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kiyo-masui / burst_search

Program to perform real-time and off-line searches for fast radio bursts in GBT GUPPI data.
GNU General Public License v2.0
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MemoryError while processing GUPPI .fits files #37

Open nategarver-daniels opened 8 years ago

nategarver-daniels commented 8 years ago

I'm probably doing something wrong, but I've been trying to run burst_guppi on some 820MHz GUPPI search data that I have. The file size is ~11G and I inevitably get a MemoryError after the code runs for 20 minutes or so. Program output is:

INFO:__main__:Rank 0, file guppi_57568_AzEl_180.021_070.000_0001_0036.fits.
INFO:burst_search.dedisperse:Using 524288 effective channels with a memory footprint of 25600.0 MB/s
INFO:__main__:Doing actions: save_plot_dm,print
INFO:burst_search.manager:Processing block 1.
INFO:burst_search.manager:Dispersion index 2.0, spectral index 0.0.
Traceback (most recent call last):
  File "/opt/pulsar/src/burst_search/scripts/burst_guppi", line 153, in <module>
    Searcher.process_all()
  File "build/bdist.linux-x86_64/egg/burst_search/manager.py", line 342, in process_all
  File "build/bdist.linux-x86_64/egg/burst_search/manager.py", line 312, in process_next_block
  File "burst_search/dedisperse.pyx", line 301, in burst_search.dedisperse.DMTransform.__call__ (burst_search/dedisperse.c:5832)
MemoryError

I suspect that there is probably something simple that I'm not doing.

kiyo-masui commented 8 years ago

Try using the 'scrunch' functionality. Right now it is up-sampling the frequency axis to 524288 channels to get to the maximum DM. With scrunching it will instead down sample the time axis for the higher DMs (where time is smeared anyhow).

kiyo-masui commented 8 years ago

Let me know if this works for you. To close this issue, I suppose I should put a note about memory requirements, and how to get around them, in the README. Your thoughts?

nategarver-daniels commented 8 years ago

Kiyo,

I think you can close the issue. Makeing a note about the memory requirements would be good though. I tried the --scrunch option but ended up with a different error (but one possibly related to compiling the package). I also tried limiting the DM range to just a few DM but was still getting memory errors. Trying to sort out if it's a system issue or if I really need to be using a lot of nodes over MPI to spread things out (and reduce the memory pressure on each individual node)

-Nate

On 07/14/2016 12:31 PM, Kiyoshi Masui wrote:

Let me know if this works for you. To close this issue, I suppose I should put a note about memory requirements, and how to get around them, in the README. Your thoughts?

You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/kiyo-masui/burst_search/issues/37#issuecomment-232718732