Open MPI logo

Open MPI User's Mailing List Archives

  |   Home   |   Support   |   FAQ   |  

This web mail archive is frozen.

This page is part of a frozen web archive of this mailing list.

You can still navigate around this archive, but know that no new mails have been added to it since July of 2016.

Click here to be taken to the new web archives of this list; it includes all the mails that are in this frozen archive plus all new mails that have been sent to the list since it was migrated to the new archives.

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 22:07:33


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_at_[hidden] [users-bounces_at_[hidden]] on behalf of Ralph Castain [rhc_at_[hidden]]
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_at_[hidden]<mailto:JYEO1_at_[hidden]>> 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_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 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
_______________________________________________
users mailing list
users_at_[hidden]<mailto:users_at_[hidden]>
http://www.open-mpi.org/mailman/listinfo.cgi/users

_______________________________________________
users mailing list
users_at_[hidden]<mailto:users_at_[hidden]>
http://www.open-mpi.org/mailman/listinfo.cgi/users

_______________________________________________
users mailing list
users_at_[hidden]<mailto:users_at_[hidden]>
http://www.open-mpi.org/mailman/listinfo.cgi/users