[ome-users] Network drive slowness

Paul van Schayck paul at vanschayck.nl
Thu Dec 11 16:29:17 GMT 2014 

Hi Melissa,

Would this bug also explain slowness in the OMERO importer while importing
files which are located on a network drive (in Windows)?

Thanks,

Paul

On Thu, Dec 11, 2014 at 3:26 PM, Niko Ehrenfeuchter <
nikolaus.ehrenfeuchter at unibas.ch> wrote:

> Hi Melissa,
>
> could you please add me to the CC list on that ticket as well? We're also
> suffering from the performance issue when opening files from network
> shares, especially on Windows.
>
> Cheers
> Niko
>
>
> On 11.12.2014 03:34, Melissa Linkert wrote:
>
>> Hi Rafael and Lorenz,
>>
>> You are both now CC'd on ticket 6586, and will receive an automated
>> email with "[OME] #6586" in the subject line each time the ticket is
>> updated.
>>
>> Regards,
>> -Melissa
>>
>> On Thu, Dec 11, 2014 at 12:55:24PM +0100, Maier, Lorenz wrote:
>>
>>> Hi Rafael,
>>>
>>> probably Zen Blue reads only the planes and zoom levels that it actually
>>> displays.
>>>
>>> Best,
>>> Lorenz
>>>
>>> PS: please CC me on that ticket!
>>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk]
>>> Im Auftrag von r b
>>> Gesendet: Donnerstag, 11. Dezember 2014 01:20
>>> An: Melissa Linkert
>>> Cc: ome-users at lists.openmicroscopy.org.uk
>>> Betreff: Re: [ome-users] Network drive slowness
>>>
>>> Hi Melissa and list,
>>>
>>> I would like to be automatically notified of updates about that ticket.
>>>
>>> Is there an obvious reason why the same file opens so much faster in Zen
>>> Blue 2012?
>>>
>>> Thank you,
>>>
>>> Rafael Buono
>>>
>>> On Wed, Dec 10, 2014 at 5:45 PM, Melissa Linkert <
>>> melissa at glencoesoftware.com> wrote:
>>>
>>>> Hi Rafael,
>>>>
>>>>  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.
>>>>>
>>>>
>>>> Thank you for the additional information.
>>>>
>>>> 20 seconds to open a 460MB file is within the range of what I would
>>>> expect - even more so if the images are compressed within the file.
>>>> The fact that only the first opening from the network drive takes 10
>>>> minutes suggests that this is not related to file format itself.  I
>>>> strongly suspect that this ticket on our issue tracking system is the
>>>> problem that you are experiencing:
>>>>
>>>> http://trac.openmicroscopy.org/ome/ticket/6586
>>>>
>>>> If you would like to be automatically notified of updates to that
>>>> ticket, please let me know.
>>>>
>>>> Regards,
>>>> -Melissa
>>>>
>>>> On Mon, Dec 08, 2014 at 06:33:51PM -0600, r b wrote:
>>>>
>>>>> 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.
>>>>>>> _______________________________________________
>>>>>>> ome-users mailing list
>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>
>>>>>> _______________________________________________
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>>
>>
> --
> Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of
> Basel | Klingelbergstr. 50/70 | CH-4056 Basel
> Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch |
> www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>
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