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* [svn-r9460] Purpose:Quincey Koziol2004-10-2622-1661/+1311
| | | | | | | | | | | | Code cleanup & optimization Description: Bring back new metadata cache code from development branch. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Linux 2.4 (heping) w/C++ & FORTRAN
* [svn-r9456] Snapshot version 1.6 release 3 (post0)HDF Admin2004-10-251-2/+2
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* [svn-r9434] Purpose:Quincey Koziol2004-10-191-1/+4
| | | | | | | | | | | | | | | | Bug fix Description: Fix core dump when flushing a file with a newly created attribute which hasn't had a value written to it still open. Solution: Write the attribute fill value when appropriate. Platforms tested: FreeBSd 4.10 (sleipnir) Linux 2.4 (verbena) Solaris 2.7 (arabica)
* [svn-r9414] Purpose:Quincey Koziol2004-10-121-2/+2
| | | | | | | | | | | Code cleanup Description: Fix a couple of return values from NULL -> FAIL. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r9403] Purpose:Quincey Koziol2004-10-129-95/+95
| | | | | | | | | | | | | | | | | Code cleanup Description: Further diff reductions against development branch, in preparation for merge of new metadata cache code. Solution: Change 'dirty' field in metadata cache info struct (H5AC_info_t) to match development branch 'is_dirty' name. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Linux 2.4 (verbena) w/FORTRAN
* [svn-r9402] Purpose:Quincey Koziol2004-10-1211-705/+230
| | | | | | | | | | | | | | | | | Port development branch changes to release branch. Description: Initial step in bringing changes to support new metadata cache from the development branch to the release branch. Solution: This checkin just aligns the H5AC* API changes, as well as bringing back various minor code cleanups, etc. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Linux 2.4 (verbena) w/FORTRAN
* [svn-r9401] This commit was manufactured by cvs2svn to create branch 'hdf5_1_6'.cvs2svn2004-10-121-0/+173
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* [svn-r9378] Purpose:Quincey Koziol2004-10-061-2/+2
| | | | | | | | | | | Typo fix Description: Fix another typo with mis-merged info. Platforms tested: Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r9377] Purpose:Quincey Koziol2004-10-061-1/+1
| | | | | | | | | | | Typo fix Description: Correct minor error value to something appropriate for the release branch. Platforms tested: FreeBSD 4.10 (sleipnir) too minor to require h5committest
* [svn-r9376] Purpose:Quincey Koziol2004-10-063-81/+109
| | | | | | | | | | | | | Bug fix Description: Close a couple of memory leaks Platforms tested: FreeBSD 4.10 (sleipnir) Solaris 2.7 (arabica) w/purify Linux 2.4 (verbena) too minor for h5committest
* [svn-r9367] Purpose: feature changeRaymond Lu2004-10-051-2/+4
| | | | | | | Description: Prevent create datatype of size 0 Platforms tested: heping(simple change)
* [svn-r9365] Raymond Lu2004-10-051-5/+5
| | | | | | | | | | | Purpose: change feature Description: Back up supporting bitfield and time datatypes in H5Tget_native_type. Leave it for future support. Simply returns "not supported" error message for now. Platforms tested: h5committest Misc. update: RELEASE.txt
* [svn-r9359] Purpose:Quincey Koziol2004-10-045-27/+26
| | | | | | | | | | | | | | | Bug fix Description: Relax restrictions on parallel I/O to allow compressed, chunked datasets to be read in parallel (collective access will be degraded to independent access, but will retrieve the information still). Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) IRIX64 6.5 (modi4) h5committest
* [svn-r9356] Purpose:Quincey Koziol2004-10-0118-1768/+775
| | | | | | | | | | | | | | | | Bug fix & code cleanup Description: More dataset cleanups to get to a point where we can fix the chunked I/O bug. Also fix a couple of errors in the recent file object resurrection changes which should hopefully address the recent daily test failres (H5T.c) Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) h5committest
* [svn-r9355] This commit was manufactured by cvs2svn to create branch 'hdf5_1_6'.cvs2svn2004-10-014-0/+5666
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* [svn-r9351] Raymond Lu2004-10-013-9/+31
| | | | | | | | | | | | | | Purpose: enhanced feature Description: enable size adjustment for compound datatype. The size can be increased and decreased(as long as the members are not cut). Solution: mainly check if any member is being cut when decreasing the size. Others are simply taking out the assertion against 0 size. Platforms tested: h5committest and fuss. Misc. update: RELEASE.txt
* [svn-r9343] Purpose:Quincey Koziol2004-09-3018-1374/+674
| | | | | | | | | | | | | | | | Bug fix/code cleanup Description: Clean up raw data I/O code to bundle the I/O parameters (dataset, DXPL ID, etc) into a single struct to pass around through the dataset I/O routines, since they are always passed together, until very near the bottom of the I/O stack. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) IRIX64 6.5 (modi4) h5committest
* [svn-r9341] Purpose:Quincey Koziol2004-09-302-4/+4
| | | | | | | | | | | Bug fix Description: Correct a couple of typos in the recent object resurrection code. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r9335] James Laird2004-09-293-4/+4
| | | | | | | | | | | | Purpose: Bug fix Description: Fix bugs found by daily tests. Platforms tested: copper
* [svn-r9334] James Laird2004-09-2841-2131/+2446
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Feature Description: (Same change to release branch) Datatypes and groups now use H5FO "file object" code that was previously only used by datasets. These objects will hold a file open if the file is closed but they have not yet been closed. If these objects are unlinked then relinked, they will not be destroyed. If they are opened twice (even by two different names), both IDs will "see" changes made to the object using the other ID. When an object is opened using two different names (e.g., if a dataset was opened under one name, then mounted and opened under its new name), calling H5Iget_name() on a given hid_t will return the name used to open that hid_t, not the current name of the object (this is a feature, and a change from the previous behavior of datasets). Solution: Used H5FO code that was already in place for datasets. Broke H5D_t's, H5T_t's, and H5G_t's into a "shared" struct and a private struct. The shared structs (H5D_shared_t, etc.) hold the object's information and are used by all IDs that point to a given object in the file. The private structs are pointed to by the hid_t and contain the object's group entry information (including its name) and a pointer to the shared struct for that object. This changed the naming of structs throughout the library (e.g., datatype->size is now datatype->shared->size). I added an updated H5Tinit.c to windows.zip. Platforms tested: Visual Studio 7, sleipnir, arabica, verbena Misc. update:
* [svn-r9331] Purpose:Quincey Koziol2004-09-281-4/+3
| | | | | | | | | | | Bug fix Description: Another attempt to fix the address overflow in the core VFL, hopefully one that works on 64-bit platforms. Platforms tested: AIX 5.1 (copper)
* [svn-r9328] Purpose:Quincey Koziol2004-09-282-12/+1
| | | | | | | | | | | | | Bug fix. Description: Fix off-by-one error in Core VFL driver which would cause spurious address or size overflow errors when an odd valued address or size was checked. Platforms tested: FreeBSD 4.10 (sleipnir) Linux 2.4 (heping) Solaris 2.7 (arabica)
* [svn-r9323] Purpose:Quincey Koziol2004-09-271-66/+104
| | | | | | | | | | | | | Bug fix Description: Fix situation where deleting a chunked datasets with B-tree nodes that weren't in the metadata cache would die with a core dump. Platforms tested: FreeBSD 4.10 (sleipnir) Linux 2.4 (heping) Solaris 2.7 (arabica)
* [svn-r9313] Purpose:Quincey Koziol2004-09-231-3/+4
| | | | | | | | | | Bug fix. Description: Allow I/O to occur on 0 element selections. Platforms tested: h5committest
* [svn-r9311] Purpose:Quincey Koziol2004-09-221-0/+36
| | | | | | | | | | | | | | Code optimization Description: Avoid performing a check on the number of objects in a group (which currently involves iterating over all entries in the group's B-tree) before calling H5G_get_obj<foo>_by_idx. Instead, just have H5G_get_obj<foo>_by_idx() notice when you've walked off the end and return fail then. Platforms tested: FreeBSD 4.10 (sleipnir) h5committest
* [svn-r9308] Purpose: Post 1.6.3 release maintenanceElena Pourmal2004-09-221-2/+2
| | | | | | | | | | Description: Changed version number to 1.6.3-post0 Solution: ran bin/h5vers script on eirene Platforms tested: Misc. update:
* [svn-r9304] Purpose: Release maintenancehdf5-1_6_3Elena Pourmal2004-09-221-2/+2
| | | | | | | | | | Description: I changed the version number to 1.6.3 Solution: Ran bin/h5vers -s 1.6.3 on eirene Platforms tested: Misc. update:
* [svn-r9263] Purpose: Maintenance for 1.6.3 third round of testingElena Pourmal2004-09-151-2/+2
| | | | | | | | | | | Description: Created test tar ball and changed version to 1.6.3-pre4 using bin/h5vers script on eirene Solution: Platforms tested: Misc. update:
* [svn-r9260] Purpose:Quincey Koziol2004-09-151-1/+1
| | | | | | | | | | | | Bug fix Description: Correct leftover issue from recent changes to dataset region reference which occurred when 1.4 backward compatibility is turned on. Platforms tested: FreeBSD 4.10 (sleipnir) w/1.4 compat Configuration not tested by h5committest
* [svn-r9251] Purpose:Quincey Koziol2004-09-143-18/+13
| | | | | | | | | | | | | | | | | | | | Bug fix Description: Correct typedef for dataset region references to avoid struct alignment issues on Crays. Solution: Change the typedef for hdset_reg_ref_t from a struct to an array of unsigned char's of the correct size and propagate the appropriate adjustments around the code. Platforms tested: FreeBSD 4.10 (sleipnir) Linux 2.4 (verbena) w/fortran Cray T90 (subzero) w/fortran Cray SV1 (wind) w/fortran & parallel Cray T3E (cyclone) w/fortran & parallel
* [svn-r9236] Purpose: Maintenance for the second round of testingElena Pourmal2004-09-091-2/+2
| | | | | | | | | | Description: I created a tar ball and changed version to 1.6.3-pre3 Solution: run bin/h5vers on eirene Platforms tested: eirene Misc. update:
* [svn-r9217] Purpose:Pedro Vicente Nunes2004-09-071-14/+16
| | | | | | | | | | | | | | | | bug fix Description: The H5O_mtime_decode function was not handling properly the case for the Code Warrior compiler Solution: Platforms tested: Code Warrior Misc. update:
* [svn-r9210] Purpose:Pedro Vicente Nunes2004-09-071-103/+112
| | | | | | | | | | | | | | | | | | | | | | | | | | | | bug fix Description: on the Cray SV1 an INT type was wrongly converted to a SHORT type by the get_native_integer function Choose the type based on the precision; this is to support cases like the Cray SV1, where the size of short is 8 but precision is 32 (e.g an INT (size 8, prec 64) would be converted to a SHORT (size 8, prec 32) if the size was the deciding factor) Solution: Platforms tested: linux solaris aix cray sv1 Misc. update:
* [svn-r9205] Purpose:Pedro Vicente Nunes2004-09-031-1/+1
| | | | | | | | | | | | updated some commnents regarding the latest cray bug fix Description: Solution: Platforms tested: Misc. update:
* [svn-r9201] Purpose:Pedro Vicente Nunes2004-09-031-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | bug fix Description: the dataset region reference data was not portable between the Cray T3E and other machines Solution: this was due to the fact that the buffer to store the heap ID and index was using a sizeof(int) for its size 4 is used instead of sizeof(int) to permit portability between the Crays and other machines (the heap ID is always encoded as an int32 anyway) Platforms tested: Cray T3E (read data from linux) linux solaris aix Misc. update:
* [svn-r9182] Purpose: Maintenance for the hdf5-1.6.3 testingElena Pourmal2004-09-011-2/+2
| | | | | | | | | | | | | | | Description: After discussing with Albert: I changed the version to hdf5-1.6.3-pre1 and created a tar ball for the first round of testing. Then I changed the version to hdf5-1.6.3-pre2 and now I am committing the changes. pre1 on ftp is the same as snap6 :-) Solution: Platforms tested: Misc. update:
* [svn-r9178] Purpose:John Mainzer2004-08-311-0/+119
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fix parallel bug reported by Thomas Guignon, in which different processes became confused as to whether they were doing collective or individual I/O. Description: When one process had a point selection, and another didn't, the first concluded that the I/O was independant, while the second presumed that it was collective. A hang resulted. Solution: Get all processes involved in an I/O to compare notes. If all agree that the I/O is collective, they proceed with same. If any think the I/O should be independant, all use independant I/O. Note that this is an interrim fix -- the correct solution is to support collective I/O on point selections. This will take a while. Platforms tested: copper h5committested Eirene (serial and parallel) In the parallel test on Eirene, I encountered a bug in h5repacktst. However the problem vanished on recompile. Since I couldn't reproduce it elsewhere, I went ahead with the checkin. Given my druthers, I would have liked to study the code more carefully before this check-in. However, there is some time pressure. The new code implementing the consensus check must not be executed unless MPI is initialized, and there is a communicator associated with the file. I think my guards against this case are adequate, but if we run into a hang or an illegal instruction error, this change should be suspect. Misc. update:
* [svn-r9177] Snapshot version 1.6 release 3 (snap5)HDF Admin2004-08-301-2/+2
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* [svn-r9171] Purpose:Albert Cheng2004-08-271-1/+1
| | | | | | | | | | | | | | | | | | | | | "bug fix" sort of. Description: The current mpicc at TG-NCSA recognizes uint64_t but not int64_t. hdf5 code rightly assumes when the unsigned type is defined, the corresponding signed type should be valid too. So, when it detected uint64_t is valid, it went ahead using int64_t which ended in compiling failure. Solution: Changed the detection to check on int64_t instead. This does not change any logic, just goes around the mpicc compiler error at TG-NCSA. Platforms tested: h5committested and tested at TG-NCSA (pp) too. Misc. update:
* [svn-r9156] Purpose:Quincey Koziol2004-08-251-2/+80
| | | | | | | | | | | | | | | Bug fix (sorta) Description: Change reading of "missing" chunks from datasets with undefined fill values to not overwrite the application buffer with random garbage from memory. Note that this is almost the same, since whatever garbage the application had in those locations will still be there... Platforms tested: FreeBSD 4.10 (sleipnir) IRIX64 6.5 (modi4) h5committested
* [svn-r9153] Elena Pourmal2004-08-252-0/+4
| | | | | | | | | | | | | | | Purpose: Maintenance/bug fix Description: On OSF1 C++ compilation failed complaining about stdint.h file being missing. Solution: By Binh-Minh's suggestion: include stdint.h file only when __cpluplus is NOT defined. inttypes.h is used by C++ compiler; it is more common than stdint.h Platforms tested: OSF1 (lemieux), Solaris 2.8 (sol), AIX 5.1 (copper) Misc. update:
* [svn-r9135] Snapshot version 1.6 release 3 (snap4)HDF Admin2004-08-231-2/+2
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* [svn-r9118] Purpose: Minor Bug FixRaymond Lu2004-08-191-2/+2
| | | | | | | | | Description: In H5O_fill_new_decode and H5O_fill_new_encode, macros UINT32DECODE and UINT32ENCODE were used to decode and encode message size, which is ssize_t. Solution: Changed to INT32DECODE and INT32ENCODE. Platforms tested: Tested v1.7 on fuss - very simple change.
* [svn-r9107] Purpose: Bug fixRaymond Lu2004-08-181-18/+5
| | | | | | | | | | | Description: In H5O_fill_new_decode, it tries to read message size(-1) when fill value is undefined for version 1. During UINT32DECODE, if the machine is 64-bit, a value 0x00000000ffffffff is returned, which is like a valid value. Solution: Don't decode message size if fill value is undefined, simply assign -1 to message size. Platforms tested: h5committest.
* [svn-r9102] Purpose:Quincey Koziol2004-08-174-308/+278
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix Description: 1 - Dataset contiguous storage cache information had a bug where it was possible to try to access invalid cache information if the cache wasn't filled the first time it attempted to loop through the list of offset/length vectors. 2 - Additionally, the contiguous storage cache information was being used in certain circumstances from the chunked dataset I/O code path, which was generally fatal since the chunk storage and contiguous storage information were stored together in a union. Solution: 1 - Avoid special case of first trip through loop over offset/length I/O vectors and always check for the contiguous storage sieve buffer buffer being NULL. 2 - Change the union containing the chunk and contiguous storage cache information into a struct, allowing both to be used at the same time. Platforms tested: FreeBSD 4.10 (sleipnir) h5committested
* [svn-r9065] Purpose:Robert E. McGrath2004-08-111-9/+9
| | | | | | | | | | | | | | | Bug fix Description: Wrong value returned for error Solution: Return correct value Platforms tested: verbena Misc. update:
* [svn-r9055] Snapshot version 1.6 release 3 (snap3)HDF Admin2004-08-091-2/+2
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* [svn-r9054] Purpose:Quincey Koziol2004-08-082-27/+45
| | | | | | | | | | | | | | | | | | | Bug fix Description: Correct possible core dump when a datatype conversion function is registered with the library after a compound datatype has been converted (having it's type conversion information cached by the library). The compound datatype must have been created by inserting the fields in non-increasing offset order to see the bug. Solution: Re-sort the fields in the compound datatypes before recalculating the cached information when performing the conversion on them. Platforms tested: FreeBSD 4.10 (sleipnir) h5committested
* [svn-r9038] Purpose:Quincey Koziol2004-08-061-1/+1
| | | | | | | | | | | | Code cleanup/bug fix Description: Check for _O_BINARY being defined instead of O_BINARY, since we actually use _O_BINARY. (Note that this only affects Windows) Platforms tested: FreeBSD 4.10 (sleipnir) Not tested w/h5committest
* [svn-r9030] Purpose:Albert Cheng2004-08-051-4/+273
| | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix (Failures when dataset size >= 1 GB, reported by Bill Loewe.) Description: In the IBM AIX system using 32bit mode, if a dataset size was 1GB or larger, when the "end" of the dataset was selected, MPI would complain it could not keep the Upper bound of a datatype within the range of MPI_Aint. This was because the old algorithm would derive the selection with extent of each row first. After all dimensions were processed, it then calculate the start position and just displace the whole MPI derived type. So, the final MPI type was actually the start position plus the whole dataset. Since the start can be as big as the whole dataset, this made the final derived twice as big as 1GB. That would hit the 2GB MPI_Aint range limit in the 32 bit mode. Solution: Use a different algorithm to include the start position in the defining of MPI type for each dimension. When all dimensions are processed, the MPI type represents the selection exactly. Platforms tested: h5committested Misc. update:
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