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<p class="MsoNormal">All,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When I attempt to run a script on a new Omer server I have recently built, I see an error that states:
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> Cannot load the script: <id><o:p></o:p></p>
<p class="MsoNormal"> Error: “No processor available!”<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have stopped, disabled, re-enabled and restarted the “Processor-0”, using the commands:
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="text-indent:36.0pt">bin/omero admin ice "server <cmd> Processor-0"<o:p></o:p></p>
<p class="MsoNormal" style="text-indent:36.0pt">(where <cmd> is stop, disable, enable and start)<o:p></o:p></p>
<p class="MsoNormal" style="text-indent:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal">Please can anyone give me some advice as to why my scripts do not seem to be working?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have checked for python and pytables on my server, and running the admin diagnostics shows the following:<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">================================================================================<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">OMERO Diagnostics 4.4.8p1-ice33-b304<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"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Commands: java -version 1.7.0 (/usr/bin/java)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Commands: python -V 2.4.3 (/usr/bin/python)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Commands: icegridnode --version 3.3.1 (/usr/bin/icegridnode)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Commands: icegridadmin --version 3.3.1 (/usr/bin/icegridadmin)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Commands: psql --version 8.4.13 (/usr/bin/psql)<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">Server: icegridnode running<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: Blitz-0 active (pid = 3331, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: DropBox active (pid = 3342, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: FileServer active (pid = 3333, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: Indexer-0 active (pid = 3334, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: MonitorServer active (pid = 3343, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: OMERO.Glacier2 active (pid = 3337, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: OMERO.IceStorm active (pid = 3344, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: PixelData-0 active (pid = 3353, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: Processor-0 active (pid = 3354, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: Tables-0 active (pid = 3341, enabled)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Server: TestDropBox inactive (enabled)<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">OMERO: SSL port 4064<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">OMERO: TCP port 4063<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">Log dir: /opt/OMERO.server-4.4.8p1-ice33-b304/var/log exists<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">Log files: Blitz-0.log 17.0 MB errors=12 warnings=64<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: DropBox.log 23.0 KB errors=8 warnings=10<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: FileServer.log 2.0 KB<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: Indexer-0.log 31.0 MB errors=54 warnings=64<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: MonitorServer.log 9.0 KB errors=0 warnings=1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: OMEROweb.log 0.0 KB<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: OMEROweb_request.log 0.0 KB<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: PixelData-0.log 266.0 KB errors=54 warnings=115<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: Processor-0.log 1.0 KB<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: Tables-0.log 0.0 KB<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: TestDropBox.log n/a<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: master.err 21.0 KB<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: master.out 0.0 KB<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Log files: Total size 48.90 MB<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">Parsing Blitz-0.log:[line:119] => Server restarted <=<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:418] => Server restarted <=<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:90500] => Server restarted <=<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:90636] => Server restarted <=<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:90766] => Server restarted <=<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:91053] => Server restarted <=<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:98690] => Server restarted <=<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:111055] Your postgres hostname and/or port is invalid<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:111166] Your postgres hostname and/or port is invalid<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:111277] Your postgres hostname and/or port is invalid<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Parsing Blitz-0.log:[line:111510] => Server restarted <=<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">Environment:OMERO_HOME=(unset)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Environment:OMERO_NODE=(unset)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Environment:OMERO_MASTER=(unset)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Environment:PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/omero/bin<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Environment:ICE_HOME=(unset)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Environment:LD_LIBRARY_PATH=(unset)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">Environment:DYLD_LIBRARY_PATH=(unset)<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">OMERO data dir: '/OMERO' Exists? True Is writable? True<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">OMERO.web status... [RUNNING] (PID 3760)<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Checking for the scripts on the server itself, I see:<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:8.0pt">[omero@v0362 Omero]$ bin/omero script list<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">Previously logged in to localhost:4064 as root<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">Server: [localhost]<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">Username: [root]<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">Password:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">Created session 4b0e346b-c123-49ea-891c-21270decc28f (root@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:8.0pt">id | Official scripts<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">----+-----------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">1 | /omero/setup_scripts/FLIM_initialise.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">2 | /omero/analysis_scripts/Plot_Profile.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">3 | /omero/analysis_scripts/Kymograph_Analysis.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">4 | /omero/analysis_scripts/Kymograph.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">5 | /omero/util_scripts/Images_From_ROIs.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">6 | /omero/util_scripts/Dataset_To_Plate.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">7 | /omero/util_scripts/Combine_Images.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">8 | /omero/util_scripts/Channel_Offsets.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">9 | /omero/import_scripts/Populate_ROI.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">10 | /omero/figure_scripts/Movie_Figure.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">11 | /omero/figure_scripts/ROI_Split_Figure.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">12 | /omero/figure_scripts/Thumbnail_Figure.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">13 | /omero/figure_scripts/Split_View_Figure.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">14 | /omero/figure_scripts/Movie_ROI_Figure.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">15 | /omero/export_scripts/Batch_Image_Export.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">16 | /omero/export_scripts/Make_Movie.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">(16 rows)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:8.0pt">[omero@v0362 Omero]$<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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" 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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