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-boun...@open-mpi.org [users-boun...@open-mpi.org] on behalf of Ralph Castain [r...@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# <jy...@e.ntu.edu.sg<mailto: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<mailto:users-boun...@open-mpi.org> [users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>] on behalf of Ralph Castain [r...@open-mpi.org<mailto: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<mailto:jy...@e.ntu.edu.sg>> wrote: Yes sir here it is: Package: Open MPI mockbu...@c6b8.bsys.dev.centos.org<mailto: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<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-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org> [users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>] on behalf of Ralph Castain [r...@open-mpi.org<mailto: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<mailto: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<mailto:us...@open-mpi.org> http://www.open-mpi.org/mailman/listinfo.cgi/users _______________________________________________ users mailing list us...@open-mpi.org<mailto:us...@open-mpi.org> http://www.open-mpi.org/mailman/listinfo.cgi/users _______________________________________________ users mailing list us...@open-mpi.org<mailto:us...@open-mpi.org> http://www.open-mpi.org/mailman/listinfo.cgi/users
