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* [svn-r6610] Purpose:Quincey Koziol2003-04-091-3/+11
| | | | | | | | | | | | | | | | | | | | | | | | Code cleanup & new features Description: Added three new API functions for working on I/O filters: H5Pmodify_filter, H5Pget_filter_by_id and H5Pall_filters_avail. Documentation on these will be added for the 1.6.0 release, until then, we'll have to use the source code. Also, simplified the H5Pset_szip and H5Pset_shuffle API interfaces, since those filters are using the new "set local" callback facility to set dataset- specific parameters. Probably, some of the changes to internal H5Z routines are captured in these changes also. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6577] Purpose:Quincey Koziol2003-04-031-1/+2
| | | | | | | | | | | | | | | | | | Code cleanup (sorta) Description: The H5Pset_szip API call was forcing users to pass in their parameters in the same way as the internal representation of the filter parameters used by the library (as an array of unsigned values). Solution: Changed to pass in separate parameters in a more user-friendly format. Platforms tested: FreeBSD 4.8 (sleipnir) IRIX64 6.5 (modi4) w/parallel Misc. update:
* [svn-r6559] Purpose:Bill Wendling2003-04-011-11/+13
| | | | | | | | | | | | Update Description: Missed this file when updating copyright statements. Platforms tested: None (comment change) Misc. update:
* [svn-r6551] Purpose:MuQun Yang2003-04-011-13/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | To support szip compression in HDF5 Description: szip compression support is required by NASA ESDIS. The compression algorithm is good for scientific data. In HDF5, we add another filter function to make szip as a default compression package as we did for gzip(or zlib). In this check-in, a new function called H5Pset_szip was added into H5Pdcpl.c, this function is very similar to H5Pset_deflate. The only difference is SZIP needs four parameters from the user to get the compression done while gzip needs only one. So we pass a pointer to this function instead of an integer number. The description of the four parameters of szip should be in different documents. H5Z.c and other header files were simply modified to have HDF5 know szip. Solution: See the decription Platforms tested: Since there are changes of configure.in and configure,I didn't use h5committest. I tested with four platforms. 1) Linux 2.4 (eirene) 2) Solaris 2.7(arabica) 3) windows 2000(VS 6.0) 4) SGI IRIX6.5-64(modi4) For test 1)-3), only basic C tests were done For modi4 test, I tested 64-bit C,parallel and fortran. All tests passed, except a warning message from szip library when checksum is used in some order, which doesn't cause any real problems. Misc. update:
* [svn-r6546] Purpose:Bill Wendling2003-03-311-11/+13
| | | | | | | | | | | | Update Description: Updated copyright statement in files which hadn't been updated yet. Platforms tested: Linux (Only comment change) Misc. update:
* [svn-r6400] Raymond Lu2003-02-121-1/+1
| | | | | | | | | | | Purpose: Change feature Description: Switch to Fletcher32 from Adler32 checksum Platforms tested: arabica, eirene, modi4 Misc. update: MANIFEST and RELEASE.txt updated.
* [svn-r6375] Raymond Lu2003-02-041-0/+5
| | | | | | | | | | | Purpose: New feature Description: Added Adler32 checksum as a filter in pipeline Platforms tested: arabica (fortran), eirene (, C++), modi4 (parallel, fortran) Misc. update: Update release_docs/RELEASE.
* [svn-r6269] Purpose:Quincey Koziol2003-01-131-4/+4
| | | | | | | | | | | | | 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-r6252] Purpose:Quincey Koziol2003-01-091-28/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r6223] Purpose:Binh-Minh Ribler2002-12-221-4/+4
| | | | | | | | | | | | | | | | | | | | | | Bug fix - informed by Kent Description: Some identifiers were flagged as unresolved symbols when building with c++ on Windows. The reason is the name of these identifiers were changed by the c++ compiler, also called name mangling. Solution: Moved #ifdef __cplusplus extern "C" { #endif to include the offending identifiers so the c++ compiler will take them as is. Platforms: SunOS 5.7 (arabica) Linux 6.2 (eirene) Windows 2000
* [svn-r6087] MuQun Yang2002-11-131-0/+1
| | | | | | | | | | | | | | | | | | | Purpose: Adding internal shuffle filter Description: With the combination of shuffling filter with general compression algorithm, the compression ratio may be improved without adding much encoding and decoding time for many real NASA datasets(especially floating data) and other application datasets(See techNotes). Solution: SHuffle the bytes within the data to utilize the locality. Platforms tested: arabica , eirene, modi4 Misc. update: Update MANIFEST if you add or remove any file. Update release_docs/RELEASE for bug fixes, new features, etc. Update applicable document files too.
* [svn-r5993] Purpose:Quincey Koziol2002-10-141-4/+7
| | | | | | | | | | | | | | New feature. Description: Add H5P_DEFAULT_HASH_SIZE macro for users to use as the default size of hash tables for H5Pcreate_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-r5964] Purpose:Quincey Koziol2002-10-081-3/+0
| | | | | | | | | | | | | | | 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 Koziol2002-10-081-0/+3
| | | | | | | | | | | | | | | | | | | | 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-r5951] Raymond Lu2002-09-301-0/+5
| | | | | | | | | | | Purpose: New API functions Description: Added API functions to return pointer to low-level file handle (H5Fget_vfd_handle and H5FDget_vfd_handle) and related property list setting functions(H5Pset_family_offset and H5Pset_multi_type). Platforms tested: Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
* [svn-r5931] MuQun Yang2002-09-201-97/+97
| | | | | | | | | | | | Purpose: __DLL__ is a keyword in some platforms and __DLL__ is also defined as a macro for windows DLL applications. That causes problems. Description: Solution: Use H5_DLL*** to replace __DLL***__ at all header files. Change the macro defination at H5api_adpt.h. Platforms tested: linux2.2.18smp, irix64, solaris 2.7 and windows 2000
* [svn-r5926] Purpose:Quincey Koziol2002-09-131-2/+2
| | | | | | | | | | | | | API name change Description: Change all "space time" references to "alloc time", including API functions and macro definitions, etc. Platforms tested: FreeBSD 4.6 (sleipnir) w/C++ Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/parallel & FORTRAN
* [svn-r5563] Purpose:Quincey Koziol2002-06-101-2/+0
| | | | | | | | | | | New Feature Description: Add H5P[set|get]_small_data_block_size API function, per our discussions at last week's HDF5 meeting. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5536] Purpose:Quincey Koziol2002-06-051-5/+4
| | | | | | | | | | | | | | | | | New feature. Description: Added a "small data" block allocation mechanism to the library, similar to the mechanism used for allocating metadata currently. See the RFC for more details: http://hdf.ncsa.uiuc.edu/RFC/SmallData/SmallData.html This reduces the number of I/O operations which hit the disk for my test program from 19 to 15 (i.e. from 393 to 15, overall). Platforms tested: Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5170] Raymond Lu2002-04-111-0/+8
| | | | | | | | | | | Purpose: New feature Description: Fill-value's behaviors for contiguous dataset have been redefined. Basicly, dataset won't allocate space until it's necessary. Full details are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment. Platforms tested: Linux 2.2.
* [svn-r4696] Raymond Lu2001-12-111-0/+2
| | | | | | | | | | | | | | | | | Purpose: Modify H5Fclose behavior Description: The HDF5 actual file close behaves in several ways in terms of if there are still objects(dataset, group, datatype) opened in file. Solution: Added a new file access property, file close degree. It has four values, H5F_CLOSE_DEFAULT H5F_CLOSE_WEAK H5F_CLOSE_SEMI H5F_CLOSE_STRONG The way a file is closed is decided by these values. Platforms tested: IRIX64 6.5, SunOS 5.6, FreeBSD 4.4
* [svn-r4680] Purpose:Quincey Koziol2001-12-061-1/+3
| | | | | | | | | | | | | Code cleanup Description: Property that H5P(g|s)et_hyper_cache uses is no longer in use inside the library. Solution: Removed H5P(g|s)et_hyper_cache API functions, except when backward compatibility is turned on. When backward compatibility is turned on, the property is defined by the library, but unused internally. Platforms tested: FreeBSD 4.4 (sleipnir)
* [svn-r4676] Purpose:Quincey Koziol2001-12-051-0/+7
| | | | | | | | | | | | | | | | Backward Compatibility Fix Description: One of H5P[gs]et_buffer's parameters changed between v1.4 and the development branch. Solution: Added v1.4 compat stuff around H5P[gs]et_buffer implementation and testing to allow v1.4.x users to continue to use their source code without modification. These changes are for everything except the FORTRAN wrappers - I spoke with Elena and she will make the FORTRAN wrapper changes. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4675] Purpose:Quincey Koziol2001-12-051-0/+5
| | | | | | | | | | | | | | | | | | Backward Compatibility Fix Description: One of H5P[gs]et_sieve_buf_size's parameters changed between v1.4 and the development branch. Solution: Added v1.4 compat stuff around H5P[gs]et_sieve_buf_size implementation and testing to allow v1.4.x users to continue to use their source code without modification. There are no C++ or FORTRAN wrappers for these functions. There are also no regression tests for these functions... :-( Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4674] Purpose:Quincey Koziol2001-12-051-0/+5
| | | | | | | | | | | | | | | | | | Backward Compatibility Fix Description: One of H5P[gs]et_meta_block_size's parameters changed between v1.4 and the development branch. Solution: Added v1.4 compat stuff around H5P[gs]et_meta_block_size implementation and testing to allow v1.4.x users to continue to use their source code without modification. There are no C++ or FORTRAN wrappers for these functions. There are also no tests for these API functions currently... :-( Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4670] Purpose:Quincey Koziol2001-12-051-0/+5
| | | | | | | | | | | | | | | | Backward Compatibility Fix Description: One of H5P[gs]et_sym_k's parameters changed between v1.4 and the development branch. Solution: Added v1.4 compat stuff around H5P[gs]et_sym_k implementation and testing to allow v1.4.x users to continue to use their source code without modification. These changes are for everything except the FORTRAN wrappers - I spoke with Elena and she will make the FORTRAN wrapper changes. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4669] Purpose:Quincey Koziol2001-12-051-0/+8
| | | | | | | | | | | | | | | | Backward Compatibility Fix Description: One of H5P[gs]et_cache's parameters changed between v1.4 and the development branch. Solution: Added v1.4 compat stuff around H5P[gs]et_cache implementation and testing to allow v1.4.x users to continue to use their source code without modification. These changes are for everything except the FORTRAN wrappers - I spoke with Elena and she will make the FORTRAN wrapper changes. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4620] Purpose:Quincey Koziol2001-11-201-1/+2
| | | | | | | | | Code cleanup Description: Get rid of IDs from internal function calls and some small cleanups from the old-stype => generic property list conversion. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4589] Purpose:Quincey Koziol2001-11-031-1/+0
| | | | | | | | Code cleanup Description: Clean up various compiler warnings from generic property updates. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4584] Raymond Lu2001-11-021-21/+6
| | | | | | | | | Purpose: Switch from old property list to new generic property list. Description: Mainly changed H5Pcreat, H5Pclose, H5Pcopy. Platforms tested: IRIX64 6.5, FreeBSD, SunOS 5.7.
* [svn-r4573] Raymond Lu2001-10-251-3/+1
| | | | | | | Purpose: Switch mount property list to the new generic property list. Platforms tested: IRIX64 6.5, SunOS 5.7, FreeBSD.
* [svn-r4569] Raymond Lu2001-10-241-19/+17
| | | | | | | | | Purpose: Generic Property List Change Description: Changed file access list to the new generic list. Platforms tested: IRIX64, SunOS5.7, FreeBSD
* [svn-r4548] Purpose:Quincey Koziol2001-10-161-2/+2
| | | | | | | | | | | Code cleanup. Description: Fix a few compiler warnings from the file creation property list -> generic property list conversion. Also change a hard-wired value (8) for the number of B-tree key values to a value that uses the enum's generated by the compiler. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4543] Raymond Lu2001-10-151-5/+3
| | | | | | | Purpose: Changed the file creation property list to the new generic property list. Platform tested: IRIX64, SunOS5.7, FreeBSD
* [svn-r4517] Raymond Lu2001-10-031-5/+4
| | | | | | | | Purpose: Changed to the new generic property list for dataset creation property list. Platforms tested: Arabica, modi4 and Hawkwind
* [svn-r4482] Purpose:Quincey Koziol2001-09-261-12/+27
| | | | | | | | | | | | | | | | | | | | | | Kludge Description: Since we're only about halfway through converting the internal use of property lists from the "old way" to the generic property lists, we turned off snapshots to avoid exposing lots of API changes to users, until the APIs settled down. Getting the snapshots rolling again seems to have become a priority, so some changes are going to have to be made now that were going to be postponed until we were completely finished with the conversion. This requires that the old API functions be able to deal with both the old and new property lists smoothly. Solution: Kludge together the property list code so that they can transparently handle dealing with both the old and new property lists Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4437] Purpose:Quincey Koziol2001-09-121-0/+1
| | | | | | | | | Adding Feature Description: Added new H5Pcopy_prop function to copy a property (value) from one property list or class to another. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4329] Purpose:Quincey Koziol2001-08-121-1/+1
| | | | | | | | | | | | | | Bug Fix Description: The datatype conversion buffer size was only halfway converted from hsize_t to size_t and was causing problems. Also, the H5P_peek_<foo> routines have a bunch of identical code. Solution: Finished converting the datatype conversion buffer size to size_t and cleaned up the implementation of the H5P_peek_<foo> routines to call a common routine instead of reimplementing a bunch of code. Platforms tested: Solaris 2.7 (arabica)
* [svn-r4324] Purpose:Quincey Koziol2001-08-101-20/+42
| | | | | | | | | | | | | | | | | | | | | | | | New Features! Description: Start migrating the internal use of property lists in the library from the older implementation to the new generic property lists. Currently, only the dataset transfer property lists are migrated to the new architecture, all the rest of the property list types are still using the older architecture. Also, the backward compatibility features are not implemented yet, so applications which use dataset transfer properties may need to make the following changes: H5Pcreate(H5P_DATASET_XFER) -> H5Pcreate_list(H5P_DATASET_XFER_NEW) and H5Pclose(<a dataset transfer property list>) -> H5Pclose_list(id) This still may have some bugs in it, especially with Fortran, but I should be wrapping up those later today. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4312] Purpose:Quincey Koziol2001-08-061-24/+0
| | | | | | | | | Feature shift Description: Take out the v1.2.x compatibility stubs and put in the hooks for v1.4.x compatibility when needed. Platforms tested: FreeBSD 4.3 (hawkwind)
* [svn-r4286] Purpose:Quincey Koziol2001-07-311-1/+1
| | | | | | | | | | | | Bug Fix Description: Header file is using incorrect macro for detecting parallel I/O when backward compability is turned on. Solution: Fix header files to define prototypes for parallel I/O property list functions when compiled with v1.2 backward compatibility turned on. Platforms tested: Eyeballed... (Elena will be testing shortly)
* [svn-r4181] Purpose:Quincey Koziol2001-07-101-7/+9
| | | | | | | | | Bug Fix, Code Cleanup, Code Optimization, etc. Description: Fold in the hyperslab speedups, clean up compile warnings and change a few things from using 'unsigned' or 'hsize_t' to use 'size_t' instead. Platforms tested: FreeBSD 4.3 (hawkwind), Solaris 2.7 (arabica), Irix64 6.5 (modi4)
* [svn-r4099] Pedro Vicente Nunes2001-07-031-0/+8
| | | | | | | | | | | Purpose: Code Cleanup Description: Updating CodeWarrior Port Solution: Move around some Windows and Metroworks ifdefs, etc. Platforms tested: Solaris 2.7 (arabica) Linux 2.2 (eirene)
* [svn-r4088] Purpose:Quincey Koziol2001-06-291-2/+0
| | | | | | | | | | | | Code cleanup Description: Recent CodeWarrior patches have broken the Unix builds and moved code around in non-portable ways. Solution: Patched things back up to try to accomodate CodeWarrior and still let the Unix builds work correctly. Platforms tested: FreeBSD 4.3 (hawkwind)
* [svn-r4083] Pedro Vicente Nunes2001-06-291-1/+1
| | | | | | | | | | | | | | code warrior support and some clean up the macros file_seek and file_offset_t that were repeated over sevral files were put only in H5private.h H5private .h was updated for win32 vthe Description: Solution: Platforms tested:
* [svn-r4011] Purpose:Quincey Koziol2001-06-161-3/+1
| | | | | | | | | | | Code fix Description: Unresolved references to the image code were left behind when it was removed from the library.. Solution: Finished taking out the image stuff... Platforms tested: FreeBSD 4.3 (hawkwind)
* [svn-r3983] Purpose:Quincey Koziol2001-06-111-1/+0
| | | | | | | | | Code cleanups Description: Fixed a small number of warnings and also took out the H5private.h header from H5Ppublic.h Platforms tested: FreeBSD 4.3 (hawkwind)
* [svn-r3980] property list modification for image and palettePedro Vicente Nunes2001-06-091-37/+41
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* [svn-r3974] code warrior portPedro Vicente Nunes2001-06-071-0/+1
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* [svn-r3781] Purpose:Bill Wendling2001-04-051-6/+6
| | | | | | | | | | | | | | | | | | Update Description: Changed #include <hdf_file.h> construct to #include "hdf_file.h" so that the GNU compiler can more easily pick up the dependencies which it places in the .depend and Dependencies files. Also regenerated the Dependencies to go along with this. Platforms tested: Linux
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