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Edgar Gabriel
c3d4ee3f73 ompi/file: add a muteex to the ompi_file_t structure 
Adding a mutex to thje ompi_file_t structure allows to have a per-file handle
mutex lock for both ROMIO and OMPIO. I double checked that the size of the
ompi_file_t structure is still below the size of the predefined_file_t structure,
so we should be good from the backward compatibility perspective.
 2016-08-21 16:09:12 -05:00
Edgar Gabriel
bc042259bc make initialization of the io framework thread safe. 
Also, remove the lock/unlock in the file_open ompi-interface routines of romio314.
The global lock in the romio component does probably not work, it is easy to construct a testcase where two threads perform collective I/O operations on different file handles. With a global lock it is easy to deadlock. THe lock has to be at least on the file handle basis.

move the mutex to file/file.c to avoid duplicate symbol problem in file_open.c pfile_open.c
 2016-08-21 16:09:00 -05:00
Nathan Hjelm
f3e9a72f1a Merge pull request #1987 from hjelmn/cid 
comm/cid: fix threaded CID allocation
 2016-08-19 14:26:39 -06:00
Nathan Hjelm
fbbf743c36 comm/cid: fix threaded CID allocation 
This commit should restore the pre-non-blocking behavior of the CID
allocator when threads are used. There are two primary changes: 1)
do not hold the cid allocator lock past the end of a request callback,
and 2) if a lower id communicator is detected during CID allocation
back off and let the lower id communicator finish before continuing.

Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
 2016-08-19 11:47:19 -06:00
Jeff Squyres
bb6b87f086 Merge pull request #1972 from jsquyres/pr/rsh-robustify-default-check 
rsh: robustify the check for plm_rsh_agent default value
 2016-08-19 13:33:38 -04:00
Ralph Castain
c9dc286f25 Update the hwloc coverity submission script 2016-08-19 09:20:48 -07:00
Nathan Hjelm
e5c7512692 Merge pull request #1983 from hjelmn/request_cb 
ompi/request: change semantics of ompi request callbacks
 2016-08-18 08:31:56 -06:00
Artem Polyakov
6ea8cccdab Merge pull request #1969 from artpol84/pmix_jobid_fix 
Pmix jobid fix
 2016-08-18 17:24:58 +07:00
Nathan Hjelm
6aa658ae33 ompi/request: change semantics of ompi request callbacks 
This commit changes the sematics of ompi request callbacks. If a
request's callback has freed or re-posted (using start) a request
the callback must return 1 instead of OMPI_SUCCESS. This indicates
to ompi_request_complete that the request should not be modified
further. This fixes a race condition in osc/pt2pt that could lead
to the req_state being inconsistent if a request is freed between
the callback and setting the request as complete.

Signed-off-by: Nathan Hjelm <hjelmn@lanl.gov>
 2016-08-17 20:14:01 -06:00
Sylvain Jeaugey
61e900eea5 Fix typo calling allreduce with the allgather module. 
That was causing CUDA collective to crash.
 2016-08-17 17:05:13 -07:00
rhc54
394e23d179 Merge pull request #1981 from rhc54/topic/timeout 
Support the PMIX_TIMEOUT key at the PMIx server when timeout=0 - this…
 2016-08-17 17:40:43 -05:00
Edgar Gabriel
e14c23ba79 Merge pull request #1980 from edgargabriel/topic/coverty-cleanup 
io/ompio: Topic/coverty cleanup
 2016-08-17 17:27:51 -05:00
Ralph Castain
7da9793fef Support the PMIX_TIMEOUT key at the PMIx server when timeout=0 - this indicates that the user doesn't want a lookup of any data from the host RM. 2016-08-17 16:26:58 -05:00
Edgar Gabriel
2c8437ce62 fs/pvfs2: fix a common symbol 2016-08-17 13:10:32 -05:00
Edgar Gabriel
eba5293586 fix coverty warning CID 1369021 2016-08-17 13:02:45 -05:00
Nathan Hjelm
cdbc94e34e Merge pull request #1977 from hjelmn/osc_pt2pt_fix 
osc/pt2pt: make receive count an unsigned int
 2016-08-17 09:38:33 -06:00
Nathan Hjelm
40b70889e5 osc/pt2pt: make receive count an unsigned int 
This receive_count MCA variable should never be negative. Change it
to an unsigned int.

Signed-off-by: Nathan Hjelm <hjelmn@me.com>
 2016-08-17 08:14:24 -06:00
Jeff Squyres
ce0124603d .gitignore: add test executable to ignore 
Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
 2016-08-17 04:27:51 -07:00
Gilles Gouaillardet
8faa1edafa osc/pt2pt: silence misc warnings 2016-08-17 14:24:14 +09:00
Gilles Gouaillardet
6b7bc64101 spml/yoda: MCA_PML(add_procs) all procs from oshmem_comm_world 
and fix oshmem_group_proc_{init,create} so they use the number of procs in oshmem_comm_world

Thanks Debendra Das for the report and Josh Ladd for the guidance

Fixes open-mpi/ompi#1966
 2016-08-17 14:24:02 +09:00
LANL OMPI Bot
96c7762050 Merge pull request #1942 from hppritcha/topic/minor_ofi_fix 
mtl/ofi: use mca param to set av type
 2016-08-16 14:14:12 -06:00
Nathan Hjelm
2e1378596f Merge pull request #1953 from hjelmn/pt2pt_fixes 
osc/pt2pt updates
 2016-08-16 08:00:24 -06:00
Jeff Squyres
71ec5cfb43 rsh: robustify the check for plm_rsh_agent default value 
Don't strcmp against the default value -- the default value may change
over time.  Instead, check to see if the MCA var source is not
DEFAULT.

Signed-off-by: Jeff Squyres <jsquyres@cisco.com>
 2016-08-16 06:58:20 -05:00
rhc54
d7cd802426 Merge pull request #1971 from rhc54/topic/sesdir 
Update the session dir structure. Restore the creation of a top-level…
 2016-08-16 03:14:08 -05:00
Ralph Castain
ae2af61ee3 Update the session dir structure. Restore the creation of a top-level dir based on userid so that everything is contained under the user's top-level dir. Make the next level down (the "job family" level) be either the pid (indicated by a name of "pid.N") or the job family if not launched by mpirun. This allows for proper rendezvous by direct-launched procs. 2016-08-15 22:46:46 -05:00
rhc54
dd05f085e9 Merge pull request #1968 from rhc54/topic/rsh 
Further cleanup getpwuid usage - try it first (unless completely disa…
 2016-08-15 22:11:21 -05:00
Gilles Gouaillardet
3126ff77e2 pmix2x: common syms: whitelist bison-generated common symbols 
Bison generates some common symbols that we can't do anything about,
so whitelist them.
 2016-08-16 11:29:06 +09:00
Artem Polyakov
c5a91c5c9d opal/pmix: fix pmix jobid calculation if external PMIx server is used. 2016-08-15 21:13:51 +03:00
Ralph Castain
9f43db7303 Further cleanup getpwuid usage - try it first (unless completely disabled), and then silently failover to try other methods. 2016-08-15 07:51:36 -07:00
Ralph Castain
ecbedee8bb Fix typo 2016-08-15 07:32:00 -07:00
Artem Polyakov
f3c816b52e opal/pmix: fix indentation in some files. 2016-08-15 18:21:50 +07:00
Gilles Gouaillardet
483685eb6a update .gitignore 
remove autogenerated opal/mca/pmix/pmix2x/pmix/src/include/pmix_config.h.in
 2016-08-15 17:00:20 +09:00
rhc54
2228d2efc2 Merge pull request #1965 from rhc54/topic/pmixfix 
Provide backward compatible keys so that the non-PMIx components in t…
 2016-08-13 13:48:12 -07:00
Ralph Castain
be8424b691 Provide backward compatible keys so that the non-PMIx components in the opal/pmix framework don't have to adjust as we continue to work on finalizing the PMIx reference scheme. Activate and utilize the new PMIx show_help capability to provide more meaningful error output when the server cannot start. 
Add a contrib script to cleanup permissions incorrectly modified due to things like smb mounts

dd
 2016-08-13 12:13:04 -07:00
rhc54
d12e50b2d6 Merge pull request #1963 from rhc54/topic/pmixfix 
Fix shared memory rendezvous
 2016-08-13 09:59:14 -07:00
Ralph Castain
08a0644df5 Fix shared memory rendezvous 2016-08-13 08:14:50 -07:00
rhc54
ddde154d28 Merge pull request #1962 from rhc54/topic/notify 
Ensure we properly convert pmix status to ORTE state before activatin…
 2016-08-13 06:59:50 -07:00
Ralph Castain
48d35a9627 Ensure we properly convert pmix status to ORTE state before activating an error state upon notification. Cleanup some conversion issues on notification info. Add a new orte_notify.c test program 2016-08-12 21:14:29 -07:00
rhc54
9868093bef Merge pull request #1961 from rhc54/topic/static 
Setup the job list in the PMIx integration so that static ports can run
 2016-08-12 15:17:31 -07:00
rhc54
9eed451916 Merge pull request #1960 from rhc54/topic/rsh 
Restore the rsh template creation code
 2016-08-12 13:38:43 -07:00
rhc54
8d67f753ca Merge pull request #1959 from rhc54/topic/nodeid 
The node index isn't normally passed with the packed node object, so …
 2016-08-12 13:30:10 -07:00
Ralph Castain
4a4c9703a9 Setup the job list in the PMIx integration so that static ports can run 2016-08-12 13:27:10 -07:00
rhc54
1ef3c86d44 Merge pull request #1931 from hjelmn/ess_fix 
ess/base: set up nidmap after pmix
 2016-08-12 13:10:30 -07:00
Ralph Castain
5717b75b45 Restore the rsh template creation code 2016-08-12 12:43:40 -07:00
rhc54
ee1ee2086c Merge pull request #1958 from rhc54/topic/path 
Fix a bug where we were requiring that all paths in $PATH be absolute
 2016-08-12 12:31:43 -07:00
Ralph Castain
d4327fd973 The node index isn't normally passed with the packed node object, so we need to set it on the remote end as the orted needs to pass it down to the procs. Refactor the registration code to better package proc-level info - we will separate out the node and app levels in a subsequent change. 2016-08-12 12:06:23 -07:00
Ralph Castain
0e58609327 Fix a bug where we were requiring that all paths in $PATH be absolute. Some users provide relative paths in their environment, and we should respect those. 2016-08-12 11:28:57 -07:00
rhc54
163999bce0 Merge pull request #1957 from rhc54/topic/rsh 
If the ssh agent hasn't been given, then check for qrsh and friends
 2016-08-12 11:18:28 -07:00
Ralph Castain
1c44543854 If the ssh agent hasn't been given, then check for qrsh and friends 2016-08-12 07:46:39 -07:00
rhc54
397faad46b Merge pull request #1954 from rhc54/topic/covpmix 
Silence Coverity warnings
 2016-08-12 06:38:04 -07:00