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Граф коммитов

1400 Коммитов

Автор SHA1 Сообщение Дата
KAWASHIMA Takahiro
5e12e0f2e5
Merge pull request #5001 from ggouaillardet/topic/javah
configury: use javac vs javah whenever possible.
2018-04-06 11:30:20 +09:00
Jeff Squyres
fc8ebbb0e0 MPI_Comm_spawn_multiple.3in: update Fortran string array notes
Per 0ab6b201fe, note in the MPI_Comm_spawn_multiple.3in man page that
the array_of_commands does not need to be terminated -- it just need
to have exactly "count" entries.  In the Fortran binding, at least,
this is different than in prior released versions of Open MPI (it's
not a backwards incompatibility, since prior versions of Open MPI
required array_of_commands to be blank-string-terminated in Fortran --
this change makes Open MPI be *less* restrictive, and therefore still
backwards compatible).

Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
2018-04-05 06:52:46 -07:00
Jeff Squyres
0ab6b201fe mpi/fortran: fix parsing arrays of Fortran strings
MPI defines the "argv" param to Fortran MPI_COMM_SPAWN as being
terminated by a blank string.  While not precisely defined (except
through a non-binding example, Example 10.2, MPI-3.1 p382:6-29), one
can infer that the "array_of_argv" param to Fortran
MPI_COMM_SPAWN_MULTIPLE is also a set of argv, each of which are
terminated by a blank line.

The "array_of_commands" argument to Fortran MPI_COMM_SPAWN_MULTIPLE is
a little less well-defined.  It is *assumed* to be of length "count"
(another parameter to MPI_COMM_SPAWN_MULTIPLE) -- and *not* be
terminated by a blank string.  This is also given credence by the same
example 10.2 in MPI-3.1.

The previous code assumed that "array_of_commands" should also be
terminated by a blank line -- but per the above, this is incorrect.
Instead, we should just parse our "count" number of strings from
"array_of_commands" and *not* look for a blank line termination.

This commit separates these two cases:

* ompi_fortran_argv_blank_f2c(): parse a Fortran array of strings out
  and stop when reaching a blank string.
* ompi_fortran_argv_count_f2c(): parse a Fortran array of strings out
  and stop when "count" number of strings have been parsed.

Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
2018-04-04 18:56:44 -07:00
Gilles Gouaillardet
5370586d98 configury: use javac vs javah whenever possible
javah is no more available from Java 10, so try
javac -h first (available since Java 8) and fallback on javah

Refs. open-mpi/ompi#5000

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-04-05 10:37:35 +09:00
Gilles Gouaillardet
132ea1a6b0 java: cleanup the list of automatically generated header files
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-04-05 09:27:34 +09:00
Jeff Squyres
dca66b9775 comm_join: fix CID 1323170
Enusre that the port name is always NULL-terminated.

Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
2018-03-26 14:21:21 -07:00
Nathan Hjelm
1c75aa82fc use-mpi-f08: fix rma function signatures
The various RMA functions need to have the asynchronous property on
all buffers. This property was missing and some buffers were
incorrectly marked as intent(in). This commit fixes the function
signatures.

Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2018-03-26 15:11:07 -06:00
Jeff Squyres
c3adcb05eb Miscellaneous compiler warnings fixes
Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
2018-03-23 11:45:30 -07:00
bosilca
bf3dd8af19
Merge pull request #4884 from bosilca/topic/fix_wtime
Improve the range and accuracy of MPI_Wtime.
2018-03-16 14:09:33 +09:00
Benoît Legat
00600c7cbb Fix typo in MPI_Cart_shift doc
Signed-off-by: Benoît Legat <benoit.legat@gmail.com>
2018-03-13 15:25:42 +01:00
George Bosilca
9bced03213
Improve the range and accuracy of MPI_Wtime.
As discussed on https://github.com/mpi-forum/mpi-issues/issues/77#issuecomment-369663119
the conversion to double in the MPI_Wtime decrease the range
and accuracy of the resulting timer. By setting the timer to
0 at the first usage we basically maintain the accuracy for
194 days even for gettimeofday.

Signed-off-by: George Bosilca <bosilca@icl.utk.edu>
2018-03-08 14:26:02 +09:00
Nathan Hjelm
5ed2fc2d48 mca/base: add support for additional variable types
This commit adds long, int32_t, uint32_t, int64_t, and uint64_t as
possible MCA variable types.

Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2018-03-01 20:42:27 -07:00
Gilles Gouaillardet
cb5dfbe5b1 man: fix indentation of MPI_Comm_spawn[_multiple]
no code change.

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-01-15 11:29:15 +09:00
Jeff Squyres
1c5664fdec
Merge pull request #4681 from nathanweeks/issue/f08_mpi_errcodes_ignore
Fix type of mpi_f08 MPI_ERRCODES_IGNORE
2018-01-10 12:34:16 -05:00
Gilles Gouaillardet
02f8215b25 ompi: enhance MPI_File_set_view datatype check.
Per MPI 3.1 chapter 13.3 :
"Derived etypes can be constructed by using any of the MPI
datatype constructor routines, provided all resulting typemap
displacements are non-negative and monotonically nondecreasing."
Same restriction applies to ftypes.

add the OMPI_DATATYPE_CHECK_FOR_VIEW() macro that is
check the underlying opal_datatype_t is monotonic, on top
of all checks performed in OMPI_DATATYPE_CHECK_FOR_RECV().

Since checking monotoniciy is expensive, check is only performed
when needed, but the result is cached by ompi_datatype_is_monotonic().

Thanks Wei-keng Liao for the valuable feedback.
Thanks George for the guidance.

Refs. open-mpi/ompi#4682

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2018-01-09 18:05:15 +09:00
Nathan T. Weeks
3158d2c5ed Fix type of mpi_f08 MPI_ERRCODES_IGNORE
Signed-off-by: Nathan T. Weeks <weeks@iastate.edu>
2018-01-07 05:36:41 -08:00
KAWASHIMA Takahiro
710080be63
Merge pull request #4667 from kawashima-fj/pr/f08-pmpi
fortran: Fix PMPI interface bugs in mpi_f08 module
2018-01-05 03:45:10 -06:00
KAWASHIMA Takahiro
bd2fe9c324 fortran: Call PMPI from PMPI_Status_set_cancelled_f08
This is a bug which was forgotten to change in c08f97b030.

Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>
2017-12-26 15:53:12 +09:00
KAWASHIMA Takahiro
00e3c7a973 fortran: Align indentation
This change makes comparison of `mpi-f08-interfaces.F90` and
`pmpi-f08-interfaces.F90` easier.

Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>
2017-12-26 14:39:09 +09:00
KAWASHIMA Takahiro
056eb39b12 fortran: Correct type of info_used
It is incorrectly typed as `MPI_Comm` in only `pmpi` in 24f7bd327e.

Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>
2017-12-26 14:39:09 +09:00
KAWASHIMA Takahiro
0c3a534b32 fortran: Use C_PTR for buffer_addr
It was changed to use `C_PTR` in only `mpi` in fc69c0be24.

Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>
2017-12-26 14:39:09 +09:00
KAWASHIMA Takahiro
d4fc404dc6 fortran: Change PMPI_Aint_{add,diff} to functions.
They were incorrectly changed to subroutines in only `pmpi`
in 258d1aa160.

Strictly speaking, this change involves binary incompatibility.
But nobody used these subroutines and nobody will be affected because
these subroutines were useless (didn't return a calculated value).

Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>
2017-12-26 14:39:09 +09:00
KAWASHIMA Takahiro
9240967b8f fortran: Remove ASYNCHRONOUS from mpi_f08 pmpi
It was removed from only `mpi` as a bug fix in db41d749c1.

Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>
2017-12-26 14:39:09 +09:00
Tsubasa Yanagibashi
3f4b373856 Add missing Fortran 2008 binding subroutines
added missing Fortran 2008 binding pmpi_{*} subroutines to Open MPI.

Signed-off-by: Tsubasa Yanagibashi <fj2505dt@aa.jp.fujitsu.com>
2017-12-22 13:45:53 +09:00
Jed Brown
533800070e MPI_Attr_get: doc fix: MPI_Comm_create_attr -> MPI_Comm_get_attr
MPI_Comm_create_attr does not exist.

Signed-off-by: Jed Brown <jed@jedbrown.org>
2017-12-17 07:44:22 -07:00
Gilles Gouaillardet
794cc09d3e mpiext: fix path to Fortran 2008 modules
OMPI_FORTRAN_USEMPIF08_MOD macro was removed in open-mpi/ompi@791bcee6c0
so this macro is now manually expanded to mpi/fortran/use-mpi-f08/mod

Thanks to Nathan T. Weeks for reporting

Refs open-mpi/ompi#3605

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-12-11 11:02:43 +09:00
Gilles Gouaillardet
b8e77ba759 mpi/c: use OPAL_THREAD[UN]LOCK() instead of opal_mutex_[un]lock()
in order to keep consistency between ompi_communicator_t, ompi_file_t
and ompi_win_t.

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-12-01 16:06:32 +09:00
Gilles Gouaillardet
5f1a967351 ompi/file: rename ompi_file_t's f_mutex into f_lock
in order to use a consistent name between ompi_file_t,
ompi_win_t and ompi_communicator_t

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-12-01 16:06:22 +09:00
Gilles Gouaillardet
f1778d2778 communicator: remove the USE_MUTEX_FOR_COMMS macro
It should have always been #define'd in order to correctly handle the
multi-threaded case.

Also fix indentation in ompi/mpi/c/comm_get_errhandler.c

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-11-30 14:29:11 +09:00
Gilles Gouaillardet
7c3e675479 fix communicator's c_lock usage
- initialize c_lock in the ompi_communicator_t constructor
 - USE_OPAL_THREAD_[UN]LOCK(c_lock)
 - #ifdef USE_MUTEX_FOR_COMMS protect c_lock access

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-11-30 14:27:59 +09:00
Nathan Hjelm
6b68d1cfc8 ompi/errhandler: make set/get actually thread safe
The current versions of these functions have a fatal flaw. If a
errhandler set and free call is made by another thread while the
thread calling get is between the cmpset and retain then we will
retain an invalid object. Fixing this by just using locking. This is
not a critical path so this should be ok.

Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2017-11-27 15:14:17 -07:00
Nathan Hjelm
3ff34af355 opal: rename opal_atomic_cmpset* to opal_atomic_bool_cmpset*
This commit renames the atomic compare-and-swap functions to indicate
the return value. This is in preperation for adding support for a
compare-and-swap that returns the old value. At the same time the
return type has been changed to bool.

Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2017-10-31 12:47:23 -06:00
George Bosilca
bdbea63a1c
Update the MPI standard reference.
Signed-off-by: George Bosilca <bosilca@icl.utk.edu>
2017-10-03 16:48:50 -04:00
Gilles Gouaillardet
b9315edb85 configury: remove the --disable-mpi-io option
Fixes open-mpi/ompi#2185

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-09-20 14:39:09 +09:00
Gilles Gouaillardet
ecb6b81a05 mpi: correctly handle MPI_IN_PLACE by memchecker in neighborhood collectives
MPI_IN_PLACE is not a valid send buffer for neighborhood collectives, so do not
invoke memchecker in this case.

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-09-04 11:21:32 +09:00
Gilles Gouaillardet
66c9485e77 MPI_Isend: memchecker do not mark send buffer as unaccessible after pml isend invokation
Today's MPI standard mandates the send buffer remains accessible during the send operation.

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-09-04 11:21:32 +09:00
Gilles Gouaillardet
6ee9366243 MPI_Wait: correctly handle MPI_STATUS_IGNORE in MEMCHECKER
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-09-04 11:18:05 +09:00
Joshua Hursey
49c40f05d4 mpi/java: Remove dlopen() workaround
* See discussion on Issue #3705 regarding why this is no longer needed.

Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
2017-08-24 11:56:17 -04:00
Jeff Squyres
ea5093fc14 mpi/info_delete: fix return code
Per MPI-3.1, ensure to raise an MPI exception with value
MPI_ERR_INFO_NOKEY if we try to MPI_INFO_DELETE a key that does not
exist.  Thanks to @dalcinl (Lisando Dalcin) for raising the issue.

Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
2017-08-22 08:56:40 -07:00
Jeff Squyres
791bcee6c0 ompi/fortran: remove proof-of-concept mpi_f08 module
This module was always intended to be a proof of concept, and was far
from complete.  If/when someone implemented F08 descriptor support for
the mpi_f08 module, this commit can either be restored or used as
reference material.

Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
2017-08-10 06:19:17 -07:00
Gilles Gouaillardet
dfe7b2be3f fortran/use-mpi-f08-desc: add a missing include file
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-08-09 13:19:22 +09:00
Gilles Gouaillardet
2c71c27882 fortran2008: fix mpiext example
in order to solve an egg and the chicken problem,  in which mpiext need mpi-f08-types.mod
and/but use-mpi-f08[-desc] needs mpiext, add an extra step
- build fortran 2008 modules only
- build fortran 2008 mpi extensions
- and then build fortran 2008 bindings

Fixes open-mpi/ompi#3605

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-08-09 13:19:22 +09:00
KAWASHIMA Takahiro
3eac4b0c9a communicator: Refine ompi_comm_set error check
The `ompi_comm_set` function never sets `NULL` to its first argument
`ncomm`.  So `NULL` check is unnecessary in its callers. Furthermore,
`NULL` check may obscure a real return code when an error occurs
if the variable is initialized to a `NULL` value.

Also, `NULL` check is added in the `ompi_comm_set` function to
avoid segmentation fault in an out-of-memory condition.

Signed-off-by: KAWASHIMA Takahiro <t-kawashima@jp.fujitsu.com>
2017-07-31 20:26:51 +09:00
KAWASHIMA Takahiro
ebc4eb347c Merge pull request #3701 from kawashima-fj/pr/non-pml-persistent
ompi/request: Support non-PML persistent requests
2017-07-31 02:36:17 -05:00
Nathan Hjelm
9b702fb9bd ompi: clean up topo helper functions
This commit removes the communicator topo helper functions in favor
of functions in mca/topo/base.

Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2017-07-17 10:30:42 -05:00
Jeff Squyres
ccf17808b6 Merge pull request #3258 from markalle/pr/symbol_name_pollution
symbol name pollution
2017-07-12 16:19:25 -05:00
Nathan Hjelm
3c0e94afab mpi/neighbor_allgatherv: fix copy&paste error and add helpers
This commit adds a helper function to get the inbound and outbound
neighbor count and updates the neighbor_allgatherv bindings to use the
correct count when checking the input parameters.

Fixes #2324

Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
2017-07-12 12:54:24 -06:00
Gilles Gouaillardet
72cfbb665c ompi/attributes: revamp attribute handling.
we now have 12 cases to deal (4 writers and 3 readers) :

1. C `void*` is written into the attribute value, and the value is read into a C `void*` (unity)
2. C `void*` is written, Fortran `INTEGER` is read
3. C `void*` is written, Fortran `INTEGER(KIND=MPI_ADDRESS_KIND)` is read
4. Fortran `INTEGER` is written, C `void*` is read
5. Fortran `INTEGER` is written, Fortran `INTEGER` is read (unity)
6. Fortran `INTEGER` is written, Fortran `INTEGER(KIND=MPI_ADDRESS_KIND)` is read
7. Fortran `INTEGER(KIND=MPI_ADDRESS_KIND)` is written, C `void*` is read
8. Fortran `INTEGER(KIND=MPI_ADDRESS_KIND)` is written, Fortran `INTEGER` is read
9. Fortran `INTEGER(KIND=MPI_ADDRESS_KIND)` is written, Fortran `INTEGER(KIND=MPI_ADDRESS_KIND)` is read (unity)
10. Intrinsic is written, C `void*` is read
11. Intrinsic is written, Fortran `INTEGER` is read
12. Intrinsic is written, Fortran `INTEGER(KIND=MPI_ADDRESS_KIND)` is read

MPI-2 Fortran "integer representation" has type `INTEGER(KIND=MPI_ADDRESS_KIND)` as clarified
at https://github.com/mpiwg-rma/rma-issues/issues/1

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2017-07-12 10:27:45 +09:00
Joshua Hursey
c81795cbda Revert "Fix MPI_SIZEOF for gfortran 4.8"
This reverts commit 5de3d5dde6.

 Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
2017-07-11 11:09:17 -05:00
Mark Allen
552216f9ba scripted symbol name change (ompi_ prefix)
Passed the below set of symbols into a script that added ompi_ to them all.

Note that if processing a symbol named "foo" the script turns
    foo  into  ompi_foo
but doesn't turn
    foobar  into  ompi_foobar

But beyond that the script is blind to C syntax, so it hits strings and
comments etc as well as vars/functions.

    coll_base_comm_get_reqs
    comm_allgather_pml
    comm_allreduce_pml
    comm_bcast_pml
    fcoll_base_coll_allgather_array
    fcoll_base_coll_allgatherv_array
    fcoll_base_coll_bcast_array
    fcoll_base_coll_gather_array
    fcoll_base_coll_gatherv_array
    fcoll_base_coll_scatterv_array
    fcoll_base_sort_iovec
    mpit_big_lock
    mpit_init_count
    mpit_lock
    mpit_unlock
    netpatterns_base_err
    netpatterns_base_verbose
    netpatterns_cleanup_narray_knomial_tree
    netpatterns_cleanup_recursive_doubling_tree_node
    netpatterns_cleanup_recursive_knomial_allgather_tree_node
    netpatterns_cleanup_recursive_knomial_tree_node
    netpatterns_init
    netpatterns_register_mca_params
    netpatterns_setup_multinomial_tree
    netpatterns_setup_narray_knomial_tree
    netpatterns_setup_narray_tree
    netpatterns_setup_narray_tree_contigous_ranks
    netpatterns_setup_recursive_doubling_n_tree_node
    netpatterns_setup_recursive_doubling_tree_node
    netpatterns_setup_recursive_knomial_allgather_tree_node
    netpatterns_setup_recursive_knomial_tree_node
    pml_v_output_close
    pml_v_output_open
    intercept_extra_state_t
    odls_base_default_wait_local_proc
    _event_debug_mode_on
    _evthread_cond_fns
    _evthread_id_fn
    _evthread_lock_debugging_enabled
    _evthread_lock_fns
    cmd_line_option_t
    cmd_line_param_t
    crs_base_self_checkpoint_fn
    crs_base_self_continue_fn
    crs_base_self_restart_fn
    event_enable_debug_output
    event_global_current_base_
    event_module_include
    eventops
    sync_wait_mt
    trigger_user_inc_callback
    var_type_names
    var_type_sizes

Signed-off-by: Mark Allen <markalle@us.ibm.com>
2017-07-11 02:13:23 -04:00