[ome-users] Network drive slowness

[r b]

Hi Melissa and list,

I did the test with a 460MB czi file.

If I copy it to the desktop and then open it, it takes ~20 seconds in Fiji.
If I open it from the network drive:
1st time: 10 minutes
2nd time: 2 minutes
3rd time: ~20 seconds
4th time: ~20 seconds

Opening the same file from the network storage or directly from the
desktop takes less than 4 seconds with Zen Blue 2012.


About the "Bio-Formats Import Options" window. I don't go through it. I go:
File>Open...> then I double click the file and it opens it without
asking anything else..
If I use the Bio-Formats Importer route to open the file from the
desktop, selecting:
-View stack with: Hyperstack
-Stack order: XYCZT
-Display metadata
-Display OME-XML metadata
-Display ROIs

I still get ~20 seconds for it to open.


Thank you

Rafael Buono

On Mon, Dec 8, 2014 at 12:27 PM, Melissa Linkert
<melissa at glencoesoftware.com> wrote:
> Hi Rafael,
>
>> First, as an example, I have a .czi of ~210MB that opens:
>> - ZEN Blue Lite 2012 loading from network drive: about 2 seconds
>> - Copying from network drive and pasting to the Desktop: about 4 seconds
>> - Fiji loading from network drive: 30 seconds
>>
>> In the ImageJ list I was informed that taking longer to load czi files
>> might be a widespread issue with czi files.
>
> How long does it take to read the file using Fiji, after it has been
> copied to the Desktop?  That would help us to know if this is strictly
> due to the network file system, or if the procedure for reading the file
> is too slow.
>
> It would also be useful to know which options you have selected in the
> "Bio-Formats Import Options" window.
>
>> The second problem was found while testing the speeds above. If I put
>> the same file one folder deeper and try to open it in Fiji, the time
>> grows from 30 seconds to 12 minutes.
>>
>> I am one of those people who organizes things by creating folder,
>> inside folder, inside folder.
>> In the following structure:
>> O:\Folder1\Folder2\Folder3\Folder4\Folder5\Folder6\Folder7
>> If I have the czi file in Folder6, it takes 30 seconds to open. If I
>> move it to Folder7, it takes 12 minutes to open.
>>
>> Is there an obvious reason for this increase in time?
>
> Having more folders can cause subtle performance degradation, but
> typically not as much as you describe.  If you open the file in Folder7
> twice in a row, does it take 12 minutes both times?
>
> Regards,
> -Melissa
>
> On Fri, Dec 05, 2014 at 11:05:21AM -0600, r b wrote:
>> Hi all,
>>
>> I recently got our lab workstation connected through the 1Gbps network
>> to the building's server. Among other reasons, I was hoping to process
>> images directly from the network drive. However, even with the upgrade
>> to 1Gbps, loading images in Fiji is still slow. I have encountered two
>> problems and I am not sure they are related.
>>
>> First, as an example, I have a .czi of ~210MB that opens:
>> - ZEN Blue Lite 2012 loading from network drive: about 2 seconds
>> - Copying from network drive and pasting to the Desktop: about 4 seconds
>> - Fiji loading from network drive: 30 seconds
>>
>> In the ImageJ list I was informed that taking longer to load czi files
>> might be a widespread issue with czi files.
>>
>> The second problem was found while testing the speeds above. If I put
>> the same file one folder deeper and try to open it in Fiji, the time
>> grows from 30 seconds to 12 minutes.
>>
>> I am one of those people who organizes things by creating folder,
>> inside folder, inside folder.
>> In the following structure:
>> O:\Folder1\Folder2\Folder3\Folder4\Folder5\Folder6\Folder7
>> If I have the czi file in Folder6, it takes 30 seconds to open. If I
>> move it to Folder7, it takes 12 minutes to open.
>>
>> Is there an obvious reason for this increase in time?
>>
>> Thank you
>>
>> Rafael Buono
>>
>> PS:
>> Some info about my system below:
>> Java information:
>>   os.arch => amd64
>>   os.name => Windows 7
>>   os.version => 6.1
>>   java.version => 1.6.0_24
>>   java.vendor => Sun Microsystems Inc.
>>   java.runtime.name => Java(TM) SE Runtime Environment
>>   java.runtime.version => 1.6.0_24-b07
>>   java.vm.name => Java HotSpot(TM) 64-Bit Server VM
>>   java.vm.version => 19.1-b02
>>   java.vm.vendor => Sun Microsystems Inc.
>>   java.vm.info => mixed mode
>>   java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
>>   java.specification.name => Java Platform API Specification
>>   java.specification.version => 1.6
>>   sun.cpu.endian => little
>>   sun.desktop => windows
>>   file.separator => \
>>
>> The up-to-date check says: UP_TO_DATE
>>
>> Information relevant to JAVA_HOME related problems:
>>
>>   JAVA_HOME is set to:
>> C:\Users\ADMINI~1\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
>>   imagej.dir => C:\Users\ADMINI~1\Desktop\Fiji.app
>>
>> Information about the version of each plugin:
>>
>> Activated update sites:
>> ImageJ: http://update.imagej.net/ (last check:20141126151327)
>> Fiji: http://fiji.sc/update/ (last check:20141125101145)
>> MOSAIC ToolSuite:
>> http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last
>> check:20141105181755)
>>
>>
>>
>> Bio-Formats information:
>> Release 5.0.6, revision 33b1150, built 10 November 2014.
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