Commit graph

435 commits

Author SHA1 Message Date
asau
bf5369e7bc Drop manual conflict registration, it conflicts with what we intend to do. 2013-02-28 07:18:15 +00:00
joerg
e50ac4f4e9 On NetBSD, link against libexecinfo when backtrace(3) is desired. 2013-02-26 23:36:17 +00:00
joerg
e3de6ad52a NetBSD/current needs _KMEMUSER and a few additional includes. 2013-02-26 11:01:32 +00:00
asau
2d29e5ff84 Update to OpenMPI 1.6.4
Here is a list of changes in v1.6.4 as compared to v1.6.3:

- Fix Cygwin shared memory and debugger plugin support.  Thanks to
  Marco Atzeri for reporting the issue and providing initial patches.
- Fix to obtaining the correct available nodes when a rankfile is
  providing the allocation.  Thanks to Siegmar Gross for reporting the
  problem.
- Fix process binding issue on Solaris.  Thanks to Siegmar Gross for
  reporting the problem.
- Updates for MXM 2.0.
- Major VT update to 5.14.2.3.
- Fixed F77 constants for Cygwin/Cmake build.
- Fix a linker error when configuring --without-hwloc.
- Automatically provide compiler flags that compile properly on some
  types of ARM systems.
- Fix slot_list behavior when multiple sockets are specified.  Thanks
  to Siegmar Gross for reporting the problem.
- Fixed memory leak in one-sided operations.  Thanks to Victor
  Vysotskiy for letting us know about this one.
- Added performance improvements to the OpenIB (OpenFabrics) BTL.
- Improved error message when process affinity fails.
- Fixed MPI_MINLOC on man pages for MPI_REDUCE(_LOCAL).  Thanks to Jed
  Brown for noticing the problem and supplying a fix.
- Made malloc hooks more friendly to IO interprosers.  Thanks to the
  bug report and suggested fix from Darshan maintainer Phil Carns.
- Restored ability to direct launch under SLURM without PMI support.
- Fixed MPI datatype issues on OpenBSD.
- Major VT update to 5.14.2.3.
- Support FCA v3.0+.
- Fixed header file problems on OpenBSD.
- Fixed issue with MPI_TYPE_CREATE_F90_REAL.
- Fix an issue with using external libltdl installations.  Thanks to
  opolawski for identifying the problem.
- Fixed MPI_IN_PLACE case for MPI_ALLGATHER for FCA.
- Allow SLURM PMI support to look in lib64 directories.  Thanks to
  Guillaume Papaure for the patch.
- Restore "use mpi" ABI compatibility with the rest of the 1.5/1.6
  series (except for v1.6.3, where it was accidentally broken).
- Fix a very old error in opal_path_access(). Thanks to Marco Atzeri
  for chasing it down.
2013-02-24 01:22:36 +00:00
wiz
d1b820f37b Recursive bump for png-1.6. 2013-02-16 11:18:58 +00:00
jperkin
becd113253 PKGREVISION bumps for the security/openssl 1.0.1d update. 2013-02-06 23:20:50 +00:00
cheusov
18698f3a82 Remove MANDIR= from MAKE_ENV which is already there (mk-c.mk) 2013-01-08 16:36:53 +00:00
markd
fac1fa996f Restructure in preparation for adding a java option. 2012-12-15 22:29:20 +00:00
markd
6b9277bc42 Support 64bit linux. 2012-12-15 22:27:01 +00:00
marino
97fd0bedd8 parallel/openmpi: Add supplemental PLIST for DragonFly
DragonFly produces an shmem library in additional to the standard PLIST.
2012-12-15 10:41:58 +00:00
cheusov
efca78433c Update to parallel-20121122 2012-12-02 10:38:51 +00:00
joerg
776f791116 Always return a value in a non-void function. 2012-11-19 03:01:07 +00:00
asau
2792fd7373 Update to OpenMPI 1.6.3
Version 1.6.3 is a minor bugfix release.
All users are encouraged to upgrade to v1.6.3 when possible.

Note that v1.6.3 is ABI compatible with the entire v1.5.x and
v1.6.x series, but is not ABI compatible with the v1.4.x series.
See http://www.open-mpi.org/software/ompi/versions/ for a
description of Open MPI's release methodology.

Here is a list of changes in v1.6.3 as compared to v1.6.2:

- Fix mpirun --launch-agent behavior when a prefix is specified.
  Thanks to Reuti for identifying the issue.
- Fixed memchecker configury.
- Brought over some compiler warning squashes from the development trunk.
- Fix spawning from a singleton to multiple hosts when the "add-host"
  MPI_Info key is used.  Thanks to Brian Budge for pointing out the
  problem.
- Add Mellanox ConnextIB IDs and max inline value.
- Fix rankfile when no -np is given.
- FreeBSD detection improvement.  Thanks to Brooks Davis for the
  patch.
- Removed TCP warnings on Windows.
- Improved collective algorithm selection for very large messages.
- Fix PSM MTL affinity settings.
- Fix issue with MPI_OP_COMMUTATIVE in the mpif.h bindings.  Thanks to
  Ake Sandgren for providing a patch to fix the issue.
- Fix issue with MPI_SIZEOF when using CHARACTER and LOGICAL types in
  the mpi module.  Thanks to Ake Sandgren for providing a patch to fix
  the issue.
2012-10-31 06:19:35 +00:00
joerg
1f80ec87e5 Avoid conflicting implicit prototype. 2012-10-26 20:23:25 +00:00
asau
394c2661b9 Reexport libxml2 from hwloc.
Reexport hwloc from openmpi.
This should fix builds with MPI_TYPE=openmpi.
2012-10-24 05:49:25 +00:00
asau
fc09dcbfdf Update to OpenMPI 1.6.2
Don't build VampirTrace anymore, it will be introduced as separate package.


Changes in v1.6.2 as compared to v1.6.1:

- Fix issue with MX MTL. Thanks to Doug Eadline for raising the issue.
- Fix singleton MPI_COMM_SPAWN when the result job spans multiple nodes.
- Fix MXM hang, and update for latest version of MXM.
- Update to support Mellanox FCA 2.5.
- Fix startup hang for large jobs.
- Ensure MPI_TESTANY / MPI_WAITANY properly set the empty status when
  count==0.
- Fix MPI_CART_SUB behavior of not copying periods to the new
  communicator properly. Thanks to John Craske for the bug report.
- Add btl_openib_abort_not_enough_reg_mem MCA parameter to cause Open
  MPI to abort MPI jobs if there is not enough registered memory
  available on the system (vs. just printing a warning). Thanks to
  Brock Palen for raising the issue.
- Minor fix to Fortran MPI_INFO_GET: only copy a value back to the
  user's buffer if the flag is .TRUE.
- Fix VampirTrace compilation issue with the PGI compiler suite.
2012-10-17 23:27:34 +00:00
asau
e1520fd682 Cleanup while here. 2012-10-17 03:36:14 +00:00
asau
55bcf55c7f Update to hwloc 1.5
v1.5 is a major new release series. It includes many new features and
changes over the v1.4.x series. The most noticeable changes are the
addition of the lstopo-no-graphics program (which does require any
heavy external library such as Cairo) and the discovery of instruction
caches. There are also many small improvements to all backends, and
some deprecated features have been removed.

Version 1.5.0
-------------
* Backends
  + Do not limit the number of processors to 1024 on Solaris anymore.
  + Gather total machine memory on FreeBSD.
  + XML topology files do not depend on the locale anymore. Float numbers
    such as NUMA distances or PCI link speeds now always use a dot as a
    decimal separator.
  + Add instruction caches detection on Linux, AIX, Windows and Darwin.
  + Add get_last_cpu_location() support for the current thread on AIX.
  + Support binding on AIX when threads or processes were bound with
    bindprocessor(). Thanks to Hendryk Bockelmann for reporting the issue
    and testing patches, and to Farid Parpia for explaining the binding
    interfaces.
  + Improve AMD topology detection in the x86 backend (for FreeBSD) using
    the topoext feature.
* API
  + Increase HWLOC_API_VERSION to 0x00010500 so that API changes may be
    detected at build-time.
  + Add a cache type attribute describind Data, Instruction and Unified
    caches. Caches with different types but same depth (for instance L1d
    and L1i) are placed on different levels.
  + Add hwloc_get_cache_type_depth() to retrieve the hwloc level depth of
    of the given cache depth and type, for instance L1i or L2.
    It helps disambiguating the case where hwloc_get_type_depth() returns
    HWLOC_TYPE_DEPTH_MULTIPLE.
  + Instruction caches are ignored unless HWLOC_TOPOLOGY_FLAG_ICACHES is
    passed to hwloc_topology_set_flags() before load.
  + Add hwloc_ibv_get_device_osdev_by_name() OpenFabrics helper in
    openfabrics-verbs.h to find the hwloc OS device object corresponding to
    an OpenFabrics device.
* Tools
  + Add lstopo-no-graphics, a lstopo built without graphical support to
    avoid dependencies on external libraries such as Cairo and X11. When
    supported, graphical outputs are only available in the original lstopo
    program.
    - Packagers splitting lstopo and lstopo-no-graphics into different
      packages are advised to use the alternatives system so that lstopo
      points to the best available binary.
  + Instruction caches are enabled in lstopo by default. User --no-icaches
    to disable them.
  + Add -t/--threads to show threads in hwloc-ps.
* Removal of obsolete components
  + Remove the old cpuset interface (hwloc/cpuset.h) which is deprecated and
    superseded by the bitmap API (hwloc/bitmap.h) since v1.1.
    hwloc_cpuset and nodeset types are still defined, but all hwloc_cpuset_*
    compatibility wrappers are now gone.
  + Remove Linux libnuma conversion helpers for the deprecated and
    broken nodemask_t interface.
  + Remove support for "Proc" type name, it was superseded by "PU" in v1.0.
  + Remove hwloc-mask symlinks, it was replaced by hwloc-calc in v1.0.
* Misc
  + Fix PCIe 3.0 link speed computation.
  + Non-printable characters are dropped from strings during XML export.
  + Fix importing of escaped characters with the minimalistic XML backend.
  + Assert hwloc_is_thissystem() in several I/O related helpers.
  + Fix some memory leaks in the x86 backend for FreeBSD.
  + Minor fixes to ease native builds on Windows.
  + Limit the number of retries when operating on all threads within a
    process on Linux if the list of threads is heavily getting modified.
2012-10-17 03:11:44 +00:00
adam
3f2cc57b2b Revbump after updating graphics/pango 2012-10-08 23:00:34 +00:00
wiz
8b5d49eb78 Bump all packages that use perl, or depend on a p5-* package, or
are called p5-*.

I hope that's all of them.
2012-10-03 21:53:53 +00:00
tron
14215633d2 Mass recursive bump after the dependence fix of the "cairo" package
requested by Thomas Klausner.
2012-10-02 17:10:28 +00:00
dholland
daca733b77 Make build stop on error. 2012-09-15 21:25:27 +00:00
obache
c38c120ee5 recursive bump from libffi shlib major bump
(additionaly, reset PKGREVISION of qt4-* sub packages from base qt4 update)
2012-09-15 10:03:29 +00:00
asau
372426dca4 "user-destdir" is default these days 2012-09-11 20:32:10 +00:00
cheusov
ff7dd60f74 Update to 0.17.0
paexec:
    - Option -x was added. With its help paexec can run one command
      per task.  If -g is also specified, command's exit status is
      analysed. Appropriate task and dependants are marked as "failed"
      if it is non-zero.
    - First character of -n argument must be alphanumeric, `+', `_',
      `:' or `/'.  Other symbols are reserved for future extentions.
    - With '-n :filename' paexec reads a list of nodes from the
      specified file.
    - With a help of new option '-m t=<eot>' end of task string
      may be specified, which is an empty line by default.
    - Option -md=<delim> was added that overrides the default
      delimiter (space character) between tasks in graph mode (-g).
    - Output line that contains failed dependants no longer ends with
      unnecessary space.
    - Long options were completely removed.

  paexec_reorder:
    - Fix. "paexec_reorder -g" now handles correctly failed tasks'
      output.  One extra line after "fatal" is expected.
    - Options -m was added. It does the same things as paexec's -m.

  More examples of use and regression tests.

  Documentation update, clean-ups and improvements.

  Regression tests:
    - Signals handling was fixed in.
    - LC_ALL is always set to C in regression tests, this fixes some
      problems in internationalized environment.

  mk-configure>=0.23.0 is required at build time
2012-09-09 23:30:26 +00:00
adam
b15c922bcc Revbump after updating graphics/cairo 2012-09-07 19:16:05 +00:00
marino
f162cdcb03 Recursive PKGREVISION bump for tcl and tk upgrade to 8.5.12 2012-08-21 23:49:18 +00:00
asau
6abbb83812 Update to SLURM 2.4.1
* Changes in SLURM 2.4.1
========================
 -- Fix bug for job state change from 2.3 -> 2.4 job state can now be preserved
    correctly when transitioning.  This also applies for 2.4.0 -> 2.4.1, no
    state will be lost. (Thanks to Carles Fenoy)

* Changes in SLURM 2.4.0
========================
 -- Cray - Improve support for zero compute note resource allocations.
    Partition used can now be configured with no nodes nodes.
 -- BGQ - make it so srun -i<taskid> works correctly.
 -- Fix parse_uint32/16 to complain if a non-digit is given.
 -- Add SUBMITHOST to job state passed to Moab vial sched/wiki2. Patch by Jon
    Bringhurst (LANL).
 -- BGQ - Fix issue when running with AllowSubBlockAllocations=Yes without
    compiling with --enable-debug
 -- Modify scontrol to require "-dd" option to report batch job's script. Patch
    from Don Albert, Bull.
 -- Modify SchedulerParamters option to match documentation: "bf_res="
    changed to "bf_resolution=". Patch from Rod Schultz, Bull.
 -- Fix bug that clears job pending reason field. Patch fron Don Lipari, LLNL.
 -- In etc/init.d/slurm move check for scontrol after sourcing
    /etc/sysconfig/slurm. Patch from Andy Wettstein, University of Chicago.
 -- Fix in scheduling logic that can delay jobs with min/max node counts.
 -- BGQ - fix issue where if a step uses the entire allocation and then
    the next step in the allocation only uses part of the allocation it gets
    the correct cnodes.
 -- BGQ - Fix checking for IO on a block with new IBM driver V1R1M1 previous
    function didn't always work correctly.
 -- BGQ - Fix issue when a nodeboard goes down and you want to combine blocks
    to make a larger small block and are running with sub-blocks.
 -- BLUEGENE - Better logic for making small blocks around bad nodeboard/card.
 -- BGQ - When using an old IBM driver cnodes that go into error because of
    a job kill timeout aren't always reported to the system.  This is now
    handled by the runjob_mux plugin.
 -- BGQ - Added information on how to setup the runjob_mux to run as SlurmUser.
 -- Improve memory consumption on step layouts with high task count.
 -- BGQ - quiter debug when the real time server comes back but there are
    still messages we find when we poll but haven't given it back to the real
    time yet.
 -- BGQ - fix for if a request comes in smaller than the smallest block and
    we must use a small block instead of a shared midplane block.
 -- Fix issues on large jobs (>64k tasks) to have the correct counter type when
    packing the step layout structure.
 -- BGQ - fix issue where if a user was asking for tasks and ntasks-per-node
    but not node count the node count is correctly figured out.
 -- Move logic to always use the 1st alphanumeric node as the batch host for
    batch jobs.
 -- BLUEGENE - fix race condition where if a nodeboard/card goes down at the
    same time a block is destroyed and that block just happens to be the
    smallest overlapping block over the bad hardware.
 -- Fix bug when querying accounting looking for a job node size.
 -- BLUEGENE - fix possible race condition if cleaning up a block and the
    removal of the job on the block failed.
 -- BLUEGENE - fix issue if a cable was in an error state make it so we can
    check if a block is still makable if the cable wasn't in error.
 -- Put nodes names in alphabetic order in node table.
 -- If preempted job should have a grace time and preempt mode is not cancel
    but job is going to be canceled because it is interactive or other reason
    it now receives the grace time.
 -- BGQ - Modified documents to explain new plugin_flags needed in bg.properties
    in order for the runjob_mux to run correctly.
 -- BGQ - change linking from libslurm.o to libslurmhelper.la to avoid warning.

* Changes in SLURM 2.4.0.rc1
=============================
 -- Improve task binding logic by making fuller use of HWLOC library,
    especially with respect to Opteron 6000 series processors. Work contributed
    by Komoto Masahiro.
 -- Add new configuration parameter PriorityFlags, based upon work by
    Carles Fenoy (Barcelona Supercomputer Center).
 -- Modify the step completion RPC between slurmd and slurmstepd in order to
    eliminate a possible deadlock. Based on work by Matthieu Hautreux, CEA.
 -- Change the owner of slurmctld and slurmdbd log files to the appropriate
    user. Without this change the files will be created by and owned by the
    user starting the daemons (likely user root).
 -- Reorganize the slurmstepd logic in order to better support NFS and
    Kerberos credentials via the AUKS plugin. Work by Matthieu Hautreux, CEA.
 -- Fix bug in allocating GRES that are associated with specific CPUs. In some
    cases the code allocated first available GRES to job instead of allocating
    GRES accessible to the specific CPUs allocated to the job.
 -- spank: Add callbacks in slurmd: slurm_spank_slurmd_{init,exit}
    and job epilog/prolog: slurm_spank_job_{prolog,epilog}
 -- spank: Add spank_option_getopt() function to api
 -- Change resolution of switch wait time from minutes to seconds.
 -- Added CrpCPUMins to the output of sshare -l for those using hard limit
    accounting.  Work contributed by Mark Nelson.
 -- Added mpi/pmi2 plugin for complete support of pmi2 including acquiring
    additional resources for newly launched tasks. Contributed by Hongjia Cao,
    NUDT.
 -- BGQ - fixed issue where if a user asked for a specific node count and more
    tasks than possible without overcommit the request would be allowed on more
    nodes than requested.
 -- Add support for new SchedulerParameters of bf_max_job_user, maximum number
    of jobs to attempt backfilling per user. Work by BjæËrn-Helge Mevik,
    University of Oslo.
 -- BLUEGENE - fixed issue where MaxNodes limit on a partition only limited
    larger than midplane jobs.
 -- Added cpu_run_min to the output of sshare --long.  Work contributed by
    Mark Nelson.
 -- BGQ - allow regular users to resolve Rack-Midplane to AXYZ coords.
 -- Add sinfo output format option of "%R" for partition name without "*"
    appended for default partition.
 -- Cray - Add support for zero compute note resource allocation to run batch
    script on front-end node with no ALPS reservation. Useful for pre- or post-
    processing.
 -- Support for cyclic distribution of cpus in task/cgroup plugin from Martin
    Perry, Bull.
 -- GrpMEM limit for QOSes and associations added Patch from BjæËrn-Helge Mevik,
    University of Oslo.
 -- Various performance improvements for up to 500% higher throughput depending
    upon configuration. Work supported by the Oak Ridge National Laboratory
    Extreme Scale Systems Center.
 -- Added jobacct_gather/cgroup plugin.  It is not advised to use this in
    production as it isn't currently complete and doesn't provide an equivalent
    substitution for jobacct_gather/linux yet. Work by Martin Perry, Bull.
2012-07-03 22:00:41 +00:00
asau
c94a30d92f Add "latest" subdirectory to look for distfiles. 2012-07-03 14:09:11 +00:00
sbd
e2bb8b5bd8 SET_LIBDIR=yes 2012-06-14 07:56:47 +00:00
sbd
21792a9296 Recursive PKGREVISION bump for libxml2 buildlink addition. 2012-06-14 07:43:06 +00:00
asau
31eaf78b3d Distfile has moved to archive subdirectory. 2012-06-13 02:47:50 +00:00
asau
ec8d0e067e Update to OpenMPI 1.6
Disable automatic detection of SGE and SLURM to avoid PLIST divergence.


Changes in OpenMPI 1.6

v1.6 is a major release; it effectively deprecates both the v1.4.x
and v1.5.x series, and replaces v1.4.x as the current "super stable" series.
A forthcoming v1.7 series will become the new "feature" series.

*All users* -- including production users and downstream providers --
are encouraged to upgrade to v1.6.

Note that v1.6 is ABI compatible with the entire v1.5.x series,
but is not ABI compatible with the v1.4.x series.
See http://www.open-mpi.org/software/ompi/versions/ for a description
of Open MPI's release methodology.


Here is a list of changes in v1.6 as compared to v1.5.5:

- Fix some process affinity issues.  When binding a process, Open MPI
  will now bind to all available hyperthreads in a core (or socket,
  depending on the binding options specified).
  --> Note that "mpirun --bind-to-socket ..." does not work on POWER6-
      and POWER7-based systems with some Linux kernel versions.  See
      the FAQ on the Open MPI web site for more information.
- Add support for ARM5 and ARM6 (in addition to the existing ARM7
  support).  Thanks to Evan Clinton for the patch.
- Minor Mellanox MXM fixes.
- Properly detect FDR10, FDR, and EDR OpenFabrics devices.
- Minor fixes to the mpirun(1) and MPI_Comm_create(3) man pages.
- Prevent segv if COMM_SPAWN_MULTIPLE fails.  Thanks to Fujitsu for
  the patch.
- Disable interposed memory management in fakeroot environments.  This
  fixes a problem in some build environments.
- Minor hwloc updates.
- Array versions of MPI_TEST and MPI_WAIT with a count==0 will now
  return immediately with MPI_SUCCESS.  Thanks to Jeremiah Willcock
  for the suggestion.
- Update VampirTrace to v5.12.2.
- Properly handle forwarding stdin to all processes when "mpirun
  --stdin all" is used.
- Workaround XLC assembly bug.
- OS X Tiger (10.3) has not been supported for a while, so forcibly
  abort configure if we detect it.
- Fix segv in the openib BTL when running on SPARC 64 systems.
- Fix some include file ordering issues on some BSD-based platforms.
  Thanks to Paul Hargove for this (and many, many other) fixes.
- Properly handle .FALSE. return parameter value to attribute copy
  callback functions.
- Fix a bunch of minor C++ API issues; thanks to Fujitsu for the patch.
- Fixed the default hostfile MCA parameter behavior.
- Per the MPI spec, ensure not to touch the port_name parameter to
  MPI_CLOSE_PORT (it's an IN parameter).
2012-06-12 23:36:30 +00:00
dholland
5510fc0bc0 Set USE_TOOLS instead of BUILD_DEPENDS to get csh, and use ${CSH}
instead of "tcsh". This builds ok for me on NetBSD; if it turns out to
cause trouble for anyone, revert it.

The motivation was that the BUILD_DEPENDS accepted either tcsh or
standalone-tcsh, and distbb was latching onto the latter and then
failing trying to install it. If the package turns out to really need
tcsh in some contexts, there are probably other ways to deal with this
issue.
2012-06-02 20:16:09 +00:00
asau
9b2aabd492 Update to OpenMPI 1.5.5
Changes in 1.5.5
----------------

- Many, many portability configure/build fixes courtesy of Paul
  Hargrove.  Thanks, Paul!
- Fixed shared memory fault tolerance support compiler errors.
- Removed not-production-quality rshd and tmd PLM launchers.
- Minor updates to the Open MPI SRPM spec file.
- Fixed mpirun's --bind-to-socket option.
- A few MPI_THREAD_MULTIPLE fixes in the shared memory BTL.
- Upgrade the GNU Autotools used to bootstrap the 1.5/1.6 series to
  all the latest versions at the time of this release.
- Categorically state in the README that if you're having a problem
  with Open MPI with the Linux Intel 12.1 compilers, *upgrade your
  Intel Compiler Suite to the latest patch version*, and the problems
  will go away. :-)
- Fix the --without-memory-manager configure option.
- Fixes for Totalview/DDT MPI-capable debuggers.
- Update rsh/ssh support to properly handle the Mac OS X library path
  (i.e., DYLD_LIBRARY_PATH).
- Make warning about shared memory backing files on a networked file
  system be optional (i.e., can be disabled via MCA parameter).
- Several fixes to processor and memory affinity.
- Various shared memory infrastructure improvements.
- Various checkpoint/restart fixes.
- Fix MPI_IN_PLACE (and other MPI sentinel values) on OS X.  Thanks to
  Dave Goodell for providing the magic OS X gcc linker flags necessary.
- Various man page corrections and typo fixes.  Thanks to Fujitsu for
  the patch.
- Updated wrapper compiler man pages to list the various --showme
  options that are available.
- Add PMI direct-launch support (e.g., "srun mpi_application" under
  SLURM).
- Correctly compute the aligned address when packing the
  datatype description. Thanks to Fujitsu for the patch.
- Fix MPI obscure corner case handling in packing MPI datatypes.
  Thanks to Fujitsu for providing the patch.
- Workaround an Intel compiler v12.1.0 2011.6.233 vector optimization
  bug.
- Output the MPI API in ompi_info output.
- Major VT update to 5.12.1.4.
- Rankfile 'P'hysical mapping is no longer available.
- Upgrade embedded Hardware Locality (hwloc) v1.3.2, plus some
  post-1.3.2-release bug fixes.  All processor and memory binding is
  now done through hwloc.  Woo hoo!  Note that this fixes core binding
  on AMD Opteron 6200 and 4200 series-based systems (sometimes known
  as Interlagos, Valencia, or other Bulldozer-based chips).
- New MCA parameters to control process-wide memory binding policy:
  hwloc_base_mem_alloc_policy, hwloc_base_mem_bind_failure_action (see
  ompi_info --param hwloc base).
- Removed direct support for libnuma.  Libnuma support may now be
  picked up through hwloc.
- Added MPI_IN_PLACE support to MPI_EXSCAN.
- Various fixes for building on Windows, including MinGW support.
- Removed support for the OpenFabrics IBCM connection manager.
- Updated Chelsio T4 and Intel NE OpenFabrics default buffer settings.
- Increased the default RDMA CM timeout to 30 seconds.
- Issue a warning if both btl_tcp_if_include and btl_tcp_if_exclude
  are specified.
- Many fixes to the Mellanox MXM transport.
2012-05-28 18:38:17 +00:00
marino
af902875ce parallel/openmpi: Fix PLIST for DragonFly 2012-05-21 16:08:51 +00:00
wiz
d7004fa306 pkglint cleanup while here. 2012-05-10 10:55:44 +00:00
wiz
6d9b01389d Fix build with automake-1.12. 2012-05-10 10:55:38 +00:00
markd
fa00fb2543 Fixup DESTDIR handling in do-install.
Add LICENSE (sun-iss + 2-clause-bsd + gpl + lgpl)
2012-04-18 21:05:30 +00:00
dholland
7722b30bfe Add missing pam.bl3.mk. (but, it builds on LP64 platforms now. yay!) 2012-04-15 19:35:15 +00:00
markd
4c36a7a000 Reinstate patch-source-utilbin_Makefile (aka patch-ak)
Dont install *.orig files
Fix build on 64bit systems
Fix arch name for Linux
Bump PKGREVISION
2012-04-15 04:07:21 +00:00
dholland
3c3ad10824 Mark sge and gridscheduler not for ${LP64PLATFORMS}. They crash during
build.
2012-04-07 22:19:13 +00:00
asau
2ff206d5ce + gridscheduler
+ hwloc
2012-03-21 20:57:14 +00:00
asau
075f7f1522 Remove empty patches, no idea how they have got through. 2012-03-21 20:52:30 +00:00
asau
509279acdd Import Open Grid Scheduler version 2011.11 as parallel/gridscheduler.
Heavily based on Sun Grid Engine package (parallel/sge).

Open Grid Scheduler/Grid Engine is a free and open-source
batch-queuing system for distributed resource management.
OGS/GE is based on Sun Grid Engine, and maintained by the same
group of external (i.e. non-Sun) developers who started
contributing code to Sun Grid Engine since 2001.
2012-03-21 20:48:53 +00:00
asau
e5fc3d3576 Import Portable Hardware Locality (hwloc) version 1.4 as parallel/hwloc.
The Portable Hardware Locality (hwloc) software package provides
a portable abstraction (across OS, versions, architectures, ...)
of the hierarchical topology of modern architectures, including
NUMA memory nodes, sockets, shared caches, cores and
simultaneous multithreading. It also gathers various system
attributes such as cache and memory information as well as the
locality of I/O devices such as network interfaces, InfiniBand
HCAs or GPUs. It primarily aims at helping applications with
gathering information about modern computing hardware so as to
exploit it accordingly and efficiently.
2012-03-21 13:31:35 +00:00
asau
7a4cb81a5b Update to the Son of Grid Engine 8.0.0d
The Son of Grid Engine is a community project to continue Sun Grid Engine.


Notable changes in Son of Grid Engine
-------------------------------------

Version 8.0.0d
--------------

* Bug fixes

  * Man and fixes
  * Fix building with older gcc versions
  * Provide load average in qstat XML output [#446, #454]
  * Partially back out Univa change which broke classic spooling
  * Fix -terse in sge_request [#777]

* Other changes (possibly-incompatible)

  * Message fixes

Version 8.0.0c
--------------

* Bug fixes

  * Man and other documentation fixes
  * Build/installation fixes (particularly for Red Hat 6 and Linux 3)
  * Fix group ids for submitted jobs [U]
  * Fix default value of boolean with JSV [U]
  * Windows fixes for helper crashes and Vista GUI jobs [U]
  * Ensure parallel jobs are dispatched to the least loaded host [U]
  * Correct ownership of qsub -pty output file; was owned by admin user [U]
  * Fix format of Windows loadcheck.exe output [U]
  * Read from stderr even if stdout is already closed in IJS [U]
  * Fix PDC_INTERVAL=NEVER execd parameter [U]
  * Fix accounting information for Windows GUI jobs [U]
  * Increase default MAX_DYN_EC qmaster param [U]
  * Fix qsub -sync y error message and enforce MAX_DYN_EC correctly [U]
  * Fix job validation (-w e) behaviour [#716] [U]
  * Fix qrsh input redirection [U]
  * Avoid warning when submitting a qrsh job [U]
  * Print start time in qstat -j -xml output [U]
  * Don't raise an error changing resource request on waiting job [#806]
  * Don't exit 0 on error with qconf -secl or -sep
  * Include string.h in drmaa.h [#712]
  * Fix process-scheduler-log with host aliases

* Enhancements

  * Base qmake and qtcsh on the current gmake and tcsh source [#289,
    #504, #832]
  * Support "-binding linear" and "-binding linear:slots"
  * Use the hwloc library for all topology information and core
    binding, supporting more operating systems (now: AIX, Darwin,
    FreeBSD, GNU/Linux, HPUX, MS Windows, OSF/1, Solaris), and more
    hardware types (specifically AMD Magny Cours and similar)
  * Add task number to execd "exceeds job ... limit"

* Other changes (possibly-incompatible)

  * Modify default paths in build files and elsewhere [U]
  * Assorted message fixes
  * In RPMs, move qsched to qmaster package, and separate drmaa4ruby
  * Default to newijs in load_sge_config.sh
  * Default to sh, not csh for configured shell

Version 8.0.0b
--------------

* Bug fixes

  * Build/installation fixes [including #424, #1349] [(U)]
  * Fix execd init script [#1348]
  * Man and other documentation fixes [including #614, #764] [(U)]
  * Fix contents of admin mail properly [#1307, #1345]
  * Fix qalter messages for -tc
  * Fix build with -DSGE_PQS_API
  * Fix group ids for submitted jobs [U]

* Enhancements

  * Update qsched and add man page

* Other changes (possibly-incompatible)

  * Avoid the use of /bin/ksh [#1306]
  * Change installation defaults to classic spooling, not adding
    shadow hosts, and not JMX. [(U)]

Version 8.0.0a
--------------

This is roughly a superset of Univa's 8.0.0 (the V800_TAG from
https://github.com/gridengine/gridengine), with thanks for that.

Changes made there which haven't been included in this version:  PLPA
source not removed; some different build/installation defaults
(e.g. for JMX); Univa/UGE "branding" (partly because trademark status
is unknown); authuser not removed (for SDM and testing use),

* Bug fixes

  * Many man and other documentation fixes [including #790, #776,
    #769, #733, #610, #587, #581, #459, #456, #439, #255, #1288, #797,
    #1271, #773] [(U)]
  * Some program message fixes [(U)]
  * Various build and installation fixes [including #761, #709, #656,
    #616, #546, #536, #521, #491, #438, #414, #411, #383, #381, #138,
    #455, #344, #438, #1311, #1272, #1273] [(U)]
  * Ask for keystore password twice on installation
  * Fix qmaster crashes with tightly integrated parallel jobs or
    un-discoverable qinstance [#789] [U]
  * Report 0 cores and sockets on unsupported Solaris hosts [U]
  * Fix malloc hooks which caused crashes, particularly with SuSE 11
    [#792, #748, #749] [U]
  * Verify the pe task start user in execd in non-CSP mode [U]
  * Fix binding parameters parsing [U]
  * Fix JSV logging with multiple users submitting jobs on same submit
    host [U]
  * Fix unresponsive qmaster when modifying the global configuration
    in a huge cluster [U]
  * Speed up finishing tightly integrated jobs [U]
  * Check consistency of JSV binding information properly [U]
  * Fix broken project spooling, which caused loss of project when
    restarting master when using core binding [U]
  * Fix slotwise preemption failure to unsuspend one job per host [#775] [U]
  * Fix problems retrieving passwd and group information with large
    responses [#1295] [(U)]
  * Fix JSV changing default of boolean [U]
  * Fix ENABLE_RESCHEDULE_SLAVE=1 [U]
  * Allow comma in CMDNAME with Perl JSV scripts [#803]
  * Don't put queue into error state when supplementary group id
    cannot be set [#185] [U]
  * Don't convert LF to CRLF with qrsh -pty [U]
  * Fix qconf segfault on bad subordination string [U]
  * Fix group ids of submitted jobs [U]
  * Disallow -masterq with serial jobs [#155] [U]
  * Fix 100% CPU use by shepherd of qsh [U]
  * Removed unnecessary binding warning on job starts [U]
  * Fix qconf error reports when tmp directory has 755 permissions [U]
  * Fix suspending of remote process on qrsh -pty yes <cmd> on Solaris [U]
  * Fix starting jobs after global host changed [U]
  * Reject invalid load_formula value [U]
  * Fix handling of implicitly-requested exclusive resources [U]
  * Fix execd vmem reporting on 64-bit Linux [U]
  * Fix startup of execd on Windows Vista [U]
  * Set xterm's path more appropriately on GNU/Linux [#557]
  * Fix generation of admin email from failed jobs [#1307]
  * Fix some ill-formed output from qstat -xml [#314]
  * Fix handling of multi-line environment variables propagated to
    shepherd [#395]
  * Fix example MPI PE templates
  * Fix bad quoting in JSV sh library
  * Fix checking of consumables for parallel jobs across multiple hosts [U]

* Enhancements

  * Additional and clarified documentation
  * PAM modules for ssh tight integration and access control for
    interactive jobs
  * Initial core binding support for Solaris/SPARC64 [U]
  * Some efficiency improvements and memory leaks fixed [U]
  * Ports to S/390 and PARISC GNU/Linux [U]
  * New complex m_thread [U]
  * Show topology by default in qhost [U]
  * qsub -pty switch [#704] [U]
  * Improved qmon graphics [#530] [(U)]
  * Include bash in default shell list [U]
  * A JSV that rejects all jobs [U]
  * Files for Scali-MPI
  * Ruby DRMAA implementation
  * Enable easy building against shared system libraries and use
    system openssl and bdb binaries
  * New scripts: "qsched" reports resource reservations; "status"
    wraps qstat; enable/disable submission; node-selection (idle etc.)
  * Restart argument for daemon init scripts
  * Improved efficiency of shell JSV if used with bash
  * Core dumps from crashing daemons enabled under Linux [U]
  * Example host_aliases file [#154]
  * Spec file for RPM packaging [#820]

* Other changes (possibly-incompatible)

  * Show core binding by default in qstat, qhost (use -ncb for
    compatibility) [U]
  * Removed Berkeley DB RPC support (recently dropped by BDB) [U]
  * Changed position in pending job list for user-rescheduled jobs
    (exit99, qmod -rj) and OLD_RESCHEDULE_BEHAVIOR,
    OLD_RESCHEDULE_BEHAVIOR_ARRAY_JOB parameters [U]
  * Unified GNU/Linux arch strings (lx-*, from lx24-* and lx26-*) [U]
  * Default to enabling core binding on GNU/Linux [U]
  * Removed Sun service tags support [U]
  * Removed obsolete SunHPCT5 files
2012-03-20 17:07:43 +00:00
asau
796a06cb68 + slurm 2012-03-20 14:53:22 +00:00
asau
22ed08e6bc Import SLURM 2.4.0pre4 as parallel/slurm
SLURM is an open-source resource manager designed for Linux
clusters of all sizes. It provides three key functions. First it
allocates exclusive and/or non-exclusive access to resources
(computer nodes) to users for some duration of time so they can
perform work. Second, it provides a framework for starting,
executing, and monitoring work (typically a parallel job) on a
set of allocated nodes. Finally, it arbitrates contention for
resources by managing a queue of pending work.
2012-03-20 14:52:15 +00:00
fhajny
81b9c78065 Add c99 support, fixes build on SunOS.
Change long xdr macros to int32 ones, fixes build on SunOS and ABI=64.

Bump PKGREVISION.
2012-03-13 12:36:25 +00:00