summaryrefslogtreecommitdiff
path: root/parallel
AgeCommit message (Collapse)AuthorFilesLines
2012-10-31Update to OpenMPI 1.6.3asau2-6/+6
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.
2012-10-26Avoid conflicting implicit prototype.joerg2-5/+6
2012-10-24Reexport libxml2 from hwloc.asau3-4/+6
Reexport hwloc from openmpi. This should fix builds with MPI_TYPE=openmpi.
2012-10-17Update to OpenMPI 1.6.2asau10-241/+99
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.
2012-10-17Cleanup while here.asau1-2/+2
2012-10-17Update to hwloc 1.5asau3-17/+26
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.
2012-10-08Revbump after updating graphics/pangoadam1-2/+2
2012-10-03Bump all packages that use perl, or depend on a p5-* package, orwiz7-10/+14
are called p5-*. I hope that's all of them.
2012-10-02Mass recursive bump after the dependence fix of the "cairo" packagetron2-4/+4
requested by Thomas Klausner.
2012-09-15Make build stop on error.dholland2-1/+18
2012-09-15recursive bump from libffi shlib major bumpobache2-4/+4
(additionaly, reset PKGREVISION of qt4-* sub packages from base qt4 update)
2012-09-11"user-destdir" is default these daysasau15-45/+15
2012-09-09Update to 0.17.0cheusov3-22/+30
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
2012-09-07Revbump after updating graphics/cairoadam2-4/+4
2012-08-21Recursive PKGREVISION bump for tcl and tk upgrade to 8.5.12marino2-3/+4
2012-07-03Update to SLURM 2.4.1asau3-8/+10
* 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.
2012-07-03Add "latest" subdirectory to look for distfiles.asau1-1/+2
2012-06-14SET_LIBDIR=yessbd1-1/+2
2012-06-14Recursive PKGREVISION bump for libxml2 buildlink addition.sbd2-3/+4
2012-06-13Distfile has moved to archive subdirectory.asau1-2/+3
2012-06-12Update to OpenMPI 1.6asau7-33/+89
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).
2012-06-02Set USE_TOOLS instead of BUILD_DEPENDS to get csh, and use ${CSH}dholland1-5/+3
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.
2012-05-28Update to OpenMPI 1.5.5asau5-23/+53
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.
2012-05-21parallel/openmpi: Fix PLIST for DragonFlymarino2-2/+10
2012-05-10pkglint cleanup while here.wiz1-4/+4
2012-05-10Fix build with automake-1.12.wiz2-1/+16
2012-04-18Fixup DESTDIR handling in do-install.markd1-5/+6
Add LICENSE (sun-iss + 2-clause-bsd + gpl + lgpl)
2012-04-15Add missing pam.bl3.mk. (but, it builds on LP64 platforms now. yay!)dholland1-1/+2
2012-04-15Reinstate patch-source-utilbin_Makefile (aka patch-ak)markd6-30/+168
Dont install *.orig files Fix build on 64bit systems Fix arch name for Linux Bump PKGREVISION
2012-04-07Mark sge and gridscheduler not for ${LP64PLATFORMS}. They crash duringdholland2-2/+8
build.
2012-03-21+ gridschedulerasau1-1/+3
+ hwloc
2012-03-21Remove empty patches, no idea how they have got through.asau11-11/+1
2012-03-21Import Open Grid Scheduler version 2011.11 as parallel/gridscheduler.asau24-0/+1287
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.
2012-03-21Import Portable Hardware Locality (hwloc) version 1.4 as parallel/hwloc.asau10-0/+648
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.
2012-03-20Update to the Son of Grid Engine 8.0.0dasau20-374/+289
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+ slurmasau1-1/+2
2012-03-20Import SLURM 2.4.0pre4 as parallel/slurmasau12-0/+517
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.
2012-03-13Add c99 support, fixes build on SunOS.fhajny3-4/+36
Change long xdr macros to int32 ones, fixes build on SunOS and ABI=64. Bump PKGREVISION.
2012-03-09clean-ups (adapted for recent mk-configure)cheusov1-4/+2
2012-03-03Recursive bump for pcre-8.30* (shlib major change)wiz2-4/+4
2012-02-06Revbump forwiz2-4/+4
a) tiff update to 4.0 (shlib major change) b) glib2 update 2.30.2 (adds libffi dependency to buildlink3.mk) Enjoy.
2012-02-06Switch to using REPLACE_CSH.sbd1-5/+2
2012-02-03Two of the install scripts use csh so add csh:run as a tools and usesbd1-2/+7
REPLACE_INTERPRETER on the scripts.
2012-02-03Set _PVM_ARCH=64 on x86_64-linux.sbd1-1/+3
2012-01-11Update to MPICH2 1.4.1p1asau6-25/+66
=============================================================================== 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
2012-01-11Update PLIST.sbd2-2/+6
Bump PKGREVISION
2011-12-27Prevent detection of OpenMP support in order to make PLIST consistent.asau1-1/+4
2011-12-09PKGREV bump for libXp-less openmotifdrochner1-2/+2
2011-12-02Recursive bump for devel/apr buildlink addition.sbd1-2/+2
2011-11-29Add pod2man and pod2html to USE_TOOLS.hans1-2/+2