157089814”,“event”: “UPDATED”,
"updateTime": "2016-03-22T17:39:30.6:00",
"owner": "jdoe" }
A
STATE
M
AA
A
A A A
Message Arrives
Compute and save state
Send messages to other actors
Create new actors
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Actor Model: Inherently Concurrent
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Actor Model: Inherently Concurrent
A
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Actor Model: Inherently Concurrent
AM
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Actor Model: Inherently Concurrent
A
A
A
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Actor Model: Inherently Concurrent
A
A
A
M
M
M
M
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Actor Model: Inherently Concurrent
A
A
A
A
A
A
A
A
A
M
M
M
M
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User-Defined Actors Via Docker
A IMAGE
● Associate an actor with a Docker image.● Assign the actor’s inbox to a unique URI.● Launch a container from the image in response to a message.
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Containers: Reproducible Environments
Infrastructure
Host Kernel/OS
App 1
Libs
App 2
Libs
App 3
Libs
Container Runtime
Isolated Userland Processes
Virtualized:Network
I/OCPU and MEM
Containers:- Include all dependencies- Ease installation- Start up in miliseconds
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Abaco: Actor Based Containers
/actorsIMAGEPOST
https://api.tacc.utexas.edu/actors/184326
{ “uuid”: “000141157089814”,“event”: “UPDATED”,
"updateTime": "2016-03-22T17:39:30.6:00",
"owner": "jdoe" }
POSThttps://api.tacc.utexas.edu/actors/184326/messages IMAGE
A M
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Abaco: Agave Event Processors
- Notifications API in Agave allows users to subscribe to events- Event subscriptions can be in of several forms:
- Email- SMS- Web callback - in this case, Agave sends details of event in
message payload.- Events API coming this summer makes registering subscriptions even
easier.
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Abaco: Agave Event Processors
● Create a Docker image to “process” an event.● Register the image as an actor in abaco.● Register the actor’s inbox URI as the callback to a
notification for the event.
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Abaco Architecture
F
F
F
REDIS
WORKER
WORKER
WORKER CC
CC
CC
RABBITMQ
H
HS
S
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Challenges
Abaco in beta, available to select “friendly” users.
Potential issues:● Accidentally subscribing to “way too many” events.● Bugy containers “hanging” during execution.
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Early Use Case: GSAF Genome Sequencing and Analysis Facility: from sequencer to SNPs
- Raw genetic material sequenced by Illumina Sequencer.- “short reads” files dumped to server - kicks off a chain of events.
- Initial quality checks- Alignment routines.- Basic analyses: Single Nucleotide Polymorphism (SNP) calls,
etc.- Data moved to scientist’s storage system.
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Conclusion● Massive data collections make real-time processing more
and more of a necessity.● The actor model provides a simple yet robust paradigm for
concurrent, event-driven programming.● Containers can be used to provide portable, reproducible
environments.
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Thanks!
Questions?
Email: [email protected]: http://agaveapi.co/
abaco: https://github.com/TACC/abaco