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Howard Pritchard
3a584fee53
Merge pull request #5723 from ggouaillardet/topic/v4.0.x/libnbc_error_path
coll/libnbc: fix various error paths
2018-09-18 09:29:45 -06:00
KAWASHIMA Takahiro
e83e118ae7 mpiext/pcollreq: fix more typos
Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>
(cherry picked from commit 4a0a2598f63b081045fdeb51256493ce2a8ec96a)
2018-09-18 15:43:06 +09:00
Gilles Gouaillardet
ece18aed45 coll/libnbc: fix various error paths
The parameter passed to NBC_Return_handle() was incorrectly casted
and not dereferenced.

Thanks Yossi for the bug report.

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>

(cherry picked from commit open-mpi/ompi@8b51862fb2)
2018-09-18 15:29:33 +09:00
Gilles Gouaillardet
73f531a8f2 mpiext/pcollreq: fix misc typos
Thanks Jeff for the report

Fixes open-mpi/ompi#5712

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>

(cherry picked from commit open-mpi/ompi@8dc6985a5a)
2018-09-18 12:47:04 +09:00
Geoff Paulsen
de0c595ca5
Merge pull request #5650 from matcabral/remove_psm2_shadow_env_40x
v4.0.x: MTL PSM2: Remove shadow variables from v4.0.x
2018-09-17 14:40:59 -05:00
Geoff Paulsen
17aab5ea5b
Merge pull request #5659 from ggouaillardet/topic/v4.0.x/misc_finalize_leaks
Plug misc leaks on MPI_Finalize()
2018-09-10 14:06:31 -05:00
KAWASHIMA Takahiro
6858028596 mpiext/pcollreq: Fix zero-count reduction
We need to return a persistent request.
`ompi_request_empty` is not a persistent request.

Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>

(cherry picked from commit 69901a515697485cf56599e206dcfb74228e7ca2)
2018-09-10 13:11:59 +09:00
Gilles Gouaillardet
ff8600f2e4 ompi/hook: plug a misc memory leak
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>

(cherry picked from commit open-mpi/ompi@b79b37465c)
2018-09-10 09:21:49 +09:00
Gilles Gouaillardet
4bd5c538a2 pml/ob1: plug a memory leak in mca_pml_ob1_component_fini()
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>

(back-ported from commit open-mpi/ompi@fed33c1530)
2018-09-10 09:21:12 +09:00
Gilles Gouaillardet
c767c63a3b ompi/info: plug memory leaks in ompi_mpiinfo_finalize()
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>

(cherry picked from commit open-mpi/ompi@d0d399c9a9)
2018-09-10 09:18:15 +09:00
Gilles Gouaillardet
080e20fa02 mtl/psm2: fix a misc memory leak
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>

(cherry picked from commit open-mpi/ompi@316e4e38f4)
2018-09-10 09:17:54 +09:00
matcabral
8fa172e60b MTL PSM2: Remove shadow variables from v4.0.x
As agreed on #4574, where removed in past release branches
to avoid perfomance impacts in the default values for
some paramters.

Signed-off-by: Matias Cabral <matias.a.cabral@intel.com>
2018-09-05 18:44:40 -04:00
Howard Pritchard
7e10bc0833
Merge pull request #5607 from edgargabriel/pr/sharedfp-naming-conflict-v4.0
sharedfp/sm and lockedfile: fix naming bug
2018-09-02 16:03:14 -04:00
Geoff Paulsen
3282c61048
Merge pull request #5625 from hoopoepg/topic/optimize-blocked-calls-v4.0
PML/UCX: blocked calls optimizations - v4.0
2018-08-31 14:11:11 -05:00
Geoff Paulsen
334748753c
Merge pull request #5626 from hoopoepg/topic/opal-mem-hooks-syno-v4.0
MCA/COMMON/UCX: added synonim to opal_mem_hook variable - v4.0
2018-08-31 14:09:14 -05:00
Geoff Paulsen
51e685ff40
Merge pull request #5622 from aravindksg/ofi_race_fix_40x
MTL OFI: Fix race condition due to global progress entries array
2018-08-31 14:07:42 -05:00
Sergey Oblomov
028bcb8a73 MCA/COMMON/UCX: added synonim to opal_mem_hook variable
- added synonim to common ucx variables to allow
  to print it in opal_info -a

Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
(cherry picked from commit e00f7a68ba0b1012f954910e39b26f6075f3d006)
2018-08-29 15:17:00 +03:00
Sergey Oblomov
9215eb9a3b PML/UCX: blocked calls optimizations
- refactoring of opal/UCX progress calls
- added UCX progress priority

Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
(cherry picked from commit b0f87f22358914ae9f8fc382daa4052b31ed2aeb)
2018-08-29 14:38:22 +03:00
Aravind Gopalakrishnan
37d1a202be MTL OFI: Fix race condition due to global progress entries array
Since progress entries array is globally allocated, it is susceptible
to race conditions when using multi-threaded applications. Allocating it
on the stack resolves any potential races as it is thread local by default.

Signed-off-by: Aravind Gopalakrishnan <Aravind.Gopalakrishnan@intel.com>
(cherry picked from commit ed2343034d09b33eb44a0a727bef97a108edc8aa)
2018-08-28 14:23:56 -07:00
Edgar Gabriel
2e3cf6fb12 io/base: fixes to file_delete selection logic
file_delete triggers underneath the hood the full component selection
logic, since we do not have a file handle, just a file name.

As part of the selection logic, we have to however initiate the
framework-open of the fs component in case of ompio, since ompio
will call the delete function of the selected fs componentn, which
is based on the file system where the file is located.

This was not handled correctly so far. The problem however only
shows up if the first I/O operatin to be executed is a file_delete,
other wise the file_open will lead to the correct opening and initialization
of the fs framework. This commit ensures that we do the right thing
even if file_delete is the first file I/O operation in the application.

Fixes issue #5611

Signed-off-by: Edgar Gabriel <egabriel@central.uh.edu>
2018-08-28 08:18:59 -05:00
Edgar Gabriel
a489a6fc9d sharedfp/sm and lockedfile: fix naming bug
If an application opens a file for reading from multiple processes
using MPI_COMM_SELF (or another communicator that has distinct
process groups but the same comm-id, as can happen as the result
of comm_split), the naming chosen for the lockedfile or the mmapped
file used by the sharedfp/sm component would collide. This patch
ensures that the filename is different by integrating the process id
of rank 0 for each sub-communicator.

This fixes one aspect of the problem reported in github issue 5593

Signed-off-by: Edgar Gabriel <egabriel@central.uh.edu>
2018-08-27 14:11:03 -05:00
Howard Pritchard
37440aca90
Merge pull request #5497 from markalle/apply_romio314_patch_to_v40x
v4.0.x: apply romio314 patch to romio321
2018-08-25 11:12:08 -04:00
Howard Pritchard
b926c35df0
Merge pull request #5562 from edgargabriel/pr/file_open_sharedfp_ordering_v4.0x
common/ompio: fix an ordering problem during file_open
2018-08-21 22:17:45 -04:00
Howard Pritchard
4c8852c2c8
Merge pull request #5555 from karasevb/v4.0.x_pmix_fence_status
v4.0.x/pmix: added check for pmix fence status
2018-08-21 09:28:17 -06:00
Edgar Gabriel
2da601a350 common/ompio: fix an ordering problem during file_open
the sharedfp component has to be selected and opened before
we set the default file view during file_open. Otherwise
there is a sperious error message from the sharefp_file_seek
operation that is called during the file_set_view.

Fixes Issue #5560

Signed-off-by: Edgar Gabriel <egabriel@central.uh.edu>
2018-08-20 10:23:32 -05:00
Boris Karasev
8873d901e8 pmix: added check for pmix fence status
Signed-off-by: Boris Karasev <karasev.b@gmail.com>
(cherry picked from commit 57683366ca300fe353e91c52dc9aa0f657120d4d)

Conflicts:
	opal/mca/common/ucx/common_ucx.c
	opal/mca/common/ucx/common_ucx.h

Modified:
	ompi/mca/pml/ucx/pml_ucx.c
	oshmem/mca/spml/ucx/spml_ucx.c
2018-08-17 21:33:50 +06:00
Jeff Squyres
7f443a159a fortran/use TKR: remove excess declaration for PMPI_Type_extent
This declaration was accidentally left behind in 89da9651bb2fe.

Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
(cherry picked from commit 8a0b5454ae26acc4984129e20ac152ca8e2214e5)
2018-08-16 13:13:14 -07:00
Howard Pritchard
cdc315c1ac
Merge pull request #5523 from tkordenbrock/topic/v4.0.x/fix.PtlMEUnlink.in.use
v4.0.x: coll-portals4: retry PtlMEUnlink() if PTL_IN_USE
2018-08-13 14:19:10 -06:00
Howard Pritchard
7b6a2da71a
Merge pull request #5504 from rhc54/cmr40/ofi
MTL OFI: send/isend split into blocking/non-blocking paths
2018-08-13 14:18:05 -06:00
Todd Kordenbrock
36369f9133 coll-portals4: retry PtlMEUnlink() if PTL_IN_USE
In the cleanup phase, it is possible for PtlMEUnlink() to return
PTL_IN_USE if the NIC is not done with the ME.  This should not
be considered an error.  This commit adds a retry loop around
PtlMEUnlink().

In some cases, the return value of PtlMEUnlink() and PtlCTFree()
was not checked at all.  Check them with the same retry loop as
above.

Signed-off-by: Todd Kordenbrock <thkgcode@gmail.com>
(cherry picked from commit f3f2a826b40cc0d4a45a63614835162ec6eef78e)
2018-08-07 11:23:51 -05:00
Howard Pritchard
9a6f6e61f0
Merge pull request #5499 from nrspruit/ns_cancel_fix_4.0
MTL OFI: Fix Deadlock in fi_cancel given completion during cancel
2018-08-07 09:16:56 -06:00
Howard Pritchard
2386994c9d
Merge pull request #5495 from hoopoepg/topic/ucx-init-c99-v4.0
PML/SPML/UCX: init global objects using C99 style - v4.0
2018-08-04 16:03:56 -06:00
Spruit, Neil R
1fbbae1907 MTL OFI: send/isend split into blocking/non-blocking paths
-Updated blocking send to directly call functionality and
set completion events expected to 0 initally. This allows for optimization for
providers that support fi_tinject up to larger sizes. This also reduces
latency on running the OFI mtl with smaller sizes without requiring
calls to progress given fi_tinject is required to complete the messaging
before returning and will not create any events in the Completion Queue.

-Updated non-blocking send to directly call fi_tsend and avoid calling
fi_tinject as the functionality should not wait on completions. This
resolves a bug where applications calling MPI_Isend can overrun the
TX buffer with small (inject) messages causing a deadlock. In addition
this improves performance in message rates by preventing
waiting on any size message to complete in non-blocking send messages.

-Created common ompi_mtl_ofi_ssend_recv function to post the ssend recv
which is common between isend and send code paths.

Signed-off-by: Spruit, Neil R <neil.r.spruit@intel.com>
(cherry picked from commit 7dc8c8ba3fa630df8c5c7ab36fcf25249a82bfe7)
2018-08-01 06:45:48 -07:00
Ralph Castain
7830d9971e
Merge pull request #5467 from rhc54/cmr40/ofi
MTL OFI: MTL_OFI_RETRY_UNTIL_DONE support for Resource overflow
2018-07-31 13:08:03 -07:00
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
Spruit, Neil R
9cc6bc1ea6 MTL OFI: Fix Deadlock in fi_cancel given completion during cancel
- If a message for a recv that is being cancelled gets completed after
the call to fi_cancel, then the OFI mtl will enter a deadlock state
waiting for ofi_req->super.ompi_req->req_status._cancelled which will
never happen since the recv was successfully finished.

- To resolve this issue, the OFI mtl now checks ofi_req->req_started
to see if the request has been started within the loop waiting for the
event to be cancelled. If the request is being completed, then the loop
is broken and fi_cancel exits setting
ofi_req->super.ompi_req->req_status._cancelled = false;

Signed-off-by: Spruit, Neil R <neil.r.spruit@intel.com>
(cherry picked from commit 767135c580f75d3dde9cb9c88601dd18afda949a)
2018-07-30 07:17:40 -07:00
Sergey Oblomov
b64502977a PML/SPML/UCX: init global objects using C99 style
- to avoid value mix used C99 style of object initializations

Signed-off-by: Sergey Oblomov <sergeyo@mellanox.com>
(cherry picked from commit 2806504290ff2fdd10f254f878e92cae6e90c854)
2018-07-28 16:47:43 +03:00
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
Spruit, Neil R
ac8d2e01f9 MTL OFI: MTL_OFI_RETRY_UNTIL_DONE support for Resource overflow
- Added support in MTL_OFI_RETRY_UNTIL_DONE to handle -FI_EAGAIN
  from the provider and correctly attempt to progress the OFI Completion
  queue by calling ompi_mtl_ofi_progress.

- If events were pending that blocked OFI operations from being enqueued
  they will be completed and the OFI operation will be retried once
  ompi_mtl_ofi_progress has successfully completed.

- Updated MTL_OFI_RETRY_UNTIL_DONE to take a RETURN variable instead of
  requiring the existance of a "ret" variable to pass back the return
  value from completing the OFI operation.

Signed-off-by: Spruit, Neil R <neil.r.spruit@intel.com>
(cherry picked from commit d4f408a7f867b2f7bab84b9c966e1eba59f59e0e)
2018-07-23 11:14:42 -07:00
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
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
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
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
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
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