| Commit message (Collapse) | Author | Age | Files | Lines |
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Brought changes from Coverity branch back to trunk, and cleaned up misc.
other warnings & formatting issues:
r20833:
Fixed Coverity 667 and 668 with real integer overflow tests this time.
r20834:
Use HDstrncpy and HDstrncat. --gh
r20835:
Change to use strncpy - use base_len + 1 for line 156, use HDstrlen(path) + 1 for line 159
r20836:
Fixed coverity 585 by casting output of fgetc() to a char.
r20837:
Changed sprintf calls to snprintf with size 1 less than the allocated buffer to address coverity issue #967.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(too minor to require h5committest)
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Rename GCC_DIAG_OFF/ON macros to H5_GCC_DIAG_OFF/ON and move from
src/H5private.h to src/H5public.h. Wrap typedef of hsize_t and hssize_t
in DIAG_OFF(long-long) macros.
Clean up a bunch of "macro '-' is unused" warnings.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/gcc 4.8.2, C++, FORTRAN, parallel
(too minor to require h5committest)
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Revert some earlier usage of strncpy, which was incorrect.
Bring Coverity changes from branch back to trunk:
r20821:
Use HDstrncpy. --gh
(Fixed already, with strdup)
r20822:
(Not merged, incorrect use of HDstrncpy())
r20823:
(Not merged, incorrect use of HDstrncpy())
r20824:
Maintenance: Bug fix: addressed CID 666.
Value stored at *expression_len should be used in the call to
HD5packFstring to avoid overflow (and unnecessary arithmetic
calculation and casting)
r20825:
Issue 642: Added check for error and handler with print to stderr and exit.
r20826:
Undo revision 20818, as that issue has already been fixed in the 1.8 branch
and trunk (but not coverity branch)
r20827:
(Not merged, incorrect use of HDstrncpy())
r20828:
Use HDstrncpy. --gh
(Corrected use of strncpy())
r20829:
Check return of H5Lget_val(print_udata->fid, path, targbuf,
linfo->u.val_size + 1, H5P_DEFAULT) and if error set trgbuf[0] to 0.
Check if H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL,
&filename, &objname) was successful and allow print. Otherwise filename
and objname are not created. (init those to NULL)
r20830:
resolved coverity issues 939, 940, 941, 944, and 947.
all were complaints about use of sprintf, and in all cases, the
buffers used were large enough for all eventualities.
Resolved issue by replacing calls to sprintf with calls
to snprintf.
r20831:
Maintenance: Addressed CID 852
Replaced sprintf with snprintf
r20832:
Purpose: Fix valgrind issues with hl/examples/ex_image2
Description:
Modified hl/examples/ex_image2 to free global "gbuf" before exit.
Tested on:
Mac OSX/64 10.9.1 (amaon) w/C++, FORTRAN & Threadsafety
(too minor to require h5committest)
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Prep work for adding a memory free function, part of HDFFV-8551.
Tested on:
32-bit LE linux (jam)
* with C++, Fortran
* with thread safety on
These are minor changes (almost entirely renaming foo functions
to HDfoo) that don't change functionality. This should not
require a full commit test.
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Clean up warnings in H5Tconv.c (down to _only_ 9000 lines of output now!)
Merge changes from Coverity branch back to trunk:
r20684:
Fix for coverity bug #1721 which was due to the fix for coverity bug #943.
r20685:
Use HDstrncpy. --gh
r20761:
Purpose: Fix valgrind issues
Description:
Free image_data and data as appropriate in test_image.
r20762:
Purpose: Fix coverity issue 600
Description:
Add check for return value of H5O_close in H5Ocopy. Also cleaned up various
warnings.
r20763:
Purpose: Fix valgrind issues with h5stat
Description:
Modified h5stat to free "iter" before exit, and free "hand" before exit if
parse_command_line exits directly.
r20764:
fixed coverity issues:
69, 327, 614, 684, 685, 696, 697, 1681, 967, 826, 660, 80
r20765:
Fixed coverity bug 668
Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning.
No actual integer overflow tests are performed since it's just a test program but I did add a check that n_elements is >= 1.
I also changed an error condition from doing its own close and returning -1 to "goto out;" like the rest of the program.
r20766:
Fixed coverity bug 667
Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning.
No actual integer overflow tests are performed since it's just a test program.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
(h5committest upcoming)
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Bring generic improvements from encode/decode property list branch to
the trunk. This includes a better version of the property list comparison
routine, cleaned up compiler warnings, and some cleaned up property list
callbacks. Also, started on changes to clean up parallel test output, so that
it doesn't report successful tests from each process.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, GCC 4.7.x, FORTRAN, C++, threadsafe and parallel
Linux 2.6/32 (jam) w/debug
Solaris 2.7/64 (linew) w/debug
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Changes resulting from Klocwork static analysis tool, from Mark Miller
@ LLNL (miller86@llnl.gov).
Tested on:
Mac OS X/64 10.7.4 (amazon) w/debug, C++ & FORTRAN, using gcc 4.7.x
(too minor to require h5committest)
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Add FUNC_ENTER macros for package-private routines and begin process of
switching package routines to use them. All H5G routines are currently
finished.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
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Correct error in loading local heap prefix & data block from the file.
Sometimes the local heap's prefix could be loaded before the data block (e.g.
using H5Oget_info), but then when the data block was loaded later, the free
list information would get lost, causing the heap's size to grow larger than
necessary. This is Jira bug #HDFFV-7767
Tested on:
Mac OS X/32 10.7.2 (amazon) w/debug
(h5committest coming up)
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defines H5_HAVE_WIN32_API and H5_HAVE_VISUAL_STUDIO defines to use. These can be properly set during configurration.
Tested: windows and local linux - reviewed internally
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Description:
Added internal tesitng routines to traverse a file and verify that symbol table
information is *always* cached, whenever possible. Added this check to the end
of many tests to check all the test files, right before the call to h5_cleanup.
Tested: jam, amani, heiwa (h5committest)
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trunk for VMS work
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dependent on the winsock2.h header so changed WIN32 to H5_HAVE_WINSOCK_H.
Tested: windows
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unresolved issues - r19441 and 19467.
Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with
the 1.8 library to compile.
I created a branch off the trunk called set_auto to continue working on the problem.
Tested on jam - backing out, simple.
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application uses -DH5_USE_16_API with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2 set
through H5Eset_auto. I changed the union in the structure H5E_auto_t. Another change is to
make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a
document for it.
Tested on heiwa, jam, and amani.
The property change in configure.in, config, and Makefile.am came from the merge of the 1.8
library change.
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replaced by WIN32_LEAN_AND_MEAN macro. This was the cause of a define conflict causing the use of grp1 and grp2 to be replaced with constants in the h5dumpgentest.c file.
This also affected the use of the #include <winsock.h> needed by gethostname. The new include: winsock2.h has been added to h5private.h and either removed or updated in the other files.
Tested: Windows
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Re-run bin/reconfigure to catch up with recent rearrangements, remove some
unused srcdir headers and duplicated code in main test header.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & prod
Linux/32 2.6 (jam)
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Unify srcdir handling for test executables and allow them to use the srcdir
setting from configure time without requiring the 'srcdir' environment variable
be set (although you still can, to override the built in setting). Attempted
to get this right for Windows builds also.
Also add dependency between src/H5Tinit.c and src/libhdf5.settings, so
that the test/testcheck_version.sh script works correctly.
Tested on:
Linux/32 2.6 (jam)
Mac OS X/32 10.6.2 (amazon)
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Trim trailing whitespace from source code files with this command:
find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//'
Tested on:
None - eyeballed only
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from v1.8 to trunk.
Tested:
amani, jam, linew (h5committest).
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TFLOPS machine has retired long ago. Removed all code specific for its
support.
Test:
h5committested.
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Bring r17266 from 1.8 branch to trunk:
Clean up various compiler warnings from IRIX64 build
Tested on:
Mac OS X/32 (amazon) debug & production
(yes, I know it's not an IRIX64 system :-)
Too minor to require h5committest
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Remove another call to H5E_clear_stack() from within the library.
Clean up lots of compiler warnings.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(followup on other platforms forthcoming)
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trunk
Description:
This checkin includes revisions 15845, 15846, and 15853 from the 1.8 branch. From the svn log:
r15845:
Purpose: Add Windows-specific version of HDftruncate
Description:
Windows doesn't include a version of the system call ftruncate. There is a similar call, _chsize_s, which performs very similarly. Thus, we map HDftruncate to _chsize_s in our Windows header file, H5win32defs.h.
r15846:
Purpose: Declare loop variable at beginning of function
Description:
On Windows, we were getting compile errors because h5test.c includes a function with variable declarations in the middle of the call. The Microsoft C compiler demands that all variables be declared at the top of the function. This checkin simply moves the declaration to the top to satisfy Visual Studio.
r15853:
Purpose: Decrease size of points array in links test
Description:
In the external_set_elink_fapl2 links test, there is a large array of points which declared on the stack for testing. Previously, the array was 1000 x 1000, which was too large for Visual Studio to handle. As a result, we were getting stack overflows during the test. We've reduced the number to 400, as this seems to be below the limit. The exact number of points in the array isn't important to the test.
Tested:
VS2005 on WinXP
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Fix various problems with a the core & sec2 VFDs.
Improve the h5_get_file_size() routine to handle files created with
VFDs that use multiple files.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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Description:
On Windows, the pthread_self function cannot be used to print the returned thread ID for debugging. Instead, we need a separate function, GetCurrentThreadId. To eliminate some Windows ifdef's in the code, we create two new function macros which can be used by all platforms. It is conditionally defined in H5win32defs.h, and globally in H5private.h.
Tested:
VS2005 w/ pthreads on WinXP
kagiso w/ pthreads
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Description:
On Linux-like systems, we can get the ID of the current thread through a pthread_self. However on Windows, the return cannot be cast as a threadID, so we simply couldn't get the ID. Previously we simply gave up and printed a message that we couldn't get an ID. Instead, though, we can use the Windows-specific call to GetCurrentThreadId(), which achieves the same goal. This way we can provide better debug output with threadsafe features.
Tested:
VS2005 on WinXP
VS.NET on WinXP
(other platforms not tested because change is within _WIN32 ifdef)
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Change H5P[gs]et_format_bounds() => H5P[gs]et_libver_bounds() and also
enumerated values H5F_FORMAT_{EARLIEST, LATEST} => H5F_LIBVER_{EARLIEST, LATEST}
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Switched from "H5P[gs]et_latest_format" to "H5P[gs]et_format_bounds".
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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- Add hash value for skip list string types, to reduce # of string
comparisons.
- Fixed bug with metadata/small data block aggregator adding size == 0
block into file free space list.
- Refactored metadata/small data block aggregator code into single set of
common routines.
- Changed block aggregator code to be smarter about releasing space in the
'other' block when the 'other' block has aggregated enough data.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Pursue calls to H5Gcreate() relentlessly and ruthlessly exterminate
them, leaving only a few tame specimens in text files and comments. ;-)
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
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First real use of API versioning code, H5E routines switched to use
new API versioning scheme.
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
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Add a bit more information to the log VFD settings.
Tested on:
FreeBSD/32 6.2 (duty) w/check-vfd
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Allow a ".h5" suffix to be added to core files also, which prevents
overwriting the test binary (and confusing the tests on copper, etc.)
Tested on:
AIX 5.3 (copper) w/check-vfd
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
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HDF5_DRIVER value to activate the use of latest_format for file access
property list.
Platform tested: h5committested.
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Fix problems with 'check-vfd' target, that were [mostly] introduced with
the recent "unique, but sharable" ISOHM optimization.
The problems were mostly with using the 'core' VFD, so the
H5Pset_fapl_core() API call was changed to re-open existing files (therefore
operating more list the sec2, stdio, etc. VFDs). This allows many more of
the tests to run using the 'core' VFD, so those were enabled also.
Tested on:
Linux/64 2.6 (chicago2) w/check-vfd
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WIN32, so I've standardized all #ifdef's to use _WIN32. This should not affect any other platform.
Tested:
Visual Studio (32- and 64-bit) on Win XP
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avoid compiler's
warning of comparing values with "==" or "!=".
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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.
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Take out separate memory type in the file for SOHM objects and create
aliases for existing memory types for SOHM use.
Tested on:
FreeBSD/32 4.11 (sleipnir)
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This feature is still in progress; Shared Object Header Messages are not
complete as a feature and are not thoroughly tested. There are still
"TODO" comments in the code (comments with the word "JAMES" in them,
so as not to be confused with other TODO comments).
Hopefully this checkin will reduce the liklihood of conflicts as I finish
implementing this feature.
All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
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systems like copper and sleipnir
doesn't require alignment for Direct I/O. If this's true, write or read data just like sec2
does.
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made the test more complete by writing
two data sets. One is aligned, and the other isn't.
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size is set through
H5Pset_fapl_direct. It's been added to H5FD_direct_read in the previous checkin. Still, a test is
needed at later checkin.
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H5Pset_fapl_direct to control
memory boundary, file block size, and maximal copy buffer size; second in H5FD_direct_write and
H5FD_direct_read, the library checks whether data buffer is aligned. If it is, then write and
read the data directly instead of making a copy buffer.
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Bug fix (related to 544)
Description:
h5_get_file_size() was coded to return 0 if failed but
file size can be 0. Changed the failure return value to -1
which is allowed by the returned type of off_t which is a signed
type.
Also changed the checking code of the stat call to just == 0
since that is how it is defined.
Test:
Could test it in heping only. Both Sol and Copper failed to
compiled due to error in the Direct IO VFD code.
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Altix (cobalt). There's a configure
option --enable-direct-vfd/--disable-direct-vfd to enable/disable Direct I/O support. The default
is enabled. There's a small test in test/vfd.c. Another way to test it is to set environment
variable HDF5_DRIVER to "direct" and run "make check" in the test/ directory. There'll be some
further improvement in the following checkin including allowing user to provide memory boundary
value, file block size, and copying buffer size.
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File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
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Code cleanup
Description:
Trim trailing whitespace in Makefile.am and C/C++ source files to make
diffing changes easier.
Platforms tested:
None necessary, whitespace only change
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Feature
Description:
Sometimes the parallel prefix is given in the form of nfs:/mnt/pfs which
if given to a non-MPIO VFD like the default H5Fcreate, it would fail.
Added a new routine h5_rmprefix which would return the non-prefix component
part of the file name which would be okay for the default H5Fcreate and
such.
Platforms tested:
Tested in heping parallel.
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