Hmmm...looks like it was built with Slurm support - is your cluster running Slurm? Do you see an "srun" command - e.g., if you do "which srun", what do you get?

You should also do an "ls -R /usr/lib64/openmpi" and see what modules were installed. Send that along and let's see why it didn't find anything.


On Jan 25, 2013, at 6:05 PM, #YEO JINGJIE# <JYEO1@e.ntu.edu.sg> wrote:

Yes sir here it is:

 


                 Package: Open MPI mockbuild@c6b8.bsys.dev.centos.org
                          Distribution
                Open MPI: 1.5.4
   Open MPI SVN revision: r25060
   Open MPI release date: Aug 18, 2011
                Open RTE: 1.5.4
   Open RTE SVN revision: r25060
   Open RTE release date: Aug 18, 2011
                    OPAL: 1.5.4
       OPAL SVN revision: r25060
       OPAL release date: Aug 18, 2011
            Ident string: 1.5.4
                  Prefix: /usr/lib64/openmpi
 Configured architecture: x86_64-unknown-linux-gnu
          Configure host: c6b8.bsys.dev.centos.org
           Configured by: mockbuild
           Configured on: Fri Jun 22 06:42:03 UTC 2012
          Configure host: c6b8.bsys.dev.centos.org
                Built by: mockbuild
                Built on: Fri Jun 22 06:46:48 UTC 2012
              Built host: c6b8.bsys.dev.centos.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 family name: GNU
      C compiler version: 4.4.6
            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_THREAD_MULTIPLE: no, progress: no)
           Sparse Groups: no
  Internal debug support: no
  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 v1.5.4)
          MCA memchecker: valgrind (MCA v2.0, API v2.0, Component v1.5.4)
              MCA memory: linux (MCA v2.0, API v2.0, Component v1.5.4)
           MCA paffinity: hwloc (MCA v2.0, API v2.0, Component v1.5.4)
               MCA carto: auto_detect (MCA v2.0, API v2.0, Component v1.5.4)
               MCA carto: file (MCA v2.0, API v2.0, Component v1.5.4)
           MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.5.4)
           MCA maffinity: libnuma (MCA v2.0, API v2.0, Component v1.5.4)
               MCA timer: linux (MCA v2.0, API v2.0, Component v1.5.4)
         MCA installdirs: env (MCA v2.0, API v2.0, Component v1.5.4)
         MCA installdirs: config (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA dpm: orte (MCA v2.0, API v2.0, Component v1.5.4)
              MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.5.4)
           MCA allocator: basic (MCA v2.0, API v2.0, Component v1.5.4)
           MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.5.4)
                MCA coll: basic (MCA v2.0, API v2.0, Component v1.5.4)
                MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.5.4)
                MCA coll: inter (MCA v2.0, API v2.0, Component v1.5.4)
                MCA coll: self (MCA v2.0, API v2.0, Component v1.5.4)
                MCA coll: sm (MCA v2.0, API v2.0, Component v1.5.4)
                MCA coll: sync (MCA v2.0, API v2.0, Component v1.5.4)
                MCA coll: tuned (MCA v2.0, API v2.0, Component v1.5.4)
               MCA mpool: fake (MCA v2.0, API v2.0, Component v1.5.4)
               MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.5.4)
               MCA mpool: sm (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA pml: bfo (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA pml: csum (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA pml: v (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA bml: r2 (MCA v2.0, API v2.0, Component v1.5.4)
              MCA rcache: vma (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA btl: ofud (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA btl: openib (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA btl: self (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA btl: sm (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA btl: tcp (MCA v2.0, API v2.0, Component v1.5.4)
                MCA topo: unity (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA osc: pt2pt (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA osc: rdma (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA iof: hnp (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA iof: orted (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA iof: tool (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA oob: tcp (MCA v2.0, API v2.0, Component v1.5.4)
                MCA odls: default (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ras: cm (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ras: loadleveler (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ras: slurm (MCA v2.0, API v2.0, Component v1.5.4)
               MCA rmaps: load_balance (MCA v2.0, API v2.0, Component v1.5.4)
               MCA rmaps: rank_file (MCA v2.0, API v2.0, Component v1.5.4)
               MCA rmaps: resilient (MCA v2.0, API v2.0, Component v1.5.4)
               MCA rmaps: round_robin (MCA v2.0, API v2.0, Component v1.5.4)
               MCA rmaps: seq (MCA v2.0, API v2.0, Component v1.5.4)
               MCA rmaps: topo (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA rml: oob (MCA v2.0, API v2.0, Component v1.5.4)
              MCA routed: binomial (MCA v2.0, API v2.0, Component v1.5.4)
              MCA routed: cm (MCA v2.0, API v2.0, Component v1.5.4)
              MCA routed: direct (MCA v2.0, API v2.0, Component v1.5.4)
              MCA routed: linear (MCA v2.0, API v2.0, Component v1.5.4)
              MCA routed: radix (MCA v2.0, API v2.0, Component v1.5.4)
              MCA routed: slave (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA plm: rsh (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA plm: rshd (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA plm: slurm (MCA v2.0, API v2.0, Component v1.5.4)
               MCA filem: rsh (MCA v2.0, API v2.0, Component v1.5.4)
              MCA errmgr: default (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ess: env (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ess: hnp (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ess: singleton (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ess: slave (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ess: slurm (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ess: slurmd (MCA v2.0, API v2.0, Component v1.5.4)
                 MCA ess: tool (MCA v2.0, API v2.0, Component v1.5.4)
             MCA grpcomm: bad (MCA v2.0, API v2.0, Component v1.5.4)
             MCA grpcomm: basic (MCA v2.0, API v2.0, Component v1.5.4)
             MCA grpcomm: hier (MCA v2.0, API v2.0, Component v1.5.4)
            MCA notifier: command (MCA v2.0, API v1.0, Component v1.5.4)
            MCA notifier: smtp (MCA v2.0, API v1.0, Component v1.5.4)
            MCA notifier: syslog (MCA v2.0, API v1.0, Component v1.5.4)

 

Regards,
Jingjie Yeo
Ph.D. Student
School of Mechanical and Aerospace Engineering
Nanyang Technological University, Singapore

From: users-bounces@open-mpi.org [users-bounces@open-mpi.org] on behalf of Ralph Castain [rhc@open-mpi.org]
Sent: Saturday, 26 January, 2013 9:58:04 AM
To: Open MPI Users
Subject: Re: [OMPI users] Error when attempting to run LAMMPS on Centos 6.2 with OpenMPI

Groan - I hate these bundled installs :-(

If you do "ompi_info", what does it tell you? Could you please send it along?

Thanks

On Jan 25, 2013, at 5:51 PM, #YEO JINGJIE# <JYEO1@e.ntu.edu.sg> wrote:

I tried to follow the installation instructions over here:

 

 

And I am using bash and yum.

 

Regards,
Jingjie Yeo
Ph.D. Student
School of Mechanical and Aerospace Engineering
Nanyang Technological University, Singapore
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