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* [svn-r11795] Snapshot version 1.7 release 54HDF Admin2005-12-142-3/+3
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* [svn-r11785] Purpose:Albert Cheng2005-12-111-0/+15
| | | | | | | | | | | | Patch for red-storm. Description: A temporary patch for redstorm, must open a file in the same parallel data filesystem before H5_init_library. Otherwise, it hangs with error: (client.c:568:ptlrpc_check_status()) @@@ type == PTL_RPC_MSG_ERR, err == -114 req@0x57a9660 x1/t0 o38->mds_l2@MDS_PEER_UUID:12 lens 240/272 ref 1 fl Rpc:R/100000/0 rc 0/-114 Platforms tested: Red-storm.
* [svn-r11771] Purpose:Quincey Koziol2005-12-087-20/+24
| | | | | | | | | | | | Code cleanup Description: Fix a bunch of warnings flagged by Windows compilers. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11761] Purpose:Albert Cheng2005-12-052-3/+3
| | | | | | | | | | | | | Unstable format version marker. Description: This marks the Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. Earlier versions (1.7.52 or earlier) have the original format. This version and later have the unstable format until further notice. Platforms tested: h5committested.
* [svn-r11758] Purpose:Quincey Koziol2005-12-0438-991/+1549
| | | | | | | | | | | | | New feature Description: Add in a combination of Peter's & my code to support copying variable-length data from one file to another, although currently only supported with contiguous data storage. Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r11742] Purpose: Minor correction.Raymond Lu2005-11-181-2/+4
| | | | | | | | | Description: H5Eset_auto_stack() and H5Eset_auto() used FUNC_ENTER_API. It would clear the error stack from the previous API call. It's better to use FUNC_ENTER_API_NOCLEAR to avoid clearing the stack. Platforms tested: fuss - simple change.
* [svn-r11741] Purpose:James Laird2005-11-181-6/+16
| | | | | | | | | | | | | | | | | Bug fix Description: Fortran type generation was broken in two ways. Fixed both. Solution: Firstly, there were a couple of path problems. Fixed a typo and specified the full path of a file. Secondly, the dependencies weren't right when building with HDF5-specific commands (make lib, make check-s, etc.). Tweaked dependencies to fix the problem. Platforms tested: mir, modi4, sleipnir
* [svn-r11739] Purpose:MuQun Yang2005-11-182-30/+5
| | | | | | | | | | | | | | slight code change for efficiency of iteration of chunk address Description: Quincey picked this up because of my inexperience of C. A pair of redundant malloc and free calls will be removed. Solution: Platforms tested: heping(Linux 2.4) too little to be tested. Misc. update:
* [svn-r11738] Purpose:James Laird2005-11-1810-3/+85
| | | | | | | | | | | | | | | | | | | Configure feature Description: Added 'make trace' target. Solution: Added tracing to 1.7. This was done automatically in 1.6, but left out of 1.7 until now (oops!). Tracing in 1.7 only happens manually, when the user types 'make trace.' Tracing automatically requires more framework than it's worth. I also fixed a couple of tracing bugs and ran trace. Platforms tested: mir, sleipnir, modi4 Misc. update:
* [svn-r11737] Purpose:James Laird2005-11-171-0/+8
| | | | | | | | | | | | | | | | | | | | | | | | Bug fix Description: Before this checkin, 'gmake check-s' would fail if there was a file in the current directory named 'check-s'. This is fixed under gmake (not sure how to fix for other makes). Solution: check, progs, install, etc. are what gmake calls "phony" targets, which means that no file should be created. These targets can be specified by a line of the form .PHONY: check progs install ... Automake adds this line for targets it knows about, but HDF5 has a lot of custom rules. This checkin adds a .PHONY line for those rules. I believe that only gmake recognizes the .PHONY line (at least, pmake doesn't seem to), but a partial solution is better than none. This error should occur very rarely anyway (the user has to manually create files with names like 'build-check-s' or '_test'). Platforms tested: mir, sleipnir, modi4
* [svn-r11735] Purpose:Albert Cheng2005-11-162-118/+2
| | | | | | | | | | | | | | | | | | Cleanup. Description: Removed the home-made version of snprintf and vsnprintf since they do not actually enforce the size parameter correctly and could corrupt memory or as a security hole. This block of code has been turned off since Aug 11, 2005 for all platforms except Tflops. No one has reported any problem since--sort of empirical evidence that all platforms except Tflops support both functions. Tflops has retired in September. So, no need to keep this block of code. Also, fixed the HDxxx macro to call the corresponding xxx function. Platforms tested: Tested in heping, both serial and parallel.
* [svn-r11733] Purpose:Quincey Koziol2005-11-167-34/+67
| | | | | | | | | | | | | | | | | | Code cleanup Description: Added some comments about the thread-specific memory for the error and function stacks. Changed H5close() to not use the function stack (since it causes it to be re-enabled after shutting it down) Changed thread-safe semaphore code to not use dynamicly allocated memory. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Too minor to require h5committest
* [svn-r11732] Purpose:Quincey Koziol2005-11-163-14/+49
| | | | | | | | | | | | | More tests Description: Add more tests for proper behavior of groups with different group creation property settings. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Solaris 2.8
* [svn-r11728] Purpose:MuQun Yang2005-11-152-0/+153
| | | | | | | | | | | | | | | | | To support collective chunk IO, obtain the chunk addresses globally from one process. Description: Implement a call-back function to iterate B-tree to do the job. Check in this code for major check-ins later. Solution: Platforms tested: heping(Linux) Should not be used by any library functions now, so won't affect library and tool tests. No need to test on 3 platforms. Misc. update:
* [svn-r11726] Purpose:James Laird2005-11-151-0/+4
| | | | | | | | | | | | | | | | | | Bug fix Description: Fixed bug in hl/src Makefile that was deleting y.tab.c. Running bin/reconfigure changed a few other files as well (somebody probably updated Makefiles.am but forgot to bin/reconfigure). Solution: Automake in its wisdom adds the line "rm *.tab.c" to every distclean in every directory. I assume that it assumes that such files are generated during the build. Supplied an empty distclean-compile target to remove this line from the Makefiles.in. Platforms tested: mir, sleipnir, shanti
* [svn-r11712] Purpose:Quincey Koziol2005-11-1588-7203/+12277
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature Description: Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! This initiates the "unstable" phase of the 1.7.x branch, leading up to the 1.8.0 release. Please test this code, but do _NOT_ keep files created with it - the format will change again before the release and you will not be able to read your old files!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! Solution: There's too many changes to really describe them all, but some of them include: - Stop abusing the H5G_entry_t structure and split it into two separate structures for non-symbol table node use within the library: H5O_loc_t for object locations in a file and H5G_name_t to store the path to an opened object. H5G_entry_t is now only used for storing symbol table entries on disk. - Retire H5G_namei() in favor of a more general mechanism for traversing group paths and issuing callbacks on objects located. This gets us out of the business of hacking H5G_namei() for new features, generally. - Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t - Lots more... Platforms tested: h5committested and maybe another dozen configurations.... :-)
* [svn-r11686] Purpose:Quincey Koziol2005-11-0740-853/+2354
| | | | | | | | | | | | | | | | | | | New feature Description: Add in baseline "object copy" code from Peter [in the form of a new API routine: H5Gcopy()]. There's still some work to do (like handling variable- length datatypes and possibly support for references) and it hasn't been tested on mounted files yet, but the core functionality is there and working correctly. I've also got a set of patches to update the 1.6 branch with tweaks to keep the branches mostly in sync, but Elena will kill me if I import them before the 1.6.5 release is out... :-) Platforms tested: FreeBSD 4.11 (sleipnir) h5committested
* [svn-r11680] Purpose:Quincey Koziol2005-11-041-9/+9
| | | | | | | | | | | Code cleanup Description: Clean up H5Dcreate a little, to prepare for coding standards discussion today. Platforms tested: Just eyeballed, too trivial to require testing.
* [svn-r11646] Purpose:James Laird2005-10-311-4/+14
| | | | | | | | | | | | | | | | | | Bug fix/feature Description: Added support for -shlib in h5fc and h5c++. Made check-install use -shlib when only shared libraries have been installed. Solution: h5fc and h5c++ didn't recognize -shlib. Stole code from h5cc to link against shared libraries. When static libraries are disabled, the examples Makefiles will automatically use the -shlib option to link against shared libraries. Thus, --disable-static and make check-install should work together. Platforms tested: heping(disable-static, enable-static, fortran, c++), modi4 (disable-static, fortran, c++, parallel, enable-static)
* [svn-r11612] Purpose:James Laird2005-10-271-1/+1
| | | | | | | | | | | | | Bug fix Description: Failed parallel tests now cause make to exit with an error. Solution: Edited config/conclude.am to throw an error if parallel test programs fail. Platforms tested: heping, modi4
* [svn-r11602] Purpose:James Laird2005-10-242-12/+0
| | | | | | | | | | | | Bug fix Description: Removed detection of pdb from configure.in as a corollary to removal of pdb2hdf5 tool. Platforms tested: mir, modi4
* [svn-r11598] Purpose:Quincey Koziol2005-10-222-15/+5
| | | | | | | | | | | | Code cleanup Description: Take out odd definition of HDalarm() and replace with standard macro like the rest of the library. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11593] Purpose:Quincey Koziol2005-10-2112-586/+294
| | | | | | | | | | | | Code cleanup Description: Clean up & standardize a bit in preparation for coding standards discussion. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11573] Purpose:James Laird2005-10-171-0/+1
| | | | | | | | | | | | | | | | | | | | Bug fix Description: Changed configure.in to use an environment variable TR to set the path to the tr utility. Solution: There are two kind of tr on Solaris with slightly different syntax. HDF5's configure relies on the "standard" tr. Traditionally, HDF5ers have needed to make sure that the "right" tr was found before the wrong one in their path; now they can use an environment variable. Platforms tested: mir, shanti, sol Misc. update: Forgot to update release notes. Off to do that now.
* [svn-r11566] Purpose:James Laird2005-10-141-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | Makefile bug fix Description: Previously, automake didn't output rules to build perform/mpi-perf or the test/gen_* programs. Now these can be built by typing 'make mpi-perf' (or 'make foo') or by configuring with --enable-build-all. Solution: Automake doesn't like having rules for programs it doesn't build. Tricked it by having these programs built "sometimes"--whenever the user enables --build-all. This should be used mostly for testing and to ensure that these helper programs compile. ***IMPORTANT*** These programs do *not* currently compile. When --enable-build-all is used (not the default), gen_new_fill fails because it uses an old API. This is an existing "bug" that has simply been exposed by this checkin. Platforms tested: sleipnir, modi4, sol Misc. update:
* [svn-r11558] Purpose:Quincey Koziol2005-10-133-15/+55
| | | | | | | | | | | | | | | | Bug fix Description: Check in Kent's fixes to hyperslab rebuilding code that should correctly detect situation when different sub-hyperslabs exist in a higher dimension. Solution: Remember previous sub-hyperslab information and compare that with newly generated sub-hyperslab to make certain they are the same. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11557] Purpose:Quincey Koziol2005-10-131-241/+97
| | | | | | | | | | | | | | | Bug fix Description: Mark continuation message & chunk as dirty for case where chunk is extended. Also refactored code to reduce duplication. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Too minor to require h5committest
* [svn-r11542] Purpose:Albert Cheng2005-10-112-0/+28
| | | | | | | Inserted Copyright notice. Platforms tested: tested in heping.
* [svn-r11519] Purpose:James Laird2005-10-101-0/+3
| | | | | | | | | | | | | | | Bug fix Description: Some platforms complain that tcp.h is present but cannot be compiled. Solution: This is because tcp.h needs in.h to be included. Checked for netinet/in.h and included it when netinet/tcp.h is being checked. Platforms tested: mir, cu11
* [svn-r11515] Purpose:Albert Cheng2005-10-101-1/+1
| | | | | | | | | | Fixed copyright notice. Description: A line is missing in the copyright notice. Fixed. Platforms tested: No test since it is only a fix in a comment block.
* [svn-r11490] Purpose:Quincey Koziol2005-10-039-17/+382
| | | | | | | | | | | | | | | Bug fix Description: Fix "double root open" bug and apply same fix to datasets & named datatypes. Also fix bug in symbol table entry lookup code that would "transfer" an object from one file handle to another file handle when the two file handles were opened on the same actual file. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11489] Snapshot version 1.7 release 51HDF Admin2005-10-022-3/+3
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* [svn-r11485] Purpose:Quincey Koziol2005-09-302-170/+173
| | | | | | | | | | | | Code cleanup Description: Clean up & optimize (a little) the recent "hyperslab rebuilding" code w/Kent. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11480] Purpose:Fang Guo2005-09-292-2/+14
| | | | | | | | | | | Maintenance on Windows Description: No alarm function on Windows, opt out Solution: Platforms tested: MSVS 6.0 on Windows XP Misc. update:
* [svn-r11478] Purpose:Albert Cheng2005-09-291-8/+7
| | | | | | | | | | | | | | | | bug fix. Description: When a parallel test script test fails, make would continue because the way it was setup inside a for loop. Fixed it by issuing an exit 1 inside the loop. There was also a typo error in the newer command comparision that it must be $${chkname} in order to be valid. Also, the test script itself was not checked in the newer lists. All fixed. Platforms tested: h5committested and also hand tested in heping pp mode.
* [svn-r11477] Purpose:Albert Cheng2005-09-291-0/+3
| | | | | | | | | | feature. Description: added the recognition of -lmpich as a form of MPI library. Platforms tested: Tested in heping. Real test will be in MCR.
* [svn-r11475] Purpose:John Mainzer2005-09-281-0/+1
| | | | | | | | | | | | | | | | | | | | | Bug fix Description: In production builds, H5MM_malloc was undefined in H5AC.c Solution: Include H5MMprivate.h in H5AC.c, which defines H5MM_malloc() in both debug and production modes. Platforms tested: h5committested, serial production build on Heping Misc. update:
* [svn-r11470] Purpose:John Mainzer2005-09-2718-401/+3972
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Repair synchronization bug in the metadata cache in PHDF5 Also repair numerous other bugs that surfaced in testing the bug fix. Description: While operations modifying metadata must be collective, we allow independant reads. This allows metadata caches on different processes to adjust to different sizes, and to place the entries on their dirty lists in different orders. Since only process 0 actually writes metadata to disk (all other processes thought they did, but the writes were discarded on the theory that they had to be collective), this made it possible for another process to modify metadata, flush it, and then read it back in in its original form (pre-modification) form. The possibilities for file corruption should be obvious. Solution: Make the policy that only process 0 can write to file explicit, and visible to the metadata caches. Thus only process 0 may flush dirty entries -- all other caches must retain dirty entries until they are informed by process 0 that the entries are clean. Synchronization is handled by counting the bytes of dirty cache entries created, and then synching up between the caches whenever the sum exceeds an (eventually user specified) limit. Dirty metadata creation is consistent across all processes because all operations modifying metadata must be collective. This change uncovered may bugs which are repaired in this checkin. It also required modification of H5HL and H5O to allocate file space on insertion rather than on flush from cache. Platforms tested: H5committest, heping(parallel & serial) Misc. update:
* [svn-r11467] Purpose:Albert Cheng2005-09-271-0/+3
| | | | | | | Add the detection of the alarm function. Platforms tested: Tested in heping.
* [svn-r11466] Purpose:MuQun Yang2005-09-271-179/+53
| | | | | | | | | | | | | | Code refinement Description: Make the re-build hyperslab selection code shorter to be maintained easily Solution: Platforms tested: Sol 2.9, linux 2.4, Aix 5.1 Misc. update:
* [svn-r11463] Purpose:Quincey Koziol2005-09-231-2/+4
| | | | | | | | | | Code cleanup Description: #ifdef out blksize field in file structure for non-GPFS builds. Platforms tested: None - just eyeballed - very minor.
* [svn-r11448] Purpose:Pedro Vicente Nunes2005-09-211-2/+6
| | | | | | | | | | | | | | | | | | | new features Description: add support for compiling the library and testphdf5 in Windows Solution: Platforms tested: Linux AIX Solaris Windows VC6 Misc. update:
* [svn-r11447] Purpose:MuQun Yang2005-09-201-0/+190
| | | | | | | | | | | | | | | | Hyperslab re-build optimization Description: Previously only singluar selection can be rebuilt from span-tree application. This optimization is supposed to rebuild for other regular selection case(such as count =2, block = 2, stride =3) Solution: Platforms tested: shanti(sol 2.9), heping(Linux 2.4), NCAR SGI(IRIX 6.5) Misc. update:
* [svn-r11446] Purpose:James Laird2005-09-201-2/+3
| | | | | | | | | | | Bug fix Description: Massaged the newer script and config/conclude.am to make SX6 happy. Platforms tested: SX6, sol, mir
* [svn-r11431] Purpose:Albert Cheng2005-09-181-2/+3
| | | | | | | | | | | | | | | | | New feature. Description: Added the time command to the make check target to report time usage of the execute of each test and test scripts. This gives us some idea how long each test takes and some vague idea it is compute bound or not. powerpc-ibm-aix5.x: Change $RUNPARALLEL default setting to allow it being invoked by the time command. Platforms tested: h5committested.
* [svn-r11424] Purpose:Quincey Koziol2005-09-173-243/+266
| | | | | | | | | | | | | | | | | | | | | Code cleanup/bug fix Description: Hoist function call out of inner loop of type conversion by retrieving source & destination precisions once, outside the loop. There's still some overhead because this information is stored in variables set at run-time, when it's really constant for the particular machine. Further work to set compiler macros would allow this code to be optimized better by the compiler with dead code removal. We'll continue to work on this area... Also, made new internal H5T_compiler_conv routine static instead of of private, until we need to reference it from another source code module. Platforms tested: h5committest FreeBSD 4.11 (sleipnir)
* [svn-r11421] Purpose:James Laird2005-09-161-4/+11
| | | | | | | | | | | | | | | Feature Description: Added H5_CFLAGS, etc. to 1.7 branch. Now compilation flags can be put in H5_*FLAGS and they'll be used when building hdf5 but not in h5cc. Platforms tested: mir, sleipnir, modi4 Misc. update:
* [svn-r11420] Purpose:James Laird2005-09-161-0/+2
| | | | | | | | | | | | | | | | | Bug fix Description: Disabled C++ shared libraries for Sun Workshop compiler. Solution: This bug only seems to happen when using the -xarch=v9 flag to compile in 64-bit mode, but disabling shared libraries entirely for this compiler is an easier fix (I don't know how to detect 64 bit mode from the command line). The framework for disabling shared libraries for other C++ compilers is in place. Platforms tested: sol, mir, sleipnir, modi4
* [svn-r11418] Purpose:James Laird2005-09-151-2/+4
| | | | | | | | | | | | | | | | Bug fix/feature Description: Disabled shared libraries for a number of Fortran compilers that don't support them. This allows other compilers to support shared Fortran libraries. Solution: Added a conditional, SHARED_FORTRAN_CONDITIONAL, which is true if Fortran supports shared libraries. It is set in configure.in. Platforms tested: mir, sleipnir, colonelk, heping
* [svn-r11415] Purpose: Internal design change.Raymond Lu2005-09-147-198/+209
| | | | | | | | | | | | | | | | | Description: H5T_register() replaces any existing data conversion path with a new path. Solution: Added a parameter to H5T_register() and H5T_path_find() to signal the library whether the new conversion path is from API function H5Tregister() or from private function like H5T_init_interface(). If it is from H5Tregister(), replace existing path. If it's from H5T_init_interface() and the library is trying to register default hard conversion functions, don't replace existing path because the path is registered by the library. For example, the library registered H5T_conv_int_float() and is trying to register H5T_conv_long_float(). The size of long is equal to int. There's no need to replace the path H5T_conv_int_float(). Platforms tested: h5committest and fuss.
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