This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MPICH primary repository". 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 Add PAMID_COLLECTIVE_REDUCE=GLUE_ALLREDUCE 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 Change PAMI_COLLECTIVES_MEMORY_OPTIMIZED to PAMID_COLLECTIVES_MEMORY_OPTIMIZED 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 Specify PAMID_COLLECTIVES_MEMORY_OPTIMIZED levels 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 ----------------------------------------------------------------------- hooks/post-receive -- MPICH primary repository