[mpich-commits] [mpich] MPICH primary repository annotated tag, v3.1b1, created. v3.1b1

mysql vizuser noreply at mpich.org
Thu Aug 8 11:44:11 CDT 2013

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The annotated tag, v3.1b1 has been created
        at  59666a207398c76cd313dd4ada91173de0b77f88 (tag)
   tagging  a56be0e75cde4afa6aeb21887cec2d6c2f74c355 (commit)
  replaces  v3.0.4
 tagged by  Pavan Balaji
        on  Thu Aug 8 10:37:55 2013 -0500

- Log -----------------------------------------------------------------
Tagging v3.1b1 release.

Antonio J. Pena (8):
      Fixes ticket #1899.
      Fixes ticket #1870.
      Small fix after 8cf54f1 fixing ticket #1870.
      Small fix after 80ad7cf8 to fix ticket #1870.
      Removing unmatched quotation sign in configure.ac.
      Patch libtool.m4 after every autoreconf and fix timestamp.
      Add weak symbol support for clang 3.2. Fixes #1815
      Regenerate configure after patching libtool.m4

Bob Cernohous (37):
      Handle count 0 allreduce
      Split large broadcasts into smaller broadcasts
      Fix BGQ compile errors
      Update PAMID with new bcast metadata changes
      Glue updates for metadata changes
      Reformat mpido_allreduce
      Use optimized protocol for more supported dt/op combinations
      Fix double allreduce when there is no cached protocol
      Revert "Ticket #632: Disable optimized alltoall[v]'s with MPI_IN_PLACE"
      Revert "Trac #636:Disable optimized allgatherv"
      Support MPI_IN_PLACE metadata
      Metadata glue fixes
      More thorough check for optimized bcast protocol
      Remove misleading verbose output
      Do optimized selection even if first protocol list is empty
      PAMI_COLLECTIVES_MEMORY_OPTIMIZED does not optimize irregular communicators
      MPI_Allgather glue protocol updates.
      Update MPI_IN_PLACE support after D188059/D188060 fixes
      Switch RankBased to SequenceBased
      Simple support for async flow control metadata
      Fix optgather flag processing
      Use new configuration options.
      After review: Use PAMI_GEOMETRY_NULL
      After review: Update comments and range checks
      After review: Fix scatter range check
      After review: Comment out [v] range checks
      Implement a simple PAMID_NUMREQUESTS for async flow control
      Use MPIDO and not MPIR internally in PAMID
      Need to read some environment variables before creating the client
      Fix M2M protocol selection
      Update scatter[v] protocol selection
      Remove ticket #595 circumvention
      BGQ must create geometries with (existing) tasklists
      Fix alltoall handling of non-PAMI datatypes and non-continuous datatypes.

Charles Archer (12):
      MPI_File_get_position_share fail in mpich2
      Added cross file for 32 bit
      Out of order message handling deadlock fix
      Change defaults for alltoall throttle to 32 outstanding sends from 4
      detect 32 bit vs 64 bit via sizeof
      use void* for sizeof detection instead of int
      Fixed assert on int env vars passed in a string
      Use pami_endpoint_t for root instead of incorrect pami_task_t
      XL compiler prototype fix
      Enable SMP aware collectives via PAMI local task detection
      PAMID device code for local task detection
      PAMID: Fix MPIC_Sendrecv interface break in dynamic tasking

Dave Goodell (15):
      attr: check for handle allocation error
      initialize mpi_errno in `MPIC_` routines
      whitespace fixup for [eed075d6]
      make `MPIR_Comm_create_intra` non-static
      Merge remote-tracking branch 'origin/pending-00' into ibm-integ
      Merge branch 'ibm-integ'
      Merge remote-tracking branch 'origin/master' into master
      tt#1816: make c99 the default for --enable-strict
      Merge branch 'ibm-integ' into master
      add `MPIU_Prod_overflows_max`
      add `MPIU_Static_assert`
      detect C11 `_Generic` in some cases
      add static type checking asserts
      add `MPIU_Assign_trunc` macro
      Merge branch 'better-large-count' (early part)

Douglas Miller (1):
      Make debugger SEND queue faster

Haizhu Liu (23):
      Dynamic tasking support
      AIX build break and mem freeup
      Fix for spawn/spaiccreate failure where the PG information needs to be broadcasted to all COMM_WORLD members that did not participated in the spawn
      Fix for concurrent_spawns
      Soft spawn bug fix in mpich2
      MPI_Abort does not abort connected world when it is in finalize process
      Dynamic cases failed with large procs
      soft spawn patch caused error msg expansion error during compile
      multi_ports failed in dynamic tasking
      Dynamic test case finalize6 hang
      spaiccreate core at MPI_Intercomm_create
      MPI_Comm_disconnect problem
      Dyntask/pgroup_intercomm_test test failure
      MPI_Win_unlock could potentially complete too soon before the remote side gets the control message
      Fix for dynamic multi threaded case
      Fix seg fault in _mpi_world_exiting_handler, fix hang at MPI_Finalize, removing calling PAMI_Context_advance in dispatch.
      MPI_Comm_disconnect hang
      Dynamic tasking MPI_Comm_disconnect HANG
      adio/common wrong checking of lseek return
      Thread level promoting w/dyn_tasking due to world exiting handler in separate thread
      second spawn reuse taskid would fail with ERROR 421
      Correct dlopen for libpoe on AIX
      Correct a 0 byte malloc failure on AIX

James Dinan (4):
      Add missing initializer
      Cleanup RMA comment in MPIDI_Reqest
      Move CH3-specific MPID_Win members into CH3
      Remove unnecessary myrank field in MPID_Win

Jed Brown (2):
      config: change PAC_FUNC_NEEDS_DECL to check by assignment
      test: add attrdeleteget, MPI_Attr_get called from delete_fn

Jeff Hammond (3):
      Replace bcopy with memmove.
      Replace bzero with memset.
      fix ticket 1863 - improper+missing RMA error checks for addr=NULL

Joe Ratterman (1):
      Trap unsupported read- and write-conversions.

Keira Zhang (1):
      Message Queue debug support

Ken Raffenetti (10):
      Revert "Debugger changes from IBM."
      Add support for MPICH_AUTOTOOLS_DIR in hwloc. Fixes 1881.
      Increase timeout for rma-contig test.
      Add configure test for __builtin_expect
      Adds framework for testing checkpointing.
      Amended write_ckpoint test.
      Adds fault tolerance tests.
      Ensure fault tolerance tests only run with hydra.
      Add FT test with communication. Tweak other FT tests.
      Mark FT tests xfail.

Michael Blocksome (49):
      Issue 6292: romio ad_bg bug fix for uninitialized struct
      fix bug in the 'is_local_task' extension.
      Utility functions originally from "7 MPI-COM error injection cases core dump with MPICH2"
      Add 'PAMID_PT2PT_LIMITS' env var to specify *all* point-to-point limit overrides
      Simplify and clarify the 'MPIDI_PT2PT_LIMIT' macro by splitting it in two.
      Create a task scaling threshold at which point internal eager is disabled
      New environment varariable: 'PAMID_DISABLE_INTERNAL_EAGER_TASK_LIMIT'
      attempt to fix pe compile error.
      BG ROMIO changes that remained unresolved after the merge.
      Enable MPIR_* non-blocking collectives implementation
      set bgq default eager limits for intra- and inter-node to 4097.
      Set appropriate wrapper flags and default error string length.
      Implement MPIX_Cart_comm_create and MPIX_Pset_* functions.
      BG ROMIO changes that remained unresolved after the merge.
      Use 'MPIU_ERR_CHKANDJUMP' for onesided parameter checks
      Add ability to customize the mpich fortran 90 library name
      Add ability to customize the OpenPA library name
      Add ability to customize the MPL library name
      Add ability to customize the PAMI library name
      Allow pkgconfig files to be installed in an arbitrary directory.
      Fix '--with-openpa-prefix=DIR' so it actually works.
      Add '--with-mpl-prefix=DIR' configure option.
      Allow f90 mod files to be installed in an arbitrary directory.
      pami_tune core w/ -collective_selection=tune
      MPIDI_TRACE tool enhancement - remaining updates
      Add dropped change from 'code review fixes'.
      Add hooks for optimized MPIX_* non-blocking collectives.
      Check for assert only if asserts are enabled.
      PAMI backward compatibility checks.
      Disable MPI_IN_PLACE for versions of pami that do not support PAMI_IN_PLACE.
      Do not assert when a pami extension is missing.
      compile fix for bgq unsupported MPID_Node_id_t
      Revert "Do not assert when a pami extension is missing."
      better bgq 'is local task' fix.
      always disable eager for synchronous sends
      Additional MPIX_IO_* functions and fortran interfaces.
      Repair the bgq system software search logic
      Use the host tuple to determine the pamid implementation if not specified.
      Allow the device to specify a default cross file.
      Allow the device to specify a default pm
      Check for the 'comm/sys' directory before adding to compiler flags
      pamid bgq fix for spi includes
      Update README.vin with bgq configure instructions.
      Debugger changes from IBM.
      update bgq pami library search process.
      add support for alternative default pami library names.
      another bg romio fix from after merge
      Clean up pamid MPID_Abort() logic
      add 'dbg_next' field to mpi request structure.

Pavan Balaji (137):
      Use VPATH builds for docs in release tarball creation.
      Cleanup unnecessary command in the release script.
      Fix PID calculation error introduced in [e04dd4b6].
      Propagate errors in autogen.sh upstream.
      Get rid of getpagesize declaration. This is already fixed in hwloc.
      Upgraded to hwloc-1.7.
      Merge hydra-specific hwloc patches.
      Bug-fix for tt#1820.
      Merge remote-tracking branch 'mpich-ibm/ticket-1824'.
      hwloc bug fix for tt#1830.
      Replace weak-symbols check in ROMIO with the confdb version.
      Cleanup confdb macros.
      VPATH bug-fix.
      (incomplete) Added new string stash/spit macros.
      Revert accidental commit [99e8252a]
      Revert accidental commit [7dc192b8]
      Missed adding back a few files in [657da4c2].
      Bug-fix in the weak symbols check for ROMIO.
      Pull in r5559 from hwloc-upstream.
      Fix minor typo.
      Fix strict build failure in hydra.
      Fix strict build errors in PMI simple.
      Fixes for hwloc to build with -D_POSIX_C_SOURCE=200112L.
      Fix check for declarations in hwloc.
      Fixes for sysctl checks in strict builds of hwloc.
      Include strings.h for strcasecmp.
      Warning squash.
      Die on autoreconf error instead of chugging along.
      Simplify C89 header checks.
      Include stdio.h in the configure test for getifaddrs.
      Include stdio.h in the configure test for the definition of NULL.
      Revert IBM hwloc versioning patch.
      hwloc fix to support c89 builds.
      Reorder compiler preference.
      Use hwloc's autogen.sh directly.
      Fix typo in hwloc's autogen.sh.
      Allow devices to override the number of handles and indices through
      Rename mpich2 to mpich.
      Initial drafts of MPID_Win_set/get_info in pamid.
      PAS_VAR_COPY cleanup.
      Get rid of PAC_EVAL_IFELSE which is a duplicate of PAC_COMMAND_IFELSE.
      Flag push/pop cleanup.
      Fix for tt#1832.
      Make MPIR_Comm_create_group visible to other MPICH utilities.
      Disable -Wcast-align and -Wshorten-64-to-32.
      Warning squash.
      Naming updates to IBM's NBC patch.
      Remove C99-ism from IBM contributed code.
      Reverted [c478a4fe] which seems to be causing build failures.
      Make parameter names consistent.
      Better arrange environment variables according to their categories.
      Update parameter generation to allow device-overrides where needed.
      Make enabling SMP collectives an environment variable instead of a
      Added ability to enable/disable individual SMP collectives.
      Cap the maximum SMP collective size.
      Allow pamid to override max message size for SMP collectives.
      Added new string stash/spit macros.
      White space cleanup.
      Correct parameter name.
      Warning squash.
      Missed check for inline in mpl.
      Warning squash for clang.
      Remove accidental debug statements.
      Warning squash.
      Fix strict build with clang on FreeBSD.
      Upgraded to hwloc-1.7.1rc1.
      Hydra-specific patches for hwloc.
      Incorrect macro for sys/sysctl.h
      Move lesser used C++ compilers down the priority list.
      Prioritize clang++ over g++.
      Added a comment explaining Jed's test.
      Enable shared builds by default.
      Memory-leak fixes.
      Bug-fix: Fix use of wrong string list.
      Bug-fix: Fix slurm node list creation.
      Check for env variables we plan to use before picking slurm.
      Pick device timer-type if available, by default.
      Remove accidentally added debug messages.
      Remove unused variable.
      Improve comment for thread-package requirement in serialized.
      Only try to find a thread package, if it is required.
      Cleanup of the --enable-threads configure option.
      Fix for tt#231.
      Added a new rma-contig test.
      Initiate the asynchronous thread only in MULTIPLE mode.
      Thread package is no longer required for SERIALIZED mode.
      ASYNC_THREAD improvements.
      Control default thread level from the environment.
      Remove arbitrary restriction on the thread-level.
      Throw warning when async thread is not started.
      Fix error in SLURM environment detection.
      Fix the slurm node query code when only one node is allocated.
      Squash memory leaks in the slurm code.
      Upgraded to hwloc-1.7.1
      Hydra-specific patches for hwloc.
      Updated version information for the 3.1b1 release.
      Added CHANGES log for mpich-3.1b1.
      Fix typo in picking the right process manager.
      Place the preferred environment variable name at the top.
      Remove MPICH_ASYNC_PROGRESS from the main README.
      Move MPICH_NAMEPUB_DIR to the PARAM format.
      Remove environment variables section from README.
      Improved README text for ASYNC_PROGRESS.
      Revert [6a4899dc].
      Improved timer-type detection.
      Fix tt#1505.
      Fixes #1882.
      Added a note on the ABI issues.
      General cleanup of RELEASE_NOTES.
      Reprioritize gcc over clang.
      Correct error string.
      Remove caching wrapper for gethostname.
      Added a file to OpenPA .gitignore.
      Replace "-" with "\-" to keep Debian lintian checks happy.
      Remove unused mpicc.conf.in and friends.
      ch3 should be creating UNIFIED windows.
      Update author list for MPICH guides.
      Get rid of PAC_CC_PREFIX.
      Correct bad parameter names.
      Better likely/unlikely hints to MPI.
      Added a badrma test program.
      Remove GCC specific pragmas.
      Added Intel-contributed patches for SCIF.
      White-space cleanup to Intel-contributed patches.
      Mention the Intel SCIF contribution in the CHANGES file.
      Update CHANGES to not describe the class of change.
      Update CHANGES to reflect the improvement to MPI_WIN_ALLOCATE.
      Error in the buffer attached to dynamic windows.
      Warning squash.
      Created a new test for a large number of outstanding RMA operations.
      Check for a NULL string before freeing.
      Intel scif code contribution.
      Make sure MPID_REQUEST_PREALLOC is always defined.
      Initialize environment parameters before MPI is initialized.
      Bug-fix: initialize string stash list early.
      Mention the missing MPI_T functionality in the README.
      Fix ABI string for libmpich.

Qi QC Zhang (11):
      7 MPI-COM error injection cases core dump with MPICH2
      handle ENOMEM errors in ADIO
      update error checkings in ADIO
      Wrong error class returned on GPFS
      check NULL size in MPI_File_get_size
      fix uninitialized `mpi_errno`
      update error checkings in ADIO
      Wrong error class returned on GPFS
      check NULL size in MPI_File_get_size
      Add dropped code change from 'Changes in PAMId layer for AIX building'
      MPI_File_close shared file fail occasionally w/ case rw_share4

Rajeev Thakur (1):
      remove check for committed type in Type_size_x. Fixes ticket #1774

Rob Latham (13):
      avoid hang if subset of procs have invalid INFO
      deal with MPI_INFO_NULL reasonably
      duped info in wrong branch of check for null
      automake doesn't like CFLAGS and CPPFLAGS
      check existance of headers before including
      some AM_INIT_AUTOMAKE invocations were missing subdir-objects
      automake subdir-object mode needs check for -c -o
      subdir-objects and top_srcdir/top_builddir conflict
      small memory management cleanups
      partial fix for tt 1742
      big redo to generalize file_info test
      memory leak in blue gene aggregator selection
      zap arch-specific stuff

Sameer Kumar (2):
      Allgather(v) optimizations to use allreduce double sum instead of integer BOR.
      Trac 665. Memory leak fix for MPI RMA.

Sameh Sharkawi (8):
      Need service variables for all collectives
      pami_tune command line changes
      Correctly handling non-continuous data in vector collectives
      Alltoallv_int is missing in the xml file
      Changing default iter count to 1000
      One more fix for correctly displaying warnings in tune mode
      pami_tune -o option renames directory
      AIX compiler pad fixes

Su Huang (23):
      Enable PAMIX extensions to enable/disable interrupts
      fix the build - replace malloc/free by MPIU_Malloc/MPIU_Free
      Memory management and token flow control for early arrivals
      mpich2 don't support mpc_statistics_write/zero in mpi program
      Support MP_BUFFER_MEM with two values
      Support MP_SHMEM_PT2PT with yes or no option
      Trace tool to include 0 byte renzevous messages
      job fail w/ MP_BUFFER_MEM set on x86_64
      NAMD core dumps due to unsafe MPICH2 iprobe() handling
      Incorrect MPI_IO default key value
      MPI job hangs at MPI_Iprobe using mpich2
      probe12 failed on MPICH2 from rcot PTF1 build
      MPIDI_TRACE tool enhancement
      multi_mpi coredump with RDMA on mpich
      MPICH missing timer only progress engine that old PEMPI has
      32bit reduce&allreduce fail MPI_LONG w/ collective_selected
      32bit(2) reduce&allreduce fail MPI_LONG w/ collective_selected
      updates for token flow control
      Hardcoded to wrong value 400000 if MP_POLLING_INTERVAL not set
      Multi mpi fail with token flow control and euidevelop=deb
      pamid updates to handling trace buffers
      negative source returned from MPI_Waitany
      Fix uninitialized parameters for one sided communication in pamid

Wesley Bland (28):
      Remove Windows instructions from README.vin
      Fixes #1868.
      Block off the highest bit of tag space.
      Add macros to manipulate error bits in tag space.
      Mask away the error bit in tag space when matching.
      Modify collective functions to propagate error bit.
      Make ENABLE_COLL_FT_RET default now that it doesn't break NBC.
      No longer need MPIR_ERROR_TAG.
      Move MPIC_* usage over to MPIC_*_ft functions.
      Combine MPIC_Send and MPIC_Send_ft. Remove MPIC_Send.
      Combine MPIC_Recv and MPIC_Recv_ft.
      Combine MPIC_Ssend and MPIC_Ssend_ft.
      Combine MPI_Sendrecv and MPI_Sendrecv_ft.
      Combine MPIC_Sendrecv_replace and MPIC_Sendrecv_replace_ft
      Combine MPIC_Irecv and MPIC_Irecv_ft
      Combine MPIC_Isend and MPIC_Isend_ft
      Rename MPIC_Recv_ft to MPIC_Recv
      Rename MPIC_Send_ft to MPIC_Send
      Rename MPIC_Ssend_ft to MPIC_Ssend
      Rename MPIC_Sendrecv_ft to MPIC_Sendrecv
      Rename MPIC_Sendrecv_replace_ft to MPIC_Sendrecv_replace
      Rename MPIC_Isend_ft to MPIC_Isend
      Rename MPIC_Irecv_ft to MPIC_Irecv
      Rename MPIC_Waitall_ft to MPIC_Waitall
      Update CHANGES with FT/NBC work.
      Deprecate ENABLE_COLL_FT_RET
      Add missing end error handling tag.
      Remove the ft tests from the default test suite.

William Gropp (16):
      Fix for #1804 - Alignment issues in Fortran with MPI_Status
      Fixes for #1804 and #1828, related to alignment issues with MPI_Status
      Suppress warnings about alignment (code already ensures correctness)
      Add casts to suppress false warnings about alignment issues.
      Fix for missing test that getsid requires a declaration.
      Corrected MPI-2 C++ interface to include the Distgraph routines
      Missed adding the change to the C++ testlist for the new topo test
      Cleaned up files to remove unused code from distgraph update
      Correct typo in usage of parameter in bcast
      Check that an MPI Error Class is provided where one is required
      Turned off the error reporting since that causes autogen.sh to abort.
      Add explicit casts to unsigned long for printing types of size_t
      Added missing delete of the created keyval
      Added a test for an invalid, size 0, determination of the sizeof a Fortran integer
      Recent versions of Cray Fortran may require a special arg to create modules
      Added Fortran tests for a few PMPI routines

Xin Zhao (37):
      bug on MPIU_INSTR_DURATION_END(rmapkt_acc_immed_op).
      bug of deleting redundant call to get win_ptr.
      fix bug:check info value of "alloc_shared_noncontig".
      Added a new test for checking for zero-byte window creations.
      fix bug of zero-byte shared window allocation.
      fix bug: return info=false in MPIDI_Win_get_info if that info is not set by user.
      Refactoring code of waiting passive RMA operations.
      Waiting for passive RMA operations to finish in MPIDI_CH3_SHM_Win_free.
      modify SHM_Win_allocate_shared and SHM_Win_free to accomodate global comm.
      Refactoring the code of SHM RMA operations from operation routines to inline functions.
      Add "alloc_shm" info to MPI_Win_allocate.
      add "alloc_shm" info to MPIDI_Win_get_info.
      Call DO_SHM_RMA_OP in fence/unlock/complete.
      In SHM RMA operations, add condition for "alloc_shm".
      Delete decrementing ref count in SHM RMA operations, but add conditions in operaiton issue routines.
      do SHM_MUTEX_LOCK/UNLOCK in packet handlers on target.
      add alloc_shm test in mcs-mutex.c test.
      add alloc_mem test in req_example.c test.
      add alloc_mem test in win_info.c test.
      Set alloc_shared_noncontig to 1 by default if alloc_shm is passed to MPI_Win_allocate.
      Fixed touch command option order
      Move shm_allocated flag from nemesis layer to CH3 layer.
      In SHM RMA operations, delete using MPI_WIN_FLAVOR_SHARED to judge if using shm_base_addrs.
      When judging if origin and target process are on the same node, using vc->node_id flag instead of vc->ch.is_local flag.
      delete assignment of (*allocate_shared) in CH3 and nemesis.
      add function pointer 'allocate_shm' to win_fns.
      In nemesis layer, change function name from MPIDI_CH3I_Win_allocate_shared to MPIDI_CH3I_Win_allocate_shm.
      In nemesis layer, change type of argument 'base_ptr' from (void**) to (void*).
      In CH3 layer, change function name from MPIDI_CH3U_Win_allocate to MPIDI_CH3U_Win_allocate_no_shm.
      delete CH3 default MPIDI_CH3U_Win_allocate_shared.
      delete CH3 default MPIDI_SHM_Win_free.
      Modify MPIDI_Win_free to handle win_allocate and win_allocate_shared in CH3.
      In (*allocate_shared), change type of argument 'base_ptr' from (void**) to (void*).
      Implement new MPIDI_CH3U_Win_allocate and call it through function pointer from MPID_Win_allocate.
      Assign new MPIDI_CH3U_Win_allocate to (*allocate_shared) so that it will be called by MPID_Win_allocate_shared.
      In MPID_Win_allocate_shared, check 'alloc_shm' info.
      Modify CH3 default MPIDI_Win_shared_query not to use shm_base_addrs.

sssharka (7):
      Implement collective algorithm selection in MPICH
      multi mpi core with collective selection enabled
      MPI_Scatterv coredump in PAMI_Type_transform_data with FCA
      External algorithm registration for collective selection
      shmcc_gather_t2 hang w/o MP_COLLECTIVE_SELECTION_FILE set
      shmcc_gather_t2 coredump w/ setMP_COLLECTIVE_SELECTION_FILE
      Fixes for parsing command line parameters in CollSel


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