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Writing H5 files

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Writing H5 files

Postby icaoberg » Tue Oct 26, 2010 8:29 pm

I am using the demo (first.py). When I run

Code: Select all
import omero
import omero_Tables_ice
import omero_SharedResources_ice

c = omero.client()
s = c.createSession()
r = s.sharedResources()
m = r.repositories()
i = m.descriptions[0].id.val
t = r.newTable(1, "/example.h5")
l = omero.grid.LongColumn('name','desc',None)
t.initialize([l])
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/afs/cs.cmu.edu/user/bhcho/<ipython console> in <module>()

AttributeError: 'NoneType' object has no attribute 'initialize'


is the first attribute from newTable an identifier?
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Location: Pittsburgh, PA

Re: Writing H5 files

Postby icaoberg » Tue Oct 26, 2010 8:59 pm

i think the problem is that no repository has been created. how can i do that at this point?

according to the diagnostics
Code: Select all
Server:     Repository-1                   error: node `repo' couldn't be reached: the node is not active
Server:     Tables-0                       inactive (disabled)
icaoberg
 
Posts: 145
Joined: Fri Sep 17, 2010 9:05 pm
Location: Pittsburgh, PA

Re: Writing H5 files

Postby jmoore » Wed Oct 27, 2010 6:59 am

The first argument at the moment is unimportant, as only one repository is used -- the default one. (Later server versions will allow creating OMERO.tables on any of the OMERO.fs mounts).

The most likely cause of this is that OMERO.tables start up has failed because of some missing library. Could you paste or attach the contents of var/log/Tables-0.log?

Thanks,
~Josh.
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Re: Writing H5 files

Postby icaoberg » Wed Oct 27, 2010 7:22 pm

josh i agree, but remember you tested it yourself when you where and you were able to create a table.

Code: Select all
2010-09-27 14:39:28,634 INFO  [                            omero.remote] (Dummy-6   )  Meth: TablesI.getTable
2010-09-27 14:39:28,635 INFO  [                    omero.tables.TablesI] (Dummy-6   ) getTable: 4461
2010-09-27 14:39:28,638 INFO  [                 omero.tables.HdfStorage] (Dummy-6   ) Size: 1 - Attaching Table-9682C295-2624-4CA0-8180-49EBED481E6F to /usr1/OMERO/Files/Dir-004/4461
2010-09-27 14:39:28,639 INFO  [                            omero.remote] (Dummy-6   )  Rslt: 9682C295-2624-4CA0-8180-49EBED481E6F -t @ Tables-0.TablesAdapter
2010-09-27 14:39:28,669 INFO  [                            omero.remote] (Dummy-5   )  Meth: TableI.getOriginalFile
2010-09-27 14:39:28,670 INFO  [                     omero.tables.TableI] (Dummy-5   ) Table-9682C295-2624-4CA0-8180-49EBED481E6F.getOriginalFile() => id=4461
2010-09-27 14:39:28,670 INFO  [                            omero.remote] (Dummy-5   )  Rslt: object #0 (::omero::model::OriginalFile)
{
    _id = object #1 (::omero::RLong)
    {
        _val = 4461
    }
    _det
2010-09-27 14:39:28,676 INFO  [                            omero.remote] (Dummy-7   )  Meth: TableI.getNumberOfRows
2010-09-27 14:39:28,676 INFO  [                     omero.tables.TableI] (Dummy-7   ) Table-9682C295-2624-4CA0-8180-49EBED481E6F.getNumberOfRows() => 300
2010-09-27 14:39:28,676 INFO  [                            omero.remote] (Dummy-7   )  Rslt: 300
2010-09-27 14:39:28,769 INFO  [                            omero.remote] (Dummy-12  )  Meth: TableI.close
2010-09-27 14:39:28,769 INFO  [                 omero.tables.HdfStorage] (Dummy-12  ) Size: 2 - Detaching Table-9682C295-2624-4CA0-8180-49EBED481E6F from /usr1/OMERO/Files/Dir-004/4461
2010-09-27 14:39:28,770 INFO  [                     omero.tables.TableI] (Dummy-12  ) Closed Table-9682C295-2624-4CA0-8180-49EBED481E6F
2010-09-27 14:39:28,770 INFO  [                            omero.remote] (Dummy-12  )  Rslt: None
2010-10-19 02:38:50,152 INFO  [                       omero.util.Server] (MainThread) Cleanup
2010-10-19 02:38:50,153 INFO  [                    omero.tables.TablesI] (MainThread) Cleaning up
2010-10-19 02:38:50,153 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-CC330B85-CDA2-457F-80A2-A69D92B19E6F from /usr1/OMERO/Files/Dir-003/3856
2010-10-19 02:38:50,153 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3856
2010-10-19 02:38:50,155 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-8727162D-C947-4B75-AFA2-55BACA299E6F from /usr1/OMERO/Files/Dir-003/3860
2010-10-19 02:38:50,155 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3860
2010-10-19 02:38:50,157 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-D50A00AE-B3D0-4C22-BB54-FC5521951E6F from /usr1/OMERO/Files/Dir-003/3864
2010-10-19 02:38:50,157 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3864
2010-10-19 02:38:50,159 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-0C523CDD-38C7-4E31-8141-7C1045DC1E6F from /usr1/OMERO/Files/Dir-003/3866
2010-10-19 02:38:50,159 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3866
2010-10-19 02:38:50,161 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-89FC7E11-2820-4AA4-B0FB-F3DB0A589E6F from /usr1/OMERO/Files/Dir-003/3868
2010-10-19 02:38:50,162 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3868
2010-10-19 02:38:50,164 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-D1621D88-9E8D-467A-AC44-FF21BD019E6F from /usr1/OMERO/Files/Dir-003/3870
2010-10-19 02:38:50,164 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3870
2010-10-19 02:38:50,166 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-E1AC196A-652B-492E-AD06-85CDAE231E6F from /usr1/OMERO/Files/Dir-003/3873
2010-10-19 02:38:50,167 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3873
2010-10-19 02:38:50,168 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-0C7178C4-8138-4A19-BB02-29C532C71E6F from /usr1/OMERO/Files/Dir-003/3878
2010-10-19 02:38:50,169 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3878
2010-10-19 02:38:50,171 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-A3A5F025-5AD6-4B91-8190-3AEC41BF9E6F from /usr1/OMERO/Files/Dir-003/3884
2010-10-19 02:38:50,171 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3884
2010-10-19 02:38:50,173 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-8245985D-5CE9-468F-A408-DA9D486E1E6F from /usr1/OMERO/Files/Dir-003/3885
2010-10-19 02:38:50,173 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3885
2010-10-19 02:38:50,175 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-B6FEB08A-4E3A-4171-9356-177CB71B9E6F from /usr1/OMERO/Files/Dir-003/3886
2010-10-19 02:38:50,176 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3886
2010-10-19 02:38:50,178 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-1A5A5342-4DCC-49EE-B9CC-EDD744271E6F from /usr1/OMERO/Files/Dir-003/3887
2010-10-19 02:38:50,178 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3887
2010-10-19 02:38:50,179 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-877ACCF8-D3C0-4BB3-B43C-357EA90A9E6F from /usr1/OMERO/Files/Dir-003/3888
2010-10-19 02:38:50,180 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3888
2010-10-19 02:38:50,181 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-AFBB69F6-556D-4CD2-8B88-A85640FE9E6F from /usr1/OMERO/Files/Dir-003/3889
2010-10-19 02:38:50,181 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3889
2010-10-19 02:38:50,183 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-4C7119D0-3C11-4B57-8B5D-58F4AD499E6F from /usr1/OMERO/Files/Dir-003/3890
2010-10-19 02:38:50,184 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3890
2010-10-19 02:38:50,185 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-B820F16D-84B4-4FE1-BBF4-4E80CE5A1E6F from /usr1/OMERO/Files/Dir-003/3891
2010-10-19 02:38:50,185 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3891
2010-10-19 02:38:50,187 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-148AD57B-CAB6-44CA-869D-D570653B9E6F from /usr1/OMERO/Files/Dir-003/3893
2010-10-19 02:38:50,187 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3893
2010-10-19 02:38:50,189 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-2D72B2AC-0681-4263-9119-876DD8299E6F from /usr1/OMERO/Files/Dir-003/3894
2010-10-19 02:38:50,189 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3894
2010-10-19 02:38:50,191 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-5DCABAFF-8640-4C0F-ADC6-B11A4BEE9E6F from /usr1/OMERO/Files/Dir-003/3895
2010-10-19 02:38:50,191 INFO  [                    omero.util.Resources] (Thread-2  ) Halted
2010-10-19 02:38:50,191 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3895
2010-10-19 02:38:50,193 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-0A7A93DE-D757-4DA3-985F-34403F479E6F from /usr1/OMERO/Files/Dir-003/3896
2010-10-19 02:38:50,193 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3896
2010-10-19 02:38:50,195 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-7B32DEA3-3BD6-4117-BC69-9708BD4D1E6F from /usr1/OMERO/Files/Dir-003/3897
2010-10-19 02:38:50,195 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3897
2010-10-19 02:38:50,196 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-0C1CD964-BA1B-4D60-84EE-7E8102451E6F from /usr1/OMERO/Files/Dir-003/3898
2010-10-19 02:38:50,197 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3898
2010-10-19 02:38:50,198 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-CD0AB790-3FBA-4703-9F6D-93D51F3D9E6F from /usr1/OMERO/Files/Dir-003/3899
2010-10-19 02:38:50,198 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3899
2010-10-19 02:38:50,200 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-6A8E3CA0-92CC-4319-8FA4-E76A75119E6F from /usr1/OMERO/Files/Dir-003/3900
2010-10-19 02:38:50,200 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3900
2010-10-19 02:38:50,202 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-669DCADC-F4B6-4DD2-860F-A3BBAB479E6F from /usr1/OMERO/Files/Dir-003/3901
2010-10-19 02:38:50,202 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3901
2010-10-19 02:38:50,204 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-D9ABDD65-9B52-4D25-8145-7FB704061E6F from /usr1/OMERO/Files/Dir-003/3902
2010-10-19 02:38:50,204 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3902
2010-10-19 02:38:50,205 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-ECEAF00B-3323-4C86-A34A-A87D2BAF9E6F from /usr1/OMERO/Files/Dir-003/3903
2010-10-19 02:38:50,206 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3903
2010-10-19 02:38:50,207 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-0E91BACB-EE2B-4DBD-89F2-45213D4D9E6F from /usr1/OMERO/Files/Dir-003/3904
2010-10-19 02:38:50,207 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-003/3904
2010-10-19 02:38:50,208 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-3390B640-4491-495E-A851-AA879FBE1E6F from /usr1/OMERO/Files/Dir-004/4080
2010-10-19 02:38:50,209 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4080
2010-10-19 02:38:50,210 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-564A497C-EC87-4CD9-B45F-9E8607839E6F from /usr1/OMERO/Files/Dir-004/4082
2010-10-19 02:38:50,211 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4082
2010-10-19 02:38:50,212 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-F1CF652D-F214-407A-AF4C-C44EC0731E6F from /usr1/OMERO/Files/Dir-004/4083
2010-10-19 02:38:50,212 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4083
2010-10-19 02:38:50,214 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-FBC66A79-8A2C-40D5-8C96-2FE4E2901E6F from /usr1/OMERO/Files/Dir-004/4393
2010-10-19 02:38:50,214 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4393
2010-10-19 02:38:50,215 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-0B6BD52A-8A3C-4939-AECC-8F53480A9E6F from /usr1/OMERO/Files/Dir-004/4394
2010-10-19 02:38:50,216 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4394
2010-10-19 02:38:50,218 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-9CF91B01-162F-4316-8641-6993C2641E6F from /usr1/OMERO/Files/Dir-004/4395
2010-10-19 02:38:50,218 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4395
2010-10-19 02:38:50,226 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-93198F04-55F7-40CF-AC72-254DF77C1E6F from /usr1/OMERO/Files/Dir-004/4396
2010-10-19 02:38:50,226 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4396
2010-10-19 02:38:50,228 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-C940F000-DCCC-4DDF-A177-64E5720F9E6F from /usr1/OMERO/Files/Dir-004/4447
2010-10-19 02:38:50,228 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4447
2010-10-19 02:38:50,230 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-02D94828-BF95-42C8-AD4A-C089A7AC1E6F from /usr1/OMERO/Files/Dir-004/4448
2010-10-19 02:38:50,230 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4448
2010-10-19 02:38:50,232 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-A828AE52-BBAC-4D3F-8D43-1F1D02EA1E6F from /usr1/OMERO/Files/Dir-004/4450
2010-10-19 02:38:50,232 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4450
2010-10-19 02:38:50,234 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-2B38B241-8F3E-4DE4-A064-6E60BE7E9E6F from /usr1/OMERO/Files/Dir-004/4451
2010-10-19 02:38:50,234 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4451
2010-10-19 02:38:50,236 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-7C07FCC1-EC05-4A8E-A0F1-3AC3C37E9E6F from /usr1/OMERO/Files/Dir-004/4452
2010-10-19 02:38:50,236 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4452
2010-10-19 02:38:50,238 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-0FF38941-C6E7-4718-92A8-624002159E6F from /usr1/OMERO/Files/Dir-004/4453
2010-10-19 02:38:50,238 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4453
2010-10-19 02:38:50,240 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-F620C4FB-F6E1-469D-8C73-22117BAF1E6F from /usr1/OMERO/Files/Dir-004/4454
2010-10-19 02:38:50,240 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4454
2010-10-19 02:38:50,242 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-75DCE64C-2595-4E95-8050-5438FEF39E6F from /usr1/OMERO/Files/Dir-004/4455
2010-10-19 02:38:50,243 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4455
2010-10-19 02:38:50,244 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-759B1413-25C1-4259-B569-FADFBF819E6F from /usr1/OMERO/Files/Dir-004/4458
2010-10-19 02:38:50,245 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4458
2010-10-19 02:38:50,247 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-8A4769A3-8CA5-46CB-8FCE-57A419769E6F from /usr1/OMERO/Files/Dir-004/4459
2010-10-19 02:38:50,247 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4459
2010-10-19 02:38:50,249 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-4DFB274F-8969-428E-88AD-4E4EDC381E6F from /usr1/OMERO/Files/Dir-004/4460
2010-10-19 02:38:50,249 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4460
2010-10-19 02:38:50,251 INFO  [                 omero.tables.HdfStorage] (MainThread) Size: 1 - Detaching Table-6C7D1838-69D0-4848-932C-AF60F5CA9E6F from /usr1/OMERO/Files/Dir-004/4461
2010-10-19 02:38:50,251 INFO  [                 omero.tables.HdfStorage] (MainThread) Cleaning storage: /usr1/OMERO/Files/Dir-004/4461
2010-10-19 02:38:50,253 INFO  [                    omero.tables.TablesI] (MainThread) Done
2010-10-19 02:38:50,254 WARNI [                omero.util.ServerContext] (MainThread) Connection failure: Ice.ConnectionRefusedException:
Connection refused
2010-10-19 02:38:50,257 INFO  [                       omero.util.Server] (MainThread) Stopped
2010-10-19 02:38:50,257 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2010-10-19 02:39:56,117 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2010-10-19 02:39:56,118 INFO  [                       omero.util.Server] (MainThread) Starting
2010-10-19 02:39:56,119 INFO  [                    omero.util.Resources] (Thread-2  ) Starting
2010-10-19 02:40:11,980 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 1
2010-10-19 02:40:22,182 INFO  [                       omero.util.Server] (MainThread) Entering main loop
2010-10-25 05:24:48,140 INFO  [                       omero.util.Server] (MainThread) Cleanup
2010-10-25 05:24:48,141 INFO  [                    omero.tables.TablesI] (MainThread) Cleaning up
2010-10-25 05:24:48,141 INFO  [                    omero.tables.TablesI] (MainThread) Done
2010-10-25 05:24:48,183 INFO  [                    omero.util.Resources] (Thread-2  ) Halted
2010-10-25 05:24:48,214 INFO  [                       omero.util.Server] (MainThread) Stopped
2010-10-25 05:24:48,215 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
icaoberg
 
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Location: Pittsburgh, PA

Re: Writing H5 files

Postby jmoore » Thu Oct 28, 2010 5:53 am

It doesn't look like OMERO.tables is running, and that it was shutdown around 5:24 AM on the 25th. Can you run bin/omero admin diagnostics and paste the output?

If the rest of OMERO is running, you can trying "enabling" OMERO.tables via
Code: Select all
bin/omero admin ice server enable Tables-0


Thanks,
~Josh
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Re: Writing H5 files

Postby icaoberg » Thu Oct 28, 2010 3:11 pm

================================================================================
OMERO Diagnostics Beta-4.2.0-r7571-b29
================================================================================

Commands: java -version 1.6.0 (/usr/local/bin/java -- 2 others)
Commands: python -V 2.5.2 (/usr/bin/python)
Commands: icegridnode --version 3.3.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.3.1 (/usr/bin/icegridadmin)
Commands: psql --version 8.3.4 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 6842, enabled)
Server: DropBox active (pid = 6860, enabled)
Server: FileServer active (pid = 6863, enabled)
Server: Indexer-0 active (pid = 6864, enabled)
Server: MonitorServer active (pid = 6866, enabled)
Server: OMERO.Glacier2 active (pid = 6879, enabled)
Server: OMERO.IceStorm active (pid = 6880, enabled)
Server: Processor-0 active (pid = 6889, enabled)
Server: Repository-1 Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)

Log dir: /usr0/local/omero.server/OMERO.server-Beta-4.2.0/var/log exists

Log files: Blitz-0.log 403.0 MB errors=1725 warnings=520
Log files: DropBox.log 13.0 KB errors=8 warnings=4
Log files: FileServer.log 1.0 KB
Log files: Indexer-0.log 471.0 MB errors=204643 warnings=215
Log files: MonitorServer.log 6.0 KB errors=0 warnings=1
Log files: OMEROweb.log 11.0 KB errors=21 warnings=0
Log files: Processor-0.log 2.0 MB errors=6 warnings=5
Log files: Processor-0.log.1 4.0 MB
Log files: Processor-0.log.2 4.0 MB
Log files: Processor-0.log.3 4.0 MB
Log files: Processor-0.log.4 4.0 MB
Log files: Processor-0.log.5 4.0 MB
Log files: Processor-0.log.6 4.0 MB
Log files: Processor-0.log.7 4.0 MB
Log files: Processor-0.log.8 4.0 MB
Log files: Processor-0.log.9 4.0 MB
Log files: Tables-0.log 110.0 KB errors=0 warnings=2
Log files: TestDropBox.log n/a
Log files: master.err 9.0 KB
Log files: master.out 0.0 KB
Log files: Total size 922.80 MB

Parsing Blitz-0.log:[line:17] => Server restarted <=
Parsing Blitz-0.log:[line:731103] => Server restarted <=
Parsing Blitz-0.log:[line:2907936] => Server restarted <=
Parsing Blitz-0.log:[line:2953559] => Server restarted <=
Parsing Blitz-0.log:[line:2995013] => Server restarted <=

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/usr/lib64/qt-3.3/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/local/sbin:/usr/sbin:/sbin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
icaoberg
 
Posts: 145
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Location: Pittsburgh, PA

Re: Writing H5 files

Postby jmoore » Thu Oct 28, 2010 3:44 pm

Code: Select all
Tables-0 inactive (disabled)


Can you try the "enable" command and see what change there is in the log? (You may want to delete it first)

~Josh.
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