MRXS 2.2 - test failures

[Agelos Pappas]

FYI I'd like to let you know that I cross compiled OpenSlide using 
libjpeg and the problems persist. I will keep looking and tell you what 
I find.

Regards
Pappas Agelos

On 13/11/2012 11:12 πμ, Agelos Pappas wrote:
> Hi Benjamin,
>
> in the first image you can see what the slide looks like zoomed out. 
> In the second, I zoomed one step in and the application crashed 
> reporting an access violation in openslide_read_region.
>
> I didn't notice any corrupted images or crashes using the java viewer 
> under windows. Is it multithreaded? I've been hunting this down the 
> past few days and I didn't find it at all easy to reproduce.
>
> It happens when threads run in parallel and is more evident when the 
> program executes quickly. I wrote a simple desktop application that 
> spawns N threads, each of which instantiates a single openslide_t, all 
> to a specific slide file.
> Every thread then walks from the top zoom level to the bottom reading 
> 256x256 tiles. If N equals to the number of CPU cores your system has, 
> so that the app runs quicker, the application crashes almost immediately.
> If I perform a lock in openslide_read_region calls, the application 
> runs fine, but slower since tiles are read in series.
>
> I have only noticed the problem in MRXS slides, but I didn't test it 
> excessively using other type of slides. It does happen on public 
> slides available in openslide.org.
>
> This is definitely a thread safety related bug, but I cannot tell for 
> sure if it lies within my application or in OpenSlide. I do know that 
> we only encountered this when we switched to the latest OpenSlide 
> binaries. This of course might very well be because the older 
> OpenSlide version was doing locks itself and this could be preventing 
> the bug in our application to show.
>
> I will try using libjpeg and tell you what I find.
>
> Regards
> Pappas Agelos
>
> On 13/11/2012 2:42 πμ, Benjamin Gilbert wrote:
>> On 11/11/2012 09:40 AM, Agelos Pappas wrote:
>>> My question therefore is, does the current GitHub version of OpenSlide
>>> pass the provided mirax test cases, as far as valgrind is concerned? In
>>> my system it looks like it does not.
>>> I am running Ubuntu 12.04 LTS 32-bit in VMWare.
>> The mirax test passes on 64-bit Fedora 17.  However, some of the other
>> tests fail, due to:
>>
>>       https://sourceforge.net/p/libjpeg-turbo/bugs/48/
>>
>> I added --track-origins=yes to the valgrind command line, ran the mirax
>> tests on a 32-bit Ubuntu 12.04 system, and got backtraces similar to the
>> ones in that bug.  I'm still tracking it down, though.
>>
>> - Could you post a screenshot of the corruption?
>>
>> - Are you seeing corruption on Linux or only on Windows?
>>
>> - On Windows, can you reproduce it using the OpenSlide Java viewer?  You
>> can run the viewer by double-clicking openslide-win32\bin\openslide.jar.
>>
>> - Can you rebuild OpenSlide against libjpeg, rather than libjpeg-turbo,
>> and see if the problem goes away?  (Install libjpeg into /usr/local,
>> then "./configure CPPFLAGS=-I/usr/local/include 
>> LDFLAGS=-L/usr/local/lib".)
>>
>> - Are you using the public test slides?
>>
>> Thanks,
>> --Benjamin Gilbert
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