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* Removes the module directory from the Automake flags as this
generated a large number of "missing include directory" warnings
and is unecessary
* Adds the module path to libhdf5.settings
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* Added support for vector I/O calls to the VFD layer, and
associated test code. Note that this includes the optimization
to allow shortened sizes and types arrays to allow more space
efficient representations of vectors in which all entries are
of the same size and/or type. See the Selection I/o RFC for
further details.
Tested serial and parallel, debug and production on Charis.
serial and parallel debug only on Jelly.
* ran code formatter
quick serial build and test on jelly
* Add H5FD_read_selection() and H5FD_write_selection(). Currently only
translate to scalar calls. Fix const buf in H5FD_write_vector().
* Format source
* Fix comments
* Add selection I/O to chunk code, used when: not using chunk cache, no
datatype conversion, no I/O filters, no page buffer, not using collective
I/O. Requires global variable H5_use_selection_io_g be set to TRUE.
Implemented selection to vector I/O transaltion at the file driver
layer.
* Fix formatting unrelated to previous change to stop github from
complaining.
* Add full API support for selection I/O. Add tests for this.
* Implement selection I/O for contiguous datasets. Fix bug in selection
I/O translation. Add const qualifiers to some internal selection I/O
routines to maintain const-correctness while avoiding memcpys.
* Added vector read / write support to the MPIO VFD, with associated
test code (see testpar/t_vfd.c).
Note that this implementation does NOT support vector entries of
size greater than 2 GB. This must be repaired before release,
but it should be good enough for correctness testing.
As MPIO requires vector I/O requests to be sorted in increasing
address order, also added a vector sort utility in H5FDint.c This
function is tested in passing by the MPIO vector I/O extension.
In passing, repaired a bug in size / type vector extension management
in H5FD_read/write_vector()
Tested parallel debug and production on charis and Jelly.
* Ran source code formatter
* Add support for independent parallel I/O with selection I/O. Add
HDF5_USE_SELECTION_IO env var to control selection I/O (default off).
* Implement parallel collective support for selection I/O.
* Fix comments and run formatter.
* Update selection IO branch with develop (#1215)
Merged branch 'develop' into selection_io
* Sync with develop (#1262)
Updated the branch with develop changes.
* Implement big I/O support for vector I/O requests in the MPIO file
driver.
* Free arrays in H5FD__mpio_read/write_vector() as soon as they're not
needed, to cut down on memory usage during I/O.
* Address comments from code review. Fix const warnings with
H5S_SEL_ITER_INIT().
* Committing clang-format changes
* Feature/subfiling (#1464)
* Initial checkin of merged sub-filing VFD.
Passes regression tests (debug/shared/paralle) on Jelly.
However, bugs and many compiler warnings remain -- not suitable
for merge to develop.
* Minor mods to src/H5FDsubfile_mpi.c to address errors reported by autogen.sh
* Code formatting run -- no test
* Merged my subfiling code fixes into the new selection_io_branch
* Forgot to add the FindMERCURY.cmake file. This will probably disappear soon
* attempting to make a more reliable subfile file open which doesn't return errors. For some unknown reason, the regular posix open will occasionally fail to create a subfile. Some better error handling for file close has been added.
* added NULL option for H5FD_subfiling_config_t in H5Pset_fapl_subfiling (#1034)
* NULL option automatically stacks IOC VFD for subfiling and returns a valid fapl.
* added doxygen subfiling APIs
* Various fixes which allow the IOR benchmark to run correctly
* Lots of updates including the packaging up of the mercury_util source files to enable easier builds for our Benchmarking
* Interim checkin of selection_io_with_subfiling_vfd branch
Moddified testpar/t_vfd.c to test the subfiling vfd with default configuration.
Must update this code to run with a variety of configurations -- most particularly
multiple IO concentrators, and stripe depth small enough to test the other IO
concentrators.
testpar/t_vfd.c exposed a large number of race condidtions -- symtoms included:
1) Crashes (usually seg faults)
2) Heap corruption
3) Stack corruption
4) Double frees of heap space
5) Hangs
6) Out of order execution of I/O requests / violations of POSIX semantics
7) Swapped write requests
Items 1 - 4 turned out to be primarily caused by file close issues --
specifically, the main I/O concentrator thread and its pool of worker threads
were not being shut down properly on file close. Addressing this issue in
combination with some other minor fixes seems to have addressed these issues.
Items 5 & 6 appear to have been caused by issue of I/O requests to the
thread pool in an order that did not maintain POSIX semantics. A rewrite of
the I/O request dispatch code appears to have solved these issues.
Item 7 seems to have been caused by multiple write requests from a given
rank being read by the wrong worker thread. Code to issue "unique" tags for
each write request via the ACK message appears to have cleaned this up.
Note that the code is still in poor condtition. A partial list of known
defects includes:
a) Race condiditon on file close that allows superblock writes to arrive
at the I/O concentrator after it has been shutdown. This defect is
most evident when testpar/t_subfiling_vfd is run with 8 ranks.
b) No error reporting from I/O concentrators -- must design and implement
this. For now, mostly just asserts, which suggests that it should be
run in debug mode.
c) Much commented out and/or un-used code.
d) Code orgnaization
e) Build system with bits of Mercury is awkward -- think of shifting
to pthreads with our own thread pool code.
f) Need to add native support for vector and selection I/O to the subfiling
VFD.
g) Need to review, and posibly rework configuration code.
h) Need to store subfile configuration data in a superblock extension message,
and add code to use this data on file open.
i) Test code is inadequate -- expect more issues as it is extended.
In particular, there is no unit test code for the I/O request dispatch code.
While I think it is correct at present, we need test code to verify this.
Similarly, we need to test with multiple I/O concentrators and much smaller
stripe depth.
My actual code changes were limited to:
src/H5FDioc.c
src/H5FDioc_threads.c
src/H5FDsubfile_int.c
src/H5FDsubfile_mpi.c
src/H5FDsubfiling.c
src/H5FDsubfiling.h
src/H5FDsubfiling_priv.h
testpar/t_subfiling_vfd.c
testpar/t_vfd.c
I'm not sure what is going on with the deletions in src/mercury/src/util.
Tested parallel/debug on Charis and Jelly
* subfiling with selection IO (#1219)
Merged branch 'selection_io' into subfiling branch.
* Subfile name fixes (#1250)
* fixed subfiling naming convention, and added leading zero to rank names.
* Merge branch 'selection_io' into selection_io_with_subfiling_vfd (#1265)
* Added script to join subfiles into a single HDF5 file (#1350)
* Modified H5FD__subfiling_query() to report that the sub-filing VFD supports MPI
This exposed issues with truncate and get EOF in the sub-filing VFD.
I believe I have addressed these issues (get EOF not as fully tested as it should be), howeer,
it exposed race conditions resulting in hangs. As of this writing, I have not been able
to chase these down.
Note that the tests that expose these race conditions are in testpar/t_subfiling_vfd.c, and
are currently skipped. Unskip these tests to reproduce the race conditions.
tested (to the extent possible) debug/parallel on charis and jelly.
* Committing clang-format changes
* fixed H5MM_free
Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Move Subfiling VFD components into H5FDsubfiling source directory
* Update Autotools build and add H5_HAVE_SUBFILING_VFD macro to H5pubconf.h
* Tidy up CMake build of subfiling sources
* Merge branch 'develop' into feature/subfiling (#1539)
Merge branch 'develop' into feature/subfiling
* Add VFD interface version field to Subfiling and IOC VFDs
* Merge branch 'develop' into feature/subfiling (#1557)
Merge branch 'develop' into feature/subfiling
* Merge branch 'develop' into feature/subfiling (#1563)
Merge branch 'develop' into feature/subfiling
* Tidy up merge artifacts after rebase on develop
* Fix incorrect variable in mirror VFD utils CMake
* Ensure VFD values are always defined
* Add subfiling to CMake VFD_LIST if built
* Mark MPI I/O driver self-initialization global as static
* Add Subfiling VFD to predefined VFDs for HDF5_DRIVER env. variable
* Initial progress towards separating private vs. public subfiling code
* include libgen.h in t_vfd tests for correct dirname/basename
* Committing clang-format changes
* removed mercury option, included subfiling header path (#1577)
Added subfiling status to configure output, installed h5fuse.sh to build directory for use in future tests.
* added check for stdatomic.h (#1578)
* added check for stdatomic.h with subfiling
* added H5_HAVE_SUBFILING_VFD for cmake
* fix old-style-definition warning (#1582)
* fix old-style-definition warning
* added test for enable parallel with subfiling VFD (#1586)
Fails if subfiling VFD is not used with parallel support.
* Subfiling/IOC VFD fixes and tidying (#1619)
* Rename CMake option for Subfiling VFD to be consistent with other VFDs
* Miscellaneous Subfiling fixes
Add error message for unset MPI communicator
Support dynamic loading of subfiling VFD with default configuration
* Temporary fix for subfile name issue
* Added subfile checks (#1634)
* added subfile checks
* Feature/subfiling (#1655)
* Subfiling/IOC VFD cleanup
Fix misuse of MPI_COMM_WORLD in IOC VFD
Propagate Subfiling FAPL MPI settings down to IOC FAPL in default
configuration case
Cleanup IOC VFD debugging code
Change sprintf to snprintf in a few places
* Major work on separating Subfiling and IOC VFDs from each other
* Re-write async_completion func to not overuse stack
* Replace usage of MPI_COMM_WORLD with file's actual MPI communicator
* Refactor H5FDsubfile_mpi.c
* Remove empty file H5FDsubfile_mpi.c
* Separate IOC VFD errors to its own error stack
* Committing clang-format changes
* Remove H5TRACE macros from H5FDioc.c
* Integrate H5FDioc_threads.c with IOC error stack
* Fix for subfile name generation
Use number of I/O concentrators from existing subfiling configuration file, if one exists
* Add temporary barrier in "Get EOF" operation to prevent races on EOF
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for retrieval of machine Host ID
* Default to MPI_COMM_WORLD if no MPI params set
* added libs rt and pthreads (#1673)
* added libs rt and pthreads
* Feature/subfiling (#1689)
* More tidying of IOC VFD and subfiling debug code
* Remove old unused log file code
* Clear FID from active file map on failure
* Fix bug in generation of subfile names when truncating file
* Change subfile names to start from 1 instead of 0
* Use long long for user-specified stripe size from environment variable
* Skip 0-sized I/Os in low-level IOC I/O routines
* Don't update EOF on read
* Convert printed warning about data size mismatch to assertion
* Don't add base file address to I/O addresses twice
Base address should already be applied as part of H5FDwrite/read_vector calls
* Account for 0-sized I/O vector entries in subfile write/read functions
* Rewrite init_indep_io for clarity
* Correction for IOC wraparound calculations
* Some corrections to iovec calculations
* Remove temporary barrier on EOF retrieval
* Complete work request queue entry on error instead of skipping over
* Account for stripe size wraparound for sf_col_offset calculation
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Re-write and fix bugs in I/O vector filling routines (#1703)
* Rewrite I/O vector filling routines for clarity
* Fix bug with iovec_fill_last when last I/O size is 0
* added subfiling_dir line read (#1714)
* added subfiling_dir line read and use it
* shellcheck fixes
* I/O request dispatch logic update (#1731)
Short-circuit I/O request dispatch when head of I/O queue is an
in-progress get EOF or truncate operation. This prevents an issue where
a write operation can be dispatched alongside a get EOF/truncate
operation, whereas all I/O requests are supposed to be ineligible for
dispatch until the get EOF/truncate is completed
* h5fuse.sh.in clean-up (#1757)
* Added command-line options
* Committing clang-format changes
* Align with changes from develop
* Mimic MPI I/O VFD for EOF handling
* Initialize context_id field for work request objects
* Use logfile for some debugging information
* Use atomic store to set IOC ready flag
* Use separate communicator for sending file EOF data
Minor IOC cleanup
* Use H5_subfile_fid_to_context to get context ID for file in Subfiling
VFD
* IOVEC calculation fixes
* Updates for debugging code
* Minor fixes for threaded code
* Committing clang-format changes
* Use separate MPI communicator for barrier operations
* Committing clang-format changes
* Rewrite EOF routine to use nonblocking MPI communication
* Committing clang-format changes
* Always dispatch I/O work requests in IOC main loop
* Return distinct MPI communicator to library when requested
* Minor warning cleanup
* Committing clang-format changes
* Generate h5fuse.sh from h5fuse.sh.in in CMake
* Send truncate messages to correct IOC rank
* Committing clang-format changes
* Miscellaneous cleanup
Post some MPI receives before sends
Free some duplicated MPI communicator/Info objects
Remove unnecessary extra MPI_Barrier
* Warning cleanup
* Fix for leaked MPI communicator
* Retrieve file EOF on single rank and bcast it
* Fixes for a few failure paths
* Cleanup of IOC file opens
* Committing clang-format changes
* Use plan MPI_Send for send of EOF messages
* Always check MPI thread support level during Subfiling init
* Committing clang-format changes
* Handle a hang on failure when IOCs can't open subfiles
* Committing clang-format changes
* Refactor file open status consensus check
* Committing clang-format changes
* Fix for MPI_Comm_free being called after MPI_Finalize
* Fix VFD test by setting MPI params before setting subfiling on FAPL
* Update Subfiling VFD error handling and error stack usage
* Improvements for Subfiling logfiles
* Remove prototypes for currently unused routines
* Disable I/O queue stat collecting by default
* Remove unused serialization mutex variable
* Update VFD testing to take subfiling VFD into account
* Fix usage of global subfiling application layout object
* Minor fixes for failure pathways
* Keep track of the number of failures in an IOC I/O queue
* Make sure not to exceed MPI_TAG_UB value for data communication messages
* Committing clang-format changes
* Update for rename of some H5FD 'ctl' opcodes
* Always include Subfiling's public header files in hdf5.h
* Remove old unused code and comments
* Implement support for per-file I/O queues
Allows the subfiling VFD to have multiple HDF5 files open simultaneously
* Use simple MPI_Iprobe over unnecessary MPI_Improbe
* Committing clang-format changes
* Update HDF5 testing to query driver for H5FD_FEAT_DEFAULT_VFD_COMPATIBLE
flag
* Fix a few bugs related to file multi-opens
* Avoid calling MPI routines if subfiling gets reinitialized
* Fix issue when files are closed in a random order
* Update HDF5 testing to query VFD for "using MPI" feature flag
* Register atexit handler in subfiling VFD to call MPI_Finalize after HDF5
closes
* Fail for collective I/O requests until support is implemented
* Correct VOL test function prototypes
* Minor cleanup of old code and comments
* Update mercury dependency
* Cleanup of subfiling configuration structure
* Committing clang-format changes
* Build system updates for Subfiling VFD
* Fix possible hang on failure in t_vfd tests caused by mismatched
MPI_Barrier calls
* Copy subfiling IOC fapl in "fapl get" method
* Mirror subfiling superblock writes to stub file for legacy POSIX-y HDF5
applications
* Allow collective I/O for MPI_BYTE types and rank 0 bcast strategy
* Committing clang-format changes
* Use different scheme for subfiling write message MPI tag calculations
* Committing clang-format changes
* Avoid performing fstat calls on all MPI ranks
* Add MPI_Barrier before finalizing IOC threads
* Use try_lock in I/O queue dispatch to minimize contention from worker threads
* Use simple Waitall for nonblocking I/O waits
* Add configurable IOC main thread delay and try_lock option to I/O queue dispatch
* Fix bug that could cause serialization of non-overlapping I/O requests
* Temporarily treat collective subfiling vector I/O calls as independent
* Removed unused mercury bits
* Add stubs for subfiling and IOC file delete callback
* Update VFD testing for Subfiling VFD
* Work around HDF5 metadata cache bug for Subfiling VFD when MPI Comm size
= 1
* Committing clang-format changes
Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
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* Enable usage of new-style references with dimension scale APIs
* Add API to check if an object ID represents a native connector object
* Modified code to use new function H5DSwith_new_ref to determine if new references should be used with
Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF
varible is define at configure time (--enable-dimension-scales-with-new-ref).
Tested on jelly.
ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references.
* Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library.
test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5
for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further
investigation; but current implementation of the new references is not portable between LE and BE systems,
and 32 and 64-bit systems.
* Minor fixes for testing issues
* Update test_ds.c
Enabled broken test; tests pass now.
* Update RELEASE.txt
Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*).
* Update MANIFEST for new 32-bit new-style references test file for H5DS APIs
* Update 'dimension scales w/ new-style refs' feature based on review
Co-authored-by: Elena <epourmal@hdfgroup.org>
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This variable is unused and was missed in the -Werror changes.
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* Works in both Autotools and CMake
* OFF by default
* Reverts "always on" -Werror behavior released in 1.10.7
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https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into feature/vfd_splitter_mirror_a
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occur. Next commit will demote the warnings promoted to errors back to
warnings again.
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* "Simultaneous and equivalent" Read-Write and Write-Only channels for
file I/O.
* Only supports drivers with the H5FD_FEAT_DEFAULT_VFD_COMPATIBLE flag for
now, preventing issues with multi-file drivers.
Add Mirror VFD to library.
* Write-only operations over a network.
* Uses TCP/IP sockets.
* Server and auxiliary server-shutdown programs provided in a new directory,
`utils/mirror_vfd`.
* Automated testing via loopback ("remote" of localhost).
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level and fixing some code.' (commit 5c911d8baf3)"
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Merge changes from update_merged_S3_HDFS branch into develop.
commit d5034315aea88629929ac0c9c59ebfafd5f21a31
Merge: 9c48823 d3fdcd8
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Thu Jul 25 08:24:53 2019 -0500
Merge branch 'develop' into update_merged_S3_HDFS
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disabling tests.
Moved h5cc.in from tools/src/misc to src directory to always create h5cc
whether or not tools are enabled.
Added configuration status of tools and tests to libhdf5.settings.
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Add line to libhdf5settings file for status of Parallel writes to
filtered datasets status
Surround Parallel Compression code in MPI_VERSION >= 3 checks
Add disabled message for Parallel Compression built w/ MPI-2
Modify Parallel Compression tests to only run the parallel filtered read
tests when parallel filtered writes are disabled
Update big I/O code to handle being built with MPI-2
Add checks to CMakeLists.txt for MPI_Mprobe and MPI_Imrecv
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settings file.
Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1
autotools serial w/Java
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debug
symbols, asserts, profiling, and optimization.
Also much refactoring, improved help, and --enable-<foo> options will
now emit errors on nonsense (e.g.: --enable-foo="asdfasdf").
The libhdf5.settings.in file was also reformatted.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial and parallel autotools w/ various options
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library.
Buffers that will be written to disk will now always be cleared since
not doing this has huge security implications.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0, x86_64) gcc 5.2.1
serial autotools
parallel autotools (MPICH 3.1.4)
serial CMake
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Add --enable-memory-alloc-sanity-check option to configure, to track and
sanity check memory allocations within the library. This is orthogonal to the
--enable-using-memchecker option and can be used with/without it.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
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Tested: h5committest --PASSED--
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--enable-fortran
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variable
from H5_CXX_SHARED (which no longer exists) to enable_static.
Tested on: jam (configure only - minor change)
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features/autotools_rework
branch.
Removed the configure option that allows selective disabling of individual
internal filters (fletcher32, shuffle, etc.).
This feature mucked up the code with a lot of #ifdefs, saved very little space,
and was not scalable to a general scheme for library size reduction. We've
decided to remove the feature while we investigate a more general scheme for
decreasing the library size.
Part of: HDFFV-9086
Tested on: h5committest
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autotools_rework branch:
- Remove Infering parallel compilers (C and Fortran) from configure.ac
- Remove restriction to build shared with parallel
- Cleanup parallel sections in configure.ac
- remove large file support checks
- MPE fixes.
tested with h5committest.
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Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
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include test.
Tested: jam
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Items merged: fortran directory,
src/libhdf5.settings.in
configure.in configure
MANIFEST
Tested: (all platforms used by daily tests, both with --enable-fortran and --enable-fortran2003)
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General shared library improvements for CYGWIN / AIX
Description:
Shared libraries are disabled on both CYGWIN and AIX due
to inability to build them correctly. Part of the problem
in both of these situations is the lack of the libtool
flag -no-undefined, which tells libtool that all needed
symbols are defined at link time (a requirement on these
systems) and that it's okay to build shared libraries.
Another problem are lack of dependencies between wrapper
libraries and core C HDF5 library.
This patch addresses both of these by fixing configure to
add in -no-undefined flag for libtool during linking and
adds automake dependencies in the Makefile.am files.
After testing, both CYGWIN and AIX now generate shared
libraries, but there are still some test failures in each.
(cache_api, dt_arith, and testerror.sh on CYGWIN, and
fortran tests on AIX).
Even though the shared libraries are not quite perfect,
this is a general improvement to what we had before, so
I'm applying the patch anyways. Note that default behavior
of shared libraries on these systems being disabled has
NOT been changed and requires the use of the
--enable-unsupported to attempt to build them.
We will need to address the test failures in each
architecture prior to formally supporting shared
libraries on each.
Tested:
h5committested & CYGWIN tested (on bangan)
(AIX tested by Albert on bp-login2)
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- Revise shared Fortran library disabling scenarios in configure
- Improve configure output summary
Description:
Shared Fortran libraries are not supported on Mac, but were being
disabled by configure in a way that also forced the C libraries
to be static-only. This has been fixed, so now only shared Fortran
is disabled while shared C can remain.
This prompted two additional changes:
1. While working on the check that addresses whether or not
shared Fortran libraries are allowed, removed old and no
longer needed check(s) that disable shared Fortran
libraries with HP, Intel 8, PGI, and Absoft compilers.
(Essentially, Mac is the only situation in which Fortran
shared are disabled by configure.)
2. Having two different states of libraries (i.e. shared C
library with static-only Fortran library) was not apparent
in the configure summary, which labeled all libraries as
either shared and/or static. I've added lines to both the
C++ and Fortran output sections to list shared/static-ness
of these libraries specifically.
Additionally, I've made sure that the new --enable-unsupported
configure option correctly overrides configure if it tries to
disable a shared library.
Tested:
jam, fred, & h5committest
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fortran and c++ compilers in libhdf5.settings file and configure output (r18836), to install examples as part of make install (r18680), and to provide scripts to compile and run the examples after they are installed (r18817).
Tested with new/h5committest on amani, heiwa, and jam.
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Improve configure's large-file support control.
Description:
Modified configure to now attempt to add defines necessary for
supporting largefiles on all systems, instead of solely on linux. This
is in response to user requests to enable largefile support on Solaris
by default, as well as to give extra control on AIX (instead of just
jamming the necessary flag into the config files).
The old --enable-linux-lfs flag has been removed in favor of the
--enable-largefile flag (enabled by default), which can be used on all
platforms.
On systems where large files cannot be supported in this manner,
configure will report as such.
Tested:
h5committest
AIX (NCSA's blue_print machine)
duty, liberty, and linew.
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Configure / Config File Fixes
Description:
1. Made AM_CPPFLAGS assignments in configure a bit safer. (i.e., check to
ensure include paths exist before adding them to AM_CPPFLAGS).
2. Change AIX config file to add -D_LARGE_FILES into AM_CXXFLAGS instead
of H5_CXXFLAGS (same with *_CFLAGS). This will propagate it into
h5c++, where it is needed to compile correctly.
3. Added missing line containing AM_CFLAGS to configure output summary.
Tested:
h5committest, and uP (AIX machine, via Albert).
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CFLAGS overhaul
Description:
Modified the way configure handles CFLAGS.
(note: all changes also apply to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS).
1. The configure process will now always preserve a user's CFLAGS
environment variable setup. Any additional flags necessary for compilation
added at configure time will be passed into the Makefiles as AM_CFLAGS,
which is an automake construct to be used in addition to CFLAGS.
This will allow a user to have the final say, as CFLAGS will always appear
later in the compile line than AM_CFLAGS. Additionally, setting CFLAGS
during make will no longer completely erase all flags set by configure,
since they're maintained in AM_CFLAGS.
2. Additionally, where possible, flags previously being assigned directly
into CFLAGS (and thus propagating into h5cc) have now been redirected into
H5_CFLAGS, so they're used ONLY for compiling hdf5, and not embedded into
the h5cc wrapper script as well.
*Note that H5_CFLAGS ultimately is assigned into AM_CFLAGS for use in the
Makefiles. Complete description of changes and build process will be
included in a Configure Document that Elena and I are working on.
3. Removed unsupported config files. This includes:
config/dec-osf*
config/hpux11.00
config/irix5.x
config/powerpc-ibm-aix4.x
config/rs6000-ibm-aix5.x
config/unicos*
4. Modified configure summary to display additional values. Specifically,
appropriate AM_* variables are being shown, as well as H5_FCFLAGS and
H5_CXXFLAGS, which were for some reason not already present.
Tested:
- H5committest
- Tested on all THG / NCSA machines, using several combinations of the more
prominent configure options (c++, fortran, szip, threadsafe, parallel,
et cetera). (Thanks to Quincey for rysnc testing setup!)
- With regards to new automated testing, anything *necessary* for
compilation will be caught by the daily tests as it stands now. (i.e.,
if LDFLAGS is not properly set when szip is used, linking will fail).
Additionally, with regards to which flags get into h5cc, if any
*necessary* flags have been improperly removed, then daily tests should
fail during make installcheck. Additional machine-specific desired
behaviors and/or checks may have to be set up separately within the
daily tests, so this is something to work on.
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Removed duplicated information due to previous incompleted changes.
Also rearranged the entries to a more logical combinations.
Tested: h5committest.
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Changed blank spacing in Fortran output so the output aligns correctly
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Fixed spacing issue for fortran summary line.
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Description: cleaning up configure related to removal of --disable-hsizet
flag, which we no longer support.
Tested: kagiso
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Improvement.
Description:
src/libhdf5.settings was the initial configure summary and is installed.
Then configure is changed to dump a summary of the configure settings to
the output and also append it to src/libhdf5.settings. That created
two different output formats and duplicated information. This is the
initial attempt to clean up this confusion and unify the output format.
It is decided to use the src/libhdf5.settings template as the unified means.
This requires more macros symbols be defined. The following symbols are
all related to generating the src/libhdf5.settings file.
AC_SUBST(EXTERNAL_FILTERS)
AC_SUBST(MPE) MPE=no
AC_SUBST(STATIC_EXEC) STATIC_EXEC=no
AC_SUBST(HDF_FORTRAN) HDF_FORTRAN=no
AC_SUBST(FC) HDF_FORTRAN=no
AC_SUBST(HDF_CXX) HDF_CXX=no
AC_SUBST(CXX) HDF_CXX=no
AC_SUBST(HDF5_HL) HDF5_HL=yes
AC_SUBST(GPFS) GPFS=no
AC_SUBST(LINUX_LFS) LINUX_LFS=no
AC_SUBST(INSTRUMENT) INSTRUMENT=no
AC_SUBST(CODESTACK) CODESTACK=no
AC_SUBST(HAVE_DMALLOC) HAVE_DMALLOC=no
AC_SUBST(DIRECT_VFD) DIRECT_VFD=no
AC_SUBST(THREADSAFE) THREADSAFE=no
AC_SUBST(STATIC_SHARED)
AC_SUBST(enable_shared)
AC_SUBST(enable_static)
AC_SUBST(UNAME_INFO) UNAME_INFO=`uname -a`
The src/libhdf5.settings.in has CONDITIONAL's added to it too. The
untrue conditions turned into a "#" and these lines are cleaned by the
post processing script.
Platform tested:
h5committest on kagiso, smirom and linew.
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Added C proprocessor flags and non-library linker flags to the
description.
./src/H5T.c [1.2, 1.3]
Changed return type in tracing macros to H5Tenum_nameof() and
H5Tenum_valueof().
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----------------------
./configure.in
./configure [REGENERATED]
./src/libhdf5.settings.in [NEW]
./config/conclude.in
./INSTALL
./MANIFEST
A file called `libhdf5.settings' is installed along with the
libraries and it contains a list of various things that might
be of interest to someone using the library (such as what
compiler/options were used and what other libraries might need
to be linked to satisfy external references). We can add more
things as it becomes necessary. Here's a sample...
SUMMARY OF THE HDF5 CONFIGURATION
=================================
HDF5 Version: hdf5-1.1.106
Configured on: Tue Jun 8 11:38:52 EDT 1999
Configured by: matzke@llnl.gov at Spizella Software
Configure mode: development
Host system: i686-pc-linux-gnulibc1
Byte sex: little-endian
Libraries: static, shared
Parallel support: mpicc
Installation point: /usr/local
Compiler: mpicc (egcs-2.91.66)
Compiler switches: -Wall -g
Extra libraries: -lmfhdf -ldf -lz -ljpeg -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages: d,e,f,g,hg,i,mm,o,p,s,v,z
API Tracing: yes
File addresses: large
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