[ome-users] Network drive slowness

Melissa Linkert melissa at glencoesoftware.com
Thu Dec 11 02:34:45 GMT 2014 

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
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

More information about the ome-users mailing list