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Thanks for that Stephen,<br>
Will try to look in deeper next week. Just for the heck of it, is
there a nice recommended way to remove everything from the database
related to a model/experiment? A clean start?<br>
<br>
Regards,<br>
<br>
On 04/01/12 20:18, <a class="moz-txt-link-abbreviated" href="mailto:stephen.pascoe@stfc.ac.uk">stephen.pascoe@stfc.ac.uk</a> wrote:
<blockquote
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<div class="WordSection1">
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">Muhammad,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">These problems are difficult to diagnose. These
errors suggest an inconsistency problem with your Gateway
database and/or THREDDS catalogs. I suspect you are missing
a root THREDDS catalog in the TDS contents directory or it
is somehow unreadable. Check what the TDS looks like in
your browser. Can you view the top-level catalog as XML?
Is the XML valid?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">I'm also concerned that your Gateway database may
be inconsistent. Check the the tables
metadata.persistent_identifier, metadata.resource and
metadata.dataset for the id </span><span style="font-size:
11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">"</span><tt><span style="font-size: 11pt;
font-family: "Calibri","sans-serif";">cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1".
They all share the same uuid: resource_id==dataset_id.</span></tt><span
style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">Stephen.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size: 10.5pt;
font-family: Consolas; color: rgb(31, 73, 125);">---<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10.5pt;
font-family: Consolas; color: rgb(31, 73, 125);">Stephen
Pascoe +44 (0)1235 445980<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10.5pt;
font-family: Consolas; color: rgb(31, 73, 125);">Centre of
Environmental Data Archival<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10.5pt;
font-family: Consolas; color: rgb(31, 73, 125);">STFC
Rutherford Appleton Laboratory, Harwell Oxford, Didcot
OX11 0QX, UK<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"><o:p> </o:p></span></p>
<div>
<div style="border-right: medium none; border-width: 1pt
medium medium; border-style: solid none none; border-color:
rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color;
padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span style="font-size: 10pt;
font-family:
"Tahoma","sans-serif"; color:
windowtext;" lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family:
"Tahoma","sans-serif"; color:
windowtext;" lang="EN-US">
<a class="moz-txt-link-abbreviated" href="mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org">esg-gateway-dev-bounces@mailman.earthsystemgrid.org</a>
[<a class="moz-txt-link-freetext" href="mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org">mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org</a>]
<b>On Behalf Of </b>
Muhammad Atif<br>
<b>Sent:</b> 04 January 2012 02:40<br>
<b>To:</b> Karl Taylor<br>
<b>Cc:</b> Pascoe, Stephen (STFC,RAL,RALSP);
<a class="moz-txt-link-abbreviated" href="mailto:go-essp-tech@ucar.edu">go-essp-tech@ucar.edu</a>;
<a class="moz-txt-link-abbreviated" href="mailto:esg-gateway-dev@earthsystemgrid.org">esg-gateway-dev@earthsystemgrid.org</a><br>
<b>Subject:</b> Re: [esg-gateway-dev] [Go-essp-tech]
publishing error (invalid hour)<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for the tips; however I am now
facing the problem that I stated in the previous email.
<br>
I wanted to pin point the file which was causing the issue and
for that tried to publish the datasets one by one. Now I
cannot even delete the said data.
<br>
<span style="font-size: 10pt; font-family: "Courier
New";"><br>
<br>
<tt><b>[root@esgnode1 debug-historicalAntNoAA]# esgunpublish
--skip-thredds
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b></tt><br>
<tt>INFO 2012-01-04 13:39:49,576 Deleting
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</tt><br>
<tt>WARNING 2012-01-04 13:39:49,687 Deletion/retraction
failed for dataset
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1
with message: Java ServiceException: The persistent
identifier=cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1
does not correspond to a dataset at
sgf.gateway.service.security.impl.acegi.AcegiCatalogAccessDecisionVoter.vote(AcegiCatalogAccessDecisionVoter.java:74)</tt><br>
<tt>INFO 2012-01-04 13:39:49,706 Result:
UNSUCCESSFUL</tt><br>
<br>
<tt><b>[root@esgnode1 debug-historicalAntNoAA]# esgunpublish
--skip-gateway
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b></tt><br>
<tt>INFO 2012-01-04 13:40:35,331 Writing THREDDS ESG
master catalog
/data/esg-node/tds-content/thredds/esgcet/catalog.xml</tt><br>
<tt>INFO 2012-01-04 13:40:35,719 Reinitializing
THREDDS server</tt><br>
<tt>Traceback (most recent call last):</tt><br>
<tt> File "/usr/local/cdat/bin/esgunpublish", line 5, in
<module></tt><br>
<tt> pkg_resources.run_script('esgcet==2.8.4',
'esgunpublish')</tt><br>
<tt> File "build/bdist.linux-x86_64/egg/pkg_resources.py",
line 489, in run_script</tt><br>
<tt> File "build/bdist.linux-x86_64/egg/pkg_resources.py",
line 1207, in run_script</tt><br>
<tt> File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 221, in <module></tt><br>
<tt> main(sys.argv[1:])</tt><br>
<tt> File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 184, in main</tt><br>
<tt> result = deleteDatasetList(datasetNames, Session,
gatewayOp, thredds, las, deleteDset, deleteAll=deleteAll,
republish=republish)</tt><br>
<tt> File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line 272, in deleteDatasetList</tt><br>
<tt> result = reinitializeThredds()</tt><br>
<tt> File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 1041, in reinitializeThredds</tt><br>
<tt> raise ESGPublishError("Error reinitializing the
THREDDS Data Server: Fatal error: %s\n%s"%(errorMessage,
str(result)))</tt><br>
<tt>esgcet.exceptions.ESGPublishError: Error reinitializing
the THREDDS Data Server: Fatal error: **Fatal:
InvCatalogFactory.readXML failed</tt><br>
<tt>Catalog init catalog.xml</tt><br>
<tt>[2012-01-04T02:40:35GMT]</tt><br>
<br>
<tt><b>[root@esgnode1 debug-historicalAntNoAA]# esgunpublish
--database-delete
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b></tt><br>
<tt>INFO 2012-01-04 13:34:34,130 Deleting
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</tt><br>
<tt>WARNING 2012-01-04 13:34:34,257 Deletion/retraction
failed for dataset
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1
with message: Java ServiceException: The persistent
identifier=cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1
does not correspond to a dataset at
sgf.gateway.service.security.impl.acegi.AcegiCatalogAccessDecisionVoter.vote(AcegiCatalogAccessDecisionVoter.java:74)</tt><br>
<tt>INFO 2012-01-04 13:34:34,274 Result:
UNSUCCESSFUL</tt><br>
<tt>INFO 2012-01-04 13:34:34,286 Writing THREDDS ESG
master catalog
/data/esg-node/tds-content/thredds/esgcet/catalog.xml</tt><br>
<tt>INFO 2012-01-04 13:34:34,661 Reinitializing
THREDDS server</tt><br>
<tt>Traceback (most recent call last):</tt><br>
<tt> File "/usr/local/cdat/bin/esgunpublish", line 5, in
<module></tt><br>
<tt> pkg_resources.run_script('esgcet==2.8.4',
'esgunpublish')</tt><br>
<tt> File "build/bdist.linux-x86_64/egg/pkg_resources.py",
line 489, in run_script</tt><br>
<tt> File "build/bdist.linux-x86_64/egg/pkg_resources.py",
line 1207, in run_script</tt><br>
<tt> File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 221, in <module></tt><br>
<tt> main(sys.argv[1:])</tt><br>
<tt> File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 184, in main</tt><br>
<tt> result = deleteDatasetList(datasetNames, Session,
gatewayOp, thredds, las, deleteDset, deleteAll=deleteAll,
republish=republish)</tt><br>
<tt> File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line 272, in deleteDatasetList</tt><br>
<tt> result = reinitializeThredds()</tt><br>
<tt> File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 1041, in reinitializeThredds</tt><br>
<tt> raise ESGPublishError("Error reinitializing the
THREDDS Data Server: Fatal error: %s\n%s"%(errorMessage,
str(result)))</tt><br>
<tt>esgcet.exceptions.ESGPublishError: Error reinitializing
the THREDDS Data Server: Fatal error: **Fatal:
InvCatalogFactory.readXML failed</tt><br>
<tt>Catalog init catalog.xml</tt><br>
<tt>[2012-01-04T02:34:34GMT]</tt><br>
<tt>readCatalog(): full
path=/data/esg-node/tds-content/thredds/catalog.xml;
path=catalog.xml</tt><br>
<tt>readCatalog(): valid catalog -- ----Catalog Validation
version 1.0.01</tt></span><br>
<br>
<tt><b><span style="font-size: 10pt;">[root@esgnode1
debug-historicalAntNoAA]# esglist_datasets cmip5 | grep
CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</span></b></tt><span
style="font-size: 10pt; font-family: "Courier
New";"><br>
<tt>| 4422 |
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1
| cmip5 | CSIRO-Mk3-6-0 | historicalAntNoAA | r10i1p1 |
False | None | restricted | mon |
ocean | Omon | r10i1p1 | CSIRO-QCCCE | 2012-01-04
13:39:49 | DELETE_DATASET_FAILED |
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0 | 20120104 |
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1.v20120104
| None |</tt></span><br>
<br>
<br>
Thanks for your help in advance. <br>
<br>
Regards,<br>
<br>
On 04/01/12 04:41, Karl Taylor wrote: <o:p></o:p></p>
<p class="MsoNormal">Hi Muhammad,<br>
<br>
Better yet, execute "ncdump -c". This will return both the
header information and the coordinate values. It would be
good to see what the time coordinate values are in the file.<br>
<br>
thanks,<br>
Karl<br>
<br>
On 1/3/12 6:34 AM, <a moz-do-not-send="true"
href="mailto:stephen.pascoe@stfc.ac.uk">stephen.pascoe@stfc.ac.uk</a>
wrote:
<o:p></o:p></p>
<pre>Hi Muhammad,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Can you send a dump of the NetCDF metadata for this file. The command is "ncdump -h". Whether a time value is valid depends on the time:units attribute and sometimes other attributes.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers,<o:p></o:p></pre>
<pre>Stephen.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>---<o:p></o:p></pre>
<pre>Stephen Pascoe +44 (0)1235 445980<o:p></o:p></pre>
<pre>Centre of Environmental Data Archival<o:p></o:p></pre>
<pre>STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: <a moz-do-not-send="true" href="mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org">esg-gateway-dev-bounces@mailman.earthsystemgrid.org</a> [<a moz-do-not-send="true" href="mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org">mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org</a>] On Behalf Of Muhammad Atif<o:p></o:p></pre>
<pre>Sent: 03 January 2012 04:37<o:p></o:p></pre>
<pre>To: <a moz-do-not-send="true" href="mailto:go-essp-tech@ucar.edu">go-essp-tech@ucar.edu</a>; <a moz-do-not-send="true" href="mailto:esg-gateway-dev@earthsystemgrid.org">esg-gateway-dev@earthsystemgrid.org</a><o:p></o:p></pre>
<pre>Subject: [esg-gateway-dev] publishing error (invalid hour)<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Dear All,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>In an unrelated problem from the previous email, we are facing another <o:p></o:p></pre>
<pre>error that gives "CDMS error: Error on time conversion: invalid hour = <o:p></o:p></pre>
<pre>28864363504146.773438"<o:p></o:p></pre>
<pre>Please let me know what to do with it. The modelers suggest that they <o:p></o:p></pre>
<pre>were not able to find any funny stuff.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>INFO 2011-12-28 12:24:32,436 Writing THREDDS catalog <o:p></o:p></pre>
<pre>/data/esg-node/tds-content/thredds/esgcet/9/cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1.v20111228.xml<o:p></o:p></pre>
<pre>CDMS error: Error on time conversion: invalid hour = 28864363504146.773438<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Traceback (most recent call last):<o:p></o:p></pre>
<pre> File "/usr/local/cdat/bin/esgpublish", line 5, in <module><o:p></o:p></pre>
<pre> pkg_resources.run_script('esgcet==2.8.4', 'esgpublish')<o:p></o:p></pre>
<pre> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in <o:p></o:p></pre>
<pre>run_script<o:p></o:p></pre>
<pre> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207, in <o:p></o:p></pre>
<pre>run_script<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgpublish", <o:p></o:p></pre>
<pre>line 434, in <module><o:p></o:p></pre>
<pre> main(sys.argv[1:])<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgpublish", <o:p></o:p></pre>
<pre>line 420, in main<o:p></o:p></pre>
<pre> result = publishDatasetList(datasetNames, Session, publish=publish, <o:p></o:p></pre>
<pre>thredds=thredds, las=las, parentId=parent, service=service, <o:p></o:p></pre>
<pre>perVariable=perVariable)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/publish.py", <o:p></o:p></pre>
<pre>line 244, in publishDatasetList<o:p></o:p></pre>
<pre> generateThredds(datasetName, Session, threddsOutput, handler, <o:p></o:p></pre>
<pre>service=service, perVariable=perVariable, versionNumber=versionno)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py", <o:p></o:p></pre>
<pre>line 726, in generateThredds<o:p></o:p></pre>
<pre> _generateThreddsV2(datasetName, outputFile, handler, session, dset, <o:p></o:p></pre>
<pre>context, project, model, experiment, config, section, genRoot=genRoot, <o:p></o:p></pre>
<pre>service=service, perVariable=perVariable, versionNumber=versionNumber)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py", <o:p></o:p></pre>
<pre>line 950, in _generateThreddsV2<o:p></o:p></pre>
<pre> _genPerVariableDatasetsV2(datasetElem, dset, datasetName, <o:p></o:p></pre>
<pre>resolution, filesRootLoc, filesRootPath, datasetRootDict, <o:p></o:p></pre>
<pre>excludeVariables, offline, serviceName, serviceDict, aggServiceName, <o:p></o:p></pre>
<pre>handler, project, model, experiment, lasConfigure, lasTimeDelta, <o:p></o:p></pre>
<pre>versionNumber, variables, variableElemDict, lasServiceSpecs, <o:p></o:p></pre>
<pre>lasServiceHash, gridftpMap=gridftpMapDatasetRoots)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py", <o:p></o:p></pre>
<pre>line 563, in _genPerVariableDatasetsV2<o:p></o:p></pre>
<pre> timeFirst = mdhandler.genTime(variable.aggdim_first, <o:p></o:p></pre>
<pre>dataset.aggdim_units, dataset.calendar)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/config/cf_handler.py", <o:p></o:p></pre>
<pre>line 179, in genTime<o:p></o:p></pre>
<pre> c = t.tocomp(_tagToCalendar[calendarTag])<o:p></o:p></pre>
<pre>Cdtime error: Invalid component time<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Regards,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Muhammad Atif<o:p></o:p></pre>
<pre>ANU Supercomputer Facility NCI National Facility<o:p></o:p></pre>
<pre>Leonard Huxley, Mills Road Room 318, Bldg # 56<o:p></o:p></pre>
<pre>Australian National University Ph: +61 2 6125 5031<o:p></o:p></pre>
<pre>Canberra, ACT 0200, Australia M: 0430 393863<o:p></o:p></pre>
<pre>CRICOS Provider #00120C <a moz-do-not-send="true" href="http://anusf.anu.edu.au">http://anusf.anu.edu.au</a><o:p></o:p></pre>
</div>
<br>
<p>-- <br>
Scanned by iCritical.
</p>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Muhammad Atif
ANU Supercomputer Facility NCI National Facility
Leonard Huxley, Mills Road Room 318, Bldg # 56
Australian National University Ph: +61 2 6125 5031
Canberra, ACT 0200, Australia M: 0430 393863
CRICOS Provider #00120C <a class="moz-txt-link-freetext" href="http://anusf.anu.edu.au">http://anusf.anu.edu.au</a></pre>
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