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Bug #3536

data bank can't be read in

Added by Brian Nord over 6 years ago. Updated over 6 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
data format
Target version:
Start date:
02/26/2013
Due date:
% Done:

0%

Estimated time:
Duration:

Description

After ctrl-c during the start of a pipeline run, and trying to run again, obtained this error:

┌(bnord@cerebro1)─(✓)─(12:02 PM Tue Feb 26)
└─(~/Cosmo/Projects/spokes/despec/Wrapper)─(8 files, 72b)─> python run_pipeline.py
=======================***
Running pipeline *** =======================***

Traceback (most recent call last):
File "run_pipeline.py", line 128, in <module>
readDatafiles(config)
File "run_pipeline.py", line 37, in readDatafiles
with archive.archive(config.get("options", "data_dir") + config.get("options", "data_bank"), 'a') as dest:
File "/Users/bnord/Cosmo/Projects/spokes/despec/Wrapper/archive.py", line 26, in init
self.file = tbl.openFile(filename, mode)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tables/file.py", line 230, in openFile
return File(filename, mode, title, rootUEP, filters, **kwargs)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tables/file.py", line 495, in init
self._g_new(filename, mode, **params)
File "hdf5Extension.pyx", line 317, in tables.hdf5Extension.File._g_new (tables/hdf5Extension.c:3039)
tables.exceptions.HDF5ExtError: HDF5 error back trace

File "H5F.c", line 1582, in H5Fopen
unable to open file
File "H5F.c", line 1373, in H5F_open
unable to read superblock
File "H5Fsuper.c", line 351, in H5F_super_read
unable to load superblock
File "H5AC.c", line 1322, in H5AC_protect
H5C_protect() failed.
File "H5C.c", line 3567, in H5C_protect
can't load entry
File "H5C.c", line 7957, in H5C_load_entry
unable to load entry
File "H5Fsuper_cache.c", line 471, in H5F_sblock_load
truncated file: eof = 135741440, sblock->base_addr = 0, stored_eoa = 169443736

End of HDF5 error back trace

Unable to open/create file '../../data/data_bank.h5'

History

#1 Updated by Laurenz Gamper over 6 years ago

  • Status changed from New to Closed

It seems to be a broken hdf5 file. Copy the clean data bank into the data bank and it should be fine.



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