[ome-devel] bio-formats slow under WIndows

[Melissa Linkert]

Hi Rubén,

> Once more by using bio-formats I address you up with a performance question.
> Maybe the answer is obvious for you people, but not for me. It could also be an issue.
> 
> Bioformats is much slower on Windows than on Linux. Could that be? I am having this for long time.
> 
> Same (local) files, same loci_tools.jar and loci.formats.tools.ImageConverter give 4x slower rates on windows.
> Does it have to do with java interpreter. Does it have to do with the filesystem?
> 
> -Xmx512m was the only argumet used (no compression).

Hmm.  I do see a performance difference when converting a small ScanR
dataset, but the cause of the difference is not obvious.

One thing you can do to narrow down the source of the problem is to
check whether there is a difference when just reading the input file(s).
On Linux:

$ showinf experiment_descriptor.xml | grep "\(Initialization\|s elapsed\)"
Initialization took 1.448s
0.411s elapsed (137.0ms per plane)

The first line shows how long file initialization took, and the second
line shows the average number of milliseconds required to read a plane.

I have also filed a ticket to investigate this further:

http://trac.openmicroscopy.org/ome/ticket/6931

but for a variety of reasons will not be able to work on it for another
1.5-2 weeks.

Regards,
-Melissa

On Fri, Oct 07, 2011 at 01:56:12PM +0200, Rubén Muñoz wrote:
> Dear bioformats developers, 
> 
> Once more by using bio-formats I address you up with a performance question.
> Maybe the answer is obvious for you people, but not for me. It could also be an issue.
> 
> Bioformats is much slower on Windows than on Linux. Could that be? I am having this for long time.
> 
> Same (local) files, same loci_tools.jar and loci.formats.tools.ImageConverter give 4x slower rates on windows.
> Does it have to do with java interpreter. Does it have to do with the filesystem?
> 
> -Xmx512m was the only argumet used (no compression).
> 
> Thanks and regards,
> Rubén
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