Commit graph

408 commits

Author SHA1 Message Date
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
cheusov
fcd614744f clean-ups (adapted for recent mk-configure) 2012-03-09 18:58:19 +00:00
wiz
ee311e3b36 Recursive bump for pcre-8.30* (shlib major change) 2012-03-03 00:11:51 +00:00
wiz
5a1e8b0499 Revbump for
a) tiff update to 4.0 (shlib major change)
b) glib2 update 2.30.2 (adds libffi dependency to buildlink3.mk)

Enjoy.
2012-02-06 12:40:37 +00:00
sbd
947244b173 Switch to using REPLACE_CSH. 2012-02-06 06:19:17 +00:00
sbd
4437884521 Two of the install scripts use csh so add csh:run as a tools and use
REPLACE_INTERPRETER on the scripts.
2012-02-03 04:29:54 +00:00
sbd
ab7fc8e756 Set _PVM_ARCH=64 on x86_64-linux. 2012-02-03 04:06:08 +00:00
asau
f479abda6b Update to MPICH2 1.4.1p1
===============================================================================
                               Changes in 1.4.1
===============================================================================

 # OVERALL: Several improvements to the ARMCI API implementation
   within MPICH2.

 # Build system: Added beta support for DESTDIR while installing
   MPICH2.

 # PM/PMI: Upgrade hwloc to 1.2.1rc2.

 # PM/PMI: Initial support for the PBS launcher.

 # Several other minor bug fixes, memory leak fixes, and code cleanup.
   A full list of changes is available using:

     svn log -r8675:HEAD https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpich2-1.4.1

     ... or at the following link:

     https://trac.mcs.anl.gov/projects/mpich2/log/mpich2/tags/release/mpich2-1.4.1?action=follow_copy&rev=HEAD&stop_rev=8675&mode=follow_copy


===============================================================================
                               Changes in 1.4
===============================================================================

 # OVERALL: Improvements to fault tolerance for collective
   operations. Thanks to Rui Wang @ ICT for reporting several of these
   issues.

 # OVERALL: Improvements to the universe size detection. Thanks to
   Yauheni Zelenko for reporting this issue.

 # OVERALL: Bug fixes for Fortran attributes on some systems. Thanks
   to Nicolai Stange for reporting this issue.

 # OVERALL: Added new ARMCI API implementation (experimental).

 # OVERALL: Added new MPIX_Group_comm_create function to allow
   non-collective creation of sub-communicators.

 # FORTRAN: Bug fixes in the MPI_DIST_GRAPH_ Fortran bindings.

 # PM/PMI: Support for a manual "none" launcher in Hydra to allow for
   higher-level tools to be built on top of Hydra. Thanks to Justin
   Wozniak for reporting this issue, for providing several patches for
   the fix, and testing it.

 # PM/PMI: Bug fixes in Hydra to handle non-uniform layouts of hosts
   better. Thanks to the MVAPICH group at OSU for reporting this issue
   and testing it.

 # PM/PMI: Bug fixes in Hydra to handle cases where only a subset of
   the available launchers or resource managers are compiled
   in. Thanks to Satish Balay @ Argonne for reporting this issue.

 # PM/PMI: Support for a different username to be provided for each
   host; this only works for launchers that support this (such as
   SSH).

 # PM/PMI: Bug fixes for using Hydra on AIX machines. Thanks to
   Kitrick Sheets @ NCSA for reporting this issue and providing the
   first draft of the patch.

 # PM/PMI: Bug fixes in memory allocation/management for environment
   variables that was showing up on older platforms. Thanks to Steven
   Sutphen for reporting the issue and providing detailed analysis to
   track down the bug.

 # PM/PMI: Added support for providing a configuration file to pick
   the default options for Hydra. Thanks to Saurabh T. for reporting
   the issues with the current implementation and working with us to
   improve this option.

 # PM/PMI: Improvements to the error code returned by Hydra.

 # PM/PMI: Bug fixes for handling "=" in environment variable values in
   hydra.

 # PM/PMI: Upgrade the hwloc version to 1.2.

 # COLLECTIVES: Performance and memory usage improvements for MPI_Bcast
   in certain cases.

 # VALGRIND: Fix incorrect Valgrind client request usage when MPICH2 is
   built for memory debugging.

 # BUILD SYSTEM: "--enable-fast" and "--disable-error-checking" are once
   again valid simultaneous options to configure.

 # TEST SUITE: Several new tests for MPI RMA operations.

 # Several other minor bug fixes, memory leak fixes, and code cleanup.
   A full list of changes is available using:

     svn log -r7838:HEAD https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpich2-1.4

     ... or at the following link:

     https://trac.mcs.anl.gov/projects/mpich2/log/mpich2/tags/release/mpich2-1.4?action=follow_copy&rev=HEAD&stop_rev=7838&mode=follow_copy


===============================================================================
                               Changes in 1.3.2
===============================================================================

 # OVERALL: MPICH2 now recognizes the OSX mach_absolute_time as a
   native timer type.

 # OVERALL: Performance improvements to MPI_Comm_split on large
   systems.

 # OVERALL: Several improvements to error returns capabilities in the
   presence of faults.

 # PM/PMI: Several fixes and improvements to Hydra's process binding
   capability.

 # PM/PMI: Upgrade the hwloc version to 1.1.1.

 # PM/PMI: Allow users to sort node lists allocated by resource
   managers in Hydra.

 # PM/PMI: Improvements to signal handling. Now Hydra respects Ctrl-Z
   signals and passes on the signal to the application.

 # PM/PMI: Improvements to STDOUT/STDERR handling including improved
   support for rank prepending on output. Improvements to STDIN
   handling for applications being run in the background.

 # PM/PMI: Split the bootstrap servers into "launchers" and "resource
   managers", allowing the user to pick a different resource manager
   from the launcher. For example, the user can now pick the "SLURM"
   resource manager and "SSH" as the launcher.

 # PM/PMI: The MPD process manager is deprecated.

 # PM/PMI: The PLPA process binding library support is deprecated.

 # WINDOWS: Adding support for gfortran and 64-bit gcc libs.

 # Several other minor bug fixes, memory leak fixes, and code cleanup.
   A full list of changes is available using:

     svn log -r7457:HEAD https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpich2-1.3.2

     ... or at the following link:

     https://trac.mcs.anl.gov/projects/mpich2/log/mpich2/tags/release/mpich2-1.3.2?action=follow_copy&rev=HEAD&stop_rev=7457&mode=follow_copy
2012-01-11 09:43:25 +00:00
sbd
f395ebe992 Update PLIST.
Bump PKGREVISION
2012-01-11 02:46:01 +00:00
asau
e017fdcad9 Prevent detection of OpenMP support in order to make PLIST consistent. 2011-12-27 23:15:35 +00:00
drochner
a03a684eb1 PKGREV bump for libXp-less openmotif 2011-12-09 14:36:32 +00:00
sbd
da993c0c08 Recursive bump for devel/apr buildlink addition. 2011-12-02 07:13:48 +00:00
hans
ecea8d6927 Add pod2man and pod2html to USE_TOOLS. 2011-11-29 18:26:09 +00:00
marino
bc8e3669e9 parallels/pvm3: Add support for DragonFly64
Include string.h unconditionally and update the configuration to
recognize DragonFly x86_64.
2011-11-27 00:28:29 +00:00
sbd
e93e5d65e3 Recursive bump for graphics/freetype2 buildlink addition. 2011-11-01 06:11:52 +00:00
sbd
04daa2f1b8 Recursive bump for graphics/freetype2 buildlink addition. 2011-11-01 06:00:33 +00:00
cheusov
98589abbad Update my email 2011-10-09 10:02:44 +00:00
cheusov
d32a7d73d7 Add missing tool "pax" 2011-09-05 20:19:52 +00:00
cheusov
7827725f0a For all packages based on mk-configure "configure" target is provided.
This fixes parallel builds.
2011-09-04 18:21:26 +00:00
asau
44592473bb + threadingbuildingblocks 2011-08-27 19:49:22 +00:00
asau
cafa437f5f Import Threading Building Blocks 3.0 Update 6 as parallel/threadingbuildingblocks.
Intel(r) Threading Building Blocks (Intel TBB) offers a rich and
complete approach to expressing parallelism in a C++ program.
It is a library that helps you take advantage of multi-core
processor performance without having to be a threading expert.
Intel TBB is not just a threads-replacement library. It represents
a higher-level, task-based parallelism that abstracts platform
details and threading mechanisms for scalability and performance.
2011-08-27 19:48:13 +00:00
asau
7d5be1f025 Update to OpenMPI 1.5.4
Changes in v1.5.4 as compared to v1.5.3:

- Add support for the (as yet unreleased) Mellanox MXM transport.
- Add support for dynamic service levels (SLs) in the openib BTL.
- Fixed C++ bindings cosmetic/warnings issue with
  MPI::Comm::NULL_COPY_FN and MPI::Comm::NULL_DELETE_FN.  Thanks to
  Julio Hoffimann for identifying the issues.
- Also allow the word "slots" in rankfiles (i.e., not just "slot").
  (** also to appear in 1.4.4)
- Add Mellanox ConnectX 3 device IDs to the openib BTL defaults.
  (** also to appear in 1.4.4)
- Various FCA updates.
- Fix 32 bit SIGBUS errors on Solaris SPARC platforms.
- Add missing ARM assembly code files.
- Update to allow more than 128 entries in an appfile.
  (** also to appear in 1.4.4)
- Various VT updates and bug fixes.
- Update description of btl_openib_cq_size to be more accurate.
  (** also to appear in 1.4.4)
- Various assembly "clobber" fixes.
- Fix a hang in carto selection in obscure situations.
- Guard the inclusion of execinfo.h since not all platforms have it.  Thanks
  to Aleksej Saushev for identifying this issue.
  (** also to appear in 1.4.4)
- Support Solaris legacy munmap prototype changes.
  (** also to appear in 1.4.4)
- Updated to Automake 1.11.1 per
  http://www.open-mpi.org/community/lists/devel/2011/07/9492.php.
- Fix compilation of LSF support.
- Update MPI_Comm_spawn_multiple.3 man page to reflect what it
  actually does.
- Fix for possible corruption of the environment.  Thanks to Peter
  Thompson for the suggestion.  (** also to appear in 1.4.4)
- Enable use of PSM on direct-launch SLURM jobs.
- Update paffinity hwloc to v1.2, and to fix minor bugs affinity
  assignment bugs on PPC64/Linux platforms.
- Let the openib BTL auto-detect its bandwidth.
- Support new MPI-2.2 datatypes.
- Updates to support more datatypes in MPI one-sided communication.
- Fix recursive locking bug when MPI-IO was used with
  MPI_THREAD_MULTIPLE.  (** also to appear in 1.4.4)
- Fix mpirun handling of prefix conflicts.
- Ensure mpirun's --xterm options leaves sessions attached.
  (** also to appear in 1.4.4)
- Fixed type of sendcounts and displs in the "use mpi" F90 module.
  ABI is preserved, but applications may well be broken.  See the
  README for more details.  Thanks to Stanislav Sazykin for
  identifying the issue.  (** also to appear in 1.4.4)
- Fix indexed datatype leaks.  Thanks to Pascal Deveze for supplying
  the initial patch.  (** also to appear in 1.4.4)
- Fix debugger mapping when mpirun's -npernode option is used.
- Fixed support for configure's --disable-dlopen option when used with
  "make distclean".
- Fix segv associated with MPI_Comm_create with MPI_GROUP_EMPTY.
  Thanks to Dominik Goeddeke for finding this.
  (** also to appear in 1.4.4)
- Improved LoadLeveler ORTE support.
- Add new WindVerbs BTL plugin, supporting native OpenFabrics verbs on
  Windows (the "wv" BTL).
- Add new btl_openib_gid_index MCA parameter to allow selecting which
  GID to use on an OpenFabrics device's GID table.
- Add support for PCI relaxed ordering in the OpenFabrics BTL (when
  available).
- Update rsh logic to allow correct SGE operation.
- Ensure that the mca_paffinity_alone MCA parameter only appears once
  in the ompi_info output.  Thanks to Gus Correa for identifying the
  issue.
- Fixed return codes from MPI_PROBE and MPI_IPROBE.
  (** also to appear in 1.4.4)
- Remove --enable-progress-thread configure option; it doesn't work on
  the v1.5 branch.  Rename --enable-mpi-threads to
  --enable-mpi-thread-multiple.  Add new --enable-opal-multi-threads
  option.
- Updates for Intel Fortran compiler version 12.
- Remove bproc support.  Farewell bproc!
- If something goes wrong during MPI_INIT, fix the error
  message to say that it's illegal to invoke MPI_INIT before
  MPI_INIT.
2011-08-27 19:32:55 +00:00
obache
3b0f2f4d0e Revision bump after updating perl5 to 5.14.1. 2011-08-14 14:14:40 +00:00
dholland
363d292038 If it's going to install tcl scripts, and use REPLACE_INTERPRETER on them,
it needs to depend on tcl. PKGREVISION -> 4
2011-07-05 01:30:52 +00:00
jym
1febc2e19f check-interpreter fix. 2011-07-03 20:01:26 +00:00
cheusov
2918c7dc88 +parallel, oked by sponsors 2011-05-23 21:40:03 +00:00
cheusov
0cffe25a6d GNU Parallel is a shell tool for executing jobs in parallel using one or
more machines.  A job is typically a single command or a small script that
has to be run for each of the lines in the input.  The typical input is a
list of files, a list of hosts, a list of users, or a list of tables.
2011-05-23 21:38:37 +00:00
cheusov
d718a633ee PR pkg/37952. Minor clean-ups. Use only one line USE_TOOLS+=... 2011-05-08 15:12:22 +00:00