#427 Threading bug in cascade-search?

[William S Noble]

I am running cascade-search, and I noticed that during the second search it will suddenly hang indefinitely. I suspect a threading bug.

The command line is

crux cascade-search --verbosity 100 --overwrite T --output-dir . --precursor-window 10 --precursor-window-type ppm --remove-precursor-peak T --exact-p-value T --concat T --num-threads 1 --estimation-method tdc small.ms2 maxMods=0,../2016-07-22mods/maxMods=1

The tar file is too big to upload to sourceforge, but you can find it here:

/net/noble/vol1/home/noble/proj/malaria/2016histone-msms/results/bill/cascade-bug.tgz

Alice, can you see if you get the same behavior? Then we can discuss potential ways to debug this.

[Alice Cheng]

One of the cmd options you specified is --num-threads 1, so there shouldn't be any threading. If it is hanging indefinitely, I don't think it would be due to threading. I'll try to reproduce the problem though.

[Alice Cheng]

Just figured out what was going on. It was a lock problem. There's a if () { continue; } branch where the lock was not getting released. The patch below should fix it. Currently testing the patch.

[William S Noble]

Yes, I have verified that (1) my test now runs to completion, (2) it get
the same results with num-threads=1 and num-threads=4, and (3) all smoke
tests pass. Code looks fine. Please check this in.

Bill

On Thu, Aug 11, 2016 at 11:12 AM, Alice Cheng acheng94@users.sf.net wrote:

Just figured out what was going on. It was a lock problem. There's a if ()
{ continue; } branch where the lock was not getting released. The patch
below should fix it. Currently testing the patch.

Attachments:

• cascadebugpatch.txt
  https://sourceforge.net/p/cruxtoolkit/issues/_discuss/thread/887ba27c/cbef/attachment/cascadebugpatch.txt
  (506 Bytes; text/plain)

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• [issues:#427] https://sourceforge.net/p/cruxtoolkit/issues/427/
  Threading bug in cascade-search?*

Status: open
Milestone: Crux v2.0
Labels: High priority
Created: Thu Aug 11, 2016 03:02 PM UTC by William S Noble
Last Updated: Thu Aug 11, 2016 05:17 PM UTC
Owner: Alice Cheng

I am running cascade-search, and I noticed that during the second search
it will suddenly hang indefinitely. I suspect a threading bug.

The command line is

crux cascade-search --verbosity 100 --overwrite T --output-dir .
--precursor-window 10 --precursor-window-type ppm --remove-precursor-peak T
--exact-p-value T --concat T --num-threads 1 --estimation-method tdc
small.ms2 maxMods=0,../2016-07-22mods/maxMods=1

The tar file is too big to upload to sourceforge, but you can find it here:

/net/noble/vol1/home/noble/proj/malaria/2016histone-msms/
results/bill/cascade-bug.tgz

Alice, can you see if you get the same behavior? Then we can discuss
potential ways to debug this.

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