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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Hi Simon,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><br>
We are indeed using an older version of Java: build 1.7.0_07-b10.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">I have updated the test server to a later version of Java (build 1.7.0_51-b13), and I have not seen the errors since.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><br>
Thanks again for your help.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">John<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> Simon Li [mailto:s.p.li@dundee.ac.uk]
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<b>Sent:</b> 26 March 2014 17:23<br>
<b>To:</b> John Webber (NBI)<br>
<b>Cc:</b> ome-users@lists.openmicroscopy.org.uk; Balaji Ramalingam<br>
<b>Subject:</b> Re: [ome-users] omero.cli error<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi John<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">What version of Java are you using? We've come across a similar error before on our daily test servers but it seemed to fix itself after we updated to Java 1.7.0_51:<o:p></o:p></p>
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<p class="MsoNormal"><a href="http://trac.openmicroscopy.org.uk/ome/ticket/11081">http://trac.openmicroscopy.org.uk/ome/ticket/11081</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Balaji's just done some testing today on importing large numbers of images, he managed to reproduce your error with 1.7.0_11-b21 but not with 1.7.0_51-b13.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Simon<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 26 Mar 2014, at 09:10, "John Webber (NBI)" <<a href="mailto:John.Webber@nbi.ac.uk">John.Webber@nbi.ac.uk</a>><o:p></o:p></p>
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<p class="MsoNormal"> wrote:<o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Simon,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><br>
Thanks for the quick response.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">My problem is that I have a bulk upload to perform and the omero.cli is now consistently failing! I can upload 60+ images to Omero before I see this error,
so switching debug on might be omerous! However, I do have the cli.err from an example of this fail – I have attached it to this email.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I have also amended my code to work around this issue so that, if it sees this error, it attempts the upload again before crashing out:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> try:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> cli.invoke(import_args, strict=True)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> except omero.cli.NonZeroReturnCode, err:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> logging.warning('%s: Omero CLI has had a NonZeroReturnCode, trying again' % (self))</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> try:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> cli.invoke(import_args, strict=True)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> except:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> logging.error('%s: Omero CLI has failed twice - exiting.' % (self))</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> sys.exit(7)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Not a particularly elegant work around – but it works.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">John</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Simon
Li [mailto:s.p.li@</span><a href="http://dundee.ac.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">dundee.ac.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">]<span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>25 March 2014 16:40<br>
<b>To:</b><span class="apple-converted-space"> </span>John Webber (NBI)<br>
<b>Cc:</b><span class="apple-converted-space"> </span></span><a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">ome-users@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] omero.cli error</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi John<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Could you try adding --debug DEBUG to your import command, and see if it gives any more information? If that doesn't help could you send us cli.err and cli.out?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Many thanks<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Simon<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">On 25 Mar 2014, at 15:46, "John Webber (NBI)" <<a href="mailto:John.Webber@nbi.ac.uk"><span style="color:purple">John.Webber@nbi.ac.uk</span></a>><o:p></o:p></p>
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<p class="MsoNormal"> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
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<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Hi,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I’m currently experiencing an issue with a bulk upload of images to Omero. This is being run from the command line.</span><o:p></o:p></p>
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<p class="MsoNormal" align="center" style="text-align:center"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am seeing the following errors, and my bulk upload fails:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif""> cli.invoke(import_args, strict=True)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif""> File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 749, in invoke</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif""> self.assertRC()</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif""> File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 738, in assertRC</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif""> raise NonZeroReturnCode(self.rv, "assert failed")</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif"">omero.cli.NonZeroReturnCode: assert failed</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">The bulk upload failed while writing an image, with the following arguments:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif"">['import', '-s', 'localhost', '-u', 'upload', '-w', '<password removed>', '-p', '4064', '-d', '1687', '-n', '11_03_14_krp4_1130_b1_boundaries.inr.gz', '---errs=cli.err', '---file=cli.out',
'--', '/tmp/tmpB3u1Gn/11_03_14_krp4_1130_b1/11_03_14_krp4_1130_b1_boundaries.inr.gz']</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">When I try to run the upload again, it fails for a different image – it does not fail on the same one upload time!</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am unable to see much additional information: I have checked in the omero logs, (/opt/Omero/var/log), but am not able to see any additional logging. I have checked filesystem
sizes, and nothing seems to have filled up!</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Please can you point me in the right direction as to how I can debug this issue further?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><br>
Thanks</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">John</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#4F81BD">-------------------------------------------------------------------------------------------------------------------------------------------- </span></b><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><b><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#548DD4">John Webber<br>
</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Computing and Information Services</span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">NBI Partnership Ltd</span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Norwich Research park</span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Colney Lane</span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Norwich</span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">NR4 7UH</span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">E-Mail:</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><a href="mailto:john.webber@nbi.ac.uk"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:purple">john.webber@nbi.ac.uk</span></a><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Web:</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <span style="color:#1F497D"> <span class="apple-converted-space"> </span></span></span><a href="http://www.nbi.ac.uk/"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:purple">http://www.nbi.ac.uk</span></a><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Tel:</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <span style="color:#1F497D">
+44(0)1603 450 818</span></span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Helpdesk (Tel): 1234</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <span style="color:#1F497D">
HPC Support (Web):</span> <span style="color:#1F497D"> <span class="apple-converted-space"> </span></span></span><a href="http://hpc.nbi.ac.uk/"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:purple">http://hpc.nbi.ac.uk</span></a><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
(NBI internal)</span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> HPC Support (Tel):</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <span style="color:#1F497D">
2003 (NBI internal)</span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><i><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury
Laboratory</span></i><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
ome-users mailing list<br>
</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif";color:#954F72">ome-users@lists.openmicroscopy.org.uk</span></a><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><br>
</span><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif";color:#954F72">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</span></a><o:p></o:p></p>
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<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><cli.err><o:p></o:p></span></p>
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<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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