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Mark Allen
e2b6e9ee09 apply romio314 patch to romio321
When romio314 was first pulled in an extra patch was applied to it, see commit
92f6c7c1e210c559471a05aaac9b19e0bd3d71bb. Most of that patch is already present
in vanilla romio321, but the fix for MPIO_DATATYPE_ISCOMMITTED() isn't.

If that macro doesn't set err_ then some paths end up with a variable being used
uninitialized. In particular you can trace through romio321/romio/mpi-io/read.c
to see what happens with error_code. It's an uninitialized stack variable that goes
through three MPIO_CHECK_* macros none of which set it. The macros consistently set
error_code to a failure if they see something wrong, but they don't consistently
set it to success when things are fine.

And then in the last macro MPIO_CHECK_DATATYPE it tries to look at the value
of error_code that was never set.

Signed-off-by: Mark Allen <markalle@us.ibm.com>
(cherry picked from commit f413ef6b142fc3498bdb575d270f9afd0a840863)
2018-07-30 17:23:59 -04:00
Howard Pritchard
5704d4fab5
Merge pull request #5474 from mkurnosov/coll-base-allgather-fix-mpi-in-place
coll/base/allgather: fix MPI_IN_PLACE processing
2018-07-26 12:32:45 -06:00
Mikhail Kurnosov
c540dfb18c coll-base-allgather: fix MPI_IN_PLACE processing
The call of MPI_Allgather with sendbuf and sendtype parameters equal to MPI_IN_PLACE and NULL correspondingly, produces the segmentation fault.

The problem is that sendtype is used even when sendbuf value is MPI_IN_PLACE. But according to the standard, sendtype and sendcount parameters should be ignored in this case.

Signed-off-by: Mikhail Kurnosov <mkurnosov@gmail.com>
(cherry picked from commit 540c2d1)
2018-07-25 08:11:28 +07:00
Howard Pritchard
12f391d435
Merge pull request #5475 from hoopoepg/topic/atomic-init-conflict-v4.0
MCA/ATOMIC: atomic_init renamed to atomic_startup - v4.0
2018-07-24 14:55:35 -06:00
Sergey Oblomov
58b7786b70 MCA/ATOMIC: atomic_init renamed to atomic_startup
- there is C11 naming conflict - atomic_init is C macro
  which cause building issue

Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
(cherry picked from commit 3295b238008a6b2e27941c60d757e64ad796fea2)
2018-07-24 17:23:42 +03:00
Geoff Paulsen
c46600fe6d
Merge pull request #5462 from hoopoepg/topic/fixed-hang-pt2pt-over-pml-ucx-v4.0
PML/UCX: fixed ucp request free on persistent request completion - v4.0
2018-07-23 14:21:34 -05:00
Howard Pritchard
4b840789e9
Merge pull request #5458 from rhc54/cmr40/px
Default to internal PMIx if newer than external
2018-07-22 14:01:35 -06:00
Sergey Oblomov
af0e7b190e PML/UCX: fixed ucp request free on persistent request completion
- in sine cases persistent request was deleted during completion
  callback, this cause double free of linked UCX request (assert
  in debug build or hang in release build)
- UCX request is freed prior completion callback

Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
(cherry picked from commit 6fe0a73861b53efac12e740c831802057391525d)
2018-07-20 22:20:14 +03:00
Ralph Castain
50e6e14020 Protect against infinite loops
Flag that we provided a notification and ignore it if it attempts to come back up.

Signed-off-by: Ralph Castain <rhc@open-mpi.org>
(cherry picked from commit ea0d70bc9396def61545e2ce492a55c4c3aa7772)
2018-07-19 13:57:52 -07:00
Geoff Paulsen
c13c320651
Merge pull request #5455 from hoopoepg/topic/osc-ucx-fox-hang-v4.0
OSC/UCX: fixed hang on OSC UCX init - v4.0
2018-07-19 14:00:28 -05:00
Ralph Castain
508c3f391f Default to internal PMIx if newer than external
Per https://github.com/open-mpi/ompi/issues/5031, if the user didn't specify a particular PMIx installation, then default back to the internal version if it is newer than the discovered external one. PMIx doesn't yet provide a full signature so we have to just get as close as possible for now.

Signed-off-by: Ralph Castain <rhc@open-mpi.org>
(cherry picked from commit 1e6aaf7f226f5a4d940e544079e3977229746c11)
2018-07-19 11:59:17 -07:00
Sergey Oblomov
74d6ad09bc OSC/UCX: fixed hang on OSC init
- there worked progress was missed on startup which caused hang
  on one of ranks

Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
(cherry picked from commit a081fba0465e0e03472fc45c9a4a7154f539e3f6)
2018-07-19 15:23:01 +03:00
Edgar Gabriel
b6b9552ca9
Merge pull request #5444 from gbossu/fix-file-delete
io/ompio: Call component-specific file_delete function instead of POSIX unlink
2018-07-18 08:45:57 -05:00
Howard Pritchard
4447738098
Merge pull request #5414 from hppritcha/topic/iwarp_only_by_default
btl/openib: only look for iwarp/roce by default
2018-07-17 20:08:00 -06:00
Howard Pritchard
bc8134dae1
Merge pull request #5448 from thananon/ofi_context
btl/ofi: Added FI_CONTEXT as requirement.
2018-07-17 19:51:13 -06:00
Howard Pritchard
6818272392 btl/openib: only look for iwarp/roce by default
Due to decreasing support by vendors/other orgs for the OpenIB BTL,
only look for iWarp/RoCE devices by default.  Allow IB HCAs
with ports configured for ethernet.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-07-17 19:11:37 -06:00
Gilles Gouaillardet
fed1e7766e
Merge pull request #5430 from ggouaillardet/pr/pcollreq-fort
mpiext/pcollreq: add Fortran bindings
2018-07-18 09:52:59 +09:00
Howard Pritchard
9ac84a92a2
Merge pull request #5449 from jladd-mlnx/topic/oshmem-bump-to-v1.4
OSHMEM Specification version: Bump to v1.4
2018-07-17 16:39:21 -06:00
Joshua Ladd
7bfcd4545d OSHMEM Specification version: Bump to v1.4
Signed-off-by: Joshua Ladd <jladd.mlnx@gmail.com>
2018-07-18 00:23:24 +03:00
Joshua Ladd
3add13c72e
Merge pull request #5441 from hoopoepg/topic/ucx-memhooks-to-common-module
MCA/COMMON/UCX: shift opal memhooks into common UCX
2018-07-17 15:52:44 -04:00
Thananon Patinyasakdikul
033c364ee0 btl/ofi: Added FI_CONTEXT as requirement.
OFI BTL uses context for completion but never ask for it in
fi_getinfo(3). This commit makes sure that we always ask for FI_CONTEXT
to eliminate any potential error.

Signed-off-by: Thananon Patinyasakdikul <thananon.patinyasakdikul@intel.com>
2018-07-17 12:18:43 -07:00
Matias Cabral
be3cb01cb4
Merge pull request #5397 from nrspruit/ns_ofi_mtl_ssend
MTL OFI: Redesign sync send with reduced tag bits and quick ack
2018-07-17 10:14:33 -07:00
Sergey Oblomov
a4b8253fa2 MCA/COMMON/UCX: fixed initialization of malloc hooks
Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
2018-07-17 20:09:50 +03:00
Gaëtan Bossu
8522ba112c MCA/IO/OMPIO: fix MPI_File_delete implementation.
OMPIO now uses the correct delete function depending on the fs

mca_common_ompio_file_delete now works this way instead
of calling POSIX unlink:
 - create a minimal file handle with the given file name
 - select the best fs component using this file handle
 - call the component-specific file delete function

Signed-off-by: Gaëtan Bossu <gbossu@ddn.com>
2018-07-17 18:17:13 +02:00
Gaëtan Bossu
ac6f75e3d1 MCA/FS: check communicator validity in query functions
It is needed because the fs components might be queried due to a MPI_File_delete call.
And in this case, we don't have a communicator value.

Signed-off-by: Gaëtan Bossu <gbossu@ddn.com>
2018-07-17 18:16:21 +02:00
Josh Hursey
9aa5168795
Merge pull request #5353 from ggouaillardet/topic/romio321_grequests
io/romio321: make grequest extensions internal
2018-07-17 10:53:53 -05:00
Gilles Gouaillardet
1a41482720 coll/libnbc: do not recursively call opal_progress()
instead of invoking ompi_request_test_all(), that will end up
calling opal_progress() recursively, manually check the status
of the requests.

the same method is used in ompi_comm_request_progress()

Refs open-mpi/ompi#3901

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-07-17 09:45:08 -06:00
Sergey Oblomov
1c7ae22dfb MCA/COMMON/UCX: shift opal memhooks into common UCX
Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
2018-07-17 13:46:38 +03:00
Yossi Itigin
9a8797a6be
Merge pull request #5440 from hoopoepg/topic/atomic-fix-build-issue
ATOMIC: fixed build issues (incorrect function proto)
2018-07-17 12:21:39 +03:00
Sergey Oblomov
36cc69d47a ATOMIC: fixed build issues (incorrect function proto)
Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
2018-07-17 10:32:15 +03:00
Gilles Gouaillardet
47351b7fac mpiext/pcollreq: Add Fortran use-mpi-f08 bindings
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-07-17 16:29:41 +09:00
Kurita, Takehiro
73e038ec18 mpiext/pcollreq: Add Fortran use-mpi bindings
Signed-off-by: Kurita, Takehiro <fj6370fp@aa.jp.fujitsu.com>
2018-07-17 16:29:41 +09:00
Gilles Gouaillardet
9e0115c980 mpiext/pcollreq: Add Fortran mpif-h bindings
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-07-17 16:29:33 +09:00
Gilles Gouaillardet
44110a575d mpiext/pcollreq: do include PMPIX_* subroutines to C bindings
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-07-17 16:29:33 +09:00
KAWASHIMA Takahiro
2ac08ddfb6
Merge pull request #5435 from kawashima-fj/pr/fortran-iscatter-inplace
mpi/fortran: Fix IN_PLACE detection of ISCATTER(V)
2018-07-17 15:07:47 +09:00
KAWASHIMA Takahiro
5ddf0f6418 mpi/fortran: Fix IN_PLACE detection of ISCATTER(V)
Blocking `MPI_SCATTER` and `MPI_SCATTERV` were fixed in 506d0e96f4
but noblocking `MPI_ISCATTER` and `MPI_ISCATTERV` were not fixed yet.

Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>
2018-07-17 14:15:21 +09:00
Joshua Ladd
1f4829b874
Merge pull request #5265 from xinzhao3/topic/openshmem-v1.4
OMPI/OSHMEM: add new functionality of OpenSHMEM v1.4.
2018-07-16 17:37:42 -04:00
Xin Zhao
c429900cd9 OMPI/OSHMEM: add new functionality of OpenSHMEM v1.4.
Signed-off-by: Xin Zhao <xinz@mellanox.com>
2018-07-16 12:55:25 -07:00
Yossi Itigin
9d0b3a42aa
Merge pull request #5423 from hoopoepg/topic/bitwise-atomics-renaming
ATOMICS: renamed atomic calls to unsigned datatypes
2018-07-16 19:08:02 +03:00
Mikhail Kurnosov
ba83cc91eb coll/base: add MPI_Bcast based on a binomial tree scatter followed by a ring allgather
Implements MPI_Bcast using a binomial tree scatter followed by a ring allgather.

Signed-off-by: Mikhail Kurnosov <mkurnosov@gmail.com>
2018-07-16 08:56:09 -06:00
Sergey Oblomov
da1afcaaaf ATOMIC/UCX: fixed typo in datatype macro
Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
2018-07-16 14:49:06 +03:00
Yossi Itigin
27b91d7564
Merge pull request #5425 from hoopoepg/topic/atomic-mxm-abstraction-viola-master
ATOMIC/MXM: fixed abstraction violation
2018-07-15 10:51:29 +03:00
Gilles Gouaillardet
99e0f96155
Merge pull request #5413 from ggouaillardet/topic/pcollreq
mpiext/pcollreq: check subroutine parameters and add profiling symbols
2018-07-14 15:02:02 +09:00
Gilles Gouaillardet
61b3308871 mpiext/pcollreq: check subroutine parameters and add profiling symbols
- check subroutine parameters
 - implement PMPIX_* subroutines

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-07-14 14:14:37 +09:00
Gilles Gouaillardet
dec1663364 spc: add missing subroutines
add counters for :
 - MPI_Exscan
 - MPI_Iexscan
 - MPI_Igatherv

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-07-14 14:14:37 +09:00
Ralph Castain
9831145020
Merge pull request #5427 from rhc54/topic/px
Remove the PMIx ext4x component
2018-07-13 20:43:09 -07:00
Ralph Castain
4a596d35f7 Remove the PMIx ext4x component
Update configury to redirect anything at or above v3 to the ext3x component

Signed-off-by: Ralph Castain <rhc@open-mpi.org>
2018-07-13 19:51:50 -07:00
Howard Pritchard
9a5fd48388
Merge pull request #5079 from jsquyres/pr/fortran-is-the-devil
status_set_cancelled: fix F08 binding
2018-07-13 15:36:02 -05:00
Joshua Ladd
b12868239c
Merge pull request #4765 from xinzhao3/topic/osc-ucx-mem-hook
OMPI/OSC/UCX: move memory hooks init in osc to win creation.
2018-07-13 09:36:20 -04:00
Sergey Oblomov
bd84165277 ATOMICS: renamed atomic calls to unsigned datatypes
Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
2018-07-13 15:32:16 +03:00