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Subject: Re: [OMPI users] Error when attempting to run LAMMPS on Centos 6.2 with OpenMPI
From: #YEO JINGJIE# (JYEO1_at_[hidden])
Date: 2013-01-25 21:22:27


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_at_[hidden] [users-bounces_at_[hidden]] on behalf of Ralph Castain [rhc_at_[hidden]]
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_at_[hidden]<mailto:JYEO1_at_[hidden]>> wrote:

Yes sir here it is:

                 Package: Open MPI mockbuild_at_[hidden]<mailto:mockbuild_at_[hidden]>
                          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<http://bsys.dev.centos.org>
           Configured by: mockbuild
           Configured on: Fri Jun 22 06:42:03 UTC 2012
          Configure host: c6b8.bsys.dev.centos.org<http://bsys.dev.centos.org>
                Built by: mockbuild
                Built on: Fri Jun 22 06:46:48 UTC 2012
              Built host: c6b8.bsys.dev.centos.org<http://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_at_[hidden]<mailto:users-bounces_at_[hidden]> [users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>] on behalf of Ralph Castain [rhc_at_[hidden]<mailto:rhc_at_[hidden]>]
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_at_[hidden]<mailto:JYEO1_at_[hidden]>> wrote:

I tried to follow the installation instructions over here:

http://amusecode.org/doc/install/install-prerequisites-redhat.html

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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