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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.<br>
<br>
Regards<br>
Pappas Agelos<br>
<br>
<div class="moz-cite-prefix">On 13/11/2012 11:12 πμ, Agelos Pappas
wrote:<br>
</div>
<blockquote cite="mid:50A20EF1.1050206@smartcode.gr" type="cite">Hi
Benjamin,
<br>
<br>
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.
<br>
<br>
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.
<br>
<br>
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.
<br>
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.
<br>
If I perform a lock in openslide_read_region calls, the
application runs fine, but slower since tiles are read in series.
<br>
<br>
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.
<br>
<br>
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.
<br>
<br>
I will try using libjpeg and tell you what I find.
<br>
<br>
Regards
<br>
Pappas Agelos
<br>
<br>
On 13/11/2012 2:42 πμ, Benjamin Gilbert wrote:
<br>
<blockquote type="cite">On 11/11/2012 09:40 AM, Agelos Pappas
wrote:
<br>
<blockquote type="cite">My question therefore is, does the
current GitHub version of OpenSlide
<br>
pass the provided mirax test cases, as far as valgrind is
concerned? In
<br>
my system it looks like it does not.
<br>
I am running Ubuntu 12.04 LTS 32-bit in VMWare.
<br>
</blockquote>
The mirax test passes on 64-bit Fedora 17. However, some of the
other
<br>
tests fail, due to:
<br>
<br>
<a class="moz-txt-link-freetext" href="https://sourceforge.net/p/libjpeg-turbo/bugs/48/">https://sourceforge.net/p/libjpeg-turbo/bugs/48/</a>
<br>
<br>
I added --track-origins=yes to the valgrind command line, ran
the mirax
<br>
tests on a 32-bit Ubuntu 12.04 system, and got backtraces
similar to the
<br>
ones in that bug. I'm still tracking it down, though.
<br>
<br>
- Could you post a screenshot of the corruption?
<br>
<br>
- Are you seeing corruption on Linux or only on Windows?
<br>
<br>
- On Windows, can you reproduce it using the OpenSlide Java
viewer? You
<br>
can run the viewer by double-clicking
openslide-win32\bin\openslide.jar.
<br>
<br>
- Can you rebuild OpenSlide against libjpeg, rather than
libjpeg-turbo,
<br>
and see if the problem goes away? (Install libjpeg into
/usr/local,
<br>
then "./configure CPPFLAGS=-I/usr/local/include
LDFLAGS=-L/usr/local/lib".)
<br>
<br>
- Are you using the public test slides?
<br>
<br>
Thanks,
<br>
--Benjamin Gilbert
<br>
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