Darshan

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* added documentation and example configuration files for using the -profile
or $MPICC_PROFILE hooks to add instrumentation to MPICH-based MPI
implementations without generating custom wrapper scripts
* Add wrappers for mkstemp(), mkostemp(), mkstemps(), and mkostemps()
(reported by Tom Peterka)
* Change OPEN_TIMESTAMP field to report timestamp right before open() is
invoked rather than after timestamp after open is completed.
NOTE: updated log format version to 2.06 to reflect this change.
* Change start_time and end_time fields in job record to use min and max
(respectively) across all ranks
* Fix bug in write volume data reported in file system table in
darshan-job-summary.pl (reported by Matthieu Dorier)
* Clean up autoconf test for zlib and make zlib mandatory (reported by Kalyana
Chadalavada)
* add --start-group and --end-group notation to Darshan libraries for Cray PE
2.x environment to fix link-time corner cases (Yushu Yao)
* improve y axis labels on time interval graphs in darshan-job-summary.pl
(reported by Tom Peterka)
* misc. improvements to darshan-parser --perf output (reported by Shane
Snyder)
- indicate which rank was slowest in unique file results
- label I/O vs. meta time more clearly
- include unique file meta time in agg_perf_by_slowest calculation
* added regression test script framework in darshan-test/regression/
- currently support platforms include:
- Linux with static linking and generated compiler wrappers
- Linux with static linking and profiler configuration files
- Linux with dynamic linking and LD_PRELOAD
- Blue Gene/Q with static linking and profiler configuration files
* update darshan-gen-fortran.pl and darshan-gen-cxx.pl to support new library
naming conventions in MPICH 3.1.1 and higher
* update documentation to reflect known issues with some versions of MPICH
* Cray platforms: modify darshan-runtime so that link-time instrumentation
options are only used when statically linking via Libs.private.
(reported by Kalyana Chadalavada)

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* Fix incorrect version numbering in darshan-runtime component of Darshan
2.2.9, reported by Jean-Guillaume Piccinali

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* Bug fixes:
- Fix mnt table overflow if a large number of file systems are mounted,
reported by David Shrader.
- Fix argument parsing for darshan-convert, reported by Mouhamed Gueye.
- Fix metadata annotation overflow in darshan-convert, reported by
Mouhamed Gueye.
- Fix const-correctness in dynamic library when built against MPI 3.x
libraries.
- Fix "undefined symbol: dlsym" error when using preloaded dynamic library
on some platforms, reported by Florin Isaila.
- Normalize timestamps to always be relative to MPI_Init().
- Better library name matching in compiler wrappers to handle more MPICH
variations on Blue Gene systems.
- Fixed header dependency problems when using darshan-logutils.h in external
programs (Shane Snyder).
* Enhancements:
- Add support (both in documentation and in provided module files) for
Cray PE 2.x.
- Honor CC variable to allow darshan-util to be built with other compilers
besides gcc.
- Update documentation to clarify the interaction between rpath and
LD_PRELOAD when instrumenting dynamic libraries, issue reported and
investigated by Davide Del Vento.
- Ability to disable shared-file reduction by setting the
DARSHAN_DISABLE_SHARED_REDUCTION environment variable.
- More thorough output from darshan-parser --perf, suggested by Huong Luu.
- Increased metadata annotation room from 64 bytes to 1KiB in header.
- CP_F_{FASTEST/SLOWEST}_RANK_TIME counters now take MPI-IO time into
account, not just POSIX time, issue reported by Huong Luu.
- Better handling of systems with many mounted file systems (after which
point Darshan will assume file resides on / file system), issue reported
and investigated by David Shrader:
- Track up to 64 rather than 32 mounted file systems at runtime.
- Increase header space available for storing mount point information in
log file from approximately 1 KiB to approximately 3 KiB.
- Prioritize storing information about non-NFS volumes over NFS volumes
if too many file systems are mounted to record them all.
- Added darshan-util pkgconfig file (Shane Snyder).
- Added --enable-shared configure option to darshan-util to build and
a shared library version of libdarshan-util

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* WARNING: please note that the Darshan module file for Cray environments has
been updated, especially in the DARSHAN_POST_LINK_OPTS variable. Please
update your module file accordingly when upgrading from 2.2.7 or earlier
on Cray platforms.
* Improved ability to analyze I/O activity related to particular files
opened by an application
- darshan-summary-per-file.sh script to generate a separate pdf summary for
each file opened by an application. Developed by Rob Latham.
- Added --file-list and --file-list-detailed options to darshan-parser to
list files opened by an application along with brief statistics
- Added --file option to darshan-convert to filter out activity for a
specific file from a Darshan log
* Add wrappers for POSIX AIO operations (fixes tracking of underlying POSIX
operations resulting from nonblocking MPI-IO operations. Bug reported by
David Shrader.)
* Fix compile-time errors when Darshan is configured for use with MPICH 3.x
installations with const correct MPI function prototypes. Also affects
MPICH 1.5+ installations with optional const support. Reported by Yushu Yao.
* Fix segmentation fault when using LD_PRELOAD instrumentation on programs
that use MPI_Init_thread() rather than MPI_Init(). Reported by Myriam
Botalla.

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* Updated Cray installation documentation for cleaner integration in Cray
environments
* Fix bug that recorded incorrect device ID (and therefore incorrect mount
point mapping) if stat() was called before open() on a file
* Store version number of the darshan runtime library in the log file
metadata (see lib_ver in darshan-parser output)

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* Bug fixes:
- make sure to honor user-specified hints passed in at runtime
via the DARSHAN_LOGHINTS env variable.
- include fread and fwrite in darshan-job-summary.pl read and write counts
- fix segmentation fault on invalid arguments to darshan-parser
* Performance enhancements:
- collect mount point information at rank 0 and broadcast to all
processes to avoid excess file system traffic on startup
- change default MPI-IO hints for writing log file to
romio_no_indep_rw=true and cb_nodes=4 to improve log creation performance
* Install libdarshan-util and headers during installation process for
darshan-util; patch contributed by Matthieu Dorier
* Detect PMPI support at link time when using compiler scripts produced
by the darshan-gen-* utilities. This avoids link problems when Darshan
compiler wrappers are used with the ADIOS dummy MPI library; reported
by Jingqing Mu
* Support MPICH_{CC/CXX/F77} environment variables in compiler scripts
produced by the darshan-gen-* utilities
* Add instrumentation of startup time, enabled via DARSHAN_INTERNAL_TIMING
environment variable
* Rename cp-shutdown-bench test utility to darshan-shutdown-bench and enable
benchmarking hooks in library by default so that darshan-shutdown-bench
can be used with any Darshan installation
* Remove deprecated --enable-st-dev-workaround configure option
* Misc. documentation updates