Darshan

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* Added enhancements to Darshan's Lustre instrumentation module to capture
extensive details on the Lustre stripe components constituting a file (e.g.,
in a progressive file layout)
- File records now composed of potentially multiple Lustre component counter
sets (e.g., LUSTRE_COMP1_*, LUSTRE_COMP2_*, etc.)
- STRIPE_OFFSET, OSTS, and MDTS counters are no longer provided
- STRIPE_WIDTH is now referred to as STRIPE_COUNT to match Lustre terminology
* Fixed bugs in Darshan's log compression/decompression routines that are
triggered when using the new zlib-ng software package
- darshan-runtime bug fix to correct problematic log compression strategy
- darshan-util bug fix to correct logs already generated with this issue
* Fixed bug leading to hangs when passing in unproperly formatted Darshan
runtime configuration settings

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* Added the ability for the Darshan runtime library to properly shutdown for
non-MPI applications that call `_exit()` directly
- This behavior has been commonly observed in the Python `multiprocessing`
package, which has traditionally prevented Darshan from properly
instrumenting applications that use it (e.g., the PyTorch DataLoader)
* Added optional integration with the LDMS data/metrics collection system,
allowing realtime analysis of Darshan instrumented I/O operations.
- For more details, see https://ovis-hpc.readthedocs.io/en/latest/ldms/ldms-streams.html#darshan
- Contributed by Sara Walton (SNL), Ana Luisa Solorzano (Northeastern), and the LDMS team
* Fixed bug to ensure Darshan includes the appropriate instrumentation wrapper
for `fscanf`/`__isoc99_fscanf`
* Fixed bug in HDF5 module causing any call to HDF5's `H5Pset_fapl_mpio()`
routine to fail

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* Fixed bug leading to inconsistent heatmap record shapes when Darshan
shared file reductions are disabled
- also added a darshan-util fix to resolve this inconsisency on already
impacted logs (any generated with 3.4.0+ versions of Darshan)
* Added workaround for potential undefined symbol errors for 'H5FD_mpio_init'
when LD_PRELOADing an HDF5-enabled runtime library
- bug triggered by 1.13+ versions of HDF5

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* Added new configure option '--with-username-env' to allow
specification of an env variable to use to find the username
associated with a job (e.g., SLURM_JOB_USER)
* Fixed bug causing crashes for applications that call fork()
and use Darshan app exclusions settings
* Fixed bug related to not closing open HDF5 file ID when
instrumenting H5Fflush() calls (reported/fixed by Zanhua
Huang)

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* Fixed segfault when defining scalar variables in PnetCDF module
* Fixed memory corruption (and potential segfault) when
reading/writing high-dimensional PnetCDF variables using
vara/vars/varm interfaces
* Fixed crashes related to using PnetCDF vard interfaces with input
MPI_DATATYPE_NULL datatypes
* Fixed bug attributing all PnetCDF variable instrumentation to the
first variable instrumented

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* Added comprehensive instrumentation of PnetCDF APIs via PNETCDF_FILE and
PNETCDF_VAR modules (contributed by Wei-Keng Liao)
- disabled by default, enabled by passing `--enable-pnetcdf-mod` to
configure
* Modified Darshan log format to support a max of 64 instrumentation
modules, since the current version of Darshan reached the old max (16)
* Modified Darshan to report job start/end times at nanosecond
granularity (previously only second granularity was possible)
* Added support for instrumenting H5Oopen family of calls
* Modified HDF5 module extraction of dataspase selection details
- Extraction of point selections now possible regardless of HDF5 version
- H5S_ALL selections are no longer counted as regular hyperslab accesses
* Fixed bug causing no instrumentation of child processes of fork() calls
(reported by Rui Wang)
* Deprecated --file-list and --file-list-detailed options in darshan-parser
* Added "darshan_accumulator" API to the logutils library
- _create(), _inject(), _emit(), and _destroy()
- generalizes the mechanism for producing summation records and derived
metrics for sets of records from a given module
- refactored darshan-parser to use new API
- implemented support for accumulators in POSIX, STDIO, and MPIIO modules
* Fixed memory leak in darshan-util helper functions used by PyDarshan
- darshan_log_get_name_records
- darshan_log_get_filtered_name_records
* Integrated the µnit Testing Framework in darshan-util
- implemented unit tests for darshan_accumlator API