CVS commit: pkgsrc/parallel/openmpi

["Aleksej Saushev" <asau%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   asau
Date:           Thu Dec 16 21:00:54 UTC 2010

Modified Files:
        pkgsrc/parallel/openmpi: Makefile PLIST PLIST.vt buildlink3.mk distinfo
        pkgsrc/parallel/openmpi/patches: patch-aa patch-ai patch-aj patch-ak
Removed Files:
        pkgsrc/parallel/openmpi/patches: patch-ab patch-ac patch-ad patch-ae
            patch-af patch-ag

Log Message:
Update to OpenMPI 1.5.1

Changes in 1.5.1

- Fixes for the Oracle Studio 12.2 Fortran compiler.
- Fix SPARC and SPARCv9 atomics.  Thanks to Nicola Stange for the
  initial patch.
- Fix Libtool issues with the IBM XL compiler in 64-bit mode.
- Restore the reset of the libevent progress counter to avoid
  over-sampling the event library.
- Update memory barrier support.
- Use memmove (instead of memcpy) when necessary (e.g., source and
  destination overlap).
- Fixed ompi-top crash.
- Fix to handle Autoconf --program-transforms properly and other
  m4/configury updates.  Thanks to the GASNet project for the
  --program transforms fix.
- Allow hostfiles to specify usernames on a per-host basis.
- Update wrapper compiler scripts to search for perl during configure,
  per request from the BSD maintainers.
- Minor man page fixes.
- Added --with-libltdl option to allow building Open MPI with an
  external installation of libltdl.
- Fixed various issues with -D_FORTIFY_SOURCE=2.
- Various VT fixes and updates.

Notable changes in 1.5

- Added "knem" support: direct process-to-process copying for shared
  memory message passing.  See http://runtime.bordeaux.inria.fr/knem/
  and the README file for more details.
- Updated shared library versioning scheme and linking style of MPI
  applications.  The MPI application ABI has been broken from the
  v1.3/v1.4 series.  MPI applications compiled against any prior
  version of Open MPI will need to, at a minimum, re-link.  See the
  README file for more details.
- Added "fca" collective component, enabling MPI collective offload
  support for Voltaire switches.
- Fixed MPI one-sided operations with large target displacements.
  Thanks to Brian Price and Jed Brown for reporting the issue.
- Fixed MPI_GET_COUNT when used with large counts.  Thanks to Jed
  Brown for reporting the issue.
- Made the openib BTL safer if extremely low SRQ settings are used.
- Fixed handling of the array_of_argv parameter in the Fortran
  binding of MPI_COMM_SPAWN_MULTIPLE (** also to appear: 1.4.3).
- Fixed malloc(0) warnings in some collectives.
- Fixed a problem with the Fortran binding for
  MPI_FILE_CREATE_ERRHANDLER.  Thanks to Secretan Yves for identifying
  the issue (** also to appear: 1.4.3).
- Updates to the LSF PLM to ensure that the path is correctly passed.
  Thanks to Teng Lin for the patch (** also to appear: 1.4.3).
- Fixes for the F90 MPI_COMM_SET_ERRHANDLER and MPI_WIN_SET_ERRHANDLER
  bindings.  Thanks to Paul Kapinos for pointing out the issue
  (** also to appear: 1.4.3).
- Fixed extra_state parameter types in F90 prototypes for
  MPI_COMM_CREATE_KEYVAL, MPI_GREQUEST_START, MPI_REGISTER_DATAREP,
  MPI_TYPE_CREATE_KEYVAL, and MPI_WIN_CREATE_KEYVAL.
- Fixes for Solaris oversubscription detection.
- If the PML determines it can't reach a peer process, print a
  slightly more helpful message.  Thanks to Nick Edmonds for the
  suggestion.
- Make btl_openib_if_include/exclude function the same way
  btl_tcp_if_include/exclude works (i.e., supplying an _include list
  overrides supplying an _exclude list).
- Apply more scalable reachability algorithm on platforms with more
  than 8 TCP interfaces.
- Various assembly code updates for more modern platforms / compilers.
- Relax restrictions on using certain kinds of MPI datatypes with
  one-sided operations.  Users beware; not all MPI datatypes are valid
  for use with one-sided operations!
- Improve behavior of MPI_COMM_SPAWN with regards to --bynode.
- Various threading fixes in the openib BTL and other core pieces of
  Open MPI.
- Various help file and man pages updates.
- Various FreeBSD and NetBSD updates and fixes.  Thanks to Kevin
  Buckley and Aleksej Saushev for their work.
- Fix case where freeing communicators in MPI_FINALIZE could cause
  process failures.
- Print warnings if shared memory state files are opened on what look
  like networked filesystems.
- Update libevent to v1.4.13.
- Allow propagating signals to processes that call fork().
- Fix bug where MPI_GATHER was sometimes incorrectly examining the
  datatype on non-root processes.  Thanks to Michael Hofmann for
  investigating the issue.
- Various Microsoft Windows fixes.
- Various Catamount fixes.
- Various checkpoint / restart fixes.
- Xgrid support has been removed until it can be fixed (patches
  would be welcome).
- Added simplistic "libompitrace" contrib package.  Using the MPI
  profiling interface, it essentially prints out to stderr when select
  MPI functions are invoked.
- Update bundled VampirTrace to v5.8.2.
- Add pkg-config(1) configuration files for ompi, ompi-c, ompi-cxx,
  ompi-f77, ompi-f90.  See the README for more details.
- Removed the libopenmpi_malloc library (added in the v1.3 series)
  since it is no longer necessary
- Add several notifier plugins (generally used when Open MPI detects
  system/network administrator-worthy problems); each have their own
  MCA parameters to govern their usage.  See "ompi_info --param
  notifier <name>" for more details.
  - command to execute arbitrary commands (e.g., run a script).
  - file to send output to a file.
  - ftb to send output to the Fault Tolerant Backplane (see
    http://wiki.mcs.anl.gov/cifts/index.php/CIFTS)
  - hnp to send the output to mpirun.
  - smtp (requires libesmtp) to send an email.


To generate a diff of this commit:
cvs rdiff -u -r1.7 -r1.8 pkgsrc/parallel/openmpi/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/parallel/openmpi/PLIST
cvs rdiff -u -r1.2 -r1.3 pkgsrc/parallel/openmpi/PLIST.vt
cvs rdiff -u -r1.1.1.1 -r1.2 pkgsrc/parallel/openmpi/buildlink3.mk
cvs rdiff -u -r1.5 -r1.6 pkgsrc/parallel/openmpi/distinfo
cvs rdiff -u -r1.1.1.1 -r1.2 pkgsrc/parallel/openmpi/patches/patch-aa \
    pkgsrc/parallel/openmpi/patches/patch-ai \
    pkgsrc/parallel/openmpi/patches/patch-aj \
    pkgsrc/parallel/openmpi/patches/patch-ak
cvs rdiff -u -r1.1.1.1 -r0 pkgsrc/parallel/openmpi/patches/patch-ab \
    pkgsrc/parallel/openmpi/patches/patch-ac \
    pkgsrc/parallel/openmpi/patches/patch-ad \
    pkgsrc/parallel/openmpi/patches/patch-ae \
    pkgsrc/parallel/openmpi/patches/patch-af \
    pkgsrc/parallel/openmpi/patches/patch-ag

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.