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* 1 12 Merges from develop (#421)Allen Byrne2021-03-041-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - files not in src or test.
* Source formattedAllen Byrne2020-10-011-18/+15
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* HDFFV-10297 add h5copy test and fix h5diff errorsAllen Byrne2017-10-161-1/+1
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* Stripped C standard library headers from tools test code.Dana Robinson2017-07-191-4/+0
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* [svn-r24480] Description:Quincey Koziol2013-11-301-8/+8
| | | | | | | | | | | Bring r24479 from 1.8 branch to trunk: Fix ph5diff worker command handling so it can correctly respond to situations where there's no work to perform. Also, a few minor code cleanups. Tested on: Mac OSX/64 10.9.0 (amazon) w/parallel (too minor to require h5committest)
* [svn-r21967] Checked all %lu references and corrected 2 that should have ↵Allen Byrne2012-02-221-6/+0
| | | | | | | | been '%"H5_PRINTF_LL_WIDTH"u' Moved lib variables windows linking declarations to proper file location. Tested: local linux windows
* [svn-r21953] HDDFV-7560: h5dump refactoringAllen Byrne2012-02-171-0/+6
| | | | Tested: local linux
* [svn-r21195] Correct windows exports for h5diff.Allen Byrne2011-08-081-18/+12
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* [svn-r20767] Purpose:Jonathan Kim2011-05-061-2/+2
| | | | | | | | | | | | HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects Description: Improved performance by eliminating duplicated action for getting object information in half from the previous fixe when comparing group vs group. This is addition to the previous commit r20676. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
* [svn-r20721] Refactor ext lib import and install.Allen Byrne2011-05-041-5/+5
| | | | Add SOVERSION for linux
* [svn-r19400] Purpose:Jonathan Kim2010-09-161-1/+2
| | | | | | | | | | Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly. Tested: jam, amani, heiwa
* [svn-r19252] Description:Quincey Koziol2010-08-191-2/+0
| | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes from branch to trunk: r19161: Fixed the part for matching the subset info with dataset r19189: BZ1646: h5dump does not check number of dimensions for subsetting parameters against the dataset Changed subset_t structure from holding hsize_t pointers to holding new subset_d pointers, which hold the original hsize_t pointer + len. this len is then checked against dataset ndims in the handle_dataset function of h5dump. Changed all references to use new data structure. Added tests for each subset parameter. r19190: Added new h5dump ddl files Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (h5committested on branch)
* [svn-r14154] Description:Quincey Koziol2007-09-251-1/+1
| | | | | | | | | | | | | | | | | | | | Finish deprecating last H5G symbol (H5G_obj_t) - yay! Lots of misc. library fixes to remove confusion between links and objects. The tools could still use another pass, to remove h5trav_type_t type and make the correct distinction between links & objects. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64 2.6 (smirom) 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 AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14144] Description:Quincey Koziol2007-09-131-7/+2
| | | | | | | | | | | | | | | | Move H5Gget_objinfo() to deprecated symbols section and retarget internal usage to H5Lget_info()/H5Oget_info(). Misc. other code cleanups... Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Linux/64 2.6 (smirom) AIX/32 5.3 (copper) Solaris/32 2.10 (linew) Mac OS X/32 10.4.10 (amazon)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r11259] Purpose:Albert Cheng2005-08-171-2/+7
| | | | | | | | | | | | | | | | | | | | Bug fix Description: ph5diff had been hanging in Tflops. Found out that vsnprintf ph5diff uses was a local coded that did not limit printing according to the size argument. That resulted in buffer overflow and other problems. Solution: Added some sort of size checking in the home-grown vsnprintf and had ph5diff checked for error return of vsnprintf. Leon also revamped the ph5diff manager's way of handling communications with the workers. That eliminated all but the last case of hanging. Platforms tested: Tflops. Misc. update:
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-3/+3
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r10996] Purpose:Leon Arber2005-06-281-0/+6
| | | | | | | | | | | | | | | | | | | | | | | Bug fix for parallel case for new "Some objects were not comparable" patch to h5diff. Description: The parallel h5diff wouldn't print out "Some objects were not comparable" because the worker tasks were not communicating the not_cmp flag of the diff_opt_t struct back to the manager, who ultimately prints everything. Also, some miscellaneous fixes for error printing. Some errors were printed out with printf instead of fprintf(stderr,...). In parallel environments, this can result in output getting lost. Solution: Had the worker tasks pass along the not_cmp flag to the manager when they sent along the number of differences they found. Platforms tested: heping (pp), sol (pp) Misc. update:
* [svn-r10659] Purpose:Leon Arber2005-04-251-1/+0
| | | | | | | | | | | | | | Optimization Description: removed an unncessary memset call. Solution: Platforms tested: heping (pp), sol (pp) Misc. update:
* [svn-r10206] Leon Arber2005-03-131-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Bug fix. Description: ph5diff fails on modi4 due to the way snprintf works on IRIX. Solution: The C99 standard says that, if there isn't enough room in the string, snprintf should return the number of characters that would have been written to the output string if there were enough room. The snprintf on modi4 would return the number of characters that is was able to write succesfully to the string if space ran out. The ph5diff logic that checks if the output buffer was full did not handle this sort of return value correctly. Used VSNPRINTF_WORKS from configure test to check how snprintf works and do the logic accordingly. Platforms tested: modi4 Misc. update:
* [svn-r10170] Purpose:Leon Arber2005-03-091-4/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fixes Description: Fixes for several bugs, including dumping of excess output to a temporary file, fix for printing hsize_t datatype, and the long awaited fix for intermixed output. Solution: Fix 1: Overflow file Previously, any output that a worker task made was buffered locally in memory, up to a point. Any output beyond the size of the buffer (used to be 10k) was discarded. Now, the memory buffer size has been changed to 1k and any output beyond this amount is sent a temporary file. This way, no output is lost and memory usage is kept under control. The temporary file is deleted as soon as a worker task finishes sending its contents to the manager. Fix 2: hsize_t printing Printing of the hsize_t datatype used to be handled by %Hu passed to HDfprintf. However, there is no corresponding HDvsnprintf that is able to print hsize_t types. These are now printed with the aid of H5_PRINTF_LL_WIDTH. Fix 3: Intermixed output fix Intermixed output would occur on some machines (although I haven't seen it happen for a while) due to the unpredictability of the underlying network and the speed at which various message would travel. This has been fixed by having all output send to the manager for printing. The worker tasks no longer print the output themselves upon receipt of a token, but instead send that data to the manager. Platforms tested: heping, eirene, tg-login (the only place that seems to still experience intermixed output every now and then) Misc. update:
* [svn-r9956] Purpose:Leon Arber2005-02-081-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fixed numerous ph5diff bugs. Description: Fixed manager output printing Fixed out of order output printing Fixed test script execution problem Temporary fix for large amounts of output overflowing buffer. Solution: The manager task buffers its output. However, since the manager task never gets a print token, this output was lost. Solution: new function called print_manager_output that prints buffered output is called in places where the manager buffers its output. printf was apparently buffering output. This means that a task would sometimes print even after it had given up its print token. Added fflush() call after printf() calls, which seems to have fixed the problem. calling rsh multiple times in succession seems to overwhelm something in Linux, as it begins to refuse new connections until the old ones reset. Since each call to mpirun in the test script starts up 4 rsh sessions, the test script eventually is unable to run any further tests. Solution: Added a short delay in the testscript between successive calls to mpirun to allow old connections to reset. The 10k output buffer was of insufficient size to hold the large amounts of output generated by some of the tests. Since code to buffer to a file has not been implemented yet, a temporary fix was to increase the size of the output buffer to 50k. Platforms tested: heping Misc. update:
* [svn-r9925] Purpose:Leon Arber2005-02-021-7/+1
| | | | | | | | | | | | | | | | | | | Bug Fix Description: Permanent fix for the incompatibilities between h5diff and h5repack. Solution: h5diff now contains the code to run both parallel and serial diffs. Depending on how the binary is called, it will run either the serial or the parallel versions respectively. Platforms tested: heping(serial + parallel), copper. Misc. update:
* [svn-r9905] Purpose:Albert Cheng2005-02-011-3/+3
| | | | | | | | | | | | | | | | | | | fix bugs. Description: The three variables, g_nTasks, outBuff, and outBuffOffset, were declared in ph5diff.h. That means they are declared in various *.c files that include it, thus having the appearance of multiple defined. Most C compilers are forgiving of this error but the g++ rejects this practice. Solution: Make it only an extern declaration in ph5diff.h but really defined them in h5diff_util.c Platforms tested: sleipnir using g++ since this only failed in Daily test. Also testes in heping, serial and parallel modes.
* [svn-r9893] Purpose:Albert Cheng2005-01-311-0/+3
| | | | | | | | | | | | | | Temporary daily tests fix. Description: The newly added ph5diff is not quite compatible with the h5repack tool. Disabled the ph5diff build (reverted back to building serial h5diff) to allow daily tests to work while ph5diff is fixed. Platforms tested: Tested in heping both serial and parallel modes. Misc. update:
* [svn-r9877] Purpose:Leon Arber2005-01-271-5/+1
| | | | | | | | | | | | | | | | | Bug fix: Temporary fix for h5repack failures in all parallel builds. Description: The parallel additions to h5diff interfered with h5repack. Solution: Added a second set of "parallel" functions to h5diff.c. h5repack uses the serial versions, whereas h5diff will use the parallel versions. Also, h5diff will now be smart about when to enter parallel mode. If is run with mpirun with more than 1 task, it will enter parallel mode. Otherwise, it will stay in serial mode as before. Platforms tested: heping (serial and parallel) Misc. update:
* [svn-r9872] Purpose:Albert Cheng2005-01-261-0/+57
New feature. Description: Added new tool ph5diff. (Code done by Leon Arber.) Code is changed but test is not working yet. For now, it skipped all tests. Platforms tested: Tested in heping, serial and parallel modes.