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Граф коммитов

8440 Коммитов

Автор SHA1 Сообщение Дата
Ralph Castain
b79cffc73b Protect ourselves - if the active pmix component doesn't have some optional functions, then gracefully decline to perform the operation OR use a required alternative (e.g., fence in place of disconnect)
This fixes the Slurm pmi2 support - still something wrong in pmi1
2015-09-09 02:29:00 -07:00
Gilles Gouaillardet
fe351f6801 io: do not cast way the const modifier when this is not necessary
update the io framework and mpi c bindings
2015-09-09 09:18:58 +09:00
Gilles Gouaillardet
e01bac962f coll: do not cast way the const modifier when this is not necessary
update the coll framework and mpi c bindings
2015-09-09 09:18:57 +09:00
Gilles Gouaillardet
6e6a3e965c pml: do not cast way the const modifier when this is not necessary
update the pml framework and mpi c bindings
2015-09-09 09:18:57 +09:00
Gilles Gouaillardet
43ef261d46 topo: do not cast way the const modifier when this is not necessary
update the topo framework and mpi c bindings
2015-09-09 09:18:57 +09:00
rhc54
3a446c9797 Merge pull request #876 from rhc54/topic/hnp
Fix segfault upon job error
2015-09-08 15:10:51 -07:00
Ralph Castain
459f169e06 Fix segfault upon job error
Silence some unnecessary error-logs
2015-09-08 14:03:06 -07:00
Ralph Castain
ae7156cabb Stop a segfault in the test by correctly passing all the argv during spawn 2015-09-08 13:42:46 -07:00
Jeff Squyres
bc9e5652ff whitespace: purge whitespace at end of lines
Generated by running "./contrib/whitespace-purge.sh".
2015-09-08 09:47:17 -07:00
Edgar Gabriel
c83e6ad0c8 fix coverty warnings 1322865 and 72136 2015-09-08 09:15:57 -05:00
Ralph Castain
e6add86e4f Deal with connect/accept between two jobs from different mpirun's. Somewhat optimize connect/accept by using MPI bcast to distribute the participants instead of another PMIx lookup. Cleanup some Coverity issues. 2015-09-07 09:19:24 -07:00
Gilles Gouaillardet
c404e98dce coll/ml: silence warnings (incorrect callback prototype) 2015-09-07 14:56:49 +09:00
Gilles Gouaillardet
56f8a7b840 coll/ml: declare a global variable as static to avoid an uninitialized common symbol. 2015-09-07 14:56:03 +09:00
Ralph Castain
37c3ed68e7 Cleanup connect/disconnect and bring comm_spawn back online! 2015-09-06 10:27:39 -07:00
Jeff Squyres
794ee4a604 treematch: remove stale test
This test was accidentally left over from
open-mpi/ompi@d97bc29102 that prevented
the treematch component from building.
2015-09-05 05:02:30 -07:00
rhc54
665b30376a Merge pull request #868 from rhc54/topic/hwloc
Remove OPAL_HAVE_HWLOC qualifier and error out if --without-hwloc is given
2015-09-04 17:58:07 -07:00
Ralph Castain
d97bc29102 Remove OPAL_HAVE_HWLOC qualifier and error out if --without-hwloc is given 2015-09-04 16:54:40 -07:00
rhc54
d45ccda813 Merge pull request #866 from rhc54/topic/updatepmix
Update PMIx support
2015-09-04 11:09:36 -07:00
Ralph Castain
f6948c2bb4 Sync with PMIx master 43e45c3. Get multi-node publish/lookup/unpublish working 2015-09-04 10:07:17 -07:00
Pavel Shamis / Pasha
c3446f363b Merge pull request #859 from shamisp/topic/ml_soft_disable
ML: Replace opal ignore with a zero priority
2015-09-04 12:37:37 -04:00
Pavel Shamis (Pasha)
32c69630ad ML: Replace opal ignore with a zero priority
The priority set by default to 0. As a result component open reports
an error and the component is not loaded (no resources allocated).
2015-09-04 11:28:47 -04:00
yohann
404393b9d7 mtl/ofi: Minor code cleanup. 2015-09-03 15:04:55 -07:00
yohann
a8cac09769 mtl/ofi: Renamed macro to prevent clash with FI_ namespace. 2015-09-03 14:42:45 -07:00
yohann
7adb9b7ab4 mtl/ofi: Handle -FI_EAGAIN on send and recv operations. 2015-09-03 10:47:00 -07:00
Edgar Gabriel
c9710660af Merge pull request #863 from edgargabriel/topic/fcoll-static-cleanup
Topic/fcoll static cleanup
2015-09-03 11:21:02 -05:00
Edgar Gabriel
a96a15a83c re-enable the contiguous buffer optimization similarly to the dynamic component. Passes all hdf5testsi and our own test suite.
Please enter the commit message for your changes. Lines starting
2015-09-03 10:13:03 -05:00
Edgar Gabriel
8007effc93 code cleanup for static component, similarly to the dynamic one 2015-09-03 10:12:45 -05:00
Jeff Squyres
6d9faf07e5 Merge pull request #858 from jsquyres/pr/fortran-use-only
fortran configiry: test for USE...ONLY support
2015-09-03 10:19:48 -04:00
Edgar Gabriel
ac3a01c39c Silence coverty warnings 1321702, 1321701, 1321700, 72331, 72330, 72327, 72326, 72325, 2015-09-03 09:10:25 -05:00
Jeff Squyres
66dda00f06 fortran configiry: test for USE...ONLY support
As of v15.7, the PGI Fortran compiler does not properly support how
Open MPI uses the "USE ... ONLY" Fortran syntax to include modules
with conflicting symbol definitions (interestingly, pgfortran only has
a problem with this when compiling with -g).

In short, OMPI uses "USE :: module_aaa, ONLY: foo" and "USE ::
module_bbb, ONLY: bar" to use modules aaa and bbb, even though they
contain conflicting definitions for some symbols.  However, the use of
the ONLY clause should preclude the inclusion of the conflicting
symbols -- as the word implies, it should direct the compiler to
*only* use the symbols identified by the clause (i.e., foo and bar, in
this example).

This commit adds a configure test for this capability.  If the
compiler fails to build a simple test that mimics this behavior, then
disable the mpi_f08 bindings.

Fixes open-mpi/ompi#857
2015-09-02 15:55:24 -07:00
Ralph Castain
a772b46c15 Bring the MPI_Publish and friends online 2015-09-02 12:04:07 -07:00
Edgar Gabriel
e95d01be97 Merge pull request #847 from edgargabriel/topic/fcoll-dynamic-cleanup
Topic/fcoll dynamic cleanup
2015-09-01 16:10:55 -05:00
Nathan Hjelm
2a8cc5e637 osc/pt2pt: remove outstanding lock only after lock/flush ack received
fixes #840

Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2015-09-01 10:54:47 -06:00
Edgar Gabriel
82efc23e8d iclean up indenting and tabs/space of fcoll_static_file_read/write_all 2015-09-01 09:39:33 -05:00
Edgar Gabriel
a1778406d6 Re-enable the contiguous buffer optimization to the read_all and the write_all routines.
After long debugging, I found last week the reason this optimization originally broke
some hdf5 tests. We now pass the hdf5 test suite with the optimization being actively used.
2015-09-01 09:29:07 -05:00
Edgar Gabriel
c2c44b11dc Code cleanup for dynamic read_all and write_all
Specifically:
 - reduce the number of realloc's and malloc's by moving
   some arrays out of the cycle loop, if we know that there
   size is not changing
 - store the rank of the aggregator in a separate variable to avoid
   continuous dereferencing
 - change the wait_all logic in write_all to use a fix number of requests
   (even if they are MPI_REQUEST_NULL)
 - fix the timing to considere the two initial allgather and the one
   allgatherv operation to be a part of it
 - add more comments.
2015-09-01 09:29:07 -05:00
Edgar Gabriel
cf1e4e0d35 step 0: clean up indenting and space vs. tabs 2015-09-01 09:29:07 -05:00
Jeff Squyres
596557e61b Fortran: update a comment
Split the list of subroutines into cases #1 and #2, just for clarity.
2015-08-31 03:10:09 -07:00
Gilles Gouaillardet
21642a2407 osc: do not cast way the const modifier when this is not necessary
update the osc framework and mpi c bindings
2015-08-31 10:34:05 +09:00
Gilles Gouaillardet
21b1e7f8c5 mpi conformance: fix prototypes
- MPI_Compare_and_swap
- MPI_Fetch_and_op
- MPI_Raccumulate
- MPI_Win_detach

Thanks to Michael Knobloch and Takahiro Kawashima for bringing this
to our attention
2015-08-31 10:34:05 +09:00
Ralph Castain
0d5814b5ca Cleanup Coverity issues 2015-08-29 21:19:27 -07:00
Ralph Castain
cf6137b530 Integrate PMIx 1.0 with OMPI.
Bring Slurm PMI-1 component online
Bring the s2 component online

Little cleanup - let the various PMIx modules set the process name during init, and then just raise it up to the ORTE level. Required as the different PMI environments all pass the jobid in different ways.

Bring the OMPI pubsub/pmi component online

Get comm_spawn working again

Ensure we always provide a cpuset, even if it is NULL

pmix/cray: adjust cray pmix component for pmix

Make changes so cray pmix can work within the integrated
ompi/pmix framework.

Bring singletons back online. Implement the comm_spawn operation using pmix - not tested yet

Cleanup comm_spawn - procs now starting, error in connect_accept

Complete integration
2015-08-29 16:04:10 -07:00
Jeff Squyres
d17497b4af Merge pull request #835 from Zhiming-Wang/master
Correct the wrong "Name Binding" of functions
2015-08-28 06:38:10 -04:00
Zhi Ming Wang
c8d4751ae6 Correct the wrong "Name Binding" of functions 2015-08-28 03:28:09 -04:00
Jeff Squyres
556c32e1d1 ompi_mpi_abort.c: use _exit(), not exit()
In an abort situation, just bail out immediately -- don't try to
invoke any atexit()/on_exit()-registered functions.

This is similar rationale to
open-mpi/ompi@17846411c3.
2015-08-27 17:08:25 -07:00
Edgar Gabriel
f214ccf499 fix the merge algorithm in the individual sharedfp component, which could
lead to file inconsistency in case of identical timestamps
Also fixes a potential buffer size problem.
2015-08-26 11:22:54 -05:00
Edgar Gabriel
423114e168 minor formatting fix. 2015-08-26 11:20:46 -05:00
Nathan Hjelm
f451876058 Merge pull request #825 from hjelmn/white_space_purge
periodic trailing whitespace purge
2015-08-25 19:23:52 -06:00
Jeff Squyres
1fdc5a5e57 Merge pull request #832 from jsquyres/pr/fortran-sizeof-fix
fortran sizeof fixes
2015-08-25 10:57:53 -04:00
Todd Kordenbrock
25c48b96bb Merge pull request #819 from tkordenbrock/allow-atomics-upto-max_fetch_atomic_size
osc-portals4: allow atomic ops on datatypes that are max_fetch_atomic_size bytes in length
2015-08-25 09:25:27 -05:00
Edgar Gabriel
70078175ee fix coverty warning 72107 2015-08-25 09:23:37 -05:00
Edgar Gabriel
a73f9470e0 fix coverty warning 1269829 2015-08-25 09:22:48 -05:00
Jeff Squyres
2cfdeff38d Fortran: these lines should not be commented out 2015-08-25 07:13:52 -07:00
Jeff Squyres
42a761e052 Fortran: remove dead Makefile.am code 2015-08-25 07:13:34 -07:00
Edgar Gabriel
6f2e8d2073 last nights coverty fix introduced a new coverty complain. This commit tries to fix the new complain by coverty. 2015-08-25 08:46:38 -05:00
Edgar Gabriel
db2d37ad93 correctly free some arrays in case of an error. This fixes a whole bunch of coverty warnings. 2015-08-24 14:13:37 -05:00
Nathan Hjelm
156ce6af21 periodic whitespace purge
Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2015-08-24 09:32:33 -06:00
Edgar Gabriel
58bd0c76b8 fix coverty warning CID 1317091 (properly freeing variables in case of an error) 2015-08-24 08:40:10 -05:00
Howard Pritchard
eb25c006eb Merge pull request #822 from nrgraham23/java_garbage_collection_bugfix
Java garbage collection bugfix
2015-08-22 14:58:01 -06:00
Jeff Squyres
0f3a3e52ba gen-mpi-sizeof: minor style change
Suggested by Paul Hargrove.
2015-08-22 03:07:44 -07:00
Jeff Squyres
9f345bd22f fortran: moar fixes for the Fortran MPI_SIZEOF debacle
Ensure to define ompi/pompi versions for platforms that don't have
weak symbols.  Also make fortran/mpif-h/profile build a separate
sizeof library, just like fortran/mpifh-h does.
2015-08-21 14:35:18 -07:00
Jeff Squyres
ede9fc17b0 gen-mpi-sizeof.pl: don't generate sub for headers
We only need the dummy subroutine when we're generating the body of a
file -- not when we're generating headers.
2015-08-20 14:24:45 -07:00
Jeff Squyres
edf485716e gen-mpi-sizeof.pl: restore execute permission
Somehow the "x" bit got reset in the last commit.
2015-08-20 13:31:02 -07:00
--quiet
d5763a8288 fortran sizeof: ensure mpi_sizeof*f90 is not empty
Per http://www.open-mpi.org/community/lists/devel/2015/08/17775.php,
some compilers don't like it when there's a .f90 file that only
contains comments (and no actual Fortran code).  So if OMPI determines
that the Fortran compiler does not support enough Fortran mojo to
support MPI_SIZEOF, generate at least one dummy Fortran subroutine
that can be compiled in an otherwise barren Fortran landscape that is
devoid of life and hope.
2015-08-20 13:01:14 -07:00
Nathaniel Graham
97422de7a8 Code cleanup
Removing the ArrayList import which is no longer needed.
2015-08-20 12:47:01 -06:00
--quiet
1e9227765a ofi mtl: also link in mtl_ofi_LIBS in the static case 2015-08-20 10:40:46 -07:00
Edgar Gabriel
4be20b119f bring the addproc component up to date with the fileview changes 2015-08-20 09:30:58 -05:00
Edgar Gabriel
8b84da5e35 bring the lockedfile component up to date with the fileview changes. 2015-08-20 09:26:30 -05:00
Nathaniel Graham
d363b5d832 Java garbage collection bugfix
This pull request adds an arraylist of type Buffer to
the Request class.  Whenever a request object is created
that has associated buffers, the buffers should be added
to this array list so the java garbage collector does
not dispose of the buffers prematurely.

This is a more robust expansion on the idea first proposed by
@ggouaillardet

Fixes #369

Signed-off-by: Nathaniel Graham <ngraham@lanl.gov>
2015-08-19 17:45:26 -06:00
Edgar Gabriel
b0461f8d3c the back pointer from the ompio_file structure to the ompi_file_t structure
has to be set earlier in case the user disables the lazy_open option.
2015-08-19 17:11:42 -05:00
Edgar Gabriel
096fe78d73 the offset provided to the read_at/write_at routines has to be a multiple of the etype. 2015-08-19 17:11:42 -05:00
Edgar Gabriel
7e370948c1 first cut on the fileview for shared filepointers fix. 2015-08-19 17:11:42 -05:00
yohann
bcc10fbcd4 mtl/ofi: remove redundant code. 2015-08-19 13:13:59 -07:00
Yossi Itigin
f9e2ede47f Merge pull request #816 from yosefe/topic/yalla-fix-on-demand-map
yalla: fix passing on-demand mapping config to mxm.
2015-08-19 17:25:30 +03:00
Jeff Squyres
699ab67598 Merge pull request #719 from ggouaillardet/poc/c_fortran_alignment
fortran: (try to) align C objects used by Fortran
2015-08-19 08:55:10 -04:00
Gilles Gouaillardet
646b9943e8 topo/treematch: initialize the global_bl symbol 2015-08-19 10:39:17 +09:00
Edgar Gabriel
1b45712595 bring the addproc component up to date with support for split collectives. No pr required
for this commit, since the addproc component is not part of v2.x
2015-08-18 12:17:46 -05:00
Todd Kordenbrock
10cf64373a osc-portals4: allow atomic ops on datatypes that are max_fetch_atomic_size bytes in length
Portals4 supports atomic ops on datatypes less than or equal to
max_fetch_atomic_size bytes.  This commit fixes a bug that required
the datatype to be less than max_fetch_atomic_size bytes.
2015-08-18 11:51:16 -05:00
Nathan Hjelm
145bac088d Merge pull request #753 from hjelmn/verbose_standard
Standardize verbosity levels
2015-08-18 09:43:28 -06:00
yosefe
85580ad055 yalla: fix passing on-demand mapping config to mxm. 2015-08-18 15:00:59 +03:00
Gilles Gouaillardet
99730f798b fortran: (try to) align C objects used by Fortran
Fortran uses objects (ompi_f08_mpi_comm_world, mpi_fortran_bottom,, ...) that are defined in C.
Some compilers have different requirements on how these objects should be aligned.
Smaller alignment in C can lead to several confusing warnings from the linker, so try to
find the alignment expected by Fortran compiler, and inform the C compiler.
2015-08-18 14:01:20 +09:00
Edgar Gabriel
5ef0632f9d cleanup the usage of printf vs. opal_output 2015-08-17 14:55:12 -05:00
Nathan Hjelm
2f447b2c4c bml/r2: use the bml framework output and set verbosity level to info
Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2015-08-17 11:48:06 -06:00
Jeff Squyres
e57861b0a5 fortran: only have one _LIBADD
Accidentally added a 2nd _LIBADD in a prior commit.  This commit
merges them back into a single _LIBADD.
2015-08-17 06:52:54 -07:00
Nathan Hjelm
dbfd6e6e5e Merge pull request #807 from hjelmn/win_update
Window updates
2015-08-15 12:33:40 -06:00
Jeff Squyres
a7f897ae49 fortran: link the opal-pal.la library directly
The libmpi_*.la fortran libraries make some direct calls to
libopen-pal.la.  In many (most?) cases, having libmpi_* link
against libmpi is sufficient (because libmpi pulls in libopen-pal).
But when building RPMs on SLES, some compiler/linker flags are used
that seem to make this implicit linking not sufficient -- we get
missing opal symbols when creating libmpi_mpifh.la.  So link in
open-pal directly (vs. indirectly), which solves the problem.
2015-08-15 06:46:01 -07:00
yohann
98b300e1bb mtl/ofi: Require proper ordering by OFI provider. 2015-08-14 16:36:10 -07:00
Rolf vandeVaart
652a685e78 Merge pull request #811 from rolfv/pr/fix-cuda-ext-again
Fix macro return value when not CUDA-aware
2015-08-14 14:40:45 -04:00
Rolf vandeVaart
0e87478e40 Fix macro return value when not CUDA-aware 2015-08-14 13:56:25 -04:00
Edgar Gabriel
022a9d8d89 Merge pull request #810 from edgargabriel/pr/coll_timing_cleanup
Code cleanup for the time breakdown feature in ompio/fcoll
2015-08-14 10:05:12 -05:00
Jeff Squyres
42b9a966d6 Makefile.am's: if calling OPAL functions, must link to it
On some OSs (e.g., Ubuntu 14.04.2 LTS), the linker is configured such
that the symbols of library dependencies are not available to the
application.  Hence, we need to explicitly list such dependencies when
creating the executable.

For this commit, these tests are use OPAL function calls, so we must
explicitly link in libopen-pal.so.
2015-08-14 07:51:55 -07:00
Edgar Gabriel
072b18e197 Code cleanup for the time breakdown feature in ompio/fcoll
- make the internal structure follow the Open MPI naming convention
 - provide a single flag/macro which controls the compilation/utilization of this
   feature, to avoid that somebody using this has to modify every single
   fcoll component. A configure option could be added later if desired.
2015-08-14 08:53:04 -05:00
Edgar Gabriel
4bfc6ae798 Performance tuning: incorporate the usage of non-blocking operations in our array group-communication operations. 2015-08-13 20:05:18 -05:00
Gilles Gouaillardet
6118236f1a Merge pull request #796 from ggouaillardet/topic/hcoll_config
configury: fix hcoll, fca and mxm detection and revamp yalla Makefile.am
Thanks to David Shrader and Ake Sandgren for bringing this issue to our attention
2015-08-14 08:55:46 +09:00
Edgar Gabriel
9f369ba515 move the inclusion of the lustre_user and lliblustreapi header files to the fs_lustre.h file. 2015-08-13 15:36:16 -05:00
Nathan Hjelm
b8356dae05 ompi/win: add internal support for returning same_size and same_disp_unit info keys
Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2015-08-13 13:19:52 -06:00
Nathan Hjelm
b933eda36b ompi: add internal error code for MPI_ERR_RMA_FLAVOR
Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2015-08-13 13:18:29 -06:00
Gilles Gouaillardet
6b2fe9120e yalla: fix Makefile.am LDFLAGS 2015-08-13 17:33:52 +09:00
Gilles Gouaillardet
1a238d3a4f configury: fix fca detection
* do not add -I/.../include/fca -I /.../include/fca_core to CPPFLAGS
 * allow configure --with-fca
 * search fca libs in both DIR/lib and DIR/lib64
 * fix the description of the --with-fca option
2015-08-13 11:09:15 +09:00
Gilles Gouaillardet
df98a73131 configury: fix hcoll detection
* do not add -I/.../include/hcoll -I /.../include/hcoll/api to CPPFLAGS
 * allow configure --with-hcoll
 * search hcoll libs in both DIR/lib and DIR/lib64
 * fix the description of the --with-hcoll option
2015-08-13 11:08:56 +09:00