Code cleanup
Description:
Platform dependent code related to the struct stat and fstat
calls polluted source codes. Hard to maintain.
Solution:
Platform dependent code are moved to H5private.h and then internal
code can #include H5private.h. Repeat those macro definition for
the stdio and multi drivers since they area examples for writing
a virtual file driver. They must not use any internal code.
Platforms tested:
eirene (parallel), modi4 (serial including gass driver.)
Users were alarmed by the OFFSET overflow and GB file size tests.
Those tests only checks the limits of the MPI implementation, not
really as an error.
Solution:
Changed the VRFY macro to indicate it is an "ERROR".
Modified the INFO macro to print messages as "REMARK (not an error)"
so that users would not be alarmed.
Added an explanation string in the GB file size write/read.
Platforms tested:
eirene and modi4 (parallel)
New test feature
Description:
Added create_faccess_plist() that create just MPIO or split+MPIO
file-access property list. This in turn can run parallel tests
with just MPIO or with Split-file VFD too.
Added -s option for split-file Plus MPIO tests.
For testphdf5.c: removed a bunch of old debug code that got left
in by mistake.
Platforms tested:
Modi4 and eirene parallel.
But it has uncovered errors in the library. The test program
is correct though. Checking the test program in so that it won't
get lost and can be used for debugging. Also, the -s is not used
by default during test. At least it won't abort "make check".
Code cleanup
Description:
This was "thrown" together in a quick way to test MPIO functionality.
Cleaned out some embrassingly useless declaration to reduce compiler
warnings.
Platforms tested:
modi4-pp and eirene-pp.
More code cleanups
Description:
Wrap up the code cleanups for changing the dataset transfer property lists
over to using the generic property list code.
Platforms tested:
IRIX64 6.5 (modi4)
Purpose:
Added attribute test
Description:
attribute test is added into t_mdset.c. At this moment, testing failed
on SunOS 5.7 and Linux. But I believe the problem is from dataset
collective writing in t_dset.c.
Platforms tested:
SGI MPI, MPICH(IRIX64 N32, IRIX64 64, IRIX, Linux, SunOS).
Multiple-group testing
Description:
Added multiple groups under root group and multiple subgroups of
certain levels. Also writes several datasets in each group in
parallel.
Solution:
Platforms tested:
MPICH(IRIX 6.5, IRIX64 6.5(64), IRIX64 6.5(N32), Linux, SunOS 5.6)
and SGI MPI(IRIX64 6.5).
Purpose:
Multiple-group testing
Description:
Added multiple groups under root group and multiple subgroups of
certain levels. Also writes several datasets in each group in
parallel.
Solution:
Platforms tested:
MPICH(IRIX 6.5, IRIX64 6.5(64), IRIX64 6.5(N32), Linux, SunOS 5.6)
and SGI MPI(IRIX64 6.5).
Bug fix
Description:
The t_mpi used to fail and exit if any error detected.
That aborted other process in a "make check" situation.
Solution:
Introduced a new error verification as INFO. INFO is for
information only. It does not increase nerrors count.
The program always exits with 0.
Platforms tested:
eirene with mpich.
Bug fix
Description:
Some mpi.h already includes MPI-IO definitions in it (e.g., SGI,
SP2). Made the #include of mpio.h be dependent on whether some
MPI-IO constant is already defined or not.
Platforms tested:
modi4 (IRIX64) and IBM SP2.
Changed MPI_File_seek then MPI_File_write or MPI_File_read to just
MPI_File_write_at and MPI_File_read_at. Some compiler, e.g., IBM
mpcc_r does not support MPI_File_seek and MPI_File_read or MPI_File_write.
This is a better measurement against HDF5 performance since HDF5
uses MPI_File_write_at and MPI_File_read_at all the times.
It is a more thread safe to use MPI_xxx_at than the other seek then
read/write approaches.
Platforms tested:
modi4 (irix64 parallel), IBM sp2.
Bug Fix
Description:
FILENAME_MAX is short on some systems. It's better to use PATH_MAX
which tends to be longer (we hope).
Solution:
Removed FILENAME_MAX and replaced it with PATH_MAX instead.
Platforms tested:
Skinner (SDSC HP N9000).
Bug fix
Description:
added a barrier to prevent racing condition before remove file and
open file.
Platforms tested:
modi4,pp
cVS: ----------------------------------------------------------------------
Feature
Description:
Show simple performance of the MPIO and the HDF5-IO.
The mpi-perf.c is contributed by Robert Ross of ANL.
The perf.c is derived from mpi-perf.c
Platforms tested:
Modi4 (O2K, parallel)
Bug fix and clean up.
Description:
The part that should test 4GB was actually testing 2GB due to
typo.
Solution:
Corrected the typo to use 4GB constant. Rearranged the code
to group 2GB and 4GB tests in their own. Removed some duplicated
testing code.
Platforms tested:
modi4.
new test
Description:
Added two new tests.
test_mpio_offset:
Verify that MPI_Offset exceeding 2**31 can be computed correctly.
test_mpio_gb_file
Test if MPIO can write file from under 2GB to over 2GB and then
from under 4GB to over 4GB.
Platforms tested:
modi4(-64), tflops.
Improvement
Description:
Changed the default value of $NPROCS from 2 to 3. This is the
value libSAF uses since 3 processes have a much bigger chance
catching parallel errors than just 2 processes.
Changed the default dataset sizes from 800 to 1200 so that it is
a multiple for 3 (and 8 too which is ofter used in the Tflops test.)
Platforms tested:
Modi4 (IRIX64) both serial and parallel modes.
New features
Description:
Some testers found the filename lengths too short.
Changed it to use the FILENAME_MAX usually defined in stdio.h.
If not, set it to 512 which should be sufficient for users
but should not exceed any system limits.
Also added a new test parameters of ndatasets so that the tester
can specific a different number of datasets for the multiple
datasets tests.
Changed the datatype of datasets created to DOUBLE. This eliminates
the current racing conditions. But the racing bugs during conversion
still need to be tracked down and squashed.
Platforms tested:
Modi4 -64.
New parallel test features
Description:
Added test cases:
INDEPENDENT write with some processes do not participate at all.
The library should not hang for this case.
COLLECTIVE read/write with some processes asking for zero elements.
The library should work properly and not hanging.
Some house cleaning: get rid of a conditional directive that was
fixed already.
Platforms tested:
IRIX64,-64,parallel
Feature, kind of
Description:
Moved the multiple dataset test out of the write-test
part so that it can be skipped or tested independent of
the other tests.
Platforms tested:
IRIX64,-64,parallel.
Backward compatibility code
Description:
Add in code to allow the library to emulate the v1.2 API and behavior.
Platforms tested:
FreeBSD 4.2 (hawkwind)
New feature
Description:
Added tests to make sure collective read or write works correctly
even if some process has no data to transfer.
ZROW--process 0 asks for zero rows of data while other processes ask
for a slab of rows.
ZCOL--process 0 asks for zero columns of data while other processes ask
for a slab of columns.
Platforms tested:
IRIX64 parallel (-64,-n32).
cvS: ----------------------------------------------------------------------
Simple changes
Description:
testphdf5.h:
Call MPI_Abort when error is detected. MPI_Finalized was used
before but it might hang if the test has already encountered errors.
Also, it does not do the H5Eprint any more since auto report is on.
t_mdest.c:
Changed the variable name of rank and nprocs to mpi_rank and mpi_size
so that it is the same with the other tests and can use the VRFY macro
call.
Platforms tested:
modi4-64.
Bug fix, cleanup,...
Description:
The test was doing the hyperslab select incorrectly (thinking
count was the block length.
Solution:
Fixed it to do the correct hyperslab selection.
Changed it to calculate different data for different datasets.
Changed output by rows instead by cols. It tests the purpose
of creating multiple datasets the same but runs faster.
Platforms tested:
modi4-64.
Features, kind of.
Description:
Separated the MPI features test into its own independent
program so that it can be tested on its own without too
much HDF5 stuff involved.
Added automatic removal of temporary test files after
the tests completed.
Reduced the size of the dataset dimensions to avoid tripping
the SGI MPI problems of running out of internal mpi type entries.
Platforms tested:
O2K -64
Added features
Description:
There were no automatic tests for transfering zero elements.
Solution:
t_dset.c:
Added two new patterns of ZROW (zero rows for process 0)
and ZCOL(zero columns for process 0).
ZROW test was added but it failed because the current library
does not accept it. Not compiled in now. Need to fix the
library before turning it back on again and also to add the
ZCOL test.
t_mdset.c:
Added statement to show progress. Also the MPI_Barrier() call
get processes synchornoized. It eliminates the racing condition
but this is not a permenant solution. The library code needs to
be fixed.
testphdf5.c:
Added a bunch of MPI_Type_XXX debug code. Added the -md
option to skip the multiple datasets tests. Changed the cosmitic
appearance of the banner messages.
testphdf5.h:
When an error is detected, the old way was to call MPI_Finalize()
before exiting. This sometimes hangs because some processes
may be waiting for a message of a different tag. Changed to
call MPI_Abort() for now so that the whole MPI job would
abort rather than hanging due resource limits exceeded.
Added the definition of ZROW and ZCOL.
Platforms tested:
Modi4 -64.
Bug fix
Description:
The old code was using count as the block size. The result was
asking for a slab of count blocks, each of 1 element. The recent
change in the hyperslab algorithm exposed this problem. (The
old algorithm merge the count blocks back into 1 big block of
count elements.) (This error was due to that the block argument
was not in the very early version of hyperslab. Then it was
not updated since it had been "working".)
Solution:
Added in the block argument to the setup and calculation of
slab and its data. Also found a dumb error in the dataset_fill
algorithm in which stride was used in the calculation. Not so
for the cases of BYROW and BYCOL.
Platforms tested:
modi4 parallel, both -64 an -n32 modes.
Makefile.in:
Added test/ as one of the -I directories to search for header files.
Needed because <h5test.h> is used.
t_file.c t_mpi.c testphdf5.c testphdf5.h:
Added FILENAME to meet the assumption in h5test.h. (May use
CLEANUP in the future.) Moved the prefix setting to the
h5_fixname().
Increase the test size to 32. Put in a check to make sure number of
processes are not bigger than SIZE.
testphdf5.c:
Fixed a mistake in the prototype of pause_proc to reflect no arguments.
** src/H5FDpublic.h
Added a #define for H5_HAVE_VFL to make life easier for application
programmers.
** config/depend1
A minor tweak to the way GNU systems generate file dependencies for
the Makefiles.
** src/H5T.c
Fixed a bug with enumeration types not having the correct object
header pointer.
** bin/rpmsync
** config/depend1.in
Tweaks for versions of `make' that can't search directories.
** examples/Dependencies
** src/Dependencies
** test/Dependencies
** testpar/Dependencies
** tools/Dependencies
Regenerated all these with more complete path names.
----------------------
./MANIFEST
./configure.in
./configure [REGENERATED]
Added more checking for `make' features.
./Makefile.in
./doc/Makefile.in
./doc/html/Makefile.in
./doc/html/Tutor/Makefile.in
./examples/Makefile.in
./pablo/Makefile.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
./config/commence.in
./config/conclude.in
./config/depend.in [REMOVED]
./config/depend1.in [NEW]
./config/depend2.in [NEW]
./config/depend3.in [NEW]
./config/depend4.in [NEW]
./config/dependN.in [NEW]
The directory search stuff was moved into commence.in, thereby
shortening the Makefile.in prologues.
./doc/html/Dependencies [NEW]
./doc/html/Tutor/Dependencies [NEW]
./examples/Dependencies [NEW]
./src/Dependencies [NEW]
./test/Dependencies [NEW]
./testpar/Dependencies [NEW]
./tools/Dependencies [NEW]
The `.distdep' files were all renamed to `Dependencies' to make them
more obvious. They are required (but may be empty) in every directory
that has a Makefile.in that ends with @CONCLUDE@ (you'll get an
obvious error from make if you forgot to create one).
./bin/trace
./src/H5.c
Added H5E_major_t and H5E_minor_t although tracing only prints the
integer value.
./src/H5E.c
./src/H5Epublic.h
Added tracing information.
./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDgass.c
./src/H5FDmpio.c
./src/H5FDsec2.c
./src/H5FDstdio.c
Fixed places where FUNC_LEAVE() evaluated it's argument more than
once.
Added tracing information.
Wrapped long lines.
./config/gnu-flags
Fixed a syntax error when we don't have a gnu compiler.
----------------------
This extensive change is the virtual file layer implementation. I've
ported and tested the sec2, family, and core drivers and only ported
the mpio driver (Albert will test it). So if you need MPIO I would
recommend sticking with the previous version for a while.
You will get a few compile warnings about split and stdio drivers not
being implemented and possibly tracing information not inserted in
some of the drivers. You can safely ignore them but I plan to fix
them.
I'm still working on the split driver because I just realized that it
needs a part of the VFL that isn't written yet.
Documentation is being updated also because there were some minor
changes (mostly just name changes). It should be available on my web
site later this week.
./MANIFEST
./src/Makefile.in
./src/hdf5.h
./src/H5Flow.c [REMOVED]
./src/H5Fstdio.c [REMOVED]
./src/H5Fsec2.c [REMOVED]
./src/H5Fsplit.c [REMOVED]
./src/H5Fmpio.c [REMOVED]
./src/H5Ffamily.c [REMOVED]
./src/H5Fcore.c [REMOVED]
./src/H5MFpublic.h [REMOVED]
./src/H5FD.c [NEW]
./src/H5FDcore.c [NEW]
./src/H5FDcore.h [NEW]
./src/H5FDfamily.c [NEW]
./src/H5FDfamily.h [NEW]
./src/H5FDmpio.c [NEW]
./src/H5FDmpio.h [NEW]
./src/H5FDprivate.h [NEW]
./src/H5FDpublic.h [NEW]
./src/H5FDsec2.c [NEW]
./src/H5FDsec2.h [NEW]
Removed/added files for virtual file layer.
./bin/trace
./src/H5.c
Removed unused public datatypes and added new VFL public
datatypes.
Changed an error message.
./config/BlankForm
./config/dec-flags
./config/gnu-flags
./config/hpux10.20
./config/hpux9.03
./config/irix5.x
./config/irix6.x
./config/solaris2.x
./config/unicosmk
Removed the H5F_OPT_SEEK and H5F_LOW_DFLT constants from the
configuration since they're no longer applicable. The default
file driver is always the sec2 driver and it always optimizes
calls to lseek() or lseek64().
./config/depend.in
C preprocessor errors generated during automatic dependency
building are sent to /dev/null to prevent them from appearing
twice in the make output.
./src/H5AC.c
./src/H5B.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Oshared.c
./src/H5T.c
./src/H5detect.c
./test/ohdr.c
Changed H5F_ADDR_UNDEF to HADDR_UNDEF to be more consistent
with the `haddr_t' datatype which is now a public type.
./src/H5D.c
./src/H5P.c
./src/H5Ppublic.h
./src/H5Tconv.c
./test/cmpd_dset.c
./test/dsets.c
./test/overhead.c
./test/tselect.c
./test/tvltypes.c
The H5P_DATASET_XFER constant was changed to H5P_DATA_XFER
because the properties apply to all types of I/O operations,
not just datasets.
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5Dpublic.h
./src/H5F.c
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5R.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Spoint.c
./src/H5Sprivate.h
./test/big.c
./test/h5test.c
./test/istore.c
./testpar/t_dset.c
./testpar/t_file.c
./tools/h5debug.c
./tools/h5ls.c
Modified to work with the virtual file layer by calling H5FD_*
functions instead of H5F_low_* functions and by passing file
access and data transfer properties by object ID instead of
pointer.
Changed H5D_transfer_t to H5FD_mpio_xfer_t since the
COLLECTIVE vs. INDEPENDENT transfer mode is specific to the
MPIO file driver.
Moved MPIO-specific stuff into the MPIO driver.
./src/H5B.c
./src/H5D.c
./src/H5Fprivate.h
The H5F_mpio_* private functions were renamed and placed in
the H5FDmpio driver except those which appeared in H5Smpio.c.
./src/H5E.c
./src/H5Epublic.h
Added major error number H5E_VFL for virtual file layer
related errors.
./src/H5F.c
./src/H5Fprivate.h
Changed the logic that controls whether the boot block is
written. Instead of assuming that the first call to write the
boot block is only to allocate space, I've added a function
argument which makes this explicit.
Changed the way files are compared so that a driver-defined
comparison function can be called. Files which belong to
different drivers are always considered different.
Removed H5F_driver_t since file drivers are now identified by
object ID instead of a special non-user-extendible datatype.
Removed all the hard-coded low-level file properties which
have been replaced by the various file drivers.
./src/H5I.c
./src/H5Iprivate.h
Added the H5I_inc_ref() which was removed a few months ago
since we finally have a use for it.
./src/H5Ipublic.h
Added the H5I_VFL object ID type to identify file drivers in
the virtual file layer.
./src/H5MF.c
./src/H5MFprivate.h
Moved all the allocation/deallocation code into the virtual
file layer which allows file drivers to override much of it.
./src/H5P.c
./src/H5Ppublic.h
Moved file driver-specific code into the various file driver
files.
The H5Pcopy() and H5Pclose() functions make calls into the
virtual file driver to manage the memory for driver-specific
file access and data transfer properties.
./src/H5private.h
./src/H5public.h
The `haddr_t' type is now public.
./test/tfile.c
Added a few more comments.
----------------------
./Makefile.in [1.3]
./examples/Makefile.in [1.3]
./pablo/Makefile.in [1.3]
./src/Makefile.in [1.3]
./test/Makefile.in [1.3]
./testpar/Makefile.in [1.3]
./tools/Makefile.in [1.3]
./config/commence.in [1.3]
./config/conclude.in [1.3]
./config/depend.in [1.3]
Added a `.PATH' target for Irix pmake which is identical to
the VPATH used by most other `make' programs. Irix 6.5 (or
6.4?) and later `make' ignores VPATH.
Started all beginning-of-line comments with `##' instead of
just `#' because Irix `pmake' barfs on things like the
following because it sees the `# if' as a directive:
# make will barf on the following line
# if running Irix pmake
./config/commence.in [1.3]
Added empty definitions for optional `make' macros because
Irix pmake complains if it sees a macro which has never been
defined. The main body of the Makefiles can redefine these
macros to whatever they need.
