[R-sig-hpc] Rmpi: Connection to lifeline [[...,0],0] lost
Sklyar, Oleg (London)
osklyar at maninvestments.com
Thu Feb 12 11:17:52 CET 2009
After moving to OpenMPI from LAM, we started to get the following error
messages with Rmpi:
[hpc01:06981] [[11499,1],0] routed:binomial: Connection to lifeline
[[11499,0],0] lost
The main script is a lengthy 3-hour long process that periodically
spawns short 2-minute long jobs onto the nodes. Any ideas what this
could be?
Thanks.
Oleg
--------------------------------------------------
*** R 2.9.0 (svn -r 47821) [/share/research/R-devel/20090203/lib64/R]
***
> library(Rmpi)
> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-02 r47821)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics utils datasets grDevices methods base
other attached packages:
[1] Rmpi_0.5-7
--------------------------------------------------
[hpc01] ~
* ompi_info
Package: Open MPI osklyar at hpc01 Distribution
Open MPI: 1.3
Open MPI SVN revision: r20295
Open MPI release date: Jan 19, 2009
Open RTE: 1.3
Open RTE SVN revision: r20295
Open RTE release date: Jan 19, 2009
OPAL: 1.3
OPAL SVN revision: r20295
OPAL release date: Jan 19, 2009
Ident string: 1.3
Prefix: /share/research/opt/openmpi
Configured architecture: x86_64-unknown-linux-gnu
Configure host: hpc01
Configured by: osklyar
Configured on: Tue Feb 3 15:04:03 GMT 2009
Configure host: hpc01
Built by: osklyar
Built on: Tue Feb 3 15:19:46 GMT 2009
Built host: hpc01
C bindings: yes
C++ bindings: yes
Fortran77 bindings: yes (all)
Fortran90 bindings: yes
Fortran90 bindings size: small
C compiler: gcc
C compiler absolute: /share/research/opt/bin/gcc
C++ compiler: g++
C++ compiler absolute: /share/research/opt/bin/g++
Fortran77 compiler: gfortran
Fortran77 compiler abs: /share/research/opt/bin/gfortran
Fortran90 compiler: gfortran
Fortran90 compiler abs: /share/research/opt/bin/gfortran
C profiling: yes
C++ profiling: yes
Fortran77 profiling: yes
Fortran90 profiling: yes
C++ exceptions: no
Thread support: posix (mpi: no, progress: no)
Sparse Groups: no
Internal debug support: 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 visibility support: yes
FT Checkpoint support: no (checkpoint thread: no)
MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.3)
MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.3)
MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.3)
MCA carto: auto_detect (MCA v2.0, API v2.0, Component
v1.3)
MCA carto: file (MCA v2.0, API v2.0, Component v1.3)
MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.3)
MCA timer: linux (MCA v2.0, API v2.0, Component v1.3)
MCA installdirs: env (MCA v2.0, API v2.0, Component v1.3)
MCA installdirs: config (MCA v2.0, API v2.0, Component v1.3)
MCA dpm: orte (MCA v2.0, API v2.0, Component v1.3)
MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.3)
MCA allocator: basic (MCA v2.0, API v2.0, Component v1.3)
MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.3)
MCA coll: basic (MCA v2.0, API v2.0, Component v1.3)
MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.3)
MCA coll: inter (MCA v2.0, API v2.0, Component v1.3)
MCA coll: self (MCA v2.0, API v2.0, Component v1.3)
MCA coll: sm (MCA v2.0, API v2.0, Component v1.3)
MCA coll: tuned (MCA v2.0, API v2.0, Component v1.3)
MCA io: romio (MCA v2.0, API v2.0, Component v1.3)
MCA mpool: fake (MCA v2.0, API v2.0, Component v1.3)
MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.3)
MCA mpool: sm (MCA v2.0, API v2.0, Component v1.3)
MCA pml: cm (MCA v2.0, API v2.0, Component v1.3)
MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.3)
MCA pml: v (MCA v2.0, API v2.0, Component v1.3)
MCA bml: r2 (MCA v2.0, API v2.0, Component v1.3)
MCA rcache: vma (MCA v2.0, API v2.0, Component v1.3)
MCA btl: self (MCA v2.0, API v2.0, Component v1.3)
MCA btl: sm (MCA v2.0, API v2.0, Component v1.3)
MCA btl: tcp (MCA v2.0, API v2.0, Component v1.3)
MCA topo: unity (MCA v2.0, API v2.0, Component v1.3)
MCA osc: pt2pt (MCA v2.0, API v2.0, Component v1.3)
MCA osc: rdma (MCA v2.0, API v2.0, Component v1.3)
MCA iof: hnp (MCA v2.0, API v2.0, Component v1.3)
MCA iof: orted (MCA v2.0, API v2.0, Component v1.3)
MCA iof: tool (MCA v2.0, API v2.0, Component v1.3)
MCA oob: tcp (MCA v2.0, API v2.0, Component v1.3)
MCA odls: default (MCA v2.0, API v2.0, Component v1.3)
MCA ras: slurm (MCA v2.0, API v2.0, Component v1.3)
MCA rmaps: rank_file (MCA v2.0, API v2.0, Component v1.3)
MCA rmaps: round_robin (MCA v2.0, API v2.0, Component
v1.3)
MCA rmaps: seq (MCA v2.0, API v2.0, Component v1.3)
MCA rml: oob (MCA v2.0, API v2.0, Component v1.3)
MCA routed: binomial (MCA v2.0, API v2.0, Component v1.3)
MCA routed: direct (MCA v2.0, API v2.0, Component v1.3)
MCA routed: linear (MCA v2.0, API v2.0, Component v1.3)
MCA plm: rsh (MCA v2.0, API v2.0, Component v1.3)
MCA plm: slurm (MCA v2.0, API v2.0, Component v1.3)
MCA filem: rsh (MCA v2.0, API v2.0, Component v1.3)
MCA errmgr: default (MCA v2.0, API v2.0, Component v1.3)
MCA ess: env (MCA v2.0, API v2.0, Component v1.3)
MCA ess: hnp (MCA v2.0, API v2.0, Component v1.3)
MCA ess: singleton (MCA v2.0, API v2.0, Component v1.3)
MCA ess: slurm (MCA v2.0, API v2.0, Component v1.3)
MCA ess: tool (MCA v2.0, API v2.0, Component v1.3)
MCA grpcomm: bad (MCA v2.0, API v2.0, Component v1.3)
MCA grpcomm: basic (MCA v2.0, API v2.0, Component v1.3)
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
osklyar at maninvestments.com
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