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Subject: Re: [OMPI users] Error when attempting to run LAMMPS on Centos 6.2 with OpenMPI
From: Ralph Castain (rhc_at_[hidden])
Date: 2013-01-25 21:29:13


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]> 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] [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]> wrote:
>
>> Yes sir here it is:
>>
>>
>> Package: Open MPI 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
>> 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_at_[hidden] [users-bounces_at_[hidden]] on behalf of Ralph Castain [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]> 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]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
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