Please help me resolve the following problems with a 306 node Rocks cluster
using SGE. Please note I can run the
job successfully on <87 slots, but not anymore than that.
We're running SGE and I'm submitting my jobs via the SGE CLI utility qsub and
the following lines from a script:
mpirun -n $NSLOTS -machinefile $TMPDIR/machines --mca btl_tcp_if_include eth0
--mca btl_tcp_if_exclude eth1 --mca oob_tcp_if_exclude eth1 --mca
opal_set_max_sys_limits 1 --mca pls_gridengine_verbose 1
/stf/billstst/ProcessColors2MPICH1
echo "MPICH1 mpirun returned #?"
eth1 is the connection to the Isilon NAS, where the object file is located.
The error messages returned are of the form:
WRT ORTE_ERROR_LOG: The system limit on number of pipes a process can open was
reached
WRT ORTE_ERROR_LOG: The system limit on number of network connections a process
can open was reached in file oob_tcp.c at line 447
We have increased the open file limit to 4096 from 1024, problem still exists.
I can run the same test code via MPICH2 successfully on all 696 slots of the
cluster, but I can't run the
same code (compiled via OpenMPI version 1.3.3) on any more than 86 slots.
Here's the details on the installed version of Open MPI:
[root}# ./ompi_info
Package: Open MPI [email protected]
Distribution
Open MPI: 1.3.3
Open MPI SVN revision: r21666
Open MPI release date: Jul 14, 2009
Open RTE: 1.3.3
Open RTE SVN revision: r21666
Open RTE release date: Jul 14, 2009
OPAL: 1.3.3
OPAL SVN revision: r21666
OPAL release date: Jul 14, 2009
Ident string: 1.3.3
Prefix: /opt/openmpi
Configured architecture: x86_64-unknown-linux-gnu
Configure host: build-x86-64.rocksclusters.org
Configured by: root
Configured on: Sat Dec 12 16:29:23 PST 2009
Configure host: build-x86-64.rocksclusters.org
Built by: bruno
Built on: Sat Dec 12 16:42:52 PST 2009
Built host: build-x86-64.rocksclusters.org
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: g++
C++ compiler absolute: /usr/bin/g++
Fortran77 compiler: gfortran
Fortran77 compiler abs: /usr/bin/gfortran
Fortran90 compiler: gfortran
Fortran90 compiler abs: /usr/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 v1.3.3)
MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.3.3)
MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.3.3)
MCA carto: auto_detect (MCA v2.0, API v2.0, Component v1.3.3)
MCA carto: file (MCA v2.0, API v2.0, Component v1.3.3)
MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.3.3)
MCA timer: linux (MCA v2.0, API v2.0, Component v1.3.3)
MCA installdirs: env (MCA v2.0, API v2.0, Component v1.3.3)
MCA installdirs: config (MCA v2.0, API v2.0, Component v1.3.3)
MCA dpm: orte (MCA v2.0, API v2.0, Component v1.3.3)
MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.3.3)
MCA allocator: basic (MCA v2.0, API v2.0, Component v1.3.3)
MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.3.3)
MCA coll: basic (MCA v2.0, API v2.0, Component v1.3.3)
MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.3.3)
MCA coll: inter (MCA v2.0, API v2.0, Component v1.3.3)
MCA coll: self (MCA v2.0, API v2.0, Component v1.3.3)
MCA coll: sm (MCA v2.0, API v2.0, Component v1.3.3)
MCA coll: sync (MCA v2.0, API v2.0, Component v1.3.3)
MCA coll: tuned (MCA v2.0, API v2.0, Component v1.3.3)
MCA io: romio (MCA v2.0, API v2.0, Component v1.3.3)
MCA mpool: fake (MCA v2.0, API v2.0, Component v1.3.3)
MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.3.3)
MCA mpool: sm (MCA v2.0, API v2.0, Component v1.3.3)
MCA pml: cm (MCA v2.0, API v2.0, Component v1.3.3)
MCA pml: csum (MCA v2.0, API v2.0, Component v1.3.3)
MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.3.3)
MCA pml: v (MCA v2.0, API v2.0, Component v1.3.3)
MCA bml: r2 (MCA v2.0, API v2.0, Component v1.3.3)
MCA rcache: vma (MCA v2.0, API v2.0, Component v1.3.3)
MCA btl: self (MCA v2.0, API v2.0, Component v1.3.3)
MCA btl: sm (MCA v2.0, API v2.0, Component v1.3.3)
MCA btl: tcp (MCA v2.0, API v2.0, Component v1.3.3)
MCA topo: unity (MCA v2.0, API v2.0, Component v1.3.3)
MCA osc: pt2pt (MCA v2.0, API v2.0, Component v1.3.3)
MCA osc: rdma (MCA v2.0, API v2.0, Component v1.3.3)
MCA iof: hnp (MCA v2.0, API v2.0, Component v1.3.3)
MCA iof: orted (MCA v2.0, API v2.0, Component v1.3.3)
MCA iof: tool (MCA v2.0, API v2.0, Component v1.3.3)
MCA oob: tcp (MCA v2.0, API v2.0, Component v1.3.3)
MCA odls: default (MCA v2.0, API v2.0, Component v1.3.3)
MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.3.3)
MCA ras: slurm (MCA v2.0, API v2.0, Component v1.3.3)
MCA rmaps: rank_file (MCA v2.0, API v2.0, Component v1.3.3)
MCA rmaps: round_robin (MCA v2.0, API v2.0, Component v1.3.3)
MCA rmaps: seq (MCA v2.0, API v2.0, Component v1.3.3)
MCA rml: oob (MCA v2.0, API v2.0, Component v1.3.3)
MCA routed: binomial (MCA v2.0, API v2.0, Component v1.3.3)
MCA routed: direct (MCA v2.0, API v2.0, Component v1.3.3)
MCA routed: linear (MCA v2.0, API v2.0, Component v1.3.3)
MCA plm: rsh (MCA v2.0, API v2.0, Component v1.3.3)
MCA plm: slurm (MCA v2.0, API v2.0, Component v1.3.3)
MCA filem: rsh (MCA v2.0, API v2.0, Component v1.3.3)
MCA errmgr: default (MCA v2.0, API v2.0, Component v1.3.3)
MCA ess: env (MCA v2.0, API v2.0, Component v1.3.3)
MCA ess: hnp (MCA v2.0, API v2.0, Component v1.3.3)
MCA ess: singleton (MCA v2.0, API v2.0, Component v1.3.3)
MCA ess: slurm (MCA v2.0, API v2.0, Component v1.3.3)
MCA ess: tool (MCA v2.0, API v2.0, Component v1.3.3)
MCA grpcomm: bad (MCA v2.0, API v2.0, Component v1.3.3)
MCA grpcomm: basic (MCA v2.0, API v2.0, Component v1.3.3)
Would upgrading to the latest version of OpenMPI (1.4.3) resolve this issue?
Thank you,
-Bill Lane
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