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Hi,
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<div class="">did you have a chance to test whether the issue can be reproduced when writing to a local disk</div>
<div class="">or whether this only applies to non-local file systems?</div>
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<div class="">Sebastien<br class="">
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<div class="">On 20 Nov 2018, at 14:52, Tarbox, Lawrence <<a href="mailto:LRTarbox@uams.edu" class="">LRTarbox@uams.edu</a>> wrote:</div>
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On second thought, it is a GPFS (aka IBM Spectrum Scale) mounted disk. It appears as a local disk (not NFS), but in actuality it is in a shared storage system (i.e. akin to a SAN, but with a shared cluster file system). These conversions were done on our
supercomputer. It normally is used to very large datasets.<o:p class=""></o:p></div>
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I was also getting errors when doing conversions on my laptop going to local disk. I switched to the cluster to take advantage of larger memory sizes (128 GB HPC versus 16 GB laptop). I could try again on the laptop to see if I get the same error, but not
until tomorrow.<o:p class=""></o:p></div>
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<b class="">From:</b><span class="Apple-converted-space"> </span>Tarbox, Lawrence<span class="Apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, November 20, 2018 8:48 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>users OME <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>RE: [ome-users] Error when converting large .svs or .vsi images<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Local disk.<o:p class=""></o:p></div>
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<b class="">From:</b><span class="Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>><span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Sebastien Besson (Staff)<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, November 20, 2018 4:58 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>users OME <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Tarbox, Lawrence <<a href="mailto:LRTarbox@uams.edu" style="color: purple; text-decoration: underline;" class="">LRTarbox@uams.edu</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Error when converting large .svs or .vsi images<o:p class=""></o:p></div>
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Dear Lawrence,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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re-reading this thread, one thing coming to mind is that we hit a very similar<o:p class=""></o:p></div>
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error internally when testing large image conversions recently [1].<o:p class=""></o:p></div>
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To make sure this is the same issue, are you writing the converted output to<o:p class=""></o:p></div>
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a local disk or to a network file system?<o:p class=""></o:p></div>
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Best,<o:p class=""></o:p></div>
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Sebastien<o:p class=""></o:p></div>
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[1] <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_openmicroscopy_bioformats_pull_3189-23issuecomment-2D410805187&d=DwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=7PfGBb2SHdaGpGKqCizhwg&m=EweMJix5DTaLSZodAecdRo0mMLAECXtN4lLoeQbaLaw&s=lU99ySOWUtgtkocrUg05hdOA41P3Wh1qm8bbffva_fo&e=" style="color: purple; text-decoration: underline;" class="">https://github.com/openmicroscopy/bioformats/pull/3189#issuecomment-410805187</a><o:p class=""></o:p></div>
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On 20 Nov 2018, at 05:39, Tarbox, Lawrence <<a href="mailto:LRTarbox@uams.edu" style="color: purple; text-decoration: underline;" class="">LRTarbox@uams.edu</a>> wrote:<o:p class=""></o:p></div>
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I tried changing tile size. The error still comes up. The conversions that are failing all stop writing the TIFF files when the size of the output file hits 1,429,209,088 bytes, consistently, regardless of the size of the input file, on both .svs and .vsi
files. It does seem to be a restriction in the size of the file that the TIFF writer can write.<o:p class=""></o:p></div>
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<b class="">From:</b><span class="apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>><span class="apple-converted-space"> </span><b class="">On
Behalf Of<span class="apple-converted-space"> </span></b>Tarbox, Lawrence<br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>Tuesday, November 6, 2018 11:22 AM<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span>David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" style="color: purple; text-decoration: underline;" class="">d.gault@dundee.ac.uk</a>>; OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] Error when converting large .svs or .vsi images<o:p class=""></o:p></div>
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These errors came up while using a compression codec. Here is the command that I was using:<o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">/home/ltarbox/bftools/bfconvert -no-upgrade -overwrite -compression JPEG \</span><o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class=""> "${FILES[MOAB_JOBARRAYINDEX-1]}" \</span><o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class=""> /home/ltarbox/CIR-scans/out/WSI-${MOAB_JOBARRAYINDEX}_S%s.ome.tif</span><o:p class=""></o:p></div>
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Are you thinking that switching from JPEG to JPEG-2000 or LZW would work better?<o:p class=""></o:p></div>
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The original .svs images use JPEG compression (I think) with a tile size of 256x256<o:p class=""></o:p></div>
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The original .vsi images use JPEG compression with a tile size of 512x512.<o:p class=""></o:p></div>
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I was somewhat hoping that if I requested -compression JPEG bfconvert would simply copy the already-JPEG-compressed tiles from the original images into the .ome.tif images. But I’m game to try a different compression scheme.<o:p class=""></o:p></div>
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<b class="">From:</b><span class="apple-converted-space"> </span>David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">d.gault@dundee.ac.uk</span></a>><span class="apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>Tuesday, November 6, 2018 9:14 AM<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a>>;
Tarbox, Lawrence <<a href="mailto:LRTarbox@uams.edu" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">LRTarbox@uams.edu</span></a>><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] Error when converting large .svs or .vsi images<o:p class=""></o:p></div>
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Hi Lawrence,<span class="apple-converted-space"> </span><o:p class=""></o:p></div>
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It does look like it is related to the file size of the converted file. Setting a compression codec should reduce the required size and might allow for easier conversion. <o:p class=""></o:p></div>
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For example using:<o:p class=""></o:p></div>
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bfconvert -compression JPEG-2000 /path/to/originalFile.svs /path/to/convertedFile.ome.tiff<o:p class=""></o:p></div>
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bfconvert -compression LZW /path/to/originalFile.svs /path/to/convertedFile.ome.tiff<o:p class=""></o:p></div>
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With Thanks,<o:p class=""></o:p></div>
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David Gault<o:p class=""></o:p></div>
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On 5 Nov 2018, at 20:19, Tarbox, Lawrence <<a href="mailto:LRTarbox@uams.edu" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">LRTarbox@uams.edu</span></a>> wrote:<o:p class=""></o:p></div>
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I am using 5.9.2, from 3 Sept 2018.<o:p class=""></o:p></div>
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The file sizes that are not converting range from 1.7 GB to 4.2 GB. The .svs images that were smaller than about 1.3 GB converted without problem.<o:p class=""></o:p></div>
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<b class="">From:</b><span class="apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">ome-users-bounces@lists.openmicroscopy.org.uk</span></a>><span class="apple-converted-space"> </span><b class="">On
Behalf Of<span class="apple-converted-space"> </span></b>David Gault (Staff)<br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>Monday, November 5, 2018 7:10 AM<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a>><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] Error when converting large .svs or .vsi images<o:p class=""></o:p></div>
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Hi Lawrence,<span class="apple-converted-space"> </span><o:p class=""></o:p></div>
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That error looks as though the buffer has been unable to successfully increase its limit for some reason.<o:p class=""></o:p></div>
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What size are the original files you are trying to convert? Also what version of Bio-Formats are you currently using?<o:p class=""></o:p></div>
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With Thanks,<o:p class=""></o:p></div>
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David Gault<o:p class=""></o:p></div>
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On 2 Nov 2018, at 15:21, Tarbox, Lawrence <<a href="mailto:LRTarbox@uams.edu" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">LRTarbox@uams.edu</span></a>> wrote:<o:p class=""></o:p></div>
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In converting large .svs or .vsi images, I get the following error:<o:p class=""></o:p></div>
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/home/ltarbox/CIR-scans<o:p class=""></o:p></div>
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SVSReader initializing 54680.svs<o:p class=""></o:p></div>
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Reading IFDs<o:p class=""></o:p></div>
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[Aperio SVS] -> /home/ltarbox/CIR-scans/out/WSI-2_S%s.ome.tif [OME-TIFF]<o:p class=""></o:p></div>
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Switching to BigTIFF (by file size)<o:p class=""></o:p></div>
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at java.nio.Buffer.limit(Buffer.java:275)<o:p class=""></o:p></div>
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Smaller images convert fine.<span class="apple-converted-space"> </span><o:p class=""></o:p></div>
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I tripled the memory size (to 40 GB), but it stll fails<o:p class=""></o:p></div>
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Ideas?<o:p class=""></o:p></div>
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<i class=""><span style="color: rgb(68, 114, 196);" class="">Lawrence Tarbox, Ph.D., Dept. of Biomedical Informatics, Univ. of Arkansas for Medical Sciences</span></i><o:p class=""></o:p></div>
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<i class=""><span style="color: rgb(68, 114, 196);" class=""><a href="mailto:LTarbox@uams.edu" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">mailto:LTarbox@uams.edu</span></a><span class="apple-converted-space"> </span>+1.314.681-2752</span></i><o:p class=""></o:p></div>
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<span style="font-size: 10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p class=""></o:p></div>
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