On 09/06/2011 04:58 PM, Ralph Castain wrote:
On Sep 6, 2011, at 12:49 PM, Simone Pellegrini wrote:
On 09/06/2011 02:57 PM, Ralph Castain wrote:
Hi Simone
Just to clarify: is your application threaded? Could you please send the OMPI
configure cmd you used?
yes, it is threaded. There are basically 3 threads, 1 for the outgoing messages
(MPI_send), 1 for incoming messages (MPI_Iprobe / MPI_Recv) and one spawning.
I am not sure what you mean with OMPI configure cmd I used... I simply do
mpirun --np 1 ./executable
How was OMPI configured when it was installed? If you didn't install it, then
provide the output of ompi_info - it will tell us.
[@arch-moto tasksys]$ ompi_info
Package: Open MPI nobody@alderaan Distribution
Open MPI: 1.5.3
Open MPI SVN revision: r24532
Open MPI release date: Mar 16, 2011
Open RTE: 1.5.3
Open RTE SVN revision: r24532
Open RTE release date: Mar 16, 2011
OPAL: 1.5.3
OPAL SVN revision: r24532
OPAL release date: Mar 16, 2011
Ident string: 1.5.3
Prefix: /usr
Configured architecture: x86_64-unknown-linux-gnu
Configure host: alderaan
Configured by: nobody
Configured on: Thu Jul 7 13:21:35 UTC 2011
Configure host: alderaan
Built by: nobody
Built on: Thu Jul 7 13:27:08 UTC 2011
Built host: alderaan
C bindings: yes
C++ bindings: yes
Fortran77 bindings: yes (all)
Fortran90 bindings: yes
Fortran90 bindings size: small
C compiler: gcc
C compiler absolute: /usr/bin/gcc
C compiler family name: GNU
C compiler version: 4.6.1
C++ compiler: g++
C++ compiler absolute: /usr/bin/g++
Fortran77 compiler: gfortran
Fortran77 compiler abs: /usr/bin/gfortran
Fortran90 compiler: /usr/bin/gfortran
Fortran90 compiler abs:
C profiling: yes
C++ profiling: yes
Fortran77 profiling: yes
Fortran90 profiling: yes
C++ exceptions: no
Thread support: posix (mpi: yes, progress: no)
Sparse Groups: no
Internal debug support: yes
MPI interface warnings: no
MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
libltdl support: yes
Heterogeneous support: no
mpirun default --prefix: no
MPI I/O support: yes
MPI_WTIME support: gettimeofday
Symbol vis. support: yes
MPI extensions: affinity example
FT Checkpoint support: no (checkpoint thread: no)
MPI_MAX_PROCESSOR_NAME: 256
MPI_MAX_ERROR_STRING: 256
MPI_MAX_OBJECT_NAME: 64
MPI_MAX_INFO_KEY: 36
MPI_MAX_INFO_VAL: 256
MPI_MAX_PORT_NAME: 1024
MPI_MAX_DATAREP_STRING: 128
MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.5.3)
MCA memchecker: valgrind (MCA v2.0, API v2.0, Component v1.5.3)
MCA memory: linux (MCA v2.0, API v2.0, Component v1.5.3)
MCA paffinity: hwloc (MCA v2.0, API v2.0, Component v1.5.3)
MCA carto: auto_detect (MCA v2.0, API v2.0, Component
v1.5.3)
MCA carto: file (MCA v2.0, API v2.0, Component v1.5.3)
MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.5.3)
MCA timer: linux (MCA v2.0, API v2.0, Component v1.5.3)
MCA installdirs: env (MCA v2.0, API v2.0, Component v1.5.3)
MCA installdirs: config (MCA v2.0, API v2.0, Component v1.5.3)
MCA dpm: orte (MCA v2.0, API v2.0, Component v1.5.3)
MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.5.3)
MCA allocator: basic (MCA v2.0, API v2.0, Component v1.5.3)
MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.5.3)
MCA coll: basic (MCA v2.0, API v2.0, Component v1.5.3)
MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.5.3)
MCA coll: inter (MCA v2.0, API v2.0, Component v1.5.3)
MCA coll: self (MCA v2.0, API v2.0, Component v1.5.3)
MCA coll: sm (MCA v2.0, API v2.0, Component v1.5.3)
MCA coll: sync (MCA v2.0, API v2.0, Component v1.5.3)
MCA coll: tuned (MCA v2.0, API v2.0, Component v1.5.3)
MCA io: romio (MCA v2.0, API v2.0, Component v1.5.3)
MCA mpool: fake (MCA v2.0, API v2.0, Component v1.5.3)
MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.5.3)
MCA mpool: sm (MCA v2.0, API v2.0, Component v1.5.3)
MCA pml: bfo (MCA v2.0, API v2.0, Component v1.5.3)
MCA pml: csum (MCA v2.0, API v2.0, Component v1.5.3)
MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.5.3)
MCA pml: v (MCA v2.0, API v2.0, Component v1.5.3)
MCA bml: r2 (MCA v2.0, API v2.0, Component v1.5.3)
MCA rcache: vma (MCA v2.0, API v2.0, Component v1.5.3)
MCA btl: self (MCA v2.0, API v2.0, Component v1.5.3)
MCA btl: sm (MCA v2.0, API v2.0, Component v1.5.3)
MCA btl: tcp (MCA v2.0, API v2.0, Component v1.5.3)
MCA topo: unity (MCA v2.0, API v2.0, Component v1.5.3)
MCA osc: pt2pt (MCA v2.0, API v2.0, Component v1.5.3)
MCA osc: rdma (MCA v2.0, API v2.0, Component v1.5.3)
MCA iof: hnp (MCA v2.0, API v2.0, Component v1.5.3)
MCA iof: orted (MCA v2.0, API v2.0, Component v1.5.3)
MCA iof: tool (MCA v2.0, API v2.0, Component v1.5.3)
MCA oob: tcp (MCA v2.0, API v2.0, Component v1.5.3)
MCA odls: default (MCA v2.0, API v2.0, Component v1.5.3)
MCA ras: cm (MCA v2.0, API v2.0, Component v1.5.3)
MCA rmaps: load_balance (MCA v2.0, API v2.0, Component
v1.5.3)
MCA rmaps: rank_file (MCA v2.0, API v2.0, Component v1.5.3)
MCA rmaps: resilient (MCA v2.0, API v2.0, Component v1.5.3)
MCA rmaps: round_robin (MCA v2.0, API v2.0, Component
v1.5.3)
MCA rmaps: seq (MCA v2.0, API v2.0, Component v1.5.3)
MCA rmaps: topo (MCA v2.0, API v2.0, Component v1.5.3)
MCA rml: oob (MCA v2.0, API v2.0, Component v1.5.3)
MCA routed: binomial (MCA v2.0, API v2.0, Component v1.5.3)
MCA routed: cm (MCA v2.0, API v2.0, Component v1.5.3)
MCA routed: direct (MCA v2.0, API v2.0, Component v1.5.3)
MCA routed: linear (MCA v2.0, API v2.0, Component v1.5.3)
MCA routed: radix (MCA v2.0, API v2.0, Component v1.5.3)
MCA routed: slave (MCA v2.0, API v2.0, Component v1.5.3)
MCA plm: rsh (MCA v2.0, API v2.0, Component v1.5.3)
MCA plm: rshd (MCA v2.0, API v2.0, Component v1.5.3)
MCA filem: rsh (MCA v2.0, API v2.0, Component v1.5.3)
MCA errmgr: default (MCA v2.0, API v2.0, Component v1.5.3)
MCA ess: env (MCA v2.0, API v2.0, Component v1.5.3)
MCA ess: hnp (MCA v2.0, API v2.0, Component v1.5.3)
MCA ess: singleton (MCA v2.0, API v2.0, Component v1.5.3)
MCA ess: slave (MCA v2.0, API v2.0, Component v1.5.3)
MCA ess: tool (MCA v2.0, API v2.0, Component v1.5.3)
MCA grpcomm: bad (MCA v2.0, API v2.0, Component v1.5.3)
MCA grpcomm: basic (MCA v2.0, API v2.0, Component v1.5.3)
MCA grpcomm: hier (MCA v2.0, API v2.0, Component v1.5.3)
MCA notifier: command (MCA v2.0, API v1.0, Component v1.5.3)
MCA notifier: syslog (MCA v2.0, API v1.0, Component v1.5.3)
Adding the debug flags just changes the race condition. Interestingly, those
values only impact the behavior of mpirun, so it looks like the race condition
is occurring there.
The problem is that the error is totally nondeterministic. Sometimes happens,
others not but the error message gives me no clue where the error is coming
from. Is is a problem of my code or internal MPI?
Can't tell, but it is likely an impact of threading. Race conditions within
threaded environments are common, and OMPI isn't particularly thread safe,
especially when it comes to comm_spawn.
cheers, Simone
On Sep 6, 2011, at 3:01 AM, Simone Pellegrini wrote:
Dear all,
I am developing an MPI application which uses heavily MPI_Spawn. Usually
everything works fine for the first hundred spawn but after a while the
application exist with a curious message:
[arch-top:27712] [[36904,165],0] ORTE_ERROR_LOG: Data unpack would read past
end of buffer in file base/grpcomm_base_modex.c at line 349
[arch-top:27712] [[36904,165],0] ORTE_ERROR_LOG: Data unpack would read past
end of buffer in file grpcomm_bad_module.c at line 518
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_proc_set_arch failed
--> Returned "Data unpack would read past end of buffer" (-26) instead of
"Success" (0)
--------------------------------------------------------------------------
*** The MPI_Init_thread() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[arch-top:27712] Abort before MPI_INIT completed successfully; not able to
guarantee that all other processes were killed!
[arch-top:27714] [[36904,165],0] ORTE_ERROR_LOG: Data unpack would read past
end of buffer in file base/grpcomm_base_modex.c at line 349
[arch-top:27714] [[36904,165],0] ORTE_ERROR_LOG: Data unpack would read past
end of buffer in file grpcomm_bad_module.c at line 518
*** The MPI_Init_thread() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[arch-top:27714] Abort before MPI_INIT completed successfully; not able to
guarantee that all other processes were killed!
[arch-top:27226] 1 more process has sent help message help-mpi-runtime /
mpi_init:startup:internal-failure
[arch-top:27226] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages
Also using MPI_init instead of MPI_Init_thread does not help, the same error
occurs.
Strangely the error does not occur if I run the code enabling debug in (-mca
plm_base_verbose 5 -mca rmaps_base_verbose 5).
I am using OpenMPI 1.5.3
cheers, Simone
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