[Nek5000-users] MPI problems
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Feb 28 18:01:46 CST 2014
Yes
you were right !
Changing mpiexec to mpiexec.mpich2 solved the problem !
Thanks a lot
Flavio
On 28/feb/2014, at 20:59, nek5000-users at lists.mcs.anl.gov wrote:
> Hi,
>
> I had a similar problem once. Changing mpiexec to mpiexec.mpich2 in the nekbmpi script solved it as far as I was concerned. Might be a similar problem?
>
> Cheers,
> JC
>
>
> 2014-02-28 17:15 GMT+01:00 <nek5000-users at lists.mcs.anl.gov>:
> Dear Nek’s
>
> I have a problem when running the code on more than one processor. The problem just appeared after a recent update of the system (debian) on our cluster. The code was working perfectly before the update but now I cannot run jobs in parallel anymore. MPI works with other softwares, but not with NEK. In particular I have the following problem:
>
> When I execute a parallel run using the script nekmpi eddy_uv 4
>
> the command execute 4 different jobs running on a single processor rather than a single job running on 4 processors. I attach the log to this mail (log.out) . After a few second three jobs are killed and only one remains active. A similar problem was also found on a new machine with a fresh installation of debian. It seems that the scripts is not able to set the correct value of the variable np (or_np).
> Anyone found a similar problem ? Any explanation for such behavior ? Any advice to solve the problem ?
>
> Thanks in advance
>
>
> Flavio
>
>
>
>
>
>
>
>
> Platform
> uname -a
> Linux cfd 2.6.32-5-amd64 #1 SMP Mon Sep 23 22:14:43 UTC 2013 x86_64 GNU/Linux
>
>
>
>
>
>
> ompi_info
> Package: Open MPI manuel at ce170155 Distribution
> Open MPI: 1.4.2
> Open MPI SVN revision: r23093
> Open MPI release date: May 04, 2010
> Open RTE: 1.4.2
> Open RTE SVN revision: r23093
> Open RTE release date: May 04, 2010
> OPAL: 1.4.2
> OPAL SVN revision: r23093
> OPAL release date: May 04, 2010
> Ident string: 1.4.2
> Prefix: /usr
> Configured architecture: x86_64-pc-linux-gnu
> Configure host: ce170155
> Configured by: manuel
> Configured on: Wed Sep 1 15:58:32 UTC 2010
> Configure host: ce170155
> Built by: root
> Built on: Wed Sep 1 16:01:42 UTC 2010
> Built host: ce170155
> C bindings: yes
> C++ bindings: yes
> Fortran77 bindings: yes (all)
> Fortran90 bindings: yes
> Fortran90 bindings size: small
> C compiler: gcc
> C compiler absolute: /usr/lib/ccache/gcc
> C++ compiler: g++
> C++ compiler absolute: /usr/lib/ccache/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: yes
> mpirun default --prefix: no
> MPI I/O support: yes
> MPI_WTIME support: gettimeofday
> Symbol visibility support: yes
> FT Checkpoint support: yes (checkpoint thread: no)
> MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.4.2)
> MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.4.2)
> MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.4.2)
> MCA carto: auto_detect (MCA v2.0, API v2.0, Component v1.4.2)
> MCA carto: file (MCA v2.0, API v2.0, Component v1.4.2)
> MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.4.2)
> MCA maffinity: libnuma (MCA v2.0, API v2.0, Component v1.4.2)
> MCA timer: linux (MCA v2.0, API v2.0, Component v1.4.2)
> MCA installdirs: env (MCA v2.0, API v2.0, Component v1.4.2)
> MCA installdirs: config (MCA v2.0, API v2.0, Component v1.4.2)
> MCA crs: none (MCA v2.0, API v2.0, Component v1.4.2)
> MCA dpm: orte (MCA v2.0, API v2.0, Component v1.4.2)
> MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.4.2)
> MCA allocator: basic (MCA v2.0, API v2.0, Component v1.4.2)
> MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: basic (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: inter (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: self (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: sm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: sync (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: tuned (MCA v2.0, API v2.0, Component v1.4.2)
> MCA io: romio (MCA v2.0, API v2.0, Component v1.4.2)
> MCA mpool: fake (MCA v2.0, API v2.0, Component v1.4.2)
> MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.4.2)
> MCA mpool: sm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA pml: cm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA pml: crcpw (MCA v2.0, API v2.0, Component v1.4.2)
> MCA pml: csum (MCA v2.0, API v2.0, Component v1.4.2)
> MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.4.2)
> MCA pml: v (MCA v2.0, API v2.0, Component v1.4.2)
> MCA bml: r2 (MCA v2.0, API v2.0, Component v1.4.2)
> MCA rcache: vma (MCA v2.0, API v2.0, Component v1.4.2)
> MCA btl: ofud (MCA v2.0, API v2.0, Component v1.4.2)
> MCA btl: openib (MCA v2.0, API v2.0, Component v1.4.2)
> MCA btl: self (MCA v2.0, API v2.0, Component v1.4.2)
> MCA btl: sm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA btl: tcp (MCA v2.0, API v2.0, Component v1.4.2)
> MCA topo: unity (MCA v2.0, API v2.0, Component v1.4.2)
> MCA osc: pt2pt (MCA v2.0, API v2.0, Component v1.4.2)
> MCA osc: rdma (MCA v2.0, API v2.0, Component v1.4.2)
> MCA crcp: bkmrk (MCA v2.0, API v2.0, Component v1.4.2)
> MCA iof: hnp (MCA v2.0, API v2.0, Component v1.4.2)
> MCA iof: orted (MCA v2.0, API v2.0, Component v1.4.2)
> MCA iof: tool (MCA v2.0, API v2.0, Component v1.4.2)
> MCA oob: tcp (MCA v2.0, API v2.0, Component v1.4.2)
> MCA odls: default (MCA v2.0, API v2.0, Component v1.4.2)
> MCA ras: slurm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA ras: tm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA rmaps: load_balance (MCA v2.0, API v2.0, Component v1.4.2)
> MCA rmaps: rank_file (MCA v2.0, API v2.0, Component v1.4.2)
> MCA rmaps: round_robin (MCA v2.0, API v2.0, Component v1.4.2)
> MCA rmaps: seq (MCA v2.0, API v2.0, Component v1.4.2)
> MCA rml: ftrm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA rml: oob (MCA v2.0, API v2.0, Component v1.4.2)
> MCA routed: binomial (MCA v2.0, API v2.0, Component v1.4.2)
> MCA routed: direct (MCA v2.0, API v2.0, Component v1.4.2)
> MCA routed: linear (MCA v2.0, API v2.0, Component v1.4.2)
> MCA plm: rsh (MCA v2.0, API v2.0, Component v1.4.2)
> MCA plm: slurm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA plm: tm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA snapc: full (MCA v2.0, API v2.0, Component v1.4.2)
> MCA filem: rsh (MCA v2.0, API v2.0, Component v1.4.2)
> MCA errmgr: default (MCA v2.0, API v2.0, Component v1.4.2)
> MCA ess: env (MCA v2.0, API v2.0, Component v1.4.2)
> MCA ess: hnp (MCA v2.0, API v2.0, Component v1.4.2)
> MCA ess: singleton (MCA v2.0, API v2.0, Component v1.4.2)
> MCA ess: slurm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA ess: tool (MCA v2.0, API v2.0, Component v1.4.2)
> MCA grpcomm: bad (MCA v2.0, API v2.0, Component v1.4.2)
> MCA grpcomm: basic (MCA v2.0, API v2.0, Component v1.4.2)
>
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