Convert indirect fractal heap blocks to use deferred file space allocation
(by using the temporary file space feature), which should ease up the metadata
fragmentation that can occur when lots of objects are added to a fractal heap
(like adding many links to a group).
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
Switch fractal heap direct blocks to use temporary file space, until they
are flushed, which makes allocation of space in file more efficient,
particularly for heaps with I/O filters.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Add private macro for testing if an address is in the 'temporary' file
space for a file.
Tested on:
FreeBSD/32 6.3 (duty)
Too minor to require h5committest
Correct latent bug in one file space allocation test which was not
getting a new file pointer when reopening a file.
Also, add a couple more asserts to the file space allocation code in
the library to help detect this problem earlier.
Tested on:
Linux/32 2.6 (jam) w/core VFD
Revert my reversion of the change to not run the 'temporary' file space
test with the family VFD. (How's that for a checkin message :-)
Tested on:
Linux/32 2.6 (jam)
Adjust 'temporary' file space code to always be within the file's
address space, even when the file uses 32-bit addresses. (It's not really
necessary to be within the file's address space, since objects with temporary
addresses can't be written to the file, but it can't really hurt and it makes
the testing easier)
Tested on:
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode and with 'make check-vfd'
Description:
When using H5T_copy on committed datatypes that are already open, H5T_copy would
properly use the already existing shared struct, but would still deep copy all
of the fields in that struct. This would cause memory leaks, and in the case of
a compound containing a vlen (or reference), the change in size would cause the
size of the resulting type to be set to an incorrect value. Changed H5T_copy to
properly avoid deep copies when using a reopened shared struct.
Tested: jam, linew, smirom (h5committest), purify on jam
Disable testing the 'temporary' space allocation code when using the
family VFD, since the test causes too many files to be opened.
Tested on:
Linux/64 2.6 (smirom) w/check-vfd
Make error handling for detecting overlaps between 'normal' and 'temporary'
space allocation more robust.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Break out the configure check for fseeko & ftello from lseek64/fseek64/
ftruncate64, since the check for the latter routines is not a valid check for
the former routines.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Rework the "proxy address" code to be more general and implement a better
"temporary address" feature, that will allow for metadata allocations to be
deferred to when the metadata is actually flushed to the file.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Bring file addres proxy additions from r16985 on the revise_chunks branch
back into the trunk, for use in allowing fractal heap direct blocks to defer
their allocation in the file.
Tested on:
Mac OS X/32 10.5.7 (amazon) debug & production
too minor to require h5committest
Bring r17005 from revise_chunks branch to trunk:
Correct error in unpinning an entry from outside the cache to correctly
unpin the entry only when it is not being used for a flush dependency relation.
Tested on:
FreeBSD/32 6.3 (duty)
h5committested on branch
Rename H5O_protect/H5O_unprotect to be H5O_pin/H5O_unpin, since that's what
that are actually doing.
Add counter of the number of times the object header is pinned, to allow
H5O_pin/H5O_unpin to be called reentrantly.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Change previous "depend/undepend" routine names to be "support/unsupport"
and add new "depend/undepend" routines, which make the extensible array a child
flush dependency of another piece of metadata in the file.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Add library private routines to allow metadata cache entries to be set as
flush dependency children on extensible array entries. This will allow chunk
proxies to be set as child flush dependencies for the extensible array, adding
another necessary layer to the flush dependency chain for SWMR access.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Description:
Tests were failing for the HDF5 trunk on Windows because Windows does not provide the strtoul function. However, there is a replacement, _strtoui64. This definition has been added to the H5win32defs.h file, similar to other such replacement functions.
Tested:
VS2005 on Vista
h5committest
Refactor extensible array metadata lookup to abstract common code into
single, reusable routine. Re-target existing 'set' & 'get' routines to use new
routine.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Correct error where data block was being marked dirty instead of index block.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Refactor chunk cache entry information to remove some [actually] unused
fields.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
ISSUE: h5ltread_dataset_string_f causes library assertion with g95.
SOLUTION: convert the fortran string buffer to a C buffer with HD5f2cstring, and pass this string to the C function
TEST: added a test call in the fortran test lite program
DOCS: added the note in RELEASE.txt "- Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions had memory problems with the g95 fortran compiler. (PVN - 5/13/2009) 1522
Modifying default cache configuration, and adding an #ifdef to allow for a
separate default configuration when parallel is enabled. This is being
modified in order to address an observed performance problem with the
current default configuration.
Description of Changes:
- increasing maximum cache size from 16MB to 32MB
- increasing maximum entry size from 10MB to 32MB
- decreasing min_clean_fraction from 0.3 to 0.01 in serial case
- increasing flash_multiple from 1.0 to 1.4 in serial case
Tested:
jam
Add test for cache client 'notify' callback.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Reduce overhead for func enter/leave & error handling macros. (Reduces
object code size by ~20% for production/~10% for debug, with gcc)
Tested on:
Mac OS X/32 10.5.6 (amazon)
(Too minor to require h5committest)
Tweak down the size of datatype created for dataset, so that the
elements are a reasonable size and the dataset's size can fit into a 64-bit
value for storing in the file.
Tested on:
FreeBSD/64 6.3 (liberty)
(too minor for h5committest)
Bring r16848 from revise_chunks branch to trunk:
Add test (and bugfixes) for detecting if a filter makes a chunk size
larger than can be encoded in a 32-bit variable (in the file).
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest not needed, multi-platform testing done on branch)
Bring r16846 from revise_chunks branch back to trunk:
Fix broken (for how long?) H5_ASSIGN_OVERFLOW macro to actually detect
overflows during assignments, along with several errors it [now] detected.
Cleaned up a fix minor warnings and/or pieces of code also.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest not needed - multi-platform test performed on branch)
Adding dependency to h5repack test script.
h5repack.sh needs h5repacktst to run first.
Tested:
Problem only appeared on Glory, but tested the dependence
manually on jam by trying to run only the script and checking
that it first ran the h5repacktst test program.
If the AR command has embedded shell separators such as the case of
"AR = ar -X 64", $AR ends up as a blank.
Solution:
Put quotes around the command substitution string to protect against embedded
separators. Applied the same to both AR and RANLIB assignments.
Tested:
At Up (AIX 5.3) only because that was where I discovered the error
when AR is ar -X 64
