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* [svn-r2774] H5FD.c:Albert Cheng2000-10-312-5/+33
| | | | | | | | | | | | | | | | | | | | Purpose: Bug fix Description: H5FD_close() wiped clean the public information before closing the FD. This caused problem to the lower level close() which wants to verify it has indeed handed a valid file-driver to close because that information is wiped out prematurely. Solution: Moved the public information part cleaning after it is closed. H5FDmpio.c: Added in a bunch of assertion to make sure the file handle is indeed an MPIO file. Platforms tested: IRIX64 -64 parallel
* [svn-r2766] ./hdf5/src/H5T.cRobb Matzke2000-10-311-1/+1
| | | | Updated API tracing calls
* [svn-r2765] ./hdf5/src/H5S.cRobb Matzke2000-10-311-1/+1
| | | | Updated API tracing calls.
* [svn-r2764] ./hdf5/src/H5FD.cRobb Matzke2000-10-311-1/+1
| | | | Updated API tracing calls.
* [svn-r2763] ./hdf5/src/H5F.cRobb Matzke2000-10-311-2/+8
| | | | | | | * 2000-10-31 Robb Matzke <matzke@llnl.gov> (H5F_dest) Do not call H5FL_FREE() if the root group object is null. This fixes a bug in h5ls when that tool is given a file which is not an hdf5 file.
* [svn-r2752] Purpose:Albert Cheng2000-10-301-1/+1
| | | | | | | | | | | Bug fix Description: There is typo in the H5D_write function which reported the optimized write failure as a H5E_READERROR. Solution: Replaced it with the correct H5E_WRITEERROR code. Platforms tested: modi4 parallel (compiled H5D.o only).
* [svn-r2748] Thomas Radke2000-10-281-0/+3
| | | | | | | | | | | | | Purpose: Detect whether the system has the netinet/tcp.h header file. Description: The Stream VFD uses setsockopt(2) to set TCP_NODELAY on an opened socket. This constant is defined normally in netinet/tcp.h except for GNU cc under Windows where this header doesn't exist. This template header file just contains the #undef HAVE_NETINET_TCP_H Platforms tested: Windows NT, GNU cc
* [svn-r2746] Thomas Radke2000-10-282-92/+257
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Port to Windows platform Bug fix Description: The Stream VFD is ported to Windows now. Also fixed a bug where an application terminated when it got a SIGPIPE due to sending/receiving on a closed socket. Solution: The socket stuff is treated different under Windows when using the MS compilers to build HDF5. They define their own socket datatype and have closesocket() instead of close(2) to close sockets. Also there are different header files for all the socket stuff. So I introduced my own socket decriptor datatype in H5FDstream.h which should be used to pass in external sockets. This datatype is mapped to either 'int' (UNIX-type sockets) or 'SOCKET' (Windows). In the code the error code checking was adapted according to the socket datatype used. Also, for Windows you have to call a routine to initialize the Socket layer before using it. As a kind of bug fix, the process signal mask is now set to ignore SIGPIPE signals which otherwise cause the application to terminate. The driver read/write routines catch this and return an error code. Platforms tested: Windows NT, both with MS Visual C++ compiler and with GNU cc It is interesting that when compiling with GNU cc under Windows it is possible to use both Windows and UNIX-type sockets (either one or the other). So I check for GNU cc and go for UNIX sockets if possible.
* [svn-r2744] Purpose:Quincey Koziol2000-10-271-0/+6
| | | | | | | | | | | | Bug fix Description: Forgot to decrement the number of objects in the group when removing each one... Solution: Decrement the ID count when successfully removing each object from a group. Platforms tested: None yet.
* [svn-r2743] Purpose:Quincey Koziol2000-10-271-37/+49
| | | | | | | | | | | | | | Bug fix Description: Fixed a very subtle bug that was corrupting the objects in a group when H5I_clear_group was called and not all the objects in the group were able to be cleared. Solution: Track whether an object as been deleted from each hash location's linked list and only destroy the list when all the objects on the list are actually removed. Platforms tested: None yet.
* [svn-r2736] Purpose:Quincey Koziol2000-10-256-268/+352
| | | | | | | | | | Code optimization Description: Minor tweaks throughout the optimized regular hyperslab code to increase speed. This set of improvements increase the benchmark time from taking ~5.46 seconds to ~4.50 seconds, or around a 20% further speedup. Platforms tested: Solaris 2.6 (baldric)
* [svn-r2735] Purpose:Albert Cheng2000-10-251-1/+1
| | | | | | | | | | | | | | | | | | Bug fix Description: Recent changes to H5FD_read() added a new argument of type of data to be written but the MPIO file driver call to H5FD_read() was not updated. Also, the prototype of H5FD_read() in H5Fprivate.h was "screened out", thus the compiler could not detect the inconsistency. With the mismatched arguments, MPIO failed badly. Solution: Update the H5FD_read() call with the new parameter. Since the call is used by H5Dread call so far, it is hardcoded to use H5FD_MEM_DRAW as the value. If the call is used besides for H5Dread, this parameter needs to be better defined. (Still need to fix the prototype being blocked off.) Platforms tested: O2K -64 parallel.
* [svn-r2722] Purpose:Quincey Koziol2000-10-2429-72/+80
| | | | | | | | | | Feature symmetry Description: A while ago I needed to get the 'type' of data being accessed during writes to the VFL driver, so I put in code to get the information down there. Albert asked for the same information during reads, so I've added that in. Tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2716] Purpose:Quincey Koziol2000-10-201-1/+1
| | | | | | | | | | Increase constant for H5S_MAX_RANK from 31 -> 32 Description: To better align the HDF5 library's maximum dimenions with HDF4 and netCDF, the maximum number of dimensions has been increased to 32. Platforms Tested: FreeBSD 4.1.1 (hawkwind) Solaris 2.5 (baldric)
* [svn-r2711] Purpose:Quincey Koziol2000-10-201-1/+1
| | | | | | | | | | | | Bug fix. Description: When the maximum number of elements in a fixed size, free-list managed array was allocated, the free-list code was writing off the end of the array. Solution: Changed definition of free-list managed arrays to allocate correct space for the array. Platforms tested: Solaris 2.5 (baldric) w/Purify
* [svn-r2707] Purpose:Quincey Koziol2000-10-191-15/+91
| | | | | | | | | | | | | Optimization for parallel I/O Description: When contiugous hyperslabs are defined (i.e. with the block=stride), the library was only aggregating the hyperslabs together for the fastest changing dimension. Solution: Add some extra code to detect when contiguous hyperslabs span more than one row and output the entire contiguous section at once. Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2702] Purpose:Quincey Koziol2000-10-191-7/+23
| | | | | | | | | | | | Code cleanup Description: There's been a compiler warning about modifying a 'const' object in the H5T_copy routine for several years now, which a few users have reported. Solution: Removed call to sort the old datatype (the const object) and changed the code to work with unsorted datatypes. Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2699] Purpose:Quincey Koziol2000-10-192-1/+24
| | | | | | | | | | | | | | | Bug fix Description: "Time" datatypes (H5T_UNIX_D*) were not being stored and retrieved in the datatype object header message correctly. Solution: Store endian-ness and precision in the datatype object header message and added test to continue to track them working correctly. This fixes bug #512. Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2694] Purpose:Quincey Koziol2000-10-183-13/+13
| | | | | | | | | | | | | Bug fix Description: H5Sget_simple_extent_npoints return type is hsize_t and the error value is 0, but it is possible to have 0 points in a dataset with an unlimited dimension, but no data written yet. Solution: Changed H5Sget_simple_extent_npoints return type to hssize_t and the error value to -1 Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2693] Purpose:Quincey Koziol2000-10-182-8/+8
| | | | | | | | | | | Bug fix (bug #446) Description: H5Tget_offset return type was size_t and the error return value was 0, but 0 is also a valid successful return value. Solution: Changed the return type to int and the error return value to -1 Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2689] Purpose:Quincey Koziol2000-10-171-0/+4
| | | | | | | | | | | | | | | | | Bug fix. Description: Previously, it has been possible to dereference deleted objects in a file. Obviously, this is incorrect and could cause all sorts of problems if the object being dereferenced had been partially over-written with other information. - This is documented in Bug #493. Solution: Check the link count for objects being dereferenced and don't allow any objects with link counts of zero to be dereferenced. This fixes bug #493. Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2679] MuQun Yang2000-10-121-0/+5
| | | | | | | | | | | | | | | | | | | Purpose: Just add a few lines so that it will not break windows platform. Description: netdb.h cannot be recognized by windows, use winsock.h in windows instead. Solution: adding the following lines at the beginning of H5FDstream.c. If you don't like, you may do it in another way, just keep it work for windows. #ifdef WIN32 > #include <winsock.h> > #else > #endif Platforms tested: I am only testing whether it will bother building objects on windows. I haven't tested whether it will affect the testing results. Hopefully not. windows 2000, eirene,arabica,gondolin,paz,opus.
* [svn-r2657] Quincey Koziol2000-10-1012-322/+64
| | | | | | | | | | | | Purpose: Parallel Bug Fixes Description: Was out of sync with header file re-arrangements I checked in last night. Solution: Fixed to use new header files, etc. Platforms tested: O2K (modi4)
* [svn-r2656] Purpose:Quincey Koziol2000-10-103-1/+29
| | | | | | | | | | | | | | Bug Fix Description: When parallel I/O is turned on, there were some macros used in the H5D routines which poked around in the H5F_t structure. This breaks the privacy of that structure and ties the H5D code too tightly to the H5F_t struct. Solution: Added a small function to retrieve the the value (driver_id) needed from the H5F_t function. Platforms tested: Eyeballed only, Albert needs this right away...
* [svn-r2652] Purpose:Quincey Koziol2000-10-1059-717/+2023
| | | | | | | | | | | | | | | Maintainance & performance enhancements Description: Re-arranged header files to protect private symbols better. Changed optimized regular hyperslab I/O to compute the offsets more efficiently from previous method of using matrix operations. Added sequential I/O operations at a more abstract level (at the same level as H5F_arr_read/write), to support the optimized hyperslab I/O. Platforms tested: Solaris 2.6 (baldric) & FreeBSD 4.1.1 (hawkwind)
* [svn-r2647] Purpose:Albert Cheng2000-10-101-15/+19
| | | | | | | | | | | | | | Bug fiX Description: H5S_hyper_select_valid would report hyperslab invalid if the one of the count values is zero. The verifying algorithm did not take into consideration that block or count can contain zeros to indicate no element is wanted. Solution: Added code to test if block or count is zero. If so, skip the rest of the validity check. Platforms tested: IRIX64 -64.
* [svn-r2646] Purpose:Albert Cheng2000-10-102-6/+28
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix (done by Kim Yates) Description: The optimized mpio code was broken and when read was done, it hanged. Solution: H5FDmpio.c: In H5FD_mpio_write, moved the 16-line block of code in which all procs other than p0 skip the actual write to be just before the call to MPI_File_write_at. Previously, the values of the local vars that controlled "allsame" were not always set correctly when the moved block was reached. H5S.c: Changed default value of H5_mpi_opt_types_g to TRUE, so that the MPI-IO hyperslab code is executed by default in parallel HDF5, rather than executing the serial hyperslab code. H5Smpio.c: In function H5S_mpio_hyper_type, added a call to free an intermediate type. Cures a small memory leak. Added code for cases of empty hyperslab Changed displacements to be MPI_Aint Platforms tested: modi4 -64: worked fine with mpich 1.2.0 but failed with the messages saying it ran out of entries for MPI_Types during the collective_read test. After tracing the code all the way to the collective read, all MPI Types have been freed properly. It aborted with the above message when it executed the line if (MPI_SUCCESS!= MPI_File_read_at_all(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat )) Could not see any problem with this line. It could be a bug in the SGI version of MPI.
* [svn-r2645] Albert Cheng2000-10-101-17/+25
| | | | | | | | | | | | | | | | Purpose: [is this a bug fix? feature? ...] Description: [describe the bug, or describe the new feature, etc] Solution: [details about the changes, algorithm, etc...] [Please as detail as you can since your own explanation is better than others guessing it from the code.] Platforms tested: [machines you have tested the changed version. This is absolute important. Test it out on at least two or three different platforms such as Big-endian-32bit (SUN/IRIX), little-endian-32(LINUX) and 64-bit (IRIX64/UNICOS/DEC-ALPHA) would be good.]
* [svn-r2638] Snapshot version 1.3 release 31HDF Admin2000-10-071-1/+1
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* [svn-r2633] Purpose:Quincey Koziol2000-10-042-20/+20
| | | | | | | | | | | | Bug Fix Description: Use H5FD_get_eoa instead of H5FD_get_eof to check for reading off the end of the allocated file space. Using H5FD_get_eof was causing the Stream VFD to fail. Solution: Switched from using H5FD_get_eof to H5FD_get_eoa Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2631] Thomas Radke2000-10-041-8/+9
| | | | | | | | | | | | Purpose: Bugfix Description: The Stream VFD was leaking memory on every opened file. Solution: In H5FD_stream_close(), finally free the file structure used to describe the closed file. Platforms tested: Linux, SGI
* [svn-r2611] Purpose:Quincey Koziol2000-09-286-254/+699
| | | | | | | | | | | | | Rearrange code Description: The data sieve buffering code for contiguously stored datasets was wedged in the H5F_arr_read/H5F_arr_write routines. Solution: Created a new H5Fcontig.c to hold I/O routines for contiguously stored datasets (like H5Fistore.c for chunked dataset I/O routines) and moved data sieving code into those routines. Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2610] Purpose:Quincey Koziol2000-09-281-28/+325
| | | | | | | | | | | | | | | | | | Code Optimization. Description: The optimized routines for copying regular hyperslabs in memory have been using the same matrix routines to copy their hyperslab pieces as the routines for irregularly shaped hyperslabs. This ends up imposing lots of extra overhead on the optimized routine, since it basically "knows" all the matrix information it needs. Solution: Keep track of the [small] amount of matrix information necessary to perform the regular hyperslab copies in the optimized routines themselves instead of using the matrix routines. This improves the performance for the benchmark I'm running from ~18 seconds to ~12 seconds and should apply to parallel I/O situations also. Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2606] Purpose:Quincey Koziol2000-09-271-32/+243
| | | | | | | | | | | | | | | Code Optimization Description: The matrix operations are currently the hot-spot in the library code for regular hyperslab operations. Solution: Unrolled loops for 3 of the more heavily used functions (H5V_stride_optimize2, H5V_hyper_stride & H5V_hyper_copy) for the common cases (i.e. up to 3-D datasets). This squeezes some more blood out of the stone (turnip? :-) and improves the h5hypers.c benchmark on baldric by another 20-25%. Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2601] Purpose:Quincey Koziol2000-09-272-5/+3
| | | | | | | | | | | | Bug Fix Description: The core and log VFL drivers were leaking small amounts of memory when they were used. Solution: Free the appropriate memory block (for the core driver) and don't allocate a block (for the log driver). Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2600] Purpose:Quincey Koziol2000-09-2615-27/+580
| | | | | | | | | | | Implemented new feature Description: Added data sieve buffering code to raw I/O data path. This is enabled for all the VFL drivers except the mpio & core drivers. Also added two new API functions to control the sieve buffer size: H5Pset_sieve_buf_size() and H5Pget_sieve_buf_size(). Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2597] Purpose:Quincey Koziol2000-09-261-2/+2
| | | | | | | | | | | Fix compiler warning Description: "HUGE_VAL" (a double value) was being put into a float type and generating a warning during compile time. Solution: Replaced "HUGE_VAL" with "FLT_MAX" Platforms tested: FreeBSD 4.1
* [svn-r2594] Purpose:Quincey Koziol2000-09-261-24/+18
| | | | | | | | | | | | Small Code Cleanup Description: Code to optimize adjacent (i.e. contiguous) hyperslab was ugly and used too many temporary variables. Solution: Computed the optimized hyperslabs slightly differently and got rid of unnecessary temporary variables. Platforms tested: FreeBSD 4.1
* [svn-r2588] Snapshot version 1.3 release 30HDF Admin2000-09-231-1/+1
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* [svn-r2587] Purpose:Quincey Koziol2000-09-223-4/+69
| | | | | | | | | | | | | | | | | | | Bug fix (sorta) Description: When the stride and block size of a hyperslab selection are equal, the blocks that are selected are contiguous in the dataset. Prior to my hyperslab optimizations, this situation used to be detected and somewhat optimized to improve performance. I've added more code to optimize for this situation and integrated it with the new hyperslab optimization that weren't very efficient for that case as they should have been. Solution: Detect contiguous hyperslab selections (i.e. block size in a dimension is the same as the stride in that dimension) and store the optimized, contiguous version of that hyperslab. We also store the original, un- optimized version of the hyperslab to give back to the user if they query the hyperslab selection they just made. Platforms tested: FreeBSD 4.1
* [svn-r2586] Purpose:Bill Wendling2000-09-221-1/+1
| | | | | | | | | | | | | Bug Fix Description: The prototype for the H5Pregister function has a variable named `class'. This is a reserved word in C++ and causes the C++ compiler to freak. Solution: This variable's name was changed to cls_id in the .c file, so I changed it in the header file to cls_id to match. Platforms tested: Linux
* [svn-r2583] Purpose:Quincey Koziol2000-09-201-0/+13
| | | | | | | | | | | | | Bug Fix. Description: An assertion in the local heap code was mistakenly checking against too large of a value for the size of new local heap created. When used with larger-sized (>10KB) variable-length objects, it was failing the check. Solution: Corrected to check against the actual size of the heap allocated, without the heap header. Platforms tested: FreeBSD 4.1
* [svn-r2581] Purpose:Quincey Koziol2000-09-191-33/+23
| | | | | | Clean up compiler warnings. Platforms tested: FreeBSD 4.1
* [svn-r2580] Purpose:Quincey Koziol2000-09-191-333/+1952
| | | | | | | | | | | | Restore file Description: It appears that Robb's checkin earlier today erroneously overwrote this file with an older version... *grumble* Solution: Found another copy of newest version, verified that it is operating correctly and re-checked it in. Platforms tested: FreeBSD 4.1
* [svn-r2579] Purpose:Quincey Koziol2000-09-199-21/+22
| | | | | | Clean up small compiler warnings and add missing function prototypes. Platforms tested: FreeBSD 4.1
* [svn-r2574] Purpose:Bill Wendling2000-09-191-6/+6
| | | | | | | | | H5FDstream.h needs to be installed. Description: H5FDstream.h is included in the hdf5.h file and needs to be installed with the other public headers. Solution: Added it to the rest of the install headers.
* [svn-r2573] Purpose:Robb Matzke2000-09-193-2039/+944
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fix Irix pmake bugs Description: Build fails on Irix when builddir != srcdir Solution: * acconfig.h * src/H5config.h.in [REGENERATED] Added definition for HAVE_STREAM * config/conclude.in * config/depend1.in * config/depend2.in * config/depend3.in * config/depend4.in The `Dependencies' file is located in the source tree. This fixes bugs for Irix pmake when compiling outside the source tree. Hopefully it still preserves Albert's changes which allow concurrent compilations to not stomp on each other's Dependencies files. * examples/Dependencies [REGENERATED] * src/Dependencies [REGENERATED] * test/Dependencies [REGENERATED] * tools/Dependencies [REGENERATED] Regenerated for testing purposes. Platforms: i686-pc-linux mips-sgi-irix6.5 sparc-sun-solaris2.6
* [svn-r2560] Purpose:Thomas Radke2000-09-151-0/+1
| | | | | | | Include the Stream VFD's header file H5FDstream.h. Description: All the VFD's header files are included by hdf5.h itself for convenience.
* [svn-r2559] Purpose:Thomas Radke2000-09-151-8/+8
| | | | | | | | Add the Stream VFD sources to the appropriate makefile variables. Description: Added H5FDstream.c to the LIB_SRC variable and H5FDstream.h to the PUB_HDR variable for building the Stream VFD.
* [svn-r2558] Purpose:Thomas Radke2000-09-151-0/+3
| | | | | | | | | | Define HAVE_STREAM. Description: If the Stream VFD was configured the configured script will expand this into '#define HAVE_STREAM 1' in H5config.h and '#define H5_STREAM 1' in H5pubconf.h.
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