[Go-essp-tech] [esg-gateway-dev] publishing error (invalid hour)
Muhammad Atif
muhammad.atif at anu.edu.au
Tue Jan 3 19:40:03 MST 2012
Thanks for the tips; however I am now facing the problem that I stated
in the previous email.
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.
*[root at esgnode1 debug-historicalAntNoAA]# esgunpublish --skip-thredds
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1*
INFO 2012-01-04 13:39:49,576 Deleting
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1
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)
INFO 2012-01-04 13:39:49,706 Result: UNSUCCESSFUL
*[root at esgnode1 debug-historicalAntNoAA]# esgunpublish --skip-gateway
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1*
INFO 2012-01-04 13:40:35,331 Writing THREDDS ESG master catalog
/data/esg-node/tds-content/thredds/esgcet/catalog.xml
INFO 2012-01-04 13:40:35,719 Reinitializing THREDDS server
Traceback (most recent call last):
File "/usr/local/cdat/bin/esgunpublish", line 5, in <module>
pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')
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/esgunpublish",
line 221, 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/esgunpublish",
line 184, in main
result = deleteDatasetList(datasetNames, Session, gatewayOp,
thredds, las, deleteDset, deleteAll=deleteAll, republish=republish)
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line 272, in deleteDatasetList
result = reinitializeThredds()
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 1041, in reinitializeThredds
raise ESGPublishError("Error reinitializing the THREDDS Data
Server: Fatal error: %s\n%s"%(errorMessage, str(result)))
esgcet.exceptions.ESGPublishError: Error reinitializing the THREDDS Data
Server: Fatal error: **Fatal: InvCatalogFactory.readXML failed
Catalog init catalog.xml
[2012-01-04T02:40:35GMT]
*[root at esgnode1 debug-historicalAntNoAA]# esgunpublish --database-delete
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1*
INFO 2012-01-04 13:34:34,130 Deleting
cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1
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)
INFO 2012-01-04 13:34:34,274 Result: UNSUCCESSFUL
INFO 2012-01-04 13:34:34,286 Writing THREDDS ESG master catalog
/data/esg-node/tds-content/thredds/esgcet/catalog.xml
INFO 2012-01-04 13:34:34,661 Reinitializing THREDDS server
Traceback (most recent call last):
File "/usr/local/cdat/bin/esgunpublish", line 5, in <module>
pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')
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/esgunpublish",
line 221, 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/esgunpublish",
line 184, in main
result = deleteDatasetList(datasetNames, Session, gatewayOp,
thredds, las, deleteDset, deleteAll=deleteAll, republish=republish)
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line 272, in deleteDatasetList
result = reinitializeThredds()
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 1041, in reinitializeThredds
raise ESGPublishError("Error reinitializing the THREDDS Data
Server: Fatal error: %s\n%s"%(errorMessage, str(result)))
esgcet.exceptions.ESGPublishError: Error reinitializing the THREDDS Data
Server: Fatal error: **Fatal: InvCatalogFactory.readXML failed
Catalog init catalog.xml
[2012-01-04T02:34:34GMT]
readCatalog(): full path=/data/esg-node/tds-content/thredds/catalog.xml;
path=catalog.xml
readCatalog(): valid catalog -- ----Catalog Validation version 1.0.01
*[root at esgnode1 debug-historicalAntNoAA]# esglist_datasets cmip5 | grep
CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1*
| 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 |
Thanks for your help in advance.
Regards,
On 04/01/12 04:41, Karl Taylor wrote:
> Hi Muhammad,
>
> 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.
>
> thanks,
> Karl
>
> On 1/3/12 6:34 AM, stephen.pascoe at stfc.ac.uk wrote:
>> 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:esg-gateway-dev-bounces at mailman.earthsystemgrid.org [mailto:esg-gateway-dev-bounces at mailman.earthsystemgrid.org] On Behalf Of Muhammad Atif
>> Sent: 03 January 2012 04:37
>> To:go-essp-tech at ucar.edu;esg-gateway-dev at earthsystemgrid.org
>> 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,
>>
--
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 http://anusf.anu.edu.au
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