"View mate region in split view" freezes IGV on distant reads

[brainstorm]

Hello @jrobinso, @igvteam

I have been chasing an IGV freeze bug for a while now. The regression appeared for sure on commit f9690c6 on Jun 13th. I bisected from release 2.8.3 (which works) an here's what I found, manually testing the sequence of steps reported by several staff and research members @umccr:

4fbb9df ... Feb 2? Works
b15e0f0 ... Mar 7? Works
4879b5e ... Jun 1? Works
ce921fd ... Jun 2? Works
6979897 ... Jun 12? Works
b0579ca ... Jun 12? Works
f9690c6 ... Jun 13? Hangs!
dd8e3c0 ... Jun 13? Hangs!
0f86206 ... Jun 14? Works but zoom on the right is not shown
b8855c5 ... Jun 20? Hangs!
...
All the way to master and prior releases which all freeze/hang IGV completely.

Would you mind revisiting that "async fix" change? I'll try to craft a minimal reproducer but it might take me a while, by reporting this in advance I hope you can figure it out faster what might be going on here.

/cc @ohofmann @reisingerf

[jrobinso]

Thanks for the report, and for narrowing it down. I'm able to reproduce this with a 1KG file, looking into it.

[brainstorm]

Epic fast response, thanks @jrobinso, much appreciated! :)

[jrobinso]

There was a thread lock contention. I'm doing a lot of profiling now, and looking at making some methods thread safe, to reduce the use of synchronization generally. This should give a performance boost in the end. However I think the fix I pushed returns us to the status quo.

…

On Fri, Jul 31, 2020 at 4:09 PM Roman Valls Guimera < ***@***.***> wrote: Epic fast response, thanks @jrobinso <https://github.com/jrobinso>, much appreciated! :) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#833 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHD2HGTUW4QRSADEPSR5XDR6NFJTANCNFSM4PPDZXSQ> .

[brainstorm]

Excellent Jim, looking forward to telling our users to download 2.8.8 IGV proper so that they can carry on with mate split view on cancer samples ;)

[davideby]

Hey, quick note here @brainstorm. There's a 2.8.8 release out there but it doesn't deal with this bug. Be on the lookout for 2.8.9 instead. It should be early next week.

I just didn't want you noticing that and thinking you're all set. We'll get this out ASAP.

[jrobinso]

The fix for this is released as 2.8.9. It was actually a separate but related bug and fix to the problem in the master branch.

…

On Sun, Aug 2, 2020 at 6:54 PM David Eby ***@***.***> wrote: Hey, quick note here @brainstorm <https://github.com/brainstorm>. There's a 2.8.8 release out there *but it doesn't deal with this bug*. Be on the lookout for *2.8.9* instead. It should be early next week. I just didn't want you noticing that and thinking you're all set. We'll get this out ASAP. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#833 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHD2HAHVUVDILTNZC7XRI3R6YKE5ANCNFSM4PPDZXSQ> .