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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