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* [svn-r13068] Ran bin/reconfigure. Some of the scripts have been changed or ↵James Laird2006-12-181-19/+19
| | | | | | | | | haven't been run in a while, so many of the source files were updated with tracing macros, etc. No code changes by me. Tested on kagiso and smirom.
* [svn-r12994] Description:Quincey Koziol2006-11-291-18/+2
| | | | | | | | | | | | | | | Propagate object creation properties up into group, dataset and named datatype property lists, when those property lists are retrieved for existing objects in a file. Also, add H5Tget_create_plist() API routine, to allow named datatype property lists to be retrieved for named datatypes. Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r12845] Description:Quincey Koziol2006-11-021-166/+146
| | | | | | | | | | | | | Finish refactoring job on the library's property list class initialization code, so that the library determines the parent class dependencies at run-time, eliminating the need for developers to initialize the classes in a particular order. Also eliminates some more redundant code... Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe & debugging turned on Linux/32 2.4 (heping) w/FORTRAN & C++ Linux/64 2.4 (mir) w/build-all & 1.6 compat enabled AIX/32 5.x (copper) w/FORTRAN & parallel
* [svn-r12842] Description:Quincey Koziol2006-11-021-292/+248
| | | | | | | | | | | | | | | | Refactor generic property list initialization code to put property list specific routines in property list modules, instead of scattered to the four winds. Also, introduce property list class initialization objects, to make adding new property list classes in the library easier. Fix daily test failure by using H5Pget_elink_prefix() API routine instead of looking at the "raw" generic property list information. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/C++ & FORTRAN Linux/64 2.4 (mir) w/build-all & 1.6 compat
* [svn-r12825] Description:Quincey Koziol2006-10-301-0/+6
| | | | | | | | Rudimentary support for creating creation order index (but not inserting links in it yet). Testedon: Mac OS X/32 10.4.8 (amazon)
* [svn-r12803] Description:Quincey Koziol2006-10-231-1/+1
| | | | | | | | | | | | | | Finish new version of the I/O pipeline message, which is much smaller than the previous version. This version is used with the "use the latest version of the format" flag. Closed several memory leaks/overruns (found with valgrind). Also, lots of compiler & formatting cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12706] Description:Quincey Koziol2006-10-021-18/+18
| | | | | | | | | Clean up some of the warnings on 64-bit Linux... Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2) Too minor to require h5committest
* [svn-r12533] Standardized the way path prefixes are passed to external links ↵James Laird2006-08-031-0/+5
| | | | | | using a LAPL. Now there are H5Pget and H5Pset functions for "elink_prefixes".
* [svn-r12531] Fixed a bug that occurred with 64-bit compilers. Types were ↵James Laird2006-08-031-1/+1
| | | | | | | used inconsistently (the nlinks property was an int in some places and a size_t elsewhere--it is now a size_t everywhere).
* [svn-r12528] Added User-Defined links to the library.James Laird2006-08-021-3/+37
| | | | | | | | | | | | | | Users can create external links using H5L_create_external(). These links point to an object in another HDF5 file. Users can alter the behavior of external links or create new kinds of links by registering callbacks using the H5L interface. Added tests, tools support, etc. Also a number of other, minor changes have been made (some restructuring of the H5L interface, for instance). Additional documentation and examples are forthcoming.
* [svn-r12452] Purpose:James Laird2006-07-051-15/+48
| | | | | | | | | | | | | | | | | | | | | | Feature Description: Revised Link APIs. Solution: New link APIs use H5L* H5*create_expand do not create links to the objects created; this must be done manually with H5Llink. Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy), and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query API (H5Lget_linkinfo instead of H5Gget_objinfo). All old APIs are still supported in H5Gdeprec.c . Platforms tested: sol, mir, copper Misc. update: Forgot to update MANIFEST and release docs. Will do after checkin.
* [svn-r12189] Purpose:Quincey Koziol2006-04-011-7/+40
| | | | | | | | | | | | | | New/expanded features Description: Check in Peter's changed for the object copy code: - Allow/fix copying datasets using named variable-length datatypes - Start adding framework for property list to control how object copying occurs. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11850] Purpose:James Laird2006-01-021-0/+13
| | | | | | | | | | | | | | Feature Description: Added character encoding and attribute creation property lists. Solution: Attributes' character encoding is set via the ACPL. The default is ASCII, with UTF-8 being the other option currently. Platforms tested: heping, mir, sleipnir, copper
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-20/+52
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r11384] Purpose:Quincey Koziol2005-09-121-17/+16
| | | | | | | | | | | | | | | | | | | | | Code cleanup Description: Merge back changes from "compact group" work that improve the infrastructure of the library and may impact others. In this round of merging, that includes: - Move datatype allocation into single internal routine, instead of duplicated code that was spread out in a dozen or so places. - Clean up guts of object header routines (H5O_*) to allow for some of the fancieroperations that need to be performed on groups, along with some general improvements. - Added a new error code - Some minor cleanups in other code.... Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Mac OS X
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-52/+52
| | | | | | | | | | | | | | | | | | | | 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-r10958] Purpose:Quincey Koziol2005-06-201-11/+124
| | | | | | | | | | | | | New feature Description: Add group creation & access property lists, dataset access property lists and named datatype creation & access property lists. Currently have <foo>_extend() API names, which will need to be changed for the final release. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (heping)
* [svn-r10736] Purpose:Quincey Koziol2005-05-071-1/+1
| | | | | | | | | | | Code cleanup Description: Clean up some compiler warnings Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r10187] Purpose:Quincey Koziol2005-03-111-9/+9
| | | | | | | | | | | | | Code cleanup, mostly Description: Remove remaining TBBT error info Add new error code for block tracker Platforms tested: FreeBSD 4.11 (sleipnir) Solaris 2.9 (shanti)
* [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-r9764] Purpose:Quincey Koziol2005-01-061-50/+33
| | | | | | | | | | | | | | | | New feature Description: Add some additional features to the skip list code that was needed to fully support all the features that the threaded, balanced binary tree code has. Also, updated the property list code to take advantage of a few of the new features. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r9734] Purpose:Quincey Koziol2004-12-301-2/+2
| | | | | | | | | | | | Code cleanup Description: Convert chunk iteration code to use skip lists instead of threaded, balanced binary trees. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & szip Too minor to require h5committest
* [svn-r9730] Purpose:Quincey Koziol2004-12-301-324/+313
| | | | | | | | | | | | | Code cleanup (sorta) Description: Transition the generic property list code from using the threaded, balanced binary tree code (H5TB<foo>() routines) to use skip lists (H5SL<foo>() routines) for internal management of properties, etc. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r9552] Purpose:Quincey Koziol2004-11-191-10/+31
| | | | | | | | | | | | | | | | | Code optimization Description: Avoid making as many copies of attribute information. Also, be smarter about which properties we've seen before when copying and closing property lists. Fix memory leak of attribute data structures. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r8781] James Laird2004-07-011-1/+0
| | | | | | | | | | | | | | | | Purpose: HDF5 now supports SZIP with no encoder. Description: SZIP can be configured to have both encoder and decoder or just to have the decoder. HDF5 can now query the configuration of any filter, and will throw errors if users try to write using a filter with encoding disabled. Solution: Added H5Zget_filter_info function, changed API for H5Pget_filter and H5P_get_filter_by_id. See SZIP RFC. Platforms tested: Copper (fortran, C++, parallel), Sleipnir (C++), Arabica (fortran, C++), Verbena (fortran, C++) Misc. update:
* [svn-r8760] Purpose:Quincey Koziol2004-06-291-3/+3
| | | | | | | | | | | | | Code cleanup & small bug fix Description: Regenerate dependency files Add htri_t as separate type from hbool_t for code tracing purposes. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8731] Purpose:Quincey Koziol2004-06-231-10/+9
| | | | | | | | | | | | | | | 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-r8707] Changed the way HDF5 handles hid_t's and added API functions to ↵James Laird2004-06-181-6/+6
| | | | allow users to register IDs and ID types at runtime.
* [svn-r8488] Purpose:Leon Arber2004-05-061-0/+1
| | | | | | | | | | | | | | | | | | | Bug fix. Description: Fixed handling of trivial data transform expressions (like 5/3 + 3) and some data coversion fixes. Also added more tests to dtransform.c Solution: Added some more checks in the H5Z_xform_reduce_tree function to see if perhaps the transform expression is complicated and is a non-trivial reduction. Added tests for data conversion to dtransform as well as tests for a trivial data transform expression. Platforms tested: h5committest'ed, except used arabica instead of sol and didn't do on copper b/c no logon there. Problem noted with mtime test...doesn't appear to be related to anything having to do with data transforms.
* [svn-r8287] Purpose:Quincey Koziol2004-03-301-1/+1
| | | | | | | | | | | | | | Bug fix/code cleanup Description: Copy Robb's feature in SSlib that checks that the name of the function used in the FUNC_ENTER macro is actually the name of function. Fixed a bunch of typos & copy-n-pasto's for functions with incorrect names. Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8038] Purpose:Quincey Koziol2004-01-081-48/+214
| | | | | | | | | | | | | | | | | | | | Bug fix Description: When two property lists are compared, the H5Pequal routine was just comparing the raw information for the property values. This causes problems when the raw information contains pointers to other information. Solution: Allow a 'compare' callback to be registered for properties, so that a user application get perform the comparison itself, allowing for "deep" compares of the property value. This was exported to the H5Pregister & H5Pinsert routines in the development branch, but not the release branch. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest
* [svn-r7930] Purpose:Quincey Koziol2003-12-111-4/+3
| | | | | | | | | | | | Bug fix/code cleanup Description: Make H5Pclose_class() decrement the ID's reference count to close a generic property class ID, which allows the new H5I routines to work correctly. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest
* [svn-r7917] Purpose:Quincey Koziol2003-12-061-37/+37
| | | | | | | | | | | | | | | | | | | 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-r7373] Purpose:Quincey Koziol2003-08-151-7/+2
| | | | | | | | | | | | Code cleanup Description: Cleanup H5Pclose code and also switch a few internal users of H5Pclose to use H5I_dec_ref instead. Platforms tested: FreeBSD 4.8 (sleipnir) too small for h5committest
* [svn-r7304] Purpose:Quincey Koziol2003-08-081-6/+2
| | | | | | | | | | Code cleanup Description: Remove some unused code and correct some error strings Platforms tested: h5committested
* [svn-r7071] Purpose:Quincey Koziol2003-06-201-1/+1
| | | | | | | | | | | Code cleanup Description: Tweak internal iterator over IDs to not require constant "operator" data. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r6952] Purpose:Quincey Koziol2003-06-041-96/+6
| | | | | | | | | | | | | Code cleanup Description: Move testing routines into their own module, to avoid linking them into user's applications needlessly. Platforms tested: FreeBSD 4.8 (sleipnir) w/C++ FreeBSD 4.8 (sleipnir) w/parallel h5committested
* [svn-r6878] Purpose:Quincey Koziol2003-05-151-46/+2
| | | | | | | | | | | Code cleanup Description: Limit the scope on more function prototypes/macros/typedefs. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest not necessary.
* [svn-r6269] Purpose:Quincey Koziol2003-01-131-4/+39
| | | | | | | | | | | | | Code cleanup Description: Various code cleanups to allow the development branch to be compiled with a C++ compiler (i.e. CC=g++ ) Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) C++
* [svn-r6266] Purpose:Quincey Koziol2003-01-101-77/+77
| | | | | | | | | | | | Code cleanup/new feature. Description: Split FUNC_LEAVE into API and non-API specific versions. This allows a solution to compiling this branch with C++, as well as reducing the size of the binaries produced. Platforms tested: FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
* [svn-r6255] Purpose:Quincey Koziol2003-01-091-24/+43
| | | | | | | | | | Code cleanup Description: Clean up a few more warnings and update dependencies. Platforms tested: Linux 2.2.18smp (eirene) serial & parallel
* [svn-r6252] Purpose:Quincey Koziol2003-01-091-654/+1237
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Lots of performance improvements & a couple new internal API interfaces. Description: Performance Improvements: - Cached file offset & length sizes in shared file struct, to avoid constantly looking them up in the FCPL. - Generic property improvements: - Added "revision" number to generic property classes to speed up comparisons. - Changed method of storing properties from using a hash-table to the TBBT routines in the library. - Share the propery names between classes and the lists derived from them. - Removed redundant 'def_value' buffer from each property. - Switching code to use a "copy on write" strategy for properties in each list, where the properties in each list are shared with the properties in the class, until a property's value is changed in a list. - Fixed error in layout code which was allocating too many buffers. - Redefined public macros of the form (H5open()/H5check, <variable>) internally to only be (<variable>), avoiding innumerable useless calls to H5open() and H5check_version(). - Reuse already zeroed buffers in H5F_contig_fill instead of constantly re-zeroing them. - Don't write fill values if writing entire dataset. - Use gettimeofday() system call instead of time() system when checking the modification time of a dataset. - Added reference counted string API and use it for tracking the names of objects opening in a file (for the ID->name code). - Removed redundant H5P_get() calls in B-tree routines. - Redefine H5T datatype macros internally to the library, to avoid calling H5check redundantly. - Keep dataspace information for dataset locally instead of reading from disk each time. Added new module to track open objects in a file, to allow this (which will be useful eventually for some FPH5 metadata caching issues). - Remove H5AC_find macro which was inlining metadata cache lookups, and call function instead. - Remove redundant memset() calls from H5G_namei() routine. - Remove redundant checking of object type when locating objects in metadata cache and rely on the address only. - Create default dataset object to use when default dataset creation property list is used to create datasets, bypassing querying for all the property list values. - Use default I/O vector size when performing raw data with the default dataset transfer property list, instead of querying for I/O vector size. - Remove H5P_DEFAULT internally to the library, replacing it with more specific default property list based on the type of property list needed. - Remove redundant memset() calls in object header message (H5O*) routines. - Remove redunant memset() calls in data I/O routines. - Split free-list allocation routines into malloc() and calloc()- like routines, instead of one combined routine. - Remove lots of indirection in H5O*() routines. - Simplify metadata cache entry comparison routine (used when flushing entire cache out). - Only enable metadata cache statistics when H5AC_DEBUG is turned on, instead of always tracking them. - Simplify address comparison macro (H5F_addr_eq). - Remove redundant metadata cache entry protections during dataset creation by protecting the object header once and making all the modifications necessary for the dataset creation before unprotecting it. - Reduce # of "number of element in extent" computations performed by computing and storing the value during dataspace creation. - Simplify checking for group location's file information, when file has not been involving in file-mounting operations. - Use binary encoding for modification time, instead of ASCII. - Hoist H5HL_peek calls (to get information in a local heap) out of loops in many group routine. - Use static variable for iterators of selections, instead of dynamically allocation them each time. - Lookup & insert new entries in one step, avoiding traversing group's B-tree twice. - Fixed memory leak in H5Gget_objname_idx() routine (tangential to performance improvements, but fixed along the way). - Use free-list for reference counted strings. - Don't bother copying object names into cached group entries, since they are re-created when an object is opened. The benchmark I used to measure these results created several thousand small (2K) datasets in a file and wrote out the data for them. This is Elena's "regular.c" benchmark. These changes resulted in approximately ~4.3x speedup of the development branch when compared to the previous code in the development branch and ~1.4x speedup compared to the release branch. Additionally, these changes reduce the total memory used (code and data) by the development branch by ~800KB, bringing the development branch back into the same ballpark as the release branch. I'll send out a more detailed description of the benchmark results as a followup note. New internal API routines: Added "reference counted strings" API for tracking strings that get used by multiple owners without duplicating the strings. Added "ternary search tree" API for text->object mappings. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} Other platforms/configurations tested? FreeBSD 4.7 (sleipnir) serial & parallel Solaris 2.6 (baldric) serial
* [svn-r6024] Purpose:Bill Wendling2002-10-231-19/+18
| | | | | | | | | Feature Add Description: Moved some functions from having only module scope to having public scope, but only available in the HDF5 internals (not public APIs). Platforms tested: Eirene, Arabica, Modi4
* [svn-r5992] Purpose:Quincey Koziol2002-10-141-23/+13
| | | | | | | | | | | | | | | | | Bug fix Description: Generic property classes where incorrectly reference counting their users, in certain cases, causing a memory leak. Solution: Cleanup reference counting code & unify in H5P_access_class() Platforms tested: FreeBSD 4.6 (sleipnir) w and w/o parallel Linux 2.2.x (eirene) w/FORTRAN & C++ Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/FORTRAN & parallel
* [svn-r5968] Purpose:Quincey Koziol2002-10-091-2/+2
| | | | | | | | | Code cleanup Description: Change new H5P_get_class_path and H5P_open_class_path functions to be non- static and put prototypes in H5Pprivate.h Platforms tested: FreeBSD 4.6 (sleipnir) (no triple-check necessary)
* [svn-r5964] Purpose:Quincey Koziol2002-10-081-32/+155
| | | | | | | | | | | | | | | Internal feature. Description: To complement the "get the class's path" functionality, there needs to be a way to open a generic property class with a path. Solution: Implement the "open a class by path" functionality. Also, add internal testing routines. Platforms tested: FreeBSD 4.6 (sleipnir) (too small for triple testing)
* [svn-r5963] Purpose:Quincey Koziol2002-10-081-7/+115
| | | | | | | | | | | | | | | | | | | | New internal feature. Description: Need some way to determine the "full path" for a generic property class, i.e. where is this class in the class hierarchy, in relation to its parent class, etc. Solution: Added an internal function "H5P_get_class_path" and a testing function "H5Pget_class_path_test" that builds the full path of a generic property class back to the top of its class hierarchy. This implementation uses '/' characters to delimit the components of the class path, but no special cases are currently supported for having a '/' character as part of the actual class name. Should this become an issue, code to support (and test) it will need to be added. Platforms tested: FreeBSD 4.6 (sleipnir) (not major enough to justify triple-test)
* [svn-r5962] Purpose:Quincey Koziol2002-10-071-13/+73
| | | | | | | | | | | | Bug fix Description: H5Pequal's algorithm for comparing property lists wasn't allowing property lists that are equal but had the properties inserted in a different order in the list's hash table. Solution: Re-did the algorithm a bit to compare the properties better. Platforms tested: FreeBSD 4.6 (sleipnir) (minor enough to not need triple testing)
* [svn-r5872] Purpose:Quincey Koziol2002-08-121-3676/+0
| | | | | | | | | | | | Code cleanup Description: Move get/set routines for each type of property list (file creation, dataset creation, file access and dataset transfer) into their own source code module. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5871] Purpose:Quincey Koziol2002-08-121-277/+108
| | | | | | | | | | | | | | | | Code cleanup Description: Combined H5P_isa_class and H5I_object functionality into a new internal H5P API function: H5P_object_verify, which checks that a property list is the appropriate class and then returns the property list object associated with the property list ID. This reduces the source code by about 200 LOC and trims the library binary some more. Platforms tested: FreeBSD 4.6 (sleipnir)
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