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# <jy...@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-boun...@open-mpi.org [users-boun...@open-mpi.org] on behalf of > Ralph Castain [r...@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# <jy...@e.ntu.edu.sg> wrote: > >> Yes sir here it is: >> >> >> Package: Open MPI mockbu...@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-boun...@open-mpi.org [users-boun...@open-mpi.org] on behalf of >> Ralph Castain [r...@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# <jy...@e.ntu.edu.sg> 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 >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
