Darshan

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* fixed bug causing corruption of Darshan common access
counters (POSIX, MPI-IO, and HDF5 modules) and potentially
other preceding counters (reported by Gerd Heber)

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* added detailed instrumentation of HDF5 library file and dataset
interfaces
* added new logutil functions: darshan_log_get_modules,
darshan_log_get_name_records, and darshan_log_get_record (contributed
by Jakob Luettgau)
* extended DXT MPIIO module to trace file offsets
* added `darshan-config --log-path` command option to display the log path(s)
configured for use with Darshan
* silenced stdout from darshan-job-summary.pl and remove --summary option
* removed Darshan stubs library traditionally used in static linking test
cases and other general simplifications of Darshan's static linking options
* fixed bug related to multiple definitions of fscanf symbols when building
Darshan (reported by Francois Trahay)
* updated Darshan's compiler wrapper generators, MPICH profiling config
hooks, and Cray software modules to explicitly link in Darshan in
dynamic linking cases using rpath
* reimplemented Darshan's MPI/PMPI wrapper macros (using functiona aliases)
to avoid potential deadlock with other PMPI tools
* made use of DESTDIR match standard automake practice (contributed by
Christopher Morrone)
* made "--with-mem-align" option optional, with a default of 8 (contributed
by Christopher Morrone)
* corrected pkgconfig path for darshan-util when using DESTDIR (reported by
Matthew Curry)
* added support for non-MPI instrumenation to Darshan, using GCC
construct/destructor attributes for bootstrapping rather than
intercepting MPI_Init()/MPI_Finalize(). This mechanism only
works for Darshan's shared library instrumentation (implemented with the
help of Glenn Lockwood)

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* added dynamic trace triggering functionality, allowing Darshan to
decide at runtime whether or not to trace specific files with DXT,
with this decision based on triggers in a user-provided config file

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* bug fix for handling DXT data in darshan-convert utility. Bug reported
by Mahzad Khoshlessan.
* bug fix for darshan-parser backwards compatibility: Darshan logs generated
by Darshan versions prior to 3.1.0 may have included stdio counters that
were not properly up-converted. Reported by Teng Wang.
* bug fix to MiB reported in I/O performance estimate of
darshan-job-summary.pl when both posix and stdio access is present
* added wrapper for __open_2(), bug reported by Cormac Garvey in which open
calls are not intercepted with some versions of glibc/gcc
* added an instrumentation module for the MDHIM key/val storage system
* added support for properly instrumenting dup(), fileno(), fdopen(), and
rename() calls

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* bug fix for linker failures caused when linking external libraries
that use MPI internally (e.g., PETSc). Reported by Bilel Hadri.
* bug fix in mapping of Darshan's MPI_File_read_all wrapper to the
underlying MPI library call in dynamic linking case

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* modify Darshan MPI instrumentation method to intercept both MPI and
PMPI symbols to workaround MPI implementations that are calling
PMPI routines directly (e.g., the Fortran bindings of OpenMPI2).
Contributed in part by Chris Zimmer.
* add a new python utility for analzying DXT trace files (dxt_analyzer).
Contributed by Alex Sim.
* bug fix to disable Darshan module instrumentation after the
Darshan shutdown procedure has began, an issue that was
leading to negative timers in some cases
* bug fix for autoconf ignoring specified libbz2 location. Contributed
by Glenn Lockwood.
* add regression tests harnesses for Cray systems at ALCF & NERSC
* add support for DARSHAN_EXCLUDE_DIRS environment variable to
explicitly disable instrumentation for files in given
directories. Contributed by Cristian Simarro.
* correct "undefined reference to `__wrap_H5get_libversion'" linker failure
when compiling some HDF5 programs, reported by Jialin Liu
* bug fix in darshan-merge utility related to logs containing DXT trace
data. Reported by Glenn Lockwood.