No earthly idea, I'm afraid - you might check "which mpirun" to ensure you are indeed running the one you think. You might also try installing OMPI from scratch yourself (into a directory under your home) so you can ensure it actually is built to match your system. You could then verify the result by building and running the code in the "examples" directory.

Not sure what else I can suggest.

On Jan 25, 2013, at 7:07 PM, #YEO JINGJIE# <JYEO1@e.ntu.edu.sg> wrote:

Does not seem to work. I did

 

export PATH=/usr/local/openmpi/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/openmpi/lib:$LD_LIBRARY_PATH

 


echo $PATH
/usr/lib64/openmpi/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:
echo $LD_LIBRARY_PATH
/usr/lib64/openmpi/lib:

 

But I still get the same error.

 

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 10:29:13 AM
To: Open MPI Users
Subject: Re: [OMPI users] Error when attempting to run LAMMPS on Centos 6.2 with OpenMPI

Okay - that's why I don't like package installs...

Still, it should work. One thing I don't like is that you have /usr/lib64/openmpi/bin at the end of your PATH - that's a bad idea. Most OS's come with a preinstalled version, usually something really old, so you want the desired version of OMPI to be at the front of your path.

Do you have LD_LIBRARY_PATH set as well? Again, you need /usr/lib64/openmpi/lib set at the very front of that envar.


On Jan 25, 2013, at 6:22 PM, #YEO JINGJIE# <JYEO1@e.ntu.edu.sg> wrote:

Ok this was what I got:

 

which srun

/usr/bin/which: no srun in (/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/usr/lib64/openmpi/bin:)

 

ls -R /usr/lib64/openmpi

/usr/lib64/openmpi:
bin  lib  share
/usr/lib64/openmpi/bin:
mpic++     mpif90         opal_wrapper       orte-top             vtc++
mpicc      mpif90-vt      opari              orte_wrapper_script  vtcc
mpiCC      mpirun         orte-bootproxy.sh  otfaux               vtCC
mpicc-vt   ompi-clean     ortec++            otfcompress          vtcxx
mpiCC-vt   ompi_info      ortecc             otfconfig            vtf77
mpic++-vt  ompi-iof       orteCC             otfdecompress        vtf90
mpicxx     ompi-probe     orte-clean         otfdump              vtfilter
mpicxx-vt  ompi-profiler  orted              otfinfo              vtunify
mpiexec    ompi-ps        orte-iof           otfmerge             vtunify-mpi
mpif77     ompi-server    orte-ps            otfprofile           vtwrapper
mpif77-vt  ompi-top       orterun            otfshrink
/usr/lib64/openmpi/lib:
libmca_common_sm.so        libompitrace.so.0      libvt-hyb.so.0.0.0
libmca_common_sm.so.2      libompitrace.so.0.0.0  libvt-mpi.a
libmca_common_sm.so.2.0.0  libopen-pal.so         libvt-mpi.so
libmpi_cxx.so              libopen-pal.so.3       libvt-mpi.so.0
libmpi_cxx.so.1            libopen-pal.so.3.0.0   libvt-mpi.so.0.0.0
libmpi_cxx.so.1.0.1        libopen-rte.so         libvt-mt.a
libmpi_f77.so              libopen-rte.so.3       libvt-mt.so
libmpi_f77.so.1            libopen-rte.so.3.0.0   libvt-mt.so.0
libmpi_f77.so.1.0.2        libotf.a               libvt-mt.so.0.0.0
libmpi_f90.so              libotf.so              libvt-pomp.a
libmpi_f90.so.1            libotf.so.0            libvt.so
libmpi_f90.so.1.1.0        libotf.so.0.0.1        libvt.so.0
libmpi.so                  libvt.a                libvt.so.0.0.0
libmpi.so.1                libvt-hyb.a            mpi.mod
libmpi.so.1.0.2            libvt-hyb.so           openmpi
libompitrace.so            libvt-hyb.so.0
/usr/lib64/openmpi/lib/openmpi:
libompi_dbg_msgq.so         mca_mtl_psm.so
mca_allocator_basic.so      mca_notifier_command.so
mca_allocator_bucket.so     mca_notifier_smtp.so
mca_bml_r2.so               mca_notifier_syslog.so
mca_btl_ofud.so             mca_odls_default.so
mca_btl_openib.so           mca_oob_tcp.so
mca_btl_self.so             mca_osc_pt2pt.so
mca_btl_sm.so               mca_osc_rdma.so
mca_btl_tcp.so              mca_paffinity_hwloc.so
mca_carto_auto_detect.so    mca_plm_rshd.so
mca_carto_file.so           mca_plm_rsh.so
mca_coll_basic.so           mca_plm_slurm.so
mca_coll_hierarch.so        mca_pml_bfo.so
mca_coll_inter.so           mca_pml_cm.so
mca_coll_self.so            mca_pml_csum.so
mca_coll_sm.so              mca_pml_ob1.so
mca_coll_sync.so            mca_pml_v.so
mca_coll_tuned.so           mca_pstat_linux.so
mca_crs_none.so             mca_pubsub_orte.so
mca_debugger_mpir.so        mca_ras_cm.so
mca_debugger_mpirx.so       mca_ras_gridengine.so
mca_dpm_orte.so             mca_ras_loadleveler.so
mca_errmgr_default.so       mca_ras_slurm.so
mca_ess_env.so              mca_rcache_vma.so
mca_ess_hnp.so              mca_rmaps_load_balance.so
mca_ess_singleton.so        mca_rmaps_rank_file.so
mca_ess_slave.so            mca_rmaps_resilient.so
mca_ess_slurmd.so           mca_rmaps_round_robin.so
mca_ess_slurm.so            mca_rmaps_seq.so
mca_ess_tool.so             mca_rmaps_topo.so
mca_filem_rsh.so            mca_rmcast_tcp.so
mca_grpcomm_bad.so          mca_rmcast_udp.so
mca_grpcomm_basic.so        mca_rml_oob.so
mca_grpcomm_hier.so         mca_routed_binomial.so
mca_iof_hnp.so              mca_routed_cm.so
mca_iof_orted.so            mca_routed_direct.so
mca_iof_tool.so             mca_routed_linear.so
mca_maffinity_first_use.so  mca_routed_radix.so
mca_maffinity_libnuma.so    mca_routed_slave.so
mca_mpool_fake.so           mca_sysinfo_linux.so
mca_mpool_rdma.so           mca_topo_unity.so
mca_mpool_sm.so             mca_vprotocol_pessimist.so
/usr/lib64/openmpi/share:
openmpi  vampirtrace
/usr/lib64/openmpi/share/openmpi:
amca-param-sets                     help-orte-filem-base.txt
doc                                 help-orte-filem-rsh.txt
help-coll-sync.txt                  help-orte-iof.txt
help-dash-host.txt                  help-orte-notifier-command.txt
help-ess-base.txt                   help-orte-notifier-smtp.txt
help-hostfile.txt                   help-orte-odls-base.txt
help-mca-base.txt                   help-orte-ps.txt
help-mca-bml-r2.txt                 help-orte-rmaps-base.txt
help-mca-coll-base.txt              help-orte-rmaps-lb.txt
help-mca-op-base.txt                help-orte-rmaps-resilient.txt
help-mca-param.txt                  help-orte-rmaps-rr.txt
help-mpi-api.txt                    help-orte-rmaps-seq.txt
help-mpi-btl-base.txt               help-orte-rmaps-topo.txt
help-mpi-btl-openib-cpc-base.txt    help-orte-rmcast-udp.txt
help-mpi-btl-openib-cpc-rdmacm.txt  help-orte-runtime.txt
help-mpi-btl-openib.txt             help-orterun.txt
help-mpi-btl-sm.txt                 help-orte-snapc-base.txt
help-mpi-btl-tcp.txt                help-orte-top.txt
help-mpi-coll-sm.txt                help-plm-base.txt
help-mpi-common-sm.txt              help-plm-rshd.txt
help-mpi-errors.txt                 help-plm-rsh.txt
help-mpi-pml-bfo.txt                help-plm-slurm.txt
help-mpi-pml-csum.txt               help-ras-base.txt
help-mpi-pml-ob1.txt                help-ras-gridengine.txt
help-mpi-runtime.txt                help-ras-slurm.txt
help-mpool-base.txt                 help-regex.txt
help-mtl-psm.txt                    help-rmaps_rank_file.txt
help-odls-default.txt               help-rmcast-base.txt
help-ompi-crcp-base.txt             mca-btl-openib-device-params.ini
help-ompi-dpm-base.txt              mpicc-vt-wrapper-data.txt
help-ompi-dpm-orte.txt              mpiCC-vt-wrapper-data.txt
help-ompi_info.txt                  mpicc-wrapper-data.txt
help-ompi-probe.txt                 mpiCC-wrapper-data.txt
help-ompi-profiler.txt              mpic++-vt-wrapper-data.txt
help-ompi-pubsub-orte.txt           mpic++-wrapper-data.txt
help-ompi-server.txt                mpicxx-vt-wrapper-data.txt
help-oob-tcp.txt                    mpicxx-wrapper-data.txt
help-opal-carto-file.txt            mpif77-vt-wrapper-data.txt
help-opal-crs-base.txt              mpif77-wrapper-data.txt
help-opal-crs-none.txt              mpif90-vt-wrapper-data.txt
help-opal-memory-linux.txt          mpif90-wrapper-data.txt
help-opal-runtime.txt               openmpi-valgrind.supp
help-opal-util.txt                  ortecc-wrapper-data.txt
help-opal-wrapper.txt               orteCC-wrapper-data.txt
help-orte-clean.txt                 ortec++-wrapper-data.txt
help-orted.txt
/usr/lib64/openmpi/share/openmpi/amca-param-sets:
btl-openib-benchmark  example.conf
/usr/lib64/openmpi/share/openmpi/doc:
COPYRIGHT-ptmalloc2.txt
/usr/lib64/openmpi/share/vampirtrace:
doc          METRICS.SPEC            vtcxx-wrapper-data.txt
FILTER.SPEC  vtcc-wrapper-data.txt   vtf77-wrapper-data.txt
GROUPS.SPEC  vtCC-wrapper-data.txt   vtf90-wrapper-data.txt
libtool      vtc++-wrapper-data.txt
/usr/lib64/openmpi/share/vampirtrace/doc:
ChangeLog  LICENSE  opari  otf  UserManual.html  UserManual.pdf
/usr/lib64/openmpi/share/vampirtrace/doc/opari:
ChangeLog  lacsi01.pdf  LICENSE  opari-logo-100.gif  Readme.html
/usr/lib64/openmpi/share/vampirtrace/doc/otf:
ChangeLog  LICENSE  otftools.pdf  specification.pdf

 

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 10:17:25 AM
To: Open MPI Users
Subject: Re: [OMPI users] Error when attempting to run LAMMPS on Centos 6.2 with OpenMPI

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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