ports/openmpi
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Gilles Gouaillardet
d3a5065288 Merge pull request #2815 from ggouaillardet/topic/opal_tsd_keys_destruct 
opal/threads: protect opal_tsd_keys_destruct() to fix Java bindings.
 2017-01-26 09:24:14 +09:00
Nysal Jan K.A
94f92f6b49 osc/base: Detect unsupported data types and abort 
Using MPI_MINLOC or MPI_MAXLOC with the following data types
leads to data corruption:
 * MPI_DOUBLE_INT
 * MPI_LONG_INT
 * MPI_SHORT_INT
 * MPI_LONG_DOUBLE_INT

Detect this print a error message and abort.
This workaround should be removed once the following issue is resolved:
 * https://github.com/open-mpi/ompi/issues/1666

Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-25 15:28:28 -06:00
Sameh S. Sharkawi
320ab3b84f pml/base: Expose some bsend varaibles so PMLs may reference them 
Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-25 15:21:53 -06:00
Ralph Castain
a7b8190fdc Per f2f meeting: if async modex is given, default to no MPI init barrier, letting the user override that if desired. 
Signed-off-by: Ralph Castain <rhc@open-mpi.org>
 2017-01-25 10:13:53 -08:00
Ralph Castain
2f4e87eae9 Have rank=1 daemon always send its topology back as this is the most common use-case 
Signed-off-by: Ralph Castain <rhc@open-mpi.org>
 2017-01-25 09:33:11 -08:00
Jeff Squyres
230bbc597d plm base: make sure to assign "node" early enough 
Make sure to assign "node" before using it in ORTE_FLAG_SET.

Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
 2017-01-25 08:02:59 -08:00
Ralph Castain
e7323fdd93 Merge pull request #2823 from rhc54/topic/oob4 
Cleanup some code so it is clear that it is executing in an event. En…
 2017-01-25 07:48:31 -08:00
Ralph Castain
184ccc8e91 Cleanup some code so it is clear that it is executing in an event. Ensure that peer event base is properly set on incoming connections 
Signed-off-by: Ralph Castain <rhc@open-mpi.org>
 2017-01-25 06:55:11 -08:00
Edgar Gabriel
4e06b96701 Merge pull request #2800 from edgargabriel/pr/sharedfp-append-fix 
Pr/sharedfp append fix
 2017-01-25 08:01:04 -06:00
Gilles Gouaillardet
142b95df87 pmix/ext2x: plug misc memory leaks regarding opal_pmix2x_event_chain_t handling 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-25 16:17:10 +09:00
Gilles Gouaillardet
7a3d39f079 pmix/ext2x: plug a memory leak in _reg_nspace() 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-25 16:17:01 +09:00
Gilles Gouaillardet
ef10d3fd7b orte: add missing include file 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-25 16:15:20 +09:00
Ralph Castain
186059cc00 Merge pull request #2803 from rhc54/topic/host 
Revamp -host and -cpu-list options per f2f meeting
 2017-01-24 18:37:24 -08:00
Gilles Gouaillardet
e1811cfe17 opal/threads: protect opal_tsd_keys_destruct() to fix Java bindings. 
When Java bindings are used, MPI_Init() is not invoked
by the main thread, and this causes some keys being destructed twice.
Reset the per thread values to NULL in order to correctly handle this

Fixes open-mpi/ompi#2811

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-25 10:58:55 +09:00
Joshua Hursey
a2d45f6e9f communicator: Fix uninitialized variable 
Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-24 16:46:13 -06:00
Joshua Hursey
0e9a06d2c3 orte/iof: Add app stderr to stdout redirection at source 
* Add an MCA parameter to combine stdout and stderr at the source
   - `iof_base_redirect_app_stderr_to_stdout`
 * Aids in user debugging when using libraries that mix stderr with stdout

Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-24 16:23:48 -06:00
Joshua Hursey
dcd9801f7c orte/iof: Add orte_map_stddiag_to_stdout option 
* Similar to `orte_map_stddiag_to_stderr` except it redirects `stddiag`
   to `stdout` instead of `stderr`.
 * Add protection so that the user canot supply both:
   - `orte_map_stddiag_to_stderr`
   - `orte_map_stddiag_to_stdout`

Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-24 16:22:59 -06:00
Joshua Hursey
2596983593 opal/output: Make sure verbose gets updated when id 0 gets updated. 
- This allows the following MCA option to have an impact on the
   framework verbose output as well.
   * `-mca mca_base_verbose stdout`

Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-24 16:14:11 -06:00
Zhi Ming Wang
9718bbac82 Fix a minor error at MPI_AINT_DIFF. 
Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-24 16:06:14 -06:00
Joshua Hursey
d6b306d716 libevent/external: Add opal_event_include to this component 
* Adds a parameter to adjust the method used by libevent.
   - Matches that of the libevent2022 component.

Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-24 16:03:09 -06:00
Mark Allen
a3452adfa9 coll/base: Allgatherv MPI_IN_PLACE Bug 
MPI_Allgatherv with MPI_IN_PLACE reads data from wrong location.

They were locating the MPI_IN_PLACE send buffer as
```c
         send_buf = (char*)rbuf;
         for (i = 0; i < rank; ++i) {
             send_buf += ((ptrdiff_t)rcounts[i] * extent);
         }
```
when it should be
```c
         send_buf = (char*)rbuf;
         send_buf += ((ptrdiff_t)disps[rank] * extent);
```
because disps[] specifies where things are in the v-style buffers.

Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-24 15:52:36 -06:00
Ralph Castain
ef86707fbe Deprecate the --slot-list paramaeter in favor of --cpu-list. Remove the --cpu-set param (mark it as deprecated) and use --cpu-list instead as it was confusing having the two params. The --cpu-list param defines the cpus to be used by procs of this job, and the binding policy will be overlayed on top of it. 
Note: since the discovered cpus are filtered against this list, #slots will be set to the #cpus in the list if no slot values are given in a -host or -hostname specification.

Signed-off-by: Ralph Castain <rhc@open-mpi.org>
 2017-01-24 13:33:22 -08:00
Ralph Castain
0bfdc0057a Extend the -host:N syntax to accept "*" or "auto" to indicate "auto-detect the #cpus and set #slots to that value" 
Signed-off-by: Ralph Castain <rhc@open-mpi.org>
 2017-01-24 10:21:01 -08:00
Ralph Castain
d3907dec98 Make master continue the -host behavior of prior releases: use of -host <foo> specifies a single slot. Requests to run more than one process will require either specifying slots using the "-host foo:N" syntax, or adding --oversubscribe to the cmd line. 
Signed-off-by: Ralph Castain <rhc@open-mpi.org>
 2017-01-24 10:11:56 -08:00
Edgar Gabriel
cbb3cb9745 fs/ufs: avoid using the exclusive flag with shared file pointer 
when a file is opened a second time for shared file pointer operations,
avoid setting the create and exclusive flag.

Signed-off-by: Edgar Gabriel <egabriel@central.uh.edu>
 2017-01-24 12:11:29 -06:00
Edgar Gabriel
f5289a1803 common/ompio: store correctly the SHAREDFP_IS_SET flag 
it looks like disabling the lazy_open flag for sharedfp components
revealead a bug that lead to a crash in file_close in some tests. Make
sure the SHAREDFP_IS_SET flag is correctly set (and not overwritten again),
and we use that to avoid a double-free of the communicator.

Signed-off-by: Edgar Gabriel <egabriel@central.uh.edu>
 2017-01-24 12:09:56 -06:00
Josh Hursey
c6595c2289 Merge pull request #2792 from jjhursey/topic/libevent-conf2 
libevent2022: Fix broken configure AC_LANG_PROGRAM
 2017-01-24 08:31:46 -06:00
Ralph Castain
4e9364b9a4 Merge pull request #2794 from rhc54/topic/regs 
Next step in reducing launch time
 2017-01-24 03:19:57 -08:00
Gilles Gouaillardet
682f5116aa Merge pull request #2781 from ggouaillardet/topic/misc_fixes_and_plugs 
fix misc bugs and plug misc memory leaks
 2017-01-24 14:41:45 +09:00
Ralph Castain
86ab751c5e Next step in reducing launch time: begin reducing the size of the launch message itself. Start by expressing the daemon map as a set of three regular expression strings. On an 8k cluster, this reduces the nidmap contribution from over 200kBytes to 21 bytes in size. 
Signed-off-by: Ralph Castain <rhc@open-mpi.org>
 2017-01-23 19:54:47 -08:00
Joshua Hursey
72ac812039 libevent2022: Fix broken configure AC_LANG_PROGRAM 
* Similar to commit 029964a748
   This removes an extra `int main` during configure.

Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-23 21:47:59 -06:00
Josh Hursey
b9b96f13ca Merge pull request #2788 from jjhursey/topic/libevent-conf 
libevent2022: Fix broken configure AC_LANG_PROGRAM
 2017-01-23 21:39:05 -06:00
Gilles Gouaillardet
d54e54538a orted/orted_submit: plug a memory leak 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:13:30 +09:00
Gilles Gouaillardet
189da7fdab pmix2x: plug a memory leak in _event_hdlr() 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:13:30 +09:00
Gilles Gouaillardet
acbc32d3b2 pmix2x: plug a memory leak in opal_lkupcbfunc() 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:13:29 +09:00
Gilles Gouaillardet
b5b21043c4 pmix2x: plug a memory leak in _reg_nspace() 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:13:29 +09:00
Gilles Gouaillardet
0f47310a75 pmix2x/pmix2x_client: plug misc memory leaks 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:13:29 +09:00
Gilles Gouaillardet
f4dc7e4134 orted/orted_submit: plug misc memory leaks 
- always invoke init_globals() before opal_cmd_line_parse(orte_cmd_line, ...)
- plug more leaks in init_globals()
- remove unused env_val and personalities fields from orte_cmd_options_t

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:13:29 +09:00
Gilles Gouaillardet
d5aa310884 mpiext/affinity: initialize all output variables of OMPI_Affinity_str() 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:13:29 +09:00
Gilles Gouaillardet
501eb8dc7e ompio: plug misc memory leaks 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:13:19 +09:00
Gilles Gouaillardet
1a6c17ec7d opal/util: plug a memory leak 
by using opal_setenv() instead of putenv()

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:12:47 +09:00
Gilles Gouaillardet
d0629f18c2 coll/libnbc: optimize size one communicators 
simply "return" with ompi_request_empty if the communicator size is 1

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:12:47 +09:00
Gilles Gouaillardet
9d6e0482a6 orte/data_server: plug a memory leak in orte_data_server() 
Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:12:47 +09:00
Gilles Gouaillardet
0bdc594b2e rml/base: plug a memory leak in orte_rml_API_recv_cancel() 
simply return when the orte event thread has gone

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:12:47 +09:00
Gilles Gouaillardet
6f2ca5809b man: fix a typo in MPI_Win_get_name() 
Thanks Nicolas Joly for the report

Fixes open-mpi/ompi#2782

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
 2017-01-24 09:08:13 +09:00
Jeff Squyres
e7588f0509 Merge pull request #2785 from edgargabriel/pr/sharedfp-append-fix 
common/ompio: update comment based on the previous commit.
 2017-01-23 14:06:13 -08:00
Joshua Hursey
029964a748 libevent2022: Fix broken configure AC_LANG_PROGRAM 
* The AC_LANG_PROGRAM macro adds the `main()` so it is erroneous
   to add it to the test program.
 * This was detected with the XL compilers which will fail to
   build the program in this situation. The GNU compiler does not
   error out or warn, but successfully compiles the program.

Signed-off-by: Joshua Hursey <jhursey@us.ibm.com>
 2017-01-23 13:44:12 -06:00
Edgar Gabriel
4dc09de3b8 common/ompio: update comment based on the previsou commit. 
No source code changed.

Signed-off-by: Edgar Gabriel <egabriel@central.uh.edu>
 2017-01-23 13:38:05 -06:00
Ralph Castain
f3920828ed Merge pull request #2784 from rhc54/topic/pmixup 
Update to latest PMIx master
 2017-01-23 11:01:19 -08:00
Edgar Gabriel
2215f29849 Merge pull request #2783 from edgargabriel/pr/sharedfp-append-fix 
Pr/sharedfp append fix
 2017-01-23 10:38:27 -06:00