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biigle / laserpoints

:m: BIIGLE module to perform a heuristic laser point detection on images
GNU General Public License v3.0
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IndexError: too many indices for array #14

Closed mzur closed 7 years ago

mzur commented 7 years ago

We've got a bug in the delphiGather script, probably a memory issue because there are too many images with too many manually annotated laserpoints. The error says:

Traceback (most recent call last):
  File "/vol/uwi/www/bias/vendor/biigle/laserpoints/src/config/../resources/scripts/delphiGather.py", line 55, in <module>
    lps.append(lpimg[j[0], j[1]])
IndexError: too many indices for array

Our best guess is that lps and lpnegativ get too large. Memory for the images read into lpimg is freed as it should.

Here is an example input file that can reproduce the issue. If the delphiGather script is called with this file, the memory comsumption increases and increases until it is exhausted and the script crashes. Command on the cluster: python -i delphiGather.py input.txt

Note: The script didn't actually crash in my tests due to memory exhaustion because the cluster has so much memory. I killed it once it consumed ~15 GB of memory. Top on wayne with 528 GB of RAM:

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
 9599 mzurowie  20   0 15.191g 0.015t  19716 S   0.0  3.0   6:30.08 python
mzur commented 7 years ago

Once the issue is resolved, restart the failed jobs in the queue.

mzur commented 7 years ago

The delphiGather script works fine now but delphiApply crashes with a core dump. We have to check delphiApply with output from the new delphiGather manually.

mzur commented 7 years ago

Note: A core dump on Solaris equals a MemoryError on a normal OS.

Since the volume where the LP detection failed has a very large number of manually set laser points the distance matrix of the delphiApply script gets huge. We have to make this more memory efficient.

Continued in #15 as this is a separate issue.