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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have an upload process running on our existing Omero server (omero version 4.4.8, Ice version 3.3) which uses the Omero CLI to upload images into Omero. This is working correctly for a bulk upload process that we have written.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am currently testing the same process on a new server which is built with Omero 5.0 and Ice 3.5. I am seeing the following error, but not after a consistent time:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Using session feccfbae-b08e-4298-9f3c-5f31139af486 (webberj@localhost:4064). Idle timeout: 10.0 min. Current group: system<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Previous session expired for webberj on localhost:4064<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">InternalException: Failed to connect: exception ::Glacier2::CannotCreateSessionException<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">{<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt"> reason = Server not fully initialized<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">}<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">A core dump is then generated. The following are the log entries (/var/log/messages) when this occurs:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:38:24 v0246 abrt[9252]: Saved core dump of pid 6130 (/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55.x86_64/jre/bin/java) to /var/spool/abrt/ccpp-2014-05-22-16:38:12-6130 (668704768
bytes)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:38:24 v0246 abrtd: Directory 'ccpp-2014-05-22-16:38:12-6130' creation detected<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:38:25 v0246 abrt[9252]: /var/spool/abrt is 1433007648 bytes (more than 1279MiB), deleting 'ccpp-2014-05-22-15:14:52-4857'<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:38:25 v0246 abrtd: Size of '/var/spool/abrt' >= 1000 MB, deleting 'ccpp-2014-05-22-15:14:52-4857'<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:38:25 v0246 abrt[9252]: Lock file '/var/spool/abrt/ccpp-2014-05-22-15:14:52-4857/.lock' is locked by process 1467<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:38:25 v0246 abrt[9252]: '/var/spool/abrt/ccpp-2014-05-22-15:14:52-4857' does not exist<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:38:34 v0246 kernel: end_request: I/O error, dev fd0, sector 0<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:38:34 v0246 kernel: end_request: I/O error, dev fd0, sector 0<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:39:52 v0246 abrtd: Sending an email...<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">May 22 16:39:52 v0246 abrtd: Email was sent to: root@localhost<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The email that is sent as a result of this crash is very long, but I have attached the first part of an example to this email.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Does anyone have any ideas why Omero / Ice is crashing in this way? Does this look like an Omero Issue, an Ice issue or a Java issue?<o:p></o:p></p>
<p class="MsoNormal"><br>
Thanks<o:p></o:p></p>
<p class="MsoNormal">John<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#4F81BD;mso-fareast-language:EN-GB">-------------------------------------------------------------------------------------------------------------------------------------------- </span></b><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><b><span style="font-family:"Arial","sans-serif";color:#548DD4;mso-fareast-language:EN-GB">John Webber<br>
</span></b><span style="color:#1F497D;mso-fareast-language:EN-GB">Computing and Information Services</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">NBI Partnership Ltd</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Norwich Research park</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Colney Lane</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Norwich</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">NR4 7UH</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB"> </span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">E-Mail:</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"><a href="mailto:john.webber@nbi.ac.uk"><span style="color:blue">john.webber@nbi.ac.uk</span></a></span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Web:</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> <a href="http://www.nbi.ac.uk/">
<span style="color:blue">http://www.nbi.ac.uk</span></a></span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Tel:</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> +44(0)1603 450 818<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Helpdesk (Tel): 1234</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> HPC Support (Web):</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> <a href="http://hpc.nbi.ac.uk/">
<span style="color:blue">http://hpc.nbi.ac.uk</span></a> (NBI internal)<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB"> HPC Support (Tel):</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> 2003 (NBI internal)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-GB"> </span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span style="color:#1F497D;mso-fareast-language:EN-GB">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><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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