| Commit message (Collapse) | Author | Age | Files | Lines |
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Purpose: Bug fix
Description: on Cray T90IEEE compact storage test (in test_misc8)
fails since dataset dimensions are too big; dataset
will not fit into the message header.
Solution: Reduced dimension sizes from 100 to 50.
Platforms tested: h5committested on arabica and mod4; verbena failed
because of the F90 license problem. I tested on verbena
by hand and C only; Cray T90IEEE
Misc. update:
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Purpose: Verify library behavior
Description: A file is first opened as read only. Then it's closed with
an object left open. A second open of the same file for read and
write should fail.
Platforms tested: arabica - simply test to verify correct library behavior.
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Code cleanup
Description:
Christi Forsythe reported that the NGROUPS macro in this file was causing
a macro redefinition warning on the QT machine.
Solution:
Rename NGROUPS to UNLINK_NGROUPS
Platforms tested:
Eyeballed, too trivial for triple check.
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Purpose: New tests added.
Description: test VL data for compact dataset; test compact dataset's
maximal size.
Platforms tested: h5committested
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removed specific code warrior debugging information
Platforms tested:
code warrior
Misc. update:
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Bug Fix
Description:
A resource leak happened if the H5Fget_access_plist() function was
called. What was happening: the driver ID and info parts of the
property list copied in H5Fget_access_plist were being overwritten,
but those properties were copied initially, so we lost information.
Added calls to the H5Fget_access_plist function to get the PList and
then immediately close it. It would cause an infinite loop if there
is a resource leak.
Solution:
Before copying over those values, call the H5F_acs_close() function
to close those values.
Platforms tested:
Modi4 (Parallel & Fortran)
Arabica (Fortran)
Verbena (Fortran & C++)
Misc. update:
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Purpose:
Fix bug in ntypes.c test.
Description:
Large arrays on stack break MacOSX
Solution:
Move arrays to static variables.
Platforms tested:
pommier
sol
modi4
Misc. update:
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Bug Fix
Description:
When using the STDIO driver, the dsets test would fail.
Solution:
Need to flush the data to disk before doing an HDopen call.
Platforms tested:
Modi4 (Parallel & Fortran)
Arabica (Fortran)
Verbena (Fortran & C++)
Misc. update:
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Purpose: Windows port
Description: Windows cannot convert from _uint64_t to double. One of
the tests (test_set_local) used conversion to fill a data
buffer. Compilation failed on Windows.
Solution: Fixed the code not to use conversion
Platforms tested: CRAY T90IEEE, arabica, modi4 with parallel, Windows 2000
Only static tests (both debug and release) passed on Windows.
DLLs have multiple problems ;-)
Misc. update:
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Code cleanup
Description:
Clean up comments, etc.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
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New feature.
Description:
Added tests to verify correct operation of re-using file space.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
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Code cleanup
Description:
Added macro for reporting line #'s of test failures more easily.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
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Bug fix
Description:
Return correct value (1 instead of -1) on test failure.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
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Code cleanup
Description:
Switched some system/library calls to use wrappers.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
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Bug fix
Description:
This fixes a bug in the low-level metadata caching code in the library
which could possibly lose metadata during file I/O when a lot of objects are
inserted into a group.
This also fixes a couple of (similar) fencepost bugs in the B-tree
deletion code.
Solution:
For the metadata bug - call the low-level driver's 'write' routine instead
of H5FD_write.
For the B-tree bug - include the correct number of keys.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
(h5committest is still not working for me on burrwhite)
Misc. update:
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Code cleanup & new tests
Description:
Updated szip and shuffle testing to reflect changes to API functions.
Added testing for new API functions: H5Pmodify_filter, H5Pget_filter_by_id
and H5Pall_filters_avail.
Added testing for "can apply" and "set local callbacks.
Cleaned up various things, also.
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir) w/szip
Linux 2.4 (sleipnir) w/szip
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel
Misc. update:
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Code cleanup
Description:
Update dependencies.
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir) w/szip
Linux 2.4 (sleipnir) w/szip
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel
Misc. update:
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Purpose: This a fix for bug #921
Description: On platforms where big test runs, it creates a set of
"solid" 1GB files. Test will take forever (modi4) or will fail
if quotas are exceeded.
Solution: Default library behavior is to allocate dataset space earlier and
to write fill values. I changed the test to use late space allocation
and never write fill values.
Platforms tested: True64 (PSC), modi4 (sequential and parallel), arabica with 64-bit
option(test was skipped there). I also enabled szip and it passed :-)
Misc. update:
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Code cleanup
Description:
Corrected a few comments.
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir)
Linux 2.4 (eirene)
Misc. update:
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Code cleanup
Description:
Updated copyright.
Removed szip-specific testing in favor of standard testing, now that bugs
in the szip filter are fixed.
Updated to latest version of H5Pset_szip API
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir)
IRIX64 6.5 (modi4) w/parallel
Misc. update:
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Cleanup
Description:
Update dependencies.
Solution:
Platforms tested:
Linux 2.4 (eirene)
Misc. update:
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To add tests for szip compression in HDF5
Description:
Three tests were added:
1) szip filter itself
3) szip + shuffle + fletch32
2) fletch32 + shuffle + szip
Solution:
Since H5Dget_storagesize returns 0(Quincey can fix it or it may be gone),
I create another function called test_internal_filter_szip, which is the almost the same
as test_internal_filter but comments out H5Dget_storage_size function.
Platforms tested:
Since there are changes of configure.in and configure,I didn't use h5committest.
I tested with four platforms.
1) Linux 2.4 (eirene) 2) Solaris 2.7(arabic
3) windows 2000(VS 6.0) 4) SGI IRIX6.5-64(modi4)
For test 1)-3), only basic C tests were done For modi4 test, I tested 64-bit C,parallel and fortran.
All tests passed, except a warning message from szip library when checksum is used in some order, which doesn't cause any real problems.
Misc. update:
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Update
Description:
Updated the Copyright statement
Platforms tested:
Linux (This change is only in the comments, so I just check that the
modules still compile)
Misc. update:
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New test feature
Description:
Added the VFD_LIST definition to support the "make check-vfd" tests.
Platforms tested:
h5committested.
Since check-vfd is not invoked by default, I went to each machine
to invoke them by hand. The target worked fine but there were
errors reported from those driver tests. (Those errors were beyond
the scope of this make target test.)
Misc. update:
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New internal feature
Description:
Add internal API for building and working with heaps (H5HP). This will be
used for the LRU algorithm in the new metadata cache code.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir)
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Code cleanup
Description:
Added more information to information printed for test failure.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
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Code cleanup
Description:
Removed extraneous __FUNCTION__ declaration that was causing warnings on
Windows.
Updated copyright information.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
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Code/comment cleanup
Description:
Made more information about reference-counted strings private to the
H5RS package by trimming the typedef used in H5RSprivate.h and switching
from using macros for a couple of operations to using functions.
Updated copyright information for a few of these files.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
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Code cleanup
Description:
Update dependencies and clean up a few warnings.
Platforms tested:
Linux 2.2 (eirene) w/parallel
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Code cleanup
Description:
Clean up miscellaneous warnings which have crept into the code.
Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD.
Adjust gcc compiler flags to be more concise for production mode.
Refactor the H5O code so that there is a stronger boundary between code
in the H5O package and code in the library which just calls H5O routines.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2
Misc. update:
Update MANIFEST if you add or remove any file.
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Purpose:
Change feature
Description:
Switch to Fletcher32 from Adler32 checksum
Platforms tested:
arabica, eirene, modi4
Misc. update:
MANIFEST and RELEASE.txt updated.
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Code cleanup
Description:
Clean up some compiler warnings
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Bug Fix
Description:
Metadata cache in parallel I/O can cause hangs in applications which
perform independent I/O on chunked datasets, because the metadata cache
can attempt to flush out dirty metadata from only a single process, instead
of collectively from all processes.
Solution:
Pass a dataset transfer property list down from every API function which
could possibly trigger metadata I/O.
Then, split the metadata cache into two sets of entries to allow dirty
metadata to be set aside when a hash table collision occurs during
independent I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Updated release_docs/RELEASE
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Bug fix
Description:
The "system scope" for threads isn't supported on all platforms.
Solution:
Add detection of this feature to the configure script and check for
"H5_HAVE_SYSTEM_SCOPE_THREADS" in the appropriate places.
Platforms tested:
modi4 w/threadsafe
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New feature for developers.
Description:
Added "function stack" tracing to library. This allows developers (there
is no public API) to call H5FS_print within the library and get a listing
of the functions traversed to reach that point in the library. Eventually,
I may add support for reporting the parameters to each function also...
Mainly for debugging parallel I/O programs, but I think it will come in
handy in other cases also.
The function stack tracking is controlled with a configure switch:
--enable-funcstack, which defaults to enabled currently. When we branch
for 1.6, we should change the default setting on the branch to be disabled.
Also, added a destructor to the thread-specific keys when thread-safety is
turned on in the library. Otherwise, they were leaking memory and causing
difficult to debug errors in threaded programs (like the test/ttsafe test).
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) w/thread-safety enabled.
Misc. update:
Updated MANIFEST with new files added (src/H5FS.c & src/H5FDprivate.h)
Update release_docs/RELEASE with thread-safety bug fix.
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Purpose:
New feature
Description:
Added Adler32 checksum as a filter in pipeline
Platforms tested:
arabica (fortran), eirene (, C++), modi4 (parallel, fortran)
Misc. update:
Update release_docs/RELEASE.
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Bug Fix
Description:
When calling H5Fopen with the core VFL driver, but without the
H5F_ACC_CREAT flag goes ahead and creates a memory file.
Solution:
Check for the H5F_ACC_CREAT flag before allowing the memory file to be
created.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Bug fix
Description:
Currently, when the library encounters an object header message that isn't
know, it fails to open that object in the file.
Solution:
Allow the library to skip over the unknown object header message and
continue to process the remaining messages, in the hope that the skipped
message isn't important later. If it is important, it will be caught at
a higher level of the library.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Code cleanup
Description:
Reduce warnings on Windows
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Code cleanup
Description:
Various code cleanups to allow the development branch to be compiled with
a C++ compiler (i.e. CC=g++ )
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) C++
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Update test
Description:
Some of the performance improvements changed the errors that are reported
for creating a duplicated dataset in a file, causing this test's hard-coded
errors to check for to fail.
Solution:
Updated error stack reported for dataset creation failure.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/threads
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Code cleanup
Description:
Clean up a few more warnings and update dependencies.
Platforms tested:
Linux 2.2.18smp (eirene) serial & parallel
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Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
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Purpose:
bug fix
Description:
some arrays were too big, running out of memory limit for some machines.
Solution:
change to dynamic memory allocation.
Platforms tested:
arabica, sleipnir
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Purpose:
Add more test
Description:
More tests on nil and zero-sized VL strings.
Platforms tested:
arabica, eirene
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Purpose:
bug fixed for windows
Description:
windows fopen functions by default opens a text mode file. It will fail for HDF5 file.
So to use HDopen HDread HDclose for test.
Solution:
Change from fopen, fread, fclose to HDopen, HDread, HDclose.
Platforms tested:
linux2.2.18smp, windows 2000
Misc. update:
Update MANIFEST if you add or remove any file.
Update release_docs/RELEASE for bug fixes, new features, etc.
Update applicable document files too.
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Purpose:
Bug fix(kinda)
Description:
Windows handle "fopen, fseek, fread, fclose" C functions slightly different.
Solution:
change to HDopen, HDlseek, HDread, HDclose to cover both Unix and Windows.
Platforms tested:
arabica
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Purpose:
more tests.
Description:
a few more test cases.
Platforms tested:
modi4, eirene, arabica
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Bug fix
Description:
Much of the VL-string testing code was recently disabled accidentally.
Solution:
Re-enable it and add test for writing/reading large string attributes.
Platforms tested:
FreeBSD 4.7 (sleipnir) - small enough to not need triple-check
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Purpose:
New feature to H5Dget_offset
Description:
If user block is set, H5Dget_offset should be able to return the absolute
offset from the beginning of file.
Platforms tested:
eirene, arabica
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