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* [svn-r13984] Description:Quincey Koziol2007-07-171-102/+88
| | | | | | | | | | | Various code cleanups and refactor recent changes for h5stat to fit into the existing library data structures better. Tested on: Mac OS X/32 10.4.10 (amazon) FreeBSD/32 6.2 (duty) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13978] purpose:Vailin Choi2007-07-131-0/+103
| | | | | | | | | | | | | | New feature. Description: Added routines to report on the amount of storage for: 1) 1.6 btree and heap storage info for groups 2) 1.8 btree, fractal heap storage info for groups, attributes and SOHM table 3) btree storage for chunked datasets 4) 1.8 superblock extension size. Platform tested: h5committested.
* [svn-r13773] Description:Quincey Koziol2007-05-201-33/+33
| | | | | | | Reduce compiler warnings w/gcc 4.2 Tested on: FreeBSD/32 6.2 (duty) w/gcc 4.2
* [svn-r13744] Description:Quincey Koziol2007-05-101-61/+57
| | | | | | | | | | | | | | | Initial changes to take advantage of readers/writer locking on metadata cache entries. Reduce the # of protect/unprotect pairs during B-tree iteration by holding reader lock on B-tree and symbol table nodes while iteration occurs. This also has the benefit of preventing an iteration callback from modifying the B-tree being iterated over (which would probably confuse the B-tree iteration code terribly) Tested on: Mac OS X/32 10.4.9 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [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-r13019] Description:Quincey Koziol2006-12-041-1/+1
| | | | | | | | | | | Further simplifications and cleanups to object header message code. Also, some changes to the "iterate" routines, in order to not override the return value from the iterator callback routine. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12949] Description:Quincey Koziol2006-11-201-4/+4
| | | | | | | | | | | | | | | | Finish implementation of H5Literate() [still needs real tests] Clean up datatype macro warnings a bit more. Unify iterator callback macros and put up in public header file, with the iterator directions. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r11686] Purpose:Quincey Koziol2005-11-071-407/+37
| | | | | | | | | | | | | | | | | | | 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-r11245] Purpose:Quincey Koziol2005-08-131-36/+36
| | | | | | | | | | | | | | | | | | | | 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-r11014] Purpose:Quincey Koziol2005-07-021-118/+64
| | | | | | | | | | | | Code cleanup Description: Refactor metadata cache to merge "dirtied" flag in with other flags for H5AC_unprotect and H5C_unprotect. Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r10978] Purpose:John Mainzer2005-06-241-61/+178
| | | | | | | | | | | | | | | | | | | | | | | | | | | Interim checkin of code changes moving management of the is_dirty flag into the cache code. Description: Prior to this checkin, management of the is_dirty flag was handled above the level of the metadata cache. This can no longer be allowed, as it introduces a race condition in the proposed fix for a cache coherency bug in PHDF5. Solution: Move management fo the is_dirty flag to the cache code proper. Entries are now marked as dirty via a flag on the unprotect call. Platforms tested: h5committested Misc. update:
* [svn-r10736] Purpose:Quincey Koziol2005-05-071-6/+6
| | | | | | | | | | | Code cleanup Description: Clean up some compiler warnings Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r10145] Purpose:Quincey Koziol2005-03-041-0/+1
| | | | | | | | | | | | Bug fix Description: Add some "safety net" sort of assertions and sanity checks contributed by user. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r9857] Purpose: MaintenanceElena Pourmal2005-01-221-3/+0
| | | | | | | | | | | | | | Description: Removed PABLO from the source Solution: Platforms tested: arabica with 64-bit, copper with parallel, heping with GNU C and C++ and PGI fortran (but I disabled hl, there is some weird problem only on heping: F9XMODFLAG is not propagated to the Makefile files Misc. update:
* [svn-r9850] Purpose:John Mainzer2005-01-201-25/+43
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) Provide facilities in cache to allow us to avoid a potential cache consistency bug in the parallel case. 2) Clean up a off by one sanity checking bug. 3) Turn off execution of long running tests in debug mode. Description: 1) In the parallel case, all writes to metadata must be collective, but reads may not be. In pricipal, this allows us to different contents in different caches. This isn't a problem as long as the correct data is always on disk, but unless we can force certain writes immediately, that need not be the case. 2) & 3) should need no further explanation. Solution: 1) Add code allowing us to mark cache entries, and then force these entries to be flushed at a later time. Note that to actually avoid the bug, we will have to modify existing code to use these new features. 2) & 3) should need no further explanation. Platforms tested: heping (serial debug and production) committest (copper, sol, and heping). test failed on heping in the c++ portion of the build, but at Quincey's siggestion, I am proceeding with the checkin. Misc. update:
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-40/+28
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-) Description: Generally speaking, this is the "signed->unsigned" change to selections. However, in the process of merging code back, things got stickier and stickier until I ended up doing a big "sync the two branches up" operation. So... I brought back all the "infrastructure" fixes from the development branch to the release branch (which I think were actually making some improvement in performance) as well as fixed several bugs which had been fixed in one branch, but not the other. I've also tagged the repository before making this checkin with the label "before_signed_unsigned_changes". Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & fphdf5 FreeBSD 4.10 (sleipnir) w/threadsafe FreeBSD 4.10 (sleipnir) w/backward compatibility Solaris 2.7 (arabica) w/"purify options" Solaris 2.8 (sol) w/FORTRAN & C++ AIX 5.x (copper) w/parallel & FORTRAN IRIX64 6.5 (modi4) w/FORTRAN Linux 2.4 (heping) w/FORTRAN & C++ Misc. update:
* [svn-r9516] Purpose:Quincey Koziol2004-11-101-2/+5
| | | | | | | | | | | | | | Bug fix Description: Fix code to allow --debug-enable=all option to work correctly. Solution: Update some ifdef'ed code with recent changes. Platforms tested: Linux 2.4 (heping) w/--enable-debug=all Too minor to require h5committest
* [svn-r8877] James Laird2004-07-141-4/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Bug Fix Description: If an HDF5 file grows larger than its address space, it dies and is unable to write any data. This is more likely to happen since users are able to change the number of bytes used to store addresses in the file. Solution: HDF5 now throws an error instead of dying. In addition, it "reserves" address space for the local heap and for object headers (which do not allocate space immediately). This ensures that after the error occurs, there is enough address space left to flush the entire file to disk, so no data is lost. A more complete explanation is at /doc/html/TechNotes/ReservedFileSpace.html Platforms tested: sleipnir, copper (parallel), verbena, arabica, Windows (Visual Studio 7) Solution: Platforms tested: Misc. update:
* [svn-r8865] Purpose:Quincey Koziol2004-07-131-52/+61
| | | | | | | | | | | | | | | | | Code optimization Description: Re-work the insertion of a new child into an existing node, to exploit some speedups for adding the rightmost child, since this is a very common case when appending records to an unlimited size dataset. Also, hoist the checks for the tree's 'K' value into a field in the shared information about the tree, instead of re-calculating them all the time. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8853] Purpose:Quincey Koziol2004-07-101-234/+192
| | | | | | | | | | | | | | | | | | | | Code optimization Description: Refactor B-tree code to extract all common information for a B-tree into a shared structure that is pointed to by all the nodes in tree (instead of being included in each node). Also re-order B-tree node comparison checks for chunked datasets to check for >= the upper node first, since the comparison is a bit "heavy" and this check is more likely to succeed when you are adding records to the dataset. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest (also, recent h5dump commits have broken testing...)
* [svn-r8847] Purpose:Quincey Koziol2004-07-091-69/+20
| | | | | | | | | | | | Code cleanup & small optimization Description: Eliminate redundant recomputation of native key pointer offsets. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8844] Purpose:Quincey Koziol2004-07-091-2/+8
| | | | | | | | | | | | | | | | | | Bug fix Description: The "shared" raw B-tree node can get freed before all the B-tree nodes had been flushed out to disk and released by the cache. Solution: Implement a simple reference counting wrapper for objects in the library and use it to hold the shared raw B-tree nodes so they aren't freed before all references to them in memory are released. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) IRIX64 6.5 (modei4)
* [svn-r8823] Purpose:Quincey Koziol2004-07-071-397/+179
| | | | | | | | | | | | | | | Code optimization Description: Since the raw B-tree nodes are the same size and only used when reading in or writing out a B-tree node, move raw B-tree node buffer from being per node to a single node that is shared among all B-tree nodes of a particular tree, freeing up a lot of space and eliminating lots of memory copies, etc. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8800] Purpose:Quincey Koziol2004-07-031-29/+29
| | | | | | | | | | | | | Code cleanup Description: Fix problems when compiling with C++ compiler. Also clean up some warnings with gcc 3.4.x Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r8791] Purpose: Rewrote metadata cache (H5AC.c, etc.) to improve ↵John Mainzer2004-07-021-0/+52
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | performance. Description: Replaced the old metadata cache with a cache with a modified LRU replacement policy. This should improve the hit rate. Solution: Since we want to flush cache entries in increasing address order, I used the threaded binary B-tree code to store the cache entries. There is a fair bit of overhead here, so we may want to consider other options. While the code is designed to allow the support of other replacement algorithms, at present, only a modified version of LRU is supported. The modified LRU algorithm requires that a user selectable portion of the cache entries be clean. The clean entries are evicted first when writes are not permitted. If the pool of clean entries is used up, the cache grows beyond its user specified maximum size. The cache can also exceed its maximum size if the combined size of the protected (or locked) entries exceeds the maximum size of the cache. Platforms tested: eirene (serial, parallel, fp), h5committested Misc. update:
* [svn-r8736] Purpose:Quincey Koziol2004-06-241-68/+24
| | | | | | | | | | | | Code cleanup Description: Some code cleanups before starting serious optimization efforts. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r8731] Purpose:Quincey Koziol2004-06-231-11/+2
| | | | | | | | | | | | | | | Code cleanup & minor optimization Description: Re-work the way interface initialization routines are specified in the library to avoid the overhead of checking for them in routines where there is no interface initialization routine. This cleans up warnings with gcc 3.4, reduces the library binary size a bit (about 2-3%) and should speedup the library's execution slightly. Platforms tested: FreeBSD 4.10 (sleipnir) w/gcc34 h5committest
* [svn-r8696] Purpose:Quincey Koziol2004-06-161-1/+1
| | | | | | | | | | | | | | | | | Code optimizations Description: Eliminate memset() call in H5S_set_extent_simple(). Use malloc() instead of calloc in H5B<mumble>. Change global heap code to track heap objects that are in use in order to allocate new objects more quickly and also to avoid memset() and calloc() calls. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8625] Purpose:Quincey Koziol2004-06-081-4/+28
| | | | | | | | | | | | | | | Code optimization Description: Avoid pushing errors on error stack when an object is not found in a B-tree. Sometimes we are just checking if the object exists before we insert it into the B-tree and the higher levels in the library should be responsible for determining if not finding the object in B-tree is really an error. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8472] Purpose:Quincey Koziol2004-05-031-13/+24
| | | | | | | | | | | | | Code optimization Description: Eliminate the B-tree "split_ratios" as a parameter and pull it from the DXPL instead. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8301] Purpose:Quincey Koziol2004-04-061-16/+16
| | | | | | | | | | | | | Code optimization Description: Move handling for free list arrays that have no maximum size to separate set of routines and optimize computations for free list arrays with maximum size to avoid re-computing sizes all the time. Platforms tested: h5committest Solaris 2.7 (arabica)
* [svn-r8109] Purpose:Quincey Koziol2004-01-241-0/+1
| | | | | Add note about B-tree not being balanced during deletion operations, pointing interested readers at the Yao & Lehman paper.
* [svn-r8079] Purpose:Quincey Koziol2004-01-191-1/+1
| | | | | | | | | | | | Add tests & docs Description: Added tests for the recent B-tree bug fixes & document their fix in the release notes. Platforms tested: FreeBSD 4.9 (sleipnir) Too minor to require h5committest
* [svn-r8075] Purpose:Quincey Koziol2004-01-161-1/+55
| | | | | | | | | | | | | | | | | | Bug fix. Description: Fix problems in B-tree deletion routine that were corrupting the data structure when the B-tree had several levels and the right-most item from a leaf node that was the right-most child of an internal node was removed. Also address similar problems when a complete internal or right-most node was removed. NOTE: The B-tree deletion routines are still _NOT_ maintaining the B-tree properties correctly, that will be addressed in a future (hopefully soon) fix. Platforms tested: FreeBSD 4.9 (sleipnir) too obscure to require h5committest
* [svn-r7917] Purpose:Quincey Koziol2003-12-061-8/+8
| | | | | | | | | | | | | | | | | | | Code cleanup Description: Clean up compiler warnings, especially the 'FUNC' variable not used which comes out in production mode. Solution: Had to add a new FUNC_ENTER_NOAPI_NOINIT_NOFUNC macro for those non-API functions which don't need the 'FUNC' variable defined. (This will be _so_ much easier when C99 is standard on all our supposed platforms, since it has a __FUNC__ macro... ) Platforms tested: FreeBSD 4.9 (sleipnir) too minor for h5committest (although there were lots of files changed, the change was minor in each one)
* [svn-r7489] Purpose:Bill Wendling2003-09-181-59/+132
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Update Description: A lot of modifications for the FPHDF5 stuff: H5AC.c H5ACprivate.h - Removed AC_find (it's replaced with AC_protect and AC_unprotect). Added flushing if it's an FPHDF5 driver and we're doing an AC_set or AC_unprotect with the dirty flag set. H5B.c - Split up the B_flush function into different functions since the one function was doing serialization which is better left as a separate entity. H5D.c - Removed some FPHDF5 code that was incorrect H5F.c - Split up the F_flush function so that it no longer allocates file space. Created new functions (F_init_superblock, F_read_superblock, and F_write_superblock) for greater modularity and so that the FPHDF5 non-captain processes can read the superblock after the captain process writes it. H5FD.c - Error message correction. H5FDfphdf5.c - Removed MPI barrier call that wasn't needed. H5FPclient.c H5FPserver.c - Modified so that if a process requests data that isn't exactly aligned, we can return it if we have the block that contains the requested address. H5G.c H5Gent.c H5Gnode.c H5HL.c H5HLpkg.h H5HLprivate.h H5Oefl.c - Removed the H5HL_peek function since it was doing a (now unsafe) holding of the information in the cache. Replaced with protect and unprotect calls. H5TB.c - Error fix. The TB_dless function wasn't working properly. H5Gstab.c - Format change. H5err.txt H5Edefin.h H5Einit.h H5Epubgen.h H5Eterm.h - Added new error code. Platforms tested: Modi4 (paralle, Fortran) Sol (Fortran) Linux (C++, Fortran) Copper (Parallel, Fortran) Misc. update:
* [svn-r7467] Purpose:Quincey Koziol2003-09-111-15/+27
| | | | | | | | | | | | | | Code cleanup Description: Patch up a few places where the metadata cache could ask for a read lock instead of a write lock and other minor code cleanups. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to need h5committest Misc. update:
* [svn-r7460] Purpose:Bill Wendling2003-09-101-19/+22
| | | | | | | | | | | | | | | Update Description: Added extra parameter to the H5AC_protect() function that indicates if the cache being asked for is going to be written to or just read from. Those AC_protect calls that were H5AC_find calls are now read-only. The rest are writes. Platforms tested: Linux (h5committest not needed due to size and small impact) Misc. update:
* [svn-r7456] Purpose:Bill Wendling2003-09-101-27/+97
| | | | | | | | | | | | | | | | | | | | | Removal of H5AC_find() Description: The H5AC_find() function is mostly redundant and with the new Flexible Parallel HDF5 stuff, we need to do locking on metadata returned from the H5AC_find() anyway. So, all of the locking stuff will be placed in the H5AC_{un}protect() functions. The H5AC_find() is no longer needed. Solution: Replaced all H5AC_finds with H5AC_protects and H5AC_unprotects. Platforms tested: Linux (Fortran & C++) Solaris (Fortran) Irix (Parallel & Fortran) Misc. update:
* [svn-r7446] Purpose:Quincey Koziol2003-09-061-29/+40
| | | | | | | | | | | | Code cleanup/bug fix Description: Move metadata cache calls around a bit so they protect the usage of the metadata better. Platforms tested: FreeBSD 4.9 (sleipnir) too small to need h5committest
* [svn-r7445] Purpose:Bill Wendling2003-09-041-7/+31
| | | | | | | | | | | | | | | | | | | | | Fix, of a sort Description: Some of the code would get an object from the cache via the H5AC_find() function and then modify the returned object. This behavior is incorrect as the pointer returned via the H5AC_find() function is supposed to be read only. Solution: Changed the H5AC_finds to H5AC_protect() instead and added the appropriate H5AC_unprotect() function. Platforms tested: (simulated h5committest by hand since it doesn't work for me) Linux (Fortran, C++) Solaris (Fortran) AIX (Fortran, C++) SGI (Parallel, Fortran)
* [svn-r7384] Purpose:Quincey Koziol2003-08-191-5/+6
| | | | | | | | | | | Code cleanup Description: More linting... Platforms tested: FreeBSD 4.8 (sleipnir) too minor to need h5committest
* [svn-r7369] Purpose:Quincey Koziol2003-08-151-3/+3
| | | | | | | | | | | | | | | | | Bug fix Description: The metadata cache 'destroy' callback routines need the file handle in order for certain callback routines (currently just the H5HG one) to perform extra cleanups. The recent change to call the 'destroy' callback from the 'clear' callback omitted this parameter. Solution: Add the file handle to the metadata cache 'clear' callbacks. Platforms tested: FreeBSD 4.8 (sleipnir) too small to need h5committest
* [svn-r7367] Purpose:Bill Wendling2003-08-151-3/+9
| | | | | | | | | | | | | | | | | | | Update Description: Added an extra flag to the clear functions that triggers a "destroy" of the object being cleared if necessary. This is a fix for the FPHDF5 stuff which had an object sticking around after it was cleared. (In FPHDF5, some processes are in charge of destroying the object, but all processes might actually allocate the object.) Platforms tested: AIX (Copper: Fortran & C++) Linux (Verbena: Fortran & C++) IRIX (Modi4: Parallel & Fortran) (Sol is down) Misc. update:
* [svn-r7204] Purpose:Quincey Koziol2003-07-101-272/+280
| | | | | | | | | | | | | Code cleanup Description: Tail end of B-tree 'K' value conversion to unsigned ints. Also, lots of misc. code cleanups suggested by lint tool Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7080] Purpose:Quincey Koziol2003-06-231-12/+6
| | | | | | | | | | | | | | | | | Bug fix (backward compatibility) Description: Changes we've made during development of the 1.5.x branch had broken the feature of allowing user's callbacks to H5Giterate to return a value through the library back to the application which called H5Giterate. Solution: Correctly pass along iterator callback return value and adjust internal library code to conform to this design. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r6878] Purpose:Quincey Koziol2003-05-151-11/+21
| | | | | | | | | | | Code cleanup Description: Limit the scope on more function prototypes/macros/typedefs. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest not necessary.
* [svn-r6647] Purpose:Quincey Koziol2003-04-141-12/+128
| | | | | | | | | | | | | | | | | | Code cleanup & new feature Description: Track changes to H5AC API (code cleanup) Added routine to delete B-tree in file. 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).
* [svn-r6632] Purpose:Quincey Koziol2003-04-111-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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:
* [svn-r6519] Purpose:Quincey Koziol2003-03-221-2/+6
| | | | | | | | | | | | | Bug fix/code cleanup/new feature Description: Fix h5debug to work correctly again, with all the changes over the past few months. Improved and cleaned up debugging output available in h5debug. Platforms tested: FreeBSD 4.7 (sleipnir)
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