De Novo Assembly using Ray

[seb567]

OK good luck with that.

Hi again Sebastian,

I think you found the problem.

I have both 1.2.8 and 1.6 versions

echo $LD_LIBRARY_PATH

/usr/bin/mpiexec --version
mpiexec (OpenRTE) 1.2.8

Report bugs to http://www.open-mpi.org/community/help/

/usr/local/bin/mpiexec --version
mpiexec (OpenRTE) 1.6

Report bugs to http://www.open-mpi.org/community/help/

Thanks for you enormous help

[Saratoga]

Hi again Sebastian,

I think you found the problem.

I have both 1.2.8 and 1.6 versions

echo $LD_LIBRARY_PATH

/usr/bin/mpiexec --version
mpiexec (OpenRTE) 1.2.8

Report bugs to http://www.open-mpi.org/community/help/

/usr/local/bin/mpiexec --version
mpiexec (OpenRTE) 1.6

Report bugs to http://www.open-mpi.org/community/help/

Thanks for you enormous help

[seb567]

You are compiling with /usr/bin/mpicxx, but you are probably not linking with the related library.

This information will be provided by

echo $LD_LIBRARY_PATH

/usr/bin/mpiexec --version

/usr/local/bin/mpiexec --version

We are closing in on the problem.

Hi again,

I got this,


echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin
echo $LD_LIBRARY_PATH

type mpiexec
mpiexec is /usr/bin/mpiexec

type mpicxx
mpicxx is /usr/bin/mpicxx

type ompi_info
ompi_info is /usr/bin/ompi_info

find /usr/local|grep mpi
/usr/local/bin/mpic++
/usr/local/bin/mpic++-vt
/usr/local/bin/mpicc
/usr/local/bin/mpicc-vt
/usr/local/bin/mpicxx
/usr/local/bin/mpicxx-vt
/usr/local/bin/mpiexec
/usr/local/bin/mpif77
/usr/local/bin/mpif77-vt
/usr/local/bin/mpif90
/usr/local/bin/mpif90-vt
/usr/local/bin/mpirun
/usr/local/bin/ompi-clean
/usr/local/bin/ompi-iof
/usr/local/bin/ompi-probe
/usr/local/bin/ompi-profiler
/usr/local/bin/ompi-ps
/usr/local/bin/ompi-server
/usr/local/bin/ompi-top
/usr/local/bin/ompi_info
/usr/local/bin/otfmerge-mpi
/usr/local/bin/otfprofile-mpi
/usr/local/bin/vtfilter-mpi
/usr/local/bin/vtfiltergen-mpi
/usr/local/bin/vtunify-mpi

[Saratoga]

Hi again,

I got this,


echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin
echo $LD_LIBRARY_PATH

type mpiexec
mpiexec is /usr/bin/mpiexec

type mpicxx
mpicxx is /usr/bin/mpicxx

type ompi_info
ompi_info is /usr/bin/ompi_info

find /usr/local|grep mpi
/usr/local/bin/mpic++
/usr/local/bin/mpic++-vt
/usr/local/bin/mpicc
/usr/local/bin/mpicc-vt
/usr/local/bin/mpicxx
/usr/local/bin/mpicxx-vt
/usr/local/bin/mpiexec
/usr/local/bin/mpif77
/usr/local/bin/mpif77-vt
/usr/local/bin/mpif90
/usr/local/bin/mpif90-vt
/usr/local/bin/mpirun
/usr/local/bin/ompi-clean
/usr/local/bin/ompi-iof
/usr/local/bin/ompi-probe
/usr/local/bin/ompi-profiler
/usr/local/bin/ompi-ps
/usr/local/bin/ompi-server
/usr/local/bin/ompi-top
/usr/local/bin/ompi_info
/usr/local/bin/otfmerge-mpi
/usr/local/bin/otfprofile-mpi
/usr/local/bin/vtfilter-mpi
/usr/local/bin/vtfiltergen-mpi
/usr/local/bin/vtunify-mpi
/usr/local/etc/openmpi-default-hostfile
/usr/local/etc/openmpi-mca-params.conf
/usr/local/etc/openmpi-totalview.tcl
/usr/local/include/c++/4.6.0/bits/regex_compiler.h
/usr/local/include/c++/4.6.0/parallel/compiletime_settings.h
/usr/local/include/mpi-ext.h
/usr/local/include/mpi.h
/usr/local/include/mpi_portable_platform.h
/usr/local/include/mpif-common.h
/usr/local/include/mpif-config.h
/usr/local/include/mpif-mpi-io.h
/usr/local/include/mpif.h
/usr/local/include/openmpi
/usr/local/include/openmpi/ompi
/usr/local/include/openmpi/ompi/mpi
/usr/local/include/openmpi/ompi/mpi/cxx
/usr/local/include/openmpi/ompi/mpi/cxx/comm.h
/usr/local/include/openmpi/ompi/mpi/cxx/comm_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/constants.h
/usr/local/include/openmpi/ompi/mpi/cxx/datatype.h
/usr/local/include/openmpi/ompi/mpi/cxx/datatype_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/errhandler.h
/usr/local/include/openmpi/ompi/mpi/cxx/errhandler_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/exception.h
/usr/local/include/openmpi/ompi/mpi/cxx/file.h
/usr/local/include/openmpi/ompi/mpi/cxx/file_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/functions.h
/usr/local/include/openmpi/ompi/mpi/cxx/functions_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/group.h
/usr/local/include/openmpi/ompi/mpi/cxx/group_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/info.h
/usr/local/include/openmpi/ompi/mpi/cxx/info_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/intercomm.h
/usr/local/include/openmpi/ompi/mpi/cxx/intercomm_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/intracomm.h
/usr/local/include/openmpi/ompi/mpi/cxx/intracomm_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/mpicxx.h
/usr/local/include/openmpi/ompi/mpi/cxx/op.h
/usr/local/include/openmpi/ompi/mpi/cxx/op_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/request.h
/usr/local/include/openmpi/ompi/mpi/cxx/request_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/status.h
/usr/local/include/openmpi/ompi/mpi/cxx/status_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/topology.h
/usr/local/include/openmpi/ompi/mpi/cxx/topology_inln.h
/usr/local/include/openmpi/ompi/mpi/cxx/win.h
/usr/local/include/openmpi/ompi/mpi/cxx/win_inln.h
/usr/local/include/vampirtrace
/usr/local/include/vampirtrace/opari_omp.h
/usr/local/include/vampirtrace/otf.h
/usr/local/include/vampirtrace/OTF_CopyHandler.h
/usr/local/include/vampirtrace/OTF_CopyHandler_stream.h
/usr/local/include/vampirtrace/OTF_Definitions.h
/usr/local/include/vampirtrace/OTF_Errno.h
/usr/local/include/vampirtrace/OTF_File.h
/usr/local/include/vampirtrace/OTF_FileManager.h
/usr/local/include/vampirtrace/OTF_Filenames.h
/usr/local/include/vampirtrace/OTF_HandlerArray.h
/usr/local/include/vampirtrace/OTF_inttypes.h
/usr/local/include/vampirtrace/OTF_inttypes_unix.h
/usr/local/include/vampirtrace/OTF_KeyValue.h
/usr/local/include/vampirtrace/OTF_MasterControl.h
/usr/local/include/vampirtrace/OTF_RBuffer.h
/usr/local/include/vampirtrace/OTF_Reader.h
/usr/local/include/vampirtrace/OTF_RStream.h
/usr/local/include/vampirtrace/OTF_Version.h
/usr/local/include/vampirtrace/OTF_WBuffer.h
/usr/local/include/vampirtrace/OTF_Writer.h
/usr/local/include/vampirtrace/OTF_WStream.h
/usr/local/include/vampirtrace/otfaux.h
/usr/local/include/vampirtrace/OTFAUX_MsgMatching.h
/usr/local/include/vampirtrace/OTFAUX_Thumbnail.h
/usr/local/include/vampirtrace/pomp_lib.h
/usr/local/include/vampirtrace/vt_inttypes.h
/usr/local/include/vampirtrace/vt_plugin_cntr.h
/usr/local/include/vampirtrace/vt_user.h
/usr/local/include/vampirtrace/vt_user.inc
/usr/local/include/vampirtrace/vt_user_comment.h
/usr/local/include/vampirtrace/vt_user_comment.inc
/usr/local/include/vampirtrace/vt_user_control.h
/usr/local/include/vampirtrace/vt_user_control.inc
/usr/local/include/vampirtrace/vt_user_count.h
/usr/local/include/vampirtrace/vt_user_count.inc
/usr/local/include/vampirtrace/vt_user_marker.h
/usr/local/include/vampirtrace/vt_user_marker.inc
/usr/local/include/vampirtrace/vt_user_message.h
/usr/local/include/vampirtrace/vt_user_message.inc
/usr/local/include/vampirtrace/vt_user_region.h
/usr/local/include/vampirtrace/vt_user_region.inc
/usr/local/include/vampirtrace/vt_wrap_pthread.h
/usr/local/lib/libmpi.1.dylib
/usr/local/lib/libmpi.dylib
/usr/local/lib/libmpi.la
/usr/local/lib/libmpi_cxx.1.dylib
/usr/local/lib/libmpi_cxx.dylib
/usr/local/lib/libmpi_cxx.la
/usr/local/lib/libmpi_f77.1.dylib
/usr/local/lib/libmpi_f77.dylib
/usr/local/lib/libmpi_f77.la
/usr/local/lib/libmpi_f90.a
/usr/local/lib/libmpi_f90.la
/usr/local/lib/libompitrace.0.dylib
/usr/local/lib/libompitrace.dylib
/usr/local/lib/libompitrace.la
/usr/local/lib/libvt-mpi-unify.0.dylib
/usr/local/lib/libvt-mpi-unify.a
/usr/local/lib/libvt-mpi-unify.dylib
/usr/local/lib/libvt-mpi-unify.la
/usr/local/lib/libvt-mpi.0.dylib
/usr/local/lib/libvt-mpi.a
/usr/local/lib/libvt-mpi.dylib
/usr/local/lib/libvt-mpi.la
/usr/local/lib/mpi.mod
/usr/local/lib/openmpi
/usr/local/lib/openmpi/libompi_dbg_msgq.la
/usr/local/lib/openmpi/libompi_dbg_msgq.so
/usr/local/lib/openmpi/mca_allocator_basic.la
/usr/local/lib/openmpi/mca_allocator_basic.so
/usr/local/lib/openmpi/mca_allocator_bucket.la
/usr/local/lib/openmpi/mca_allocator_bucket.so
/usr/local/lib/openmpi/mca_bml_r2.la
/usr/local/lib/openmpi/mca_bml_r2.so
/usr/local/lib/openmpi/mca_btl_self.la
/usr/local/lib/openmpi/mca_btl_self.so
/usr/local/lib/openmpi/mca_btl_sm.la
/usr/local/lib/openmpi/mca_btl_sm.so
/usr/local/lib/openmpi/mca_btl_tcp.la
/usr/local/lib/openmpi/mca_btl_tcp.so
/usr/local/lib/openmpi/mca_carto_auto_detect.la
/usr/local/lib/openmpi/mca_carto_auto_detect.so
/usr/local/lib/openmpi/mca_carto_file.la
/usr/local/lib/openmpi/mca_carto_file.so
/usr/local/lib/openmpi/mca_coll_basic.la
/usr/local/lib/openmpi/mca_coll_basic.so
/usr/local/lib/openmpi/mca_coll_hierarch.la
/usr/local/lib/openmpi/mca_coll_hierarch.so
/usr/local/lib/openmpi/mca_coll_inter.la
/usr/local/lib/openmpi/mca_coll_inter.so
/usr/local/lib/openmpi/mca_coll_self.la
/usr/local/lib/openmpi/mca_coll_self.so
/usr/local/lib/openmpi/mca_coll_sm.la
/usr/local/lib/openmpi/mca_coll_sm.so
/usr/local/lib/openmpi/mca_coll_sync.la
/usr/local/lib/openmpi/mca_coll_sync.so
/usr/local/lib/openmpi/mca_coll_tuned.la
/usr/local/lib/openmpi/mca_coll_tuned.so
/usr/local/lib/openmpi/mca_crs_none.la
/usr/local/lib/openmpi/mca_crs_none.so
/usr/local/lib/openmpi/mca_dpm_orte.la
/usr/local/lib/openmpi/mca_dpm_orte.so
/usr/local/lib/openmpi/mca_errmgr_default.la
/usr/local/lib/openmpi/mca_errmgr_default.so
/usr/local/lib/openmpi/mca_ess_env.la
/usr/local/lib/openmpi/mca_ess_env.so
/usr/local/lib/openmpi/mca_ess_hnp.la
/usr/local/lib/openmpi/mca_ess_hnp.so
/usr/local/lib/openmpi/mca_ess_singleton.la
/usr/local/lib/openmpi/mca_ess_singleton.so
/usr/local/lib/openmpi/mca_ess_slave.la
/usr/local/lib/openmpi/mca_ess_slave.so
/usr/local/lib/openmpi/mca_ess_slurm.la
/usr/local/lib/openmpi/mca_ess_slurm.so
/usr/local/lib/openmpi/mca_ess_slurmd.la
/usr/local/lib/openmpi/mca_ess_slurmd.so
/usr/local/lib/openmpi/mca_ess_tool.la
/usr/local/lib/openmpi/mca_ess_tool.so
/usr/local/lib/openmpi/mca_filem_rsh.la
/usr/local/lib/openmpi/mca_filem_rsh.so
/usr/local/lib/openmpi/mca_grpcomm_bad.la
/usr/local/lib/openmpi/mca_grpcomm_bad.so
/usr/local/lib/openmpi/mca_grpcomm_basic.la
/usr/local/lib/openmpi/mca_grpcomm_basic.so
/usr/local/lib/openmpi/mca_grpcomm_hier.la
/usr/local/lib/openmpi/mca_grpcomm_hier.so
/usr/local/lib/openmpi/mca_io_romio.la
/usr/local/lib/openmpi/mca_io_romio.so
/usr/local/lib/openmpi/mca_iof_hnp.la
/usr/local/lib/openmpi/mca_iof_hnp.so
/usr/local/lib/openmpi/mca_iof_orted.la
/usr/local/lib/openmpi/mca_iof_orted.so
/usr/local/lib/openmpi/mca_iof_tool.la
/usr/local/lib/openmpi/mca_iof_tool.so
/usr/local/lib/openmpi/mca_maffinity_first_use.la
/usr/local/lib/openmpi/mca_maffinity_first_use.so
/usr/local/lib/openmpi/mca_maffinity_hwloc.la
/usr/local/lib/openmpi/mca_maffinity_hwloc.so
/usr/local/lib/openmpi/mca_mpool_fake.la
/usr/local/lib/openmpi/mca_mpool_fake.so
/usr/local/lib/openmpi/mca_mpool_rdma.la
/usr/local/lib/openmpi/mca_mpool_rdma.so
/usr/local/lib/openmpi/mca_mpool_sm.la
/usr/local/lib/openmpi/mca_mpool_sm.so
/usr/local/lib/openmpi/mca_notifier_command.la
/usr/local/lib/openmpi/mca_notifier_command.so
/usr/local/lib/openmpi/mca_notifier_syslog.la
/usr/local/lib/openmpi/mca_notifier_syslog.so
/usr/local/lib/openmpi/mca_odls_default.la
/usr/local/lib/openmpi/mca_odls_default.so
/usr/local/lib/openmpi/mca_oob_tcp.la
/usr/local/lib/openmpi/mca_oob_tcp.so
/usr/local/lib/openmpi/mca_osc_pt2pt.la
/usr/local/lib/openmpi/mca_osc_pt2pt.so
/usr/local/lib/openmpi/mca_osc_rdma.la
/usr/local/lib/openmpi/mca_osc_rdma.so
/usr/local/lib/openmpi/mca_paffinity_hwloc.la
/usr/local/lib/openmpi/mca_paffinity_hwloc.so
/usr/local/lib/openmpi/mca_plm_rsh.la
/usr/local/lib/openmpi/mca_plm_rsh.so
/usr/local/lib/openmpi/mca_plm_slurm.la
/usr/local/lib/openmpi/mca_plm_slurm.so
/usr/local/lib/openmpi/mca_pml_bfo.la
/usr/local/lib/openmpi/mca_pml_bfo.so
/usr/local/lib/openmpi/mca_pml_cm.la
/usr/local/lib/openmpi/mca_pml_cm.so
/usr/local/lib/openmpi/mca_pml_csum.la
/usr/local/lib/openmpi/mca_pml_csum.so
/usr/local/lib/openmpi/mca_pml_ob1.la
/usr/local/lib/openmpi/mca_pml_ob1.so
/usr/local/lib/openmpi/mca_pml_v.la
/usr/local/lib/openmpi/mca_pml_v.so
/usr/local/lib/openmpi/mca_pstat_darwin.la
/usr/local/lib/openmpi/mca_pstat_darwin.so
/usr/local/lib/openmpi/mca_pubsub_orte.la
/usr/local/lib/openmpi/mca_pubsub_orte.so
/usr/local/lib/openmpi/mca_ras_cm.la
/usr/local/lib/openmpi/mca_ras_cm.so
/usr/local/lib/openmpi/mca_ras_slurm.la
/usr/local/lib/openmpi/mca_ras_slurm.so
/usr/local/lib/openmpi/mca_rcache_vma.la
/usr/local/lib/openmpi/mca_rcache_vma.so
/usr/local/lib/openmpi/mca_rmaps_load_balance.la
/usr/local/lib/openmpi/mca_rmaps_load_balance.so
/usr/local/lib/openmpi/mca_rmaps_rank_file.la
/usr/local/lib/openmpi/mca_rmaps_rank_file.so
/usr/local/lib/openmpi/mca_rmaps_resilient.la
/usr/local/lib/openmpi/mca_rmaps_resilient.so
/usr/local/lib/openmpi/mca_rmaps_round_robin.la
/usr/local/lib/openmpi/mca_rmaps_round_robin.so
/usr/local/lib/openmpi/mca_rmaps_seq.la
/usr/local/lib/openmpi/mca_rmaps_seq.so
/usr/local/lib/openmpi/mca_rmaps_topo.la
/usr/local/lib/openmpi/mca_rmaps_topo.so
/usr/local/lib/openmpi/mca_rmcast_tcp.la
/usr/local/lib/openmpi/mca_rmcast_tcp.so
/usr/local/lib/openmpi/mca_rmcast_udp.la
/usr/local/lib/openmpi/mca_rmcast_udp.so
/usr/local/lib/openmpi/mca_rml_oob.la
/usr/local/lib/openmpi/mca_rml_oob.so
/usr/local/lib/openmpi/mca_routed_binomial.la
/usr/local/lib/openmpi/mca_routed_binomial.so
/usr/local/lib/openmpi/mca_routed_cm.la
/usr/local/lib/openmpi/mca_routed_cm.so
/usr/local/lib/openmpi/mca_routed_direct.la
/usr/local/lib/openmpi/mca_routed_direct.so
/usr/local/lib/openmpi/mca_routed_linear.la
/usr/local/lib/openmpi/mca_routed_linear.so
/usr/local/lib/openmpi/mca_routed_radix.la
/usr/local/lib/openmpi/mca_routed_radix.so
/usr/local/lib/openmpi/mca_routed_slave.la
/usr/local/lib/openmpi/mca_routed_slave.so
/usr/local/lib/openmpi/mca_shmem_mmap.la
/usr/local/lib/openmpi/mca_shmem_mmap.so
/usr/local/lib/openmpi/mca_shmem_posix.la
/usr/local/lib/openmpi/mca_shmem_posix.so
/usr/local/lib/openmpi/mca_shmem_sysv.la
/usr/local/lib/openmpi/mca_shmem_sysv.so
/usr/local/lib/openmpi/mca_sysinfo_darwin.la
/usr/local/lib/openmpi/mca_sysinfo_darwin.so
/usr/local/lib/openmpi/mca_topo_unity.la
/usr/local/lib/openmpi/mca_topo_unity.so
/usr/local/lib/openmpi/mca_vprotocol_pessimist.la
/usr/local/lib/openmpi/mca_vprotocol_pessimist.so
/usr/local/lib/pkgconfig/ompi-c.pc
/usr/local/lib/pkgconfig/ompi-cxx.pc
/usr/local/lib/pkgconfig/ompi-f77.pc
/usr/local/lib/pkgconfig/ompi-f90.pc
/usr/local/lib/pkgconfig/ompi.pc
find: /usr/local/mysql-5.5.22-osx10.6-x86/data/performance_schema: Permission denied
/usr/local/mysql-5.5.22-osx10.6-x86/include/my_compiler.h
/usr/local/mysql-5.5.22-osx10.6-x86/mysql-test/suite/sys_vars/r/version_compile_machine_basic.result
/usr/local/mysql-5.5.22-osx10.6-x86/mysql-test/suite/sys_vars/r/version_compile_os_basic.result
/usr/local/mysql-5.5.22-osx10.6-x86/mysql-test/suite/sys_vars/t/version_compile_machine_basic.test
/usr/local/mysql-5.5.22-osx10.6-x86/mysql-test/suite/sys_vars/t/version_compile_os_basic.test
/usr/local/share/man/man1/mpic++.1
/usr/local/share/man/man1/mpicc.1
/usr/local/share/man/man1/mpicxx.1
/usr/local/share/man/man1/mpiexec.1
/usr/local/share/man/man1/mpif77.1
/usr/local/share/man/man1/mpif90.1
/usr/local/share/man/man1/mpirun.1
/usr/local/share/man/man1/ompi-clean.1
/usr/local/share/man/man1/ompi-iof.1
/usr/local/share/man/man1/ompi-probe.1
/usr/local/share/man/man1/ompi-profiler.1
/usr/local/share/man/man1/ompi-ps.1
/usr/local/share/man/man1/ompi-server.1
/usr/local/share/man/man1/ompi-top.1
/usr/local/share/man/man1/ompi_info.1
/usr/local/share/man/man7/ompi_crcp.7
/usr/local/share/openmpi
/usr/local/share/openmpi/amca-param-sets
/usr/local/share/openmpi/amca-param-sets/example.conf
/usr/local/share/openmpi/help-coll-sync.txt
/usr/local/share/openmpi/help-dash-host.txt
/usr/local/share/openmpi/help-ess-base.txt
/usr/local/share/openmpi/help-hostfile.txt
/usr/local/share/openmpi/help-mca-base.txt
/usr/local/share/openmpi/help-mca-bml-r2.txt
/usr/local/share/openmpi/help-mca-coll-base.txt
/usr/local/share/openmpi/help-mca-op-base.txt
/usr/local/share/openmpi/help-mca-param.txt
/usr/local/share/openmpi/help-mpi-api.txt
/usr/local/share/openmpi/help-mpi-btl-base.txt
/usr/local/share/openmpi/help-mpi-btl-sm.txt
/usr/local/share/openmpi/help-mpi-btl-tcp.txt
/usr/local/share/openmpi/help-mpi-coll-sm.txt
/usr/local/share/openmpi/help-mpi-common-sm.txt
/usr/local/share/openmpi/help-mpi-errors.txt
/usr/local/share/openmpi/help-mpi-pml-bfo.txt
/usr/local/share/openmpi/help-mpi-pml-csum.txt
/usr/local/share/openmpi/help-mpi-pml-ob1.txt
/usr/local/share/openmpi/help-mpi-runtime.txt
/usr/local/share/openmpi/help-mpool-base.txt
/usr/local/share/openmpi/help-odls-default.txt
/usr/local/share/openmpi/help-ompi-crcp-base.txt
/usr/local/share/openmpi/help-ompi-dpm-base.txt
/usr/local/share/openmpi/help-ompi-dpm-orte.txt
/usr/local/share/openmpi/help-ompi-probe.txt
/usr/local/share/openmpi/help-ompi-profiler.txt
/usr/local/share/openmpi/help-ompi-pubsub-orte.txt
/usr/local/share/openmpi/help-ompi-server.txt
/usr/local/share/openmpi/help-ompi_info.txt
/usr/local/share/openmpi/help-oob-tcp.txt
/usr/local/share/openmpi/help-opal-carto-file.txt
/usr/local/share/openmpi/help-opal-crs-base.txt
/usr/local/share/openmpi/help-opal-crs-none.txt
/usr/local/share/openmpi/help-opal-maffinity-hwloc.txt
/usr/local/share/openmpi/help-opal-runtime.txt
/usr/local/share/openmpi/help-opal-shmem-mmap.txt
/usr/local/share/openmpi/help-opal-shmem-posix.txt
/usr/local/share/openmpi/help-opal-shmem-sysv.txt
/usr/local/share/openmpi/help-opal-util.txt
/usr/local/share/openmpi/help-opal-wrapper.txt
/usr/local/share/openmpi/help-orte-clean.txt
/usr/local/share/openmpi/help-orte-filem-base.txt
/usr/local/share/openmpi/help-orte-filem-rsh.txt
/usr/local/share/openmpi/help-orte-iof.txt
/usr/local/share/openmpi/help-orte-notifier-command.txt
/usr/local/share/openmpi/help-orte-odls-base.txt
/usr/local/share/openmpi/help-orte-ps.txt
/usr/local/share/openmpi/help-orte-rmaps-base.txt
/usr/local/share/openmpi/help-orte-rmaps-lb.txt
/usr/local/share/openmpi/help-orte-rmaps-resilient.txt
/usr/local/share/openmpi/help-orte-rmaps-rr.txt
/usr/local/share/openmpi/help-orte-rmaps-seq.txt
/usr/local/share/openmpi/help-orte-rmaps-topo.txt
/usr/local/share/openmpi/help-orte-rmcast-udp.txt
/usr/local/share/openmpi/help-orte-runtime.txt
/usr/local/share/openmpi/help-orte-snapc-base.txt
/usr/local/share/openmpi/help-orte-top.txt
/usr/local/share/openmpi/help-orted.txt
/usr/local/share/openmpi/help-orterun.txt
/usr/local/share/openmpi/help-plm-base.txt
/usr/local/share/openmpi/help-plm-rsh.txt
/usr/local/share/openmpi/help-plm-slurm.txt
/usr/local/share/openmpi/help-ras-base.txt
/usr/local/share/openmpi/help-ras-slurm.txt
/usr/local/share/openmpi/help-regex.txt
/usr/local/share/openmpi/help-rmaps_rank_file.txt
/usr/local/share/openmpi/help-rmcast-base.txt
/usr/local/share/openmpi/mpic++-vt-wrapper-data.txt
/usr/local/share/openmpi/mpic++-wrapper-data.txt
/usr/local/share/openmpi/mpicc-vt-wrapper-data.txt
/usr/local/share/openmpi/mpicc-wrapper-data.txt
/usr/local/share/openmpi/mpicxx-vt-wrapper-data.txt
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/usr/local/share/openmpi/mpif77-wrapper-data.txt
/usr/local/share/openmpi/mpif90-vt-wrapper-data.txt
/usr/local/share/openmpi/mpif90-wrapper-data.txt
/usr/local/share/openmpi/openmpi-valgrind.supp
/usr/local/share/openmpi/ortec++-wrapper-data.txt
/usr/local/share/openmpi/ortecc-wrapper-data.txt
/usr/local/share/vampirtrace
/usr/local/share/vampirtrace/doc
/usr/local/share/vampirtrace/doc/ChangeLog
/usr/local/share/vampirtrace/doc/LICENSE
/usr/local/share/vampirtrace/doc/opari
/usr/local/share/vampirtrace/doc/opari/ChangeLog
/usr/local/share/vampirtrace/doc/opari/lacsi01.pdf
/usr/local/share/vampirtrace/doc/opari/LICENSE
/usr/local/share/vampirtrace/doc/opari/opari-logo-100.gif
/usr/local/share/vampirtrace/doc/opari/Readme.html
/usr/local/share/vampirtrace/doc/otf
/usr/local/share/vampirtrace/doc/otf/ChangeLog
/usr/local/share/vampirtrace/doc/otf/LICENSE
/usr/local/share/vampirtrace/doc/otf/otfprofile.pdf
/usr/local/share/vampirtrace/doc/otf/otfprofile_clustering.pdf
/usr/local/share/vampirtrace/doc/otf/otftools.pdf
/usr/local/share/vampirtrace/doc/otf/specification.pdf
/usr/local/share/vampirtrace/doc/UserManual.html
/usr/local/share/vampirtrace/doc/UserManual.pdf
/usr/local/share/vampirtrace/doc/vtsetup
/usr/local/share/vampirtrace/doc/vtsetup/ChangeLog
/usr/local/share/vampirtrace/doc/vtsetup/LICENSE
/usr/local/share/vampirtrace/FILTER.SPEC
/usr/local/share/vampirtrace/GROUPS.SPEC
/usr/local/share/vampirtrace/libtool
/usr/local/share/vampirtrace/METRICS.SPEC
/usr/local/share/vampirtrace/TAUINST.SPEC
/usr/local/share/vampirtrace/vtc++-wrapper-data.txt
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/usr/local/share/vampirtrace/vtf90-wrapper-data.txt
/usr/local/share/vampirtrace/vtsetup-data.dtd
/usr/local/share/vampirtrace/vtsetup-data.xml
/usr/local/texlive/2011/bin/universal-darwin/teckit_compile
/usr/local/texlive/2011/bin/x86_64-darwin/teckit_compile
/usr/local/texlive/2011/texmf-dist/doc/generic/wsuipa/compilefonts
/usr/local/texlive/2011/texmf-dist/doc/latex/apprends-latex/exemples/seraphin-lampion.jpg
/usr/local/texlive/2011/texmf-dist/doc/latex/arsclassica/Italian/Immagini/esempio_1.jpg
/usr/local/texlive/2011/texmf-dist/doc/latex/arsclassica/Italian/Immagini/esempio_2.jpg
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/usr/local/texlive/2011/texmf-dist/doc/latex/arsclassica/Italian/Immagini/esempio_4.jpg
/usr/local/texlive/2011/texmf-dist/doc/latex/bardiag/example/compile.all
/usr/local/texlive/2011/texmf-dist/doc/latex/cmpica
/usr/local/texlive/2011/texmf-dist/doc/latex/cmpica/README
/usr/local/texlive/2011/texmf-dist/doc/latex/oberdiek/stampinclude.pdf
/usr/local/texlive/2011/texmf-dist/doc/latex/suftesi/esempiofrontespizio.pdf
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/usr/local/texlive/2011/texmf-dist/doc/latex/xmpincl
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/usr/local/texlive/2011/tlpkg/texworks/Lib/sre_compile.pyc
/usr/local/texlive/2011/tlpkg/texworks/texworks-help/TeXworks-manual/en/CompilingTw.html
/usr/local/texlive/2011/tlpkg/tlpobj/cmpica.tlpobj
/usr/local/texlive/2011/tlpkg/tlpobj/xmpincl.tlpobj

[seb567]

I am pretty sure you have two versions of Open-MPI installed (v1.4.3 and v1.2.8)


Run these:

echo $PATH

echo $LD_LIBRARY_PATH

type mpiexec

type mpicxx

type ompi_info

find /usr/local|grep mpi

Hi,

Thank you so much for your effort helping me,

I did it but I got the following


-- The C compiler identification is GNU 4.2.1
-- The CXX compiler identification is GNU 4.2.1
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done

collect2: ld returned 1 exit status
make[2]: *** [Ray] Error 1
make[1]: *** [CMakeFiles/Ray.dir/all] Error 2
make: *** [all] Error 2

[Saratoga]

Hi,

Thank you so much for your effort helping me,

I did it but I got the following


-- The C compiler identification is GNU 4.2.1
-- The CXX compiler identification is GNU 4.2.1
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /Phylos/Build-with-CMAKE
cyanelle:Build-with-CMAKE cyanelle$ make
Scanning dependencies of target Ray
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/Phylos/Ray-v2.0.0-rc7/code/plugin_SequencesLoader/SequencesLoader.cpp:189: warning: format ?%lu? expects type ?long unsigned int?, but argument 3 has type ?long long unsigned int?
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/Phylos/Ray-v2.0.0-rc7/code/plugin_MessageProcessor/MessageProcessor.cpp:727: warning: comparison between signed and unsigned integer expressions
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/Phylos/Ray-v2.0.0-rc7/code/plugin_Amos/Amos.cpp:136: warning: format ?%lu? expects type ?long unsigned int?, but argument 4 has type ?long long unsigned int?
/Phylos/Ray-v2.0.0-rc7/code/plugin_Amos/Amos.cpp:206: warning: format ?%li? expects type ?long int?, but argument 3 has type ?ReadHandle?
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[ 80%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationDeBruijn.cpp.o
[ 81%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationRandom.cpp.o
[ 82%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/scheduling/TaskCreator.cpp.o
[ 82%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/scheduling/SwitchMan.cpp.o
[ 83%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/scheduling/VirtualProcessor.cpp.o
[ 84%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/profiling/Derivative.cpp.o
[ 85%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/profiling/TimePrinter.cpp.o
[ 85%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/profiling/Profiler.cpp.o
[ 86%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/profiling/TickLogger.cpp.o
[ 87%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/cryptography/crypto.cpp.o
[ 88%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/structures/StaticVector.cpp.o
[ 89%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/ReusableMemoryStore.cpp.o
[ 89%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/ChunkAllocatorWithDefragmentation.cpp.o
[ 90%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/DefragmentationGroup.cpp.o
[ 91%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/RingAllocator.cpp.o
[ 92%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/MyAllocator.cpp.o
[ 92%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/allocator.cpp.o
[ 93%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/DefragmentationLane.cpp.o
[ 94%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/plugins/CorePlugin.cpp.o
[ 95%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/plugins/RegisteredPlugin.cpp.o
[ 96%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/VirtualCommunicator.cpp.o
[ 96%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/MessagesHandler.cpp.o
[ 97%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/MessageRouter.cpp.o
[ 98%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/Message.cpp.o
[ 99%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/mpi_tags.cpp.o
[100%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/BufferedData.cpp.o
Linking CXX executable Ray
Undefined symbols:
"_MPI_Reduce_local", referenced from:
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MachineHelper.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Library.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin LibraryWorker.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin FusionTaskCreator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin NetworkTest.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SequencesLoader.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin GridTable.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin VerticesExtractor.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin JoinerTaskCreator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SeedingData.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin FusionData.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin CoverageGatherer.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TipWatchdog.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SeedExtender.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin VertexMessenger.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin ReadFetcher.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin DepthFirstSearchData.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MessageProcessor.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Partitioner.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SequencesIndexer.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Parameters.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin ray_main.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin common_functions.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Machine.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Amos.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin KmerAcademyBuilder.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin KmerAcademy.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin EdgePurger.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Searcher.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Scaffolder.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin GeneOntology.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin GenomeNeighbourhood.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin PhylogenyViewer.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin ComputeCore.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin OperatingSystem.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SwitchMan.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin VirtualProcessor.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Derivative.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TimePrinter.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Profiler.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TickLogger.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MyAllocator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin allocator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin VirtualCommunicator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MessagesHandler.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MessageRouter.cpp.o
"_MPI_Op_commutative", referenced from:
MPI::Op::Is_commutative() constin MachineHelper.cpp.o
MPI::Op::Is_commutative() constin Library.cpp.o
MPI::Op::Is_commutative() constin LibraryWorker.cpp.o
MPI::Op::Is_commutative() constin FusionTaskCreator.cpp.o
MPI::Op::Is_commutative() constin NetworkTest.cpp.o
MPI::Op::Is_commutative() constin SequencesLoader.cpp.o
MPI::Op::Is_commutative() constin GridTable.cpp.o
MPI::Op::Is_commutative() constin VerticesExtractor.cpp.o
MPI::Op::Is_commutative() constin JoinerTaskCreator.cpp.o
MPI::Op::Is_commutative() constin SeedingData.cpp.o
MPI::Op::Is_commutative() constin FusionData.cpp.o
MPI::Op::Is_commutative() constin CoverageGatherer.cpp.o
MPI::Op::Is_commutative() constin TipWatchdog.cpp.o
MPI::Op::Is_commutative() constin SeedExtender.cpp.o
MPI::Op::Is_commutative() constin VertexMessenger.cpp.o
MPI::Op::Is_commutative() constin ReadFetcher.cpp.o
MPI::Op::Is_commutative() constin DepthFirstSearchData.cpp.o
MPI::Op::Is_commutative() constin MessageProcessor.cpp.o
MPI::Op::Is_commutative() constin Partitioner.cpp.o
MPI::Op::Is_commutative() constin SequencesIndexer.cpp.o
MPI::Op::Is_commutative() constin Parameters.cpp.o
MPI::Op::Is_commutative() constin ray_main.cpp.o
MPI::Op::Is_commutative() constin common_functions.cpp.o
MPI::Op::Is_commutative() constin Machine.cpp.o
MPI::Op::Is_commutative() constin Amos.cpp.o
MPI::Op::Is_commutative() constin KmerAcademyBuilder.cpp.o
MPI::Op::Is_commutative() constin KmerAcademy.cpp.o
MPI::Op::Is_commutative() constin EdgePurger.cpp.o
MPI::Op::Is_commutative() constin Searcher.cpp.o
MPI::Op::Is_commutative() constin Scaffolder.cpp.o
MPI::Op::Is_commutative() constin GeneOntology.cpp.o
MPI::Op::Is_commutative() constin GenomeNeighbourhood.cpp.o
MPI::Op::Is_commutative() constin PhylogenyViewer.cpp.o
MPI::Op::Is_commutative() constin ComputeCore.cpp.o
MPI::Op::Is_commutative() constin OperatingSystem.cpp.o
MPI::Op::Is_commutative() constin SwitchMan.cpp.o
MPI::Op::Is_commutative() constin VirtualProcessor.cpp.o
MPI::Op::Is_commutative() constin Derivative.cpp.o
MPI::Op::Is_commutative() constin TimePrinter.cpp.o
MPI::Op::Is_commutative() constin Profiler.cpp.o
MPI::Op::Is_commutative() constin TickLogger.cpp.o
MPI::Op::Is_commutative() constin MyAllocator.cpp.o
MPI::Op::Is_commutative() constin allocator.cpp.o
MPI::Op::Is_commutative() constin VirtualCommunicator.cpp.o
MPI::Op::Is_commutative() constin MessagesHandler.cpp.o
MPI::Op::Is_commutative() constin MessageRouter.cpp.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [Ray] Error 1
make[1]: *** [CMakeFiles/Ray.dir/all] Error 2
make: *** [all] Error 2

[seb567]

Hi,

You said you used this tutorial to install Open-MPI. In this tutorial, Open-MPI 1.4.3 is installed.

So I guess you installed Open-MPI 1.4.3.

But ompi_info indicates that you have (also) Open-MPI 1.2.8.

I think you are compiling the code with one version, but linking with the other version. That is why there are unresolved symbols.

Can you try what I describe in the next section.



Alternate way


If you have cmake installed, you can build Ray with it instead. CMake is cross-platform.



To build Ray with CMake:


tar xjf Ray-v2.0.0-rc7.tar.bz2

cd Ray-v2.0.0-rc7

remove the line " RayPlatform/scheduling/SwitchMan_adapters.cpp" from CMakeLists.txt

cd ..

mkdir Build-with-CMAKE

cd Build-with-CMAKE

cmake ../Ray-v2.0.0-rc7

make

ls Ray



Let me know if that works for you.

mpicxx -showme:compile
-D_REENTRANT

mpicxx -showme:link
-Wl,-u,_munmap -Wl,-multiply_defined,suppress -lmpi_cxx -lmpi -lopen-rte -lopen-pal

ompi_info -a|head
Open MPI: 1.2.8
Open MPI SVN revision: r19718
Open RTE: 1.2.8
Open RTE SVN revision: r19718
OPAL: 1.2.8
OPAL SVN revision: r19718
MCA backtrace: execinfo (MCA v1.0, API v1.0, Component v1.2.8)
MCA memory: darwin (MCA v1.0, API v1.0, Component v1.2.8)
MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2.8)
MCA timer: darwin (MCA v1.0, API v1.0, Component v1.2.8)

ompi_info -a|grep compiler
C compiler: gcc
C compiler absolute: /usr/bin/gcc
C++ compiler: g++
C++ compiler absolute: /usr/bin/g++
Fortran77 compiler: none
Fortran77 compiler abs: none
Fortran90 compiler: none
Fortran90 compiler abs: none

[Saratoga]

mpicxx -showme:compile
-D_REENTRANT

mpicxx -showme:link
-Wl,-u,_munmap -Wl,-multiply_defined,suppress -lmpi_cxx -lmpi -lopen-rte -lopen-pal

ompi_info -a|head
Open MPI: 1.2.8
Open MPI SVN revision: r19718
Open RTE: 1.2.8
Open RTE SVN revision: r19718
OPAL: 1.2.8
OPAL SVN revision: r19718
MCA backtrace: execinfo (MCA v1.0, API v1.0, Component v1.2.8)
MCA memory: darwin (MCA v1.0, API v1.0, Component v1.2.8)
MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2.8)
MCA timer: darwin (MCA v1.0, API v1.0, Component v1.2.8)

ompi_info -a|grep compiler
C compiler: gcc
C compiler absolute: /usr/bin/gcc
C++ compiler: g++
C++ compiler absolute: /usr/bin/g++
Fortran77 compiler: none
Fortran77 compiler abs: none
Fortran90 compiler: none
Fortran90 compiler abs: none

[seb567]

What is the output of this:

mpicxx -showme:compile

mpicxx -showme:link

ompi_info -a|head

ompi_info -a|grep compiler

Maybe you installed 2 MPI libraries and it is linking against the wrong one.

Hi,

This is the log



Compilation options (you can change them of course)

PREFIX = install-prefix
MAXKMERLENGTH = 32
FORCE_PACKING = n
ASSERT = n
HAVE_LIBZ = n
HAVE_LIBBZ2 = n
INTEL_COMPILER = n
MPICXX = mpicxx
GPROF = n
OPTIMIZE = y
DEBUG = n


mpicxx code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
Undefined symbols:
"_MPI_Reduce_local", referenced from:
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(ray_main.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) TheRayGenomeAssembler.a(CoverageGatherer.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GenomeNeighbourhood.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(PhylogenyViewer.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(TimePrinter.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(FusionTaskCreator.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GeneOntology.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(MessageRouter.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(FusionData.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Partitioner.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(TipWatchdog.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [Ray] Error 1

[seb567]

Where did it seg fault exactly ?

My Mac is a MacPro 2x2.66 6-core Intel xeon
16 GB RAM

Ray was running but causing segmentation faults. So I decided to recompile after the compilers update and then the problem showed up.

Thanks!

[Saratoga]

My Mac is a MacPro 2x2.66 6-core Intel xeon
16 GB RAM

Ray was running but causing segmentation faults. So I decided to recompile after the compilers update and then the problem showed up.

Thanks!

[Saratoga]

Hi,

This is the log



Compilation options (you can change them of course)

PREFIX = install-prefix
MAXKMERLENGTH = 32
FORCE_PACKING = n
ASSERT = n
HAVE_LIBZ = n
HAVE_LIBBZ2 = n
INTEL_COMPILER = n
MPICXX = mpicxx
GPROF = n
OPTIMIZE = y
DEBUG = n

Compilation and linking flags (generated automatically)

CXXFLAGS = -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\"
LDFLAGS =

mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/ReusableMemoryStore.o memory/ReusableMemoryStore.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/MyAllocator.o memory/MyAllocator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/RingAllocator.o memory/RingAllocator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/allocator.o memory/allocator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/DefragmentationGroup.o memory/DefragmentationGroup.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/ChunkAllocatorWithDefragmentation.o memory/ChunkAllocatorWithDefragmentation.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/DefragmentationLane.o memory/DefragmentationLane.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementation.o routing/GraphImplementation.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationRandom.o routing/GraphImplementationRandom.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationComplete.o routing/GraphImplementationComplete.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationDeBruijn.o routing/GraphImplementationDeBruijn.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationKautz.o routing/GraphImplementationKautz.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationExperimental.o routing/GraphImplementationExperimental.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationGroup.o routing/GraphImplementationGroup.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/ConnectionGraph.o routing/ConnectionGraph.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/mpi_tags.o communication/mpi_tags.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/VirtualCommunicator.o communication/VirtualCommunicator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/BufferedData.o communication/BufferedData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/Message.o communication/Message.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/MessagesHandler.o communication/MessagesHandler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/MessageRouter.o communication/MessageRouter.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o scheduling/VirtualProcessor.o scheduling/VirtualProcessor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o scheduling/TaskCreator.o scheduling/TaskCreator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o scheduling/SwitchMan.o scheduling/SwitchMan.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/slave_modes.o core/slave_modes.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/OperatingSystem.o core/OperatingSystem.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/master_modes.o core/master_modes.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/ComputeCore.o core/ComputeCore.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/statistics.o core/statistics.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o plugins/CorePlugin.o plugins/CorePlugin.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o plugins/RegisteredPlugin.o plugins/RegisteredPlugin.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o structures/StaticVector.o structures/StaticVector.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o profiling/Profiler.o profiling/Profiler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o profiling/Derivative.o profiling/Derivative.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o profiling/TickLogger.o profiling/TickLogger.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o profiling/TimePrinter.o profiling/TimePrinter.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/SlaveModeHandler.o handlers/SlaveModeHandler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/MasterModeHandler.o handlers/MasterModeHandler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/MessageTagHandler.o handlers/MessageTagHandler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/MasterModeExecutor.o handlers/MasterModeExecutor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/SlaveModeExecutor.o handlers/SlaveModeExecutor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/MessageTagExecutor.o handlers/MessageTagExecutor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o cryptography/crypto.o cryptography/crypto.cpp
ar rcs libRayPlatform.a memory/ReusableMemoryStore.o memory/MyAllocator.o memory/RingAllocator.o memory/allocator.o memory/DefragmentationGroup.o memory/ChunkAllocatorWithDefragmentation.o memory/DefragmentationLane.o routing/GraphImplementation.o routing/GraphImplementationRandom.o routing/GraphImplementationComplete.o routing/GraphImplementationDeBruijn.o routing/GraphImplementationKautz.o routing/GraphImplementationExperimental.o routing/GraphImplementationGroup.o routing/ConnectionGraph.o communication/mpi_tags.o communication/VirtualCommunicator.o communication/BufferedData.o communication/Message.o communication/MessagesHandler.o communication/MessageRouter.o scheduling/VirtualProcessor.o scheduling/TaskCreator.o scheduling/SwitchMan.o core/slave_modes.o core/OperatingSystem.o core/master_modes.o core/ComputeCore.o core/statistics.o plugins/CorePlugin.o plugins/RegisteredPlugin.o structures/StaticVector.o profiling/Profiler.o profiling/Derivative.o profiling/TickLogger.o profiling/TimePrinter.o handlers/SlaveModeHandler.o handlers/MasterModeHandler.o handlers/MessageTagHandler.o handlers/MasterModeExecutor.o handlers/SlaveModeExecutor.o handlers/MessageTagExecutor.o cryptography/crypto.o
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o application_core/ray_main.o application_core/ray_main.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o application_core/Machine.o application_core/Machine.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o application_core/Parameters.o application_core/Parameters.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o application_core/common_functions.o application_core/common_functions.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Amos/Amos.o plugin_Amos/Amos.cpp
plugin_Amos/Amos.cpp: In member function ‘void Amos::call_RAY_SLAVE_MODE_AMOS()’:
plugin_Amos/Amos.cpp:136: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’
plugin_Amos/Amos.cpp:206: warning: format ‘%li’ expects type ‘long int’, but argument 3 has type ‘ReadHandle’
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_CoverageGatherer/CoverageGatherer.o plugin_CoverageGatherer/CoverageGatherer.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_CoverageGatherer/CoverageDistribution.o plugin_CoverageGatherer/CoverageDistribution.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_EdgePurger/EdgePurger.o plugin_EdgePurger/EdgePurger.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_EdgePurger/EdgePurgerWorker.o plugin_EdgePurger/EdgePurgerWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_FusionData/FusionData.o plugin_FusionData/FusionData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_FusionTaskCreator/FusionWorker.o plugin_FusionTaskCreator/FusionWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_FusionTaskCreator/FusionTaskCreator.o plugin_FusionTaskCreator/FusionTaskCreator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GeneOntology/KeyEncoder.o plugin_GeneOntology/KeyEncoder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GeneOntology/GeneOntology.o plugin_GeneOntology/GeneOntology.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GenomeNeighbourhood/GenomeNeighbourhood.o plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GenomeNeighbourhood/Neighbour.o plugin_GenomeNeighbourhood/Neighbour.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GenomeNeighbourhood/NeighbourPair.o plugin_GenomeNeighbourhood/NeighbourPair.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_JoinerTaskCreator/JoinerWorker.o plugin_JoinerTaskCreator/JoinerWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_JoinerTaskCreator/JoinerTaskCreator.o plugin_JoinerTaskCreator/JoinerTaskCreator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/KmerAcademyBuilder.o plugin_KmerAcademyBuilder/KmerAcademyBuilder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/BloomFilter.o plugin_KmerAcademyBuilder/BloomFilter.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/Kmer.o plugin_KmerAcademyBuilder/Kmer.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/KmerAcademy.o plugin_KmerAcademyBuilder/KmerAcademy.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/KmerAcademyIterator.o plugin_KmerAcademyBuilder/KmerAcademyIterator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Library/LibraryPeakFinder.o plugin_Library/LibraryPeakFinder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Library/LibraryWorker.o plugin_Library/LibraryWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Library/Library.o plugin_Library/Library.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_MachineHelper/MachineHelper.o plugin_MachineHelper/MachineHelper.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_MessageProcessor/MessageProcessor.o plugin_MessageProcessor/MessageProcessor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_NetworkTest/NetworkTest.o plugin_NetworkTest/NetworkTest.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Partitioner/Partitioner.o plugin_Partitioner/Partitioner.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/PhylogenyViewer.o plugin_PhylogenyViewer/PhylogenyViewer.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/GenomeToTaxonLoader.o plugin_PhylogenyViewer/GenomeToTaxonLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/PhylogeneticTreeLoader.o plugin_PhylogenyViewer/PhylogeneticTreeLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/TaxonNameLoader.o plugin_PhylogenyViewer/TaxonNameLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/Scaffolder.o plugin_Scaffolder/Scaffolder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingLink.o plugin_Scaffolder/ScaffoldingLink.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/SummarizedLink.o plugin_Scaffolder/SummarizedLink.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingAlgorithm.o plugin_Scaffolder/ScaffoldingAlgorithm.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingVertex.o plugin_Scaffolder/ScaffoldingVertex.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingEdge.o plugin_Scaffolder/ScaffoldingEdge.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/Searcher.o plugin_Searcher/Searcher.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/SearchDirectory.o plugin_Searcher/SearchDirectory.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/ContigSearchEntry.o plugin_Searcher/ContigSearchEntry.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/ContigHit.o plugin_Searcher/ContigHit.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/ColorSet.o plugin_Searcher/ColorSet.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/VirtualKmerColor.o plugin_Searcher/VirtualKmerColor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/QualityCaller.o plugin_Searcher/QualityCaller.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/DistributionWriter.o plugin_Searcher/DistributionWriter.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/ColoredPeakFinder.o plugin_Searcher/ColoredPeakFinder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/SeedExtender.o plugin_SeedExtender/SeedExtender.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/Direction.o plugin_SeedExtender/Direction.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/VertexMessenger.o plugin_SeedExtender/VertexMessenger.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/ReadFetcher.o plugin_SeedExtender/ReadFetcher.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/BubbleTool.o plugin_SeedExtender/BubbleTool.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/Chooser.o plugin_SeedExtender/Chooser.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/OpenAssemblerChooser.o plugin_SeedExtender/OpenAssemblerChooser.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/TipWatchdog.o plugin_SeedExtender/TipWatchdog.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/NovaEngine.o plugin_SeedExtender/NovaEngine.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/ExtensionElement.o plugin_SeedExtender/ExtensionElement.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/DepthFirstSearchData.o plugin_SeedExtender/DepthFirstSearchData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/ExtensionData.o plugin_SeedExtender/ExtensionData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedingData/AssemblySeed.o plugin_SeedingData/AssemblySeed.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedingData/SeedWorker.o plugin_SeedingData/SeedWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedingData/SeedingData.o plugin_SeedingData/SeedingData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/SequencesIndexer.o plugin_SequencesIndexer/SequencesIndexer.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/IndexerWorker.o plugin_SequencesIndexer/IndexerWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/PairedRead.o plugin_SequencesIndexer/PairedRead.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/ReadAnnotation.o plugin_SequencesIndexer/ReadAnnotation.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/SequencesLoader.o plugin_SequencesLoader/SequencesLoader.cpp
plugin_SequencesLoader/SequencesLoader.cpp: In member function ‘bool SequencesLoader::writeSequencesToAMOSFile(int, int, StaticVector*, RingAllocator*, bool*, BubbleData*, time_t*, Parameters*, int*, int*)’:
plugin_SequencesLoader/SequencesLoader.cpp:189: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’
plugin_SequencesLoader/SequencesLoader.cpp:189: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/Read.o plugin_SequencesLoader/Read.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/ArrayOfReads.o plugin_SequencesLoader/ArrayOfReads.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/ColorSpaceDecoder.o plugin_SequencesLoader/ColorSpaceDecoder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/ColorSpaceLoader.o plugin_SequencesLoader/ColorSpaceLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/FastaLoader.o plugin_SequencesLoader/FastaLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/FastqLoader.o plugin_SequencesLoader/FastqLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/SffLoader.o plugin_SequencesLoader/SffLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/Loader.o plugin_SequencesLoader/Loader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/VerticesExtractor.o plugin_VerticesExtractor/VerticesExtractor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/GridTable.o plugin_VerticesExtractor/GridTable.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/GridTableIterator.o plugin_VerticesExtractor/GridTableIterator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/Vertex.o plugin_VerticesExtractor/Vertex.cpp
ar rcs TheRayGenomeAssembler.a application_core/ray_main.o application_core/Machine.o application_core/Parameters.o application_core/common_functions.o plugin_Amos/Amos.o plugin_CoverageGatherer/CoverageGatherer.o plugin_CoverageGatherer/CoverageDistribution.o plugin_EdgePurger/EdgePurger.o plugin_EdgePurger/EdgePurgerWorker.o plugin_FusionData/FusionData.o plugin_FusionTaskCreator/FusionWorker.o plugin_FusionTaskCreator/FusionTaskCreator.o plugin_GeneOntology/KeyEncoder.o plugin_GeneOntology/GeneOntology.o plugin_GenomeNeighbourhood/GenomeNeighbourhood.o plugin_GenomeNeighbourhood/Neighbour.o plugin_GenomeNeighbourhood/NeighbourPair.o plugin_JoinerTaskCreator/JoinerWorker.o plugin_JoinerTaskCreator/JoinerTaskCreator.o plugin_KmerAcademyBuilder/KmerAcademyBuilder.o plugin_KmerAcademyBuilder/BloomFilter.o plugin_KmerAcademyBuilder/Kmer.o plugin_KmerAcademyBuilder/KmerAcademy.o plugin_KmerAcademyBuilder/KmerAcademyIterator.o plugin_Library/LibraryPeakFinder.o plugin_Library/LibraryWorker.o plugin_Library/Library.o plugin_MachineHelper/MachineHelper.o plugin_MessageProcessor/MessageProcessor.o plugin_NetworkTest/NetworkTest.o plugin_Partitioner/Partitioner.o plugin_PhylogenyViewer/PhylogenyViewer.o plugin_PhylogenyViewer/GenomeToTaxonLoader.o plugin_PhylogenyViewer/PhylogeneticTreeLoader.o plugin_PhylogenyViewer/TaxonNameLoader.o plugin_Scaffolder/Scaffolder.o plugin_Scaffolder/ScaffoldingLink.o plugin_Scaffolder/SummarizedLink.o plugin_Scaffolder/ScaffoldingAlgorithm.o plugin_Scaffolder/ScaffoldingVertex.o plugin_Scaffolder/ScaffoldingEdge.o plugin_Searcher/Searcher.o plugin_Searcher/SearchDirectory.o plugin_Searcher/ContigSearchEntry.o plugin_Searcher/ContigHit.o plugin_Searcher/ColorSet.o plugin_Searcher/VirtualKmerColor.o plugin_Searcher/QualityCaller.o plugin_Searcher/DistributionWriter.o plugin_Searcher/ColoredPeakFinder.o plugin_SeedExtender/SeedExtender.o plugin_SeedExtender/Direction.o plugin_SeedExtender/VertexMessenger.o plugin_SeedExtender/ReadFetcher.o plugin_SeedExtender/BubbleTool.o plugin_SeedExtender/Chooser.o plugin_SeedExtender/OpenAssemblerChooser.o plugin_SeedExtender/TipWatchdog.o plugin_SeedExtender/NovaEngine.o plugin_SeedExtender/ExtensionElement.o plugin_SeedExtender/DepthFirstSearchData.o plugin_SeedExtender/ExtensionData.o plugin_SeedingData/AssemblySeed.o plugin_SeedingData/SeedWorker.o plugin_SeedingData/SeedingData.o plugin_SequencesIndexer/SequencesIndexer.o plugin_SequencesIndexer/IndexerWorker.o plugin_SequencesIndexer/PairedRead.o plugin_SequencesIndexer/ReadAnnotation.o plugin_SequencesLoader/SequencesLoader.o plugin_SequencesLoader/Read.o plugin_SequencesLoader/ArrayOfReads.o plugin_SequencesLoader/ColorSpaceDecoder.o plugin_SequencesLoader/ColorSpaceLoader.o plugin_SequencesLoader/FastaLoader.o plugin_SequencesLoader/FastqLoader.o plugin_SequencesLoader/SffLoader.o plugin_SequencesLoader/Loader.o plugin_VerticesExtractor/VerticesExtractor.o plugin_VerticesExtractor/GridTable.o plugin_VerticesExtractor/GridTableIterator.o plugin_VerticesExtractor/Vertex.o
mpicxx code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
Undefined symbols:
"_MPI_Reduce_local", referenced from:
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(ray_main.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Machine.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(MachineHelper.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(MessageProcessor.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(EdgePurger.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Searcher.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(OperatingSystem.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(JoinerTaskCreator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Parameters.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(SeedExtender.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(ComputeCore.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(SwitchMan.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(MessagesHandler.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(SequencesLoader.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Amos.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(CoverageGatherer.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(GenomeNeighbourhood.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(PhylogenyViewer.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(TimePrinter.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(FusionTaskCreator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(GeneOntology.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(MessageRouter.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(FusionData.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Partitioner.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(SeedingData.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(VerticesExtractor.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(VirtualProcessor.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Scaffolder.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(TickLogger.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(KmerAcademyBuilder.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Library.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(NetworkTest.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(GridTable.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(Derivative.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(SequencesIndexer.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(MyAllocator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(VirtualCommunicator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(Profiler.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(LibraryWorker.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(KmerAcademy.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(common_functions.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(VertexMessenger.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(ReadFetcher.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(allocator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(DepthFirstSearchData.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(TipWatchdog.o)
"_MPI_Op_commutative", referenced from:
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(ray_main.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Machine.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(MachineHelper.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(MessageProcessor.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(EdgePurger.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Searcher.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(OperatingSystem.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(JoinerTaskCreator.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Parameters.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(SeedExtender.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(ComputeCore.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(SwitchMan.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(MessagesHandler.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(SequencesLoader.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Amos.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(CoverageGatherer.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GenomeNeighbourhood.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(PhylogenyViewer.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(TimePrinter.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(FusionTaskCreator.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GeneOntology.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(MessageRouter.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(FusionData.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Partitioner.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(SeedingData.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(VerticesExtractor.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(VirtualProcessor.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Scaffolder.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(TickLogger.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(KmerAcademyBuilder.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Library.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(NetworkTest.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GridTable.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(Derivative.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(SequencesIndexer.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(MyAllocator.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(VirtualCommunicator.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(Profiler.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(LibraryWorker.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(KmerAcademy.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(common_functions.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(VertexMessenger.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(ReadFetcher.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(allocator.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(DepthFirstSearchData.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(TipWatchdog.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [Ray] Error 1

[seb567]

I did test Ray on a Apple PowerBook G4 (PowerPC) running Linux and a Sun SunBlade 100 (Sparc).

What is the hardware of your Mac ?

Is it an Intel processor ?

I think Xcode on Mac OS is based of LLVM.

I remember that LLVM had problems linking sometimes of GNU/Linux for various applications.

Does that work at all on your Mac ?


mpiexec -n 3 date

Hi,

I'm very new in this arena.

I installed Ray 2.0 in MacOS (Snow Leopard) and I got a segmentation fault. Then I decided to update the compilers following http://sites.google.com/site/dwhipp/.../mac_compilers and then installed Open MPI http://sites.google.com/site/dwhipp/...pi-on-mac-os-x.

After that I tried to compile again but now I get a this error

ld: symbol(s) not found collect2:
ld returned 1 exit status make:
*** [Ray] Error 1

Please Advice

[seb567]

Hi,

You probably installed Ray v2.0.0-rc7 or v2.0.0-rc5 as v2.0.0 is not released yet !

Can you provide all the log of your compilation.

cd Ray-v2.0.0-rc7
make clean
make &> make.log

You can use http://pastebin.com

Hi,

I'm very new in this arena.

I installed Ray 2.0 in MacOS (Snow Leopard) and I got a segmentation fault. Then I decided to update the compilers following http://sites.google.com/site/dwhipp/.../mac_compilers and then installed Open MPI http://sites.google.com/site/dwhipp/...pi-on-mac-os-x.

After that I tried to compile again but now I get a this error

ld: symbol(s) not found collect2:
ld returned 1 exit status make:
*** [Ray] Error 1

Please Advice

[Saratoga]

Hi,

I'm very new in this arena.

I installed Ray 2.0 in MacOS (Snow Leopard) and I got a segmentation fault. Then I decided to update the compilers following http://sites.google.com/site/dwhipp/.../mac_compilers and then installed Open MPI http://sites.google.com/site/dwhipp/...pi-on-mac-os-x.

After that I tried to compile again but now I get a this error

ld: symbol(s) not found collect2:
ld returned 1 exit status make:
*** [Ray] Error 1

Please Advice