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Hi Martin,
<div><br>
</div>
<div>Looking at the content of the server logs, there are lots of "Too many open files"</div>
<div>exceptions in it which are likely related to the import failures including pyramid</div>
<div>generation failures.</div>
<div><br>
</div>
<div>What is your `ulimit -a` output? Could you try increasing the maximum number of</div>
<div>open files per process and see if that fixes your issues?</div>
<div><br>
</div>
<div>See also</div>
<div><a href="https://www.openmicroscopy.org/site/support/omero5.0/sysadmins/limitations.html#limitations-openfiles">https://www.openmicroscopy.org/site/support/omero5.0/sysadmins/limitations.html#limitations-openfiles</a></div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div>On 24 Feb 2015, at 20:14, Martin Schorb <<a href="mailto:martin.schorb@embl.de">martin.schorb@embl.de</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Hi Sebastien,<br>
<br>
the only log file that I found something related to the import s<br>
blitz.log which is raw 293MB. I have uploaded it here:<br>
* snip *<br>
<br>
let me know if I can provide more useful files.<br>
<br>
Martin<br>
<br>
Am 2/24/15 um 5:44 PM schrieb Sebastien Besson:<br>
<blockquote type="cite">Hi Martin,<br>
<br>
I tried to reproduce your failures with a 5.0.8 server while performing an in-place<br>
import of 6000 fake files but could not reproduce. I will give it another go with tiff<br>
files tomorrow.<br>
<br>
In the meantime, do you have access to the server logs corresponding to the failing<br>
import? Would it be possible to upload them for our examination?<br>
<br>
Best,<br>
Sebastien<br>
<br>
On 23 Feb 2015, at 20:48, Josh Moore <<a href="mailto:josh@glencoesoftware.com">josh@glencoesoftware.com</a>> wrote:<br>
<br>
<blockquote type="cite">Forwarding conversation to the list.<br>
<br>
<br>
---------- Forwarded message ----------<br>
From: Martin Schorb <<a href="mailto:martin.schorb@embl.de">martin.schorb@embl.de</a>><br>
Date: Mon, Feb 23, 2015 at 9:45 PM<br>
Subject: Re: OMERO.qa - new comment<br>
To: Josh Moore <<a href="mailto:josh@glencoesoftware.com">josh@glencoesoftware.com</a>><br>
<br>
<br>
I have a set of ~6000 tif files from a FIB-SEM. 15 MB each that I try<br>
to import using<br>
OMERO.server/bin/omero -s localhost -u $user import -- -d 1<br>
--transfer=ln_s $imagedir<br>
<br>
It manages to do so for part of the files but randomly exits with the<br>
following complaint (first line shows last successful import):<br>
2015-02-20 17:41:53,539 3097900 [l.Client-0] INFO<br>
ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file:<br>
/home/emcf/images/MB1-ROI9-FIBSEM-AliCropAli-InvCLAHE/MB1-ROI9-FIBSEM_s1000-1999_InvCLAHE0781.tif<br>
Imported pixels:<br>
3197<br>
Other imported objects:<br>
Fileset:3198<br>
Image:3197<br>
<br>
...<br>
<br>
2015-02-20 17:41:53,539 3097900 [l.Client-0] INFO<br>
ome.formats.importer.cli.ErrorHandler - Number of errors: 0<br>
2015-02-20 17:41:53,558 3097919 [ main] INFO<br>
ome.formats.OMEROMetadataStoreClient - Call context: {omero.group:3}<br>
2015-02-20 17:41:53,565 3097926 [ main] INFO<br>
ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION<br>
2015-02-20 17:41:53,689 3098050 [ main] INFO<br>
ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START<br>
2015-02-20 17:41:53,690 3098051 [ main] INFO<br>
s.importer.transfers.SymlinkFileTransfer - Transferring<br>
/home/emcf/images/MB1-ROI9-FIBSEM-AliCropAli-InvCLAHE/MB1-ROI9-FIBSEM_s1000-1999_InvCLAHE0764.tif...<br>
2015-02-20 17:41:53,707 3098068 [ main] INFO<br>
ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED:<br>
/home/emcf/images/MB1-ROI9-FIBSEM-AliCropAli-InvCLAHE/MB1-ROI9-FIBSEM_s1000-1999_InvCLAHE0764.tif<br>
2015-02-20 17:41:53,813 3098174 [ main] ERROR<br>
ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION:<br>
/home/emcf/images/MB1-ROI9-FIBSEM-AliCropAli-InvCLAHE/MB1-ROI9-FIBSEM_s1000-1999_InvCLAHE0764.tif<br>
omero.ResourceError: null<br>
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native<br>
Method) ~[na:1.7.0_75]<br>
<br>
....<br>
<br>
I run the import command as the omero system user on the actual server<br>
(thru ssh). It succeeds with 3197 files and then causes the problem. The<br>
target dir in ManagedRepositories is empty and writable, there is no<br>
quota and plenty of free disk space.<br>
<br>
Martin<br>
<br>
<br>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="https://www.openmicroscopy.org/qa2/qa/feedback/10523/?token=515b9ee71de697b8f25684d282d61532">https://www.openmicroscopy.org/qa2/qa/feedback/10523/?token=515b9ee71de697b8f25684d282d61532</a><br>
</blockquote>
</blockquote>
</blockquote>
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</blockquote>
<br>
</blockquote>
<br>
</blockquote>
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<br>
<br>
<div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
</div>
</span></div>
</span></span></div>
<br>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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