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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>
<tt><br>
<br>
<b>[root@esgnode1 debug-historicalAntNoAA]# esgunpublish
--skip-thredds
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b><br>
INFO 2012-01-04 13:39:49,576 Deleting
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1<br>
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)<br>
INFO 2012-01-04 13:39:49,706 Result: UNSUCCESSFUL<br>
<br>
<b>[root@esgnode1 debug-historicalAntNoAA]# esgunpublish
--skip-gateway
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b><br>
INFO 2012-01-04 13:40:35,331 Writing THREDDS ESG master
catalog /data/esg-node/tds-content/thredds/esgcet/catalog.xml<br>
INFO 2012-01-04 13:40:35,719 Reinitializing THREDDS server<br>
Traceback (most recent call last):<br>
File "/usr/local/cdat/bin/esgunpublish", line 5, in
<module><br>
pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')<br>
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489,
in run_script<br>
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207,
in run_script<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 221, in <module><br>
main(sys.argv[1:])<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 184, in main<br>
result = deleteDatasetList(datasetNames, Session, gatewayOp,
thredds, las, deleteDset, deleteAll=deleteAll,
republish=republish)<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line 272, in deleteDatasetList<br>
result = reinitializeThredds()<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 1041, in reinitializeThredds<br>
raise ESGPublishError("Error reinitializing the THREDDS Data
Server: Fatal error: %s\n%s"%(errorMessage, str(result)))<br>
esgcet.exceptions.ESGPublishError: Error reinitializing the
THREDDS Data Server: Fatal error: **Fatal:
InvCatalogFactory.readXML failed<br>
Catalog init catalog.xml<br>
[2012-01-04T02:40:35GMT]<br>
<br>
<b>[root@esgnode1 debug-historicalAntNoAA]# esgunpublish
--database-delete
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b><br>
INFO 2012-01-04 13:34:34,130 Deleting
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1<br>
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)<br>
INFO 2012-01-04 13:34:34,274 Result: UNSUCCESSFUL<br>
INFO 2012-01-04 13:34:34,286 Writing THREDDS ESG master
catalog /data/esg-node/tds-content/thredds/esgcet/catalog.xml<br>
INFO 2012-01-04 13:34:34,661 Reinitializing THREDDS server<br>
Traceback (most recent call last):<br>
File "/usr/local/cdat/bin/esgunpublish", line 5, in
<module><br>
pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')<br>
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489,
in run_script<br>
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207,
in run_script<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 221, in <module><br>
main(sys.argv[1:])<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 184, in main<br>
result = deleteDatasetList(datasetNames, Session, gatewayOp,
thredds, las, deleteDset, deleteAll=deleteAll,
republish=republish)<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line 272, in deleteDatasetList<br>
result = reinitializeThredds()<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 1041, in reinitializeThredds<br>
raise ESGPublishError("Error reinitializing the THREDDS Data
Server: Fatal error: %s\n%s"%(errorMessage, str(result)))<br>
esgcet.exceptions.ESGPublishError: Error reinitializing the
THREDDS Data Server: Fatal error: **Fatal:
InvCatalogFactory.readXML failed<br>
Catalog init catalog.xml<br>
[2012-01-04T02:34:34GMT]<br>
readCatalog(): full
path=/data/esg-node/tds-content/thredds/catalog.xml;
path=catalog.xml<br>
readCatalog(): valid catalog -- ----Catalog Validation version
1.0.01</tt><br>
<br>
<tt><b>[root@esgnode1 debug-historicalAntNoAA]# esglist_datasets
cmip5 | grep
CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b><br>
| 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><br>
<br>
<br>
Thanks for your help in advance. <br>
<br>
Regards,<br>
<br>
On 04/01/12 04:41, Karl Taylor wrote:
<blockquote cite="mid:4F033DC0.4010901@llnl.gov" type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<font face="Times New Roman">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>
</font><br>
On 1/3/12 6:34 AM, <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:stephen.pascoe@stfc.ac.uk">stephen.pascoe@stfc.ac.uk</a>
wrote:
<blockquote
cite="mid:4C353E6E4A08AE4792B350DAA392B5211C95F5D3@EXCHMBX01.fed.cclrc.ac.uk"
type="cite">
<pre wrap="">Hi Muhammad,
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.
Cheers,
Stephen.
---
Stephen Pascoe +44 (0)1235 445980
Centre of Environmental Data Archival
STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK
-----Original Message-----
From: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org">esg-gateway-dev-bounces@mailman.earthsystemgrid.org</a> [<a moz-do-not-send="true" class="moz-txt-link-freetext" href="mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org">mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org</a>] On Behalf Of Muhammad Atif
Sent: 03 January 2012 04:37
To: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:go-essp-tech@ucar.edu">go-essp-tech@ucar.edu</a>; <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:esg-gateway-dev@earthsystemgrid.org">esg-gateway-dev@earthsystemgrid.org</a>
Subject: [esg-gateway-dev] publishing error (invalid hour)
Dear All,
In an unrelated problem from the previous email, we are facing another
error that gives "CDMS error: Error on time conversion: invalid hour =
28864363504146.773438"
Please let me know what to do with it. The modelers suggest that they
were not able to find any funny stuff.
INFO 2011-12-28 12:24:32,436 Writing THREDDS catalog
/data/esg-node/tds-content/thredds/esgcet/9/cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1.v20111228.xml
CDMS error: Error on time conversion: invalid hour = 28864363504146.773438
Traceback (most recent call last):
File "/usr/local/cdat/bin/esgpublish", line 5, in <module>
pkg_resources.run_script('esgcet==2.8.4', 'esgpublish')
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in
run_script
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207, in
run_script
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgpublish",
line 434, in <module>
main(sys.argv[1:])
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgpublish",
line 420, in main
result = publishDatasetList(datasetNames, Session, publish=publish,
thredds=thredds, las=las, parentId=parent, service=service,
perVariable=perVariable)
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/publish.py",
line 244, in publishDatasetList
generateThredds(datasetName, Session, threddsOutput, handler,
service=service, perVariable=perVariable, versionNumber=versionno)
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 726, in generateThredds
_generateThreddsV2(datasetName, outputFile, handler, session, dset,
context, project, model, experiment, config, section, genRoot=genRoot,
service=service, perVariable=perVariable, versionNumber=versionNumber)
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 950, in _generateThreddsV2
_genPerVariableDatasetsV2(datasetElem, dset, datasetName,
resolution, filesRootLoc, filesRootPath, datasetRootDict,
excludeVariables, offline, serviceName, serviceDict, aggServiceName,
handler, project, model, experiment, lasConfigure, lasTimeDelta,
versionNumber, variables, variableElemDict, lasServiceSpecs,
lasServiceHash, gridftpMap=gridftpMapDatasetRoots)
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 563, in _genPerVariableDatasetsV2
timeFirst = mdhandler.genTime(variable.aggdim_first,
dataset.aggdim_units, dataset.calendar)
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/config/cf_handler.py",
line 179, in genTime
c = t.tocomp(_tagToCalendar[calendarTag])
Cdtime error: Invalid component time
Regards,
</pre>
</blockquote>
</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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