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LOFAR & Python



  Gijs Molenaar
 gijs@pythonic.nl
Agenda
●   LOFAR
●   AARTFAAC / TKP
●   Python
●   MonetDB
Non Python stuff
What is LOFAR
What is LOFAR
●   Low-Frequency Array
●   Distributed sensor network
●   No dishes
●   Simple and cheap antenna's
●   Omni-directional
●   Concurrent observations
●   Software telescope
    –   Flexible
    –   Requires supercomputer
What is LOFAR
    Biggest Radio telescope
    array in the world
●   7000 antennas
●   10 to 80 MHz (LBA)
●   120 to 240 MHz (HBA)
●   Multiple small stations
●   NL, DE, UK, FR, SE
●   New (unique) design
New design
●   Many unsolved problems
●   Multi-terabit/s data scale
●   How to
    –   Process
    –   Store
    –   Distribute
    –   Make results useful
●   Small scale example for SKA
Usage
●   Epoch of re-ionization
●   Cosmic rays
●   Extragalactic surveys

●   Transients
●   Pulsars
Correlation
Correlation
●   IBM blue Gene/P
●   Groningen
●   Alotta computer power
●   Will be replaced with
    FPGA's (for our
    purpose)
●   No Python
Example output – Cygnus A
Actual data
Transient Key Project
●   Static sources are boring

●
    Transient – something that changes

●   Detect sources
●
    Store extracted information
●
    Associate with existing observations
●
    Did something change?

●
    This is where the Python fun starts!
●   The glue

●   Distributing computation
●   Image processing
●   Source extraction
●   Source association
●   Database interactions
Why Python
●   A lot of existing code
●   Good (scientific) libraries
●   Good astronomical libraries
●   Easy to use

●   Get it working first, then fast
●   NumPy is quite fast when used correctly
What do we use?
●   Python
●   NumPy / SciPy
●   Django
●   MonetDB
●   Pyrap (casacore wrapper)
    –   Does all astro shizzle you can imagine
Distributed Computation
●   Home made (ASTRON)
●
    SSH based
●
    Calling remote scripts
●   Shared code base (NFS)
●   Protocol for passing arguments and results
●
    Uses logging module a lot

●
    Difficult to debug
●   Difficult to profile
●
    Hadoop probably better
The Lofar Cluster
●   100 nodes
●   24 cores each
●   20 TB raid5 storage
●   40 Gbps InfiniBand

●   But for AARTFAAC we build our own
●   Eventually
Main loop
●   Extract source properties

●   Store properties

●   Do association

●   Detect transients
The data
●   1 datacube per second
●   10 frequency bands

●   In the future 10 images per second
●   In the future 4 different polarization

●   Non stop
Source extraction
Source extraction & NumPy
●   Calculate average noise
●   Subtract
●   Find 'islands'
●   Fit gauss
Store the data
Database
●   Move calculation to the data
●   Independent data
●   Naturally separable by sky coordinates

●   ~100 TB/year
●   10.000 insert/second
MonetDB
●   Don't believe the hype
●   NoNoSQL
●   Relational
●   Column store DB
●   Fast
●   Auto tuning!
●   Developers next door (CWI)
●   Cross research funding
INSERT INTO tempbasesources
(xtrsrc_id
,datapoints
,I_peak_sum
,I_peak_sq_sum
,weight_peak_sum
,weight_I_peak_sum
,weight_I_peak_sq_sum
)
SELECT b0.xtrsrc_id
,b0.datapoints
+ 1 AS datapoints
,b0.I_peak_sum
+ x0.I_peak AS i_peak_sum
,b0.I_peak_sq_sum
+ x0.I_peak * x0.I_peak AS i_peak_sq_sum
,b0.weight_peak_sum
+ 1 / (x0.I_peak_err * x0.I_peak_err) AS weight_peak_sum
,b0.weight_I_peak_sum
+ x0.I_peak / (x0.I_peak_err * x0.I_peak_err)
AS weight_i_peak_sum
,b0.weight_I_peak_sq_sum
+ x0.I_peak * x0.I_peak / (x0.I_peak_err * x0.I_peak_err)
AS weight_i_peak_sq_sum
FROM basesources b0
,extractedsources x0
WHERE x0.image_id = @imageid
AND b0.zone BETWEEN CAST(FLOOR((x0.decl - @theta) / x0.zoneheight
) AS INTEGER)
AND CAST(FLOOR((x0.decl + @theta) / x0.zoneheight
) AS INTEGER)
AND ASIN(SQRT((x0.x - b0.x)*(x0.x - b0.x)
+(x0.y - b0.y)*(x0.y - b0.y)
+(x0.z - b0.z)*(x0.z - b0.z)
)/2
)
/
SQRT(x0.ra_err * x0.ra_err + b0.ra_err * b0.ra_err
+x0.decl_err * x0.decl_err + b0.decl_err * b0.decl_err)
< @assoc_r;
MonetDB vs MySQL
MonetDB and Python

●   We maintain the MonetDB Python API

●   http://pypi.python.org/pypi/python-monetdb/

●   Problems? Ask me :)
Challenges
●   Debugging queries

●   MonetDB still in active development
Djonet
●   MonetDB backend for Django
●   https://github.com/gijzelaerr/djonet

●   brew install monetdb
●   pip install python-monetdb djonet

●   Contributions are welcome!
VO events
●   Standardized language
●   Report observations of astronomical events

●   Hey world, check this supernova out over
    there

●   http://comet.transientskp.org
VOevents
Visualisation
●   Web interface
●   Django!
●   Not public (yet)
Source code?
●   No sorry.
●   Maybe some day
●   Legal issues, bureaucracy

●   UvA, Astron
●
More
●   http://www.transientskp.org/
●   http://www.lofar.org/
●   http://www.aartfaac.org/
Questions?

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Lofar python meetup jan9 2013

  • 1. LOFAR & Python Gijs Molenaar gijs@pythonic.nl
  • 2. Agenda ● LOFAR ● AARTFAAC / TKP ● Python ● MonetDB
  • 5. What is LOFAR ● Low-Frequency Array ● Distributed sensor network ● No dishes ● Simple and cheap antenna's ● Omni-directional ● Concurrent observations ● Software telescope – Flexible – Requires supercomputer
  • 6. What is LOFAR Biggest Radio telescope array in the world ● 7000 antennas ● 10 to 80 MHz (LBA) ● 120 to 240 MHz (HBA) ● Multiple small stations ● NL, DE, UK, FR, SE ● New (unique) design
  • 7. New design ● Many unsolved problems ● Multi-terabit/s data scale ● How to – Process – Store – Distribute – Make results useful ● Small scale example for SKA
  • 8. Usage ● Epoch of re-ionization ● Cosmic rays ● Extragalactic surveys ● Transients ● Pulsars
  • 9.
  • 11. Correlation ● IBM blue Gene/P ● Groningen ● Alotta computer power ● Will be replaced with FPGA's (for our purpose) ● No Python
  • 12. Example output – Cygnus A
  • 14. Transient Key Project ● Static sources are boring ● Transient – something that changes ● Detect sources ● Store extracted information ● Associate with existing observations ● Did something change? ● This is where the Python fun starts!
  • 15. The glue ● Distributing computation ● Image processing ● Source extraction ● Source association ● Database interactions
  • 16. Why Python ● A lot of existing code ● Good (scientific) libraries ● Good astronomical libraries ● Easy to use ● Get it working first, then fast ● NumPy is quite fast when used correctly
  • 17. What do we use? ● Python ● NumPy / SciPy ● Django ● MonetDB ● Pyrap (casacore wrapper) – Does all astro shizzle you can imagine
  • 18. Distributed Computation ● Home made (ASTRON) ● SSH based ● Calling remote scripts ● Shared code base (NFS) ● Protocol for passing arguments and results ● Uses logging module a lot ● Difficult to debug ● Difficult to profile ● Hadoop probably better
  • 19. The Lofar Cluster ● 100 nodes ● 24 cores each ● 20 TB raid5 storage ● 40 Gbps InfiniBand ● But for AARTFAAC we build our own ● Eventually
  • 20. Main loop ● Extract source properties ● Store properties ● Do association ● Detect transients
  • 21. The data ● 1 datacube per second ● 10 frequency bands ● In the future 10 images per second ● In the future 4 different polarization ● Non stop
  • 23. Source extraction & NumPy ● Calculate average noise ● Subtract ● Find 'islands' ● Fit gauss
  • 25. Database ● Move calculation to the data ● Independent data ● Naturally separable by sky coordinates ● ~100 TB/year ● 10.000 insert/second
  • 26. MonetDB ● Don't believe the hype ● NoNoSQL ● Relational ● Column store DB ● Fast ● Auto tuning! ● Developers next door (CWI) ● Cross research funding
  • 27. INSERT INTO tempbasesources (xtrsrc_id ,datapoints ,I_peak_sum ,I_peak_sq_sum ,weight_peak_sum ,weight_I_peak_sum ,weight_I_peak_sq_sum ) SELECT b0.xtrsrc_id ,b0.datapoints + 1 AS datapoints ,b0.I_peak_sum + x0.I_peak AS i_peak_sum ,b0.I_peak_sq_sum + x0.I_peak * x0.I_peak AS i_peak_sq_sum ,b0.weight_peak_sum + 1 / (x0.I_peak_err * x0.I_peak_err) AS weight_peak_sum ,b0.weight_I_peak_sum + x0.I_peak / (x0.I_peak_err * x0.I_peak_err) AS weight_i_peak_sum ,b0.weight_I_peak_sq_sum + x0.I_peak * x0.I_peak / (x0.I_peak_err * x0.I_peak_err) AS weight_i_peak_sq_sum FROM basesources b0 ,extractedsources x0 WHERE x0.image_id = @imageid AND b0.zone BETWEEN CAST(FLOOR((x0.decl - @theta) / x0.zoneheight ) AS INTEGER) AND CAST(FLOOR((x0.decl + @theta) / x0.zoneheight ) AS INTEGER) AND ASIN(SQRT((x0.x - b0.x)*(x0.x - b0.x) +(x0.y - b0.y)*(x0.y - b0.y) +(x0.z - b0.z)*(x0.z - b0.z) )/2 ) / SQRT(x0.ra_err * x0.ra_err + b0.ra_err * b0.ra_err +x0.decl_err * x0.decl_err + b0.decl_err * b0.decl_err) < @assoc_r;
  • 29. MonetDB and Python ● We maintain the MonetDB Python API ● http://pypi.python.org/pypi/python-monetdb/ ● Problems? Ask me :)
  • 30. Challenges ● Debugging queries ● MonetDB still in active development
  • 31. Djonet ● MonetDB backend for Django ● https://github.com/gijzelaerr/djonet ● brew install monetdb ● pip install python-monetdb djonet ● Contributions are welcome!
  • 32. VO events ● Standardized language ● Report observations of astronomical events ● Hey world, check this supernova out over there ● http://comet.transientskp.org
  • 34. Visualisation ● Web interface ● Django! ● Not public (yet)
  • 35. Source code? ● No sorry. ● Maybe some day ● Legal issues, bureaucracy ● UvA, Astron ●
  • 36. More ● http://www.transientskp.org/ ● http://www.lofar.org/ ● http://www.aartfaac.org/