Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • seb567
    replied
    OK good luck with that.



    Originally posted by Saratoga View Post
    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

    Leave a comment:


  • Saratoga
    replied
    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

    Leave a comment:


  • seb567
    replied
    You are compiling with /usr/bin/mpicxx, but you are probably not linking with the related library.

    This information will be provided by


    Code:
    echo $LD_LIBRARY_PATH
    Code:
    /usr/bin/mpiexec --version
    Code:
    /usr/local/bin/mpiexec --version
    We are closing in on the problem.

    Originally posted by Saratoga View Post
    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

    Leave a comment:


  • Saratoga
    replied
    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
    /usr/local/share/openmpi/mpicxx-wrapper-data.txt
    /usr/local/share/openmpi/mpif77-vt-wrapper-data.txt
    /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
    /usr/local/share/vampirtrace/vtcc-wrapper-data.txt
    /usr/local/share/vampirtrace/vtcxx-wrapper-data.txt
    /usr/local/share/vampirtrace/vtf77-wrapper-data.txt
    /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
    /usr/local/texlive/2011/texmf-dist/doc/latex/arsclassica/Italian/Immagini/esempio_3.jpg
    /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
    /usr/local/texlive/2011/texmf-dist/doc/latex/tkz-fct/latex/TKZdoc-fct-compilation.tex
    /usr/local/texlive/2011/texmf-dist/doc/latex/xmpincl
    /usr/local/texlive/2011/texmf-dist/doc/latex/xmpincl/license.xmp
    /usr/local/texlive/2011/texmf-dist/doc/latex/xmpincl/README
    /usr/local/texlive/2011/texmf-dist/doc/latex/xmpincl/xmpincl.pdf
    /usr/local/texlive/2011/texmf-dist/doc/metapost/base/mpintro.pdf
    /usr/local/texlive/2011/texmf-dist/doc/metapost/base/source-tutorial/compilation.tex
    /usr/local/texlive/2011/texmf-dist/doc/metapost/base/source-tutorial/mpintro.bib
    /usr/local/texlive/2011/texmf-dist/doc/metapost/base/source-tutorial/mpintro.ltx
    /usr/local/texlive/2011/texmf-dist/fonts/source/public/cmpica
    /usr/local/texlive/2011/texmf-dist/fonts/source/public/cmpica/cmpica.mf
    /usr/local/texlive/2011/texmf-dist/fonts/source/public/cmpica/cmpicab.mf
    /usr/local/texlive/2011/texmf-dist/fonts/source/public/cmpica/cmpicati.mf
    /usr/local/texlive/2011/texmf-dist/fonts/source/public/cmpica/pcpunct.mf
    /usr/local/texlive/2011/texmf-dist/fonts/source/public/cmpica/pica.mf
    /usr/local/texlive/2011/texmf-dist/fonts/source/public/ibygrk/sampi4.mf
    /usr/local/texlive/2011/texmf-dist/fonts/tfm/public/cmpica
    /usr/local/texlive/2011/texmf-dist/fonts/tfm/public/cmpica/cmpica.tfm
    /usr/local/texlive/2011/texmf-dist/fonts/tfm/public/cmpica/cmpicab.tfm
    /usr/local/texlive/2011/texmf-dist/fonts/tfm/public/cmpica/cmpicati.tfm
    /usr/local/texlive/2011/texmf-dist/source/latex/oberdiek/stampinclude.dtx
    /usr/local/texlive/2011/texmf-dist/source/latex/prosper/compilation.fig
    /usr/local/texlive/2011/texmf-dist/source/latex/xmpincl
    /usr/local/texlive/2011/texmf-dist/source/latex/xmpincl/xmpincl.dtx
    /usr/local/texlive/2011/texmf-dist/source/latex/xmpincl/xmpincl.ins
    /usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/stampinclude.sty
    /usr/local/texlive/2011/texmf-dist/tex/latex/prosper/compilation.eps
    /usr/local/texlive/2011/texmf-dist/tex/latex/xmpincl
    /usr/local/texlive/2011/texmf-dist/tex/latex/xmpincl/xmpincl.sty
    /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

    Leave a comment:


  • seb567
    replied
    I am pretty sure you have two versions of Open-MPI installed (v1.4.3 and v1.2.8)


    Run these:


    Code:
    echo $PATH
    Code:
    echo $LD_LIBRARY_PATH
    Code:
    type mpiexec
    Code:
    type mpicxx
    Code:
    type ompi_info
    Code:
    find /usr/local|grep mpi

    Originally posted by Saratoga View Post
    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

    Leave a comment:


  • Saratoga
    replied
    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
    [ 0%] Building CXX object CMakeFiles/Ray.dir/code/plugin_MachineHelper/MachineHelper.cpp.o
    [ 1%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Library/Library.cpp.o
    [ 2%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Library/LibraryPeakFinder.cpp.o
    [ 3%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Library/LibraryWorker.cpp.o
    [ 3%] Building CXX object CMakeFiles/Ray.dir/code/plugin_FusionTaskCreator/FusionTaskCreator.cpp.o
    [ 4%] Building CXX object CMakeFiles/Ray.dir/code/plugin_FusionTaskCreator/FusionWorker.cpp.o
    [ 5%] Building CXX object CMakeFiles/Ray.dir/code/plugin_NetworkTest/NetworkTest.cpp.o
    [ 6%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/SequencesLoader.cpp.o
    /Phylos/Ray-v2.0.0-rc7/code/plugin_SequencesLoader/SequencesLoader.cpp: In member function ?bool SequencesLoader::writeSequencesToAMOSFile(int, int, StaticVector*, RingAllocator*, bool*, BubbleData*, time_t*, Parameters*, int*, int*)?:
    /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?
    /Phylos/Ray-v2.0.0-rc7/code/plugin_SequencesLoader/SequencesLoader.cpp:189: warning: format ?%lu? expects type ?long unsigned int?, but argument 4 has type ?long long unsigned int?
    [ 7%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/ArrayOfReads.cpp.o
    [ 7%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/ColorSpaceDecoder.cpp.o
    [ 8%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/FastqGzLoader.cpp.o
    [ 9%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/SffLoader.cpp.o
    [ 10%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/Read.cpp.o
    [ 10%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/FastaLoader.cpp.o
    [ 11%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/BzReader.cpp.o
    [ 12%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/FastqBz2Loader.cpp.o
    [ 13%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/Loader.cpp.o
    [ 14%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/FastqLoader.cpp.o
    [ 14%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/ColorSpaceLoader.cpp.o
    [ 15%] Building CXX object CMakeFiles/Ray.dir/code/plugin_VerticesExtractor/Vertex.cpp.o
    [ 16%] Building CXX object CMakeFiles/Ray.dir/code/plugin_VerticesExtractor/GridTable.cpp.o
    [ 17%] Building CXX object CMakeFiles/Ray.dir/code/plugin_VerticesExtractor/GridTableIterator.cpp.o
    [ 17%] Building CXX object CMakeFiles/Ray.dir/code/plugin_VerticesExtractor/VerticesExtractor.cpp.o
    [ 18%] Building CXX object CMakeFiles/Ray.dir/code/plugin_JoinerTaskCreator/JoinerTaskCreator.cpp.o
    [ 19%] Building CXX object CMakeFiles/Ray.dir/code/plugin_JoinerTaskCreator/JoinerWorker.cpp.o
    [ 20%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedingData/SeedingData.cpp.o
    [ 21%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedingData/SeedWorker.cpp.o
    [ 21%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedingData/AssemblySeed.cpp.o
    [ 22%] Building CXX object CMakeFiles/Ray.dir/code/plugin_FusionData/FusionData.cpp.o
    [ 23%] Building CXX object CMakeFiles/Ray.dir/code/plugin_CoverageGatherer/CoverageGatherer.cpp.o
    [ 24%] Building CXX object CMakeFiles/Ray.dir/code/plugin_CoverageGatherer/CoverageDistribution.cpp.o
    [ 25%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/Direction.cpp.o
    [ 25%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/TipWatchdog.cpp.o
    [ 26%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/Chooser.cpp.o
    [ 27%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/ExtensionElement.cpp.o
    [ 28%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/SeedExtender.cpp.o
    [ 28%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/ExtensionData.cpp.o
    [ 29%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/VertexMessenger.cpp.o
    [ 30%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/ReadFetcher.cpp.o
    [ 31%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/BubbleTool.cpp.o
    [ 32%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/NovaEngine.cpp.o
    [ 32%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/DepthFirstSearchData.cpp.o
    [ 33%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/OpenAssemblerChooser.cpp.o
    [ 34%] Building CXX object CMakeFiles/Ray.dir/code/plugin_MessageProcessor/MessageProcessor.cpp.o
    /Phylos/Ray-v2.0.0-rc7/code/plugin_MessageProcessor/MessageProcessor.cpp: In member function ?void MessageProcessor::call_RAY_MPI_TAG_VERTICES_DATA(Message*)?:
    /Phylos/Ray-v2.0.0-rc7/code/plugin_MessageProcessor/MessageProcessor.cpp:727: warning: comparison between signed and unsigned integer expressions
    [ 35%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Partitioner/Partitioner.cpp.o
    [ 35%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesIndexer/SequencesIndexer.cpp.o
    [ 36%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesIndexer/PairedRead.cpp.o
    [ 37%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesIndexer/ReadAnnotation.cpp.o
    [ 38%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesIndexer/IndexerWorker.cpp.o
    [ 39%] Building CXX object CMakeFiles/Ray.dir/code/application_core/Parameters.cpp.o
    [ 39%] Building CXX object CMakeFiles/Ray.dir/code/application_core/ray_main.cpp.o
    [ 40%] Building CXX object CMakeFiles/Ray.dir/code/application_core/common_functions.cpp.o
    [ 41%] Building CXX object CMakeFiles/Ray.dir/code/application_core/Machine.cpp.o
    [ 42%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Amos/Amos.cpp.o
    /Phylos/Ray-v2.0.0-rc7/code/plugin_Amos/Amos.cpp: In member function ?void Amos::call_RAY_SLAVE_MODE_AMOS()?:
    /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?
    [ 42%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/Kmer.cpp.o
    [ 43%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/KmerAcademyBuilder.cpp.o
    [ 44%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/KmerAcademy.cpp.o
    [ 45%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/BloomFilter.cpp.o
    [ 46%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/KmerAcademyIterator.cpp.o
    [ 46%] Building CXX object CMakeFiles/Ray.dir/code/plugin_EdgePurger/EdgePurger.cpp.o
    [ 47%] Building CXX object CMakeFiles/Ray.dir/code/plugin_EdgePurger/EdgePurgerWorker.cpp.o
    [ 48%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/ColorSet.cpp.o
    [ 49%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/ContigHit.cpp.o
    [ 50%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/Searcher.cpp.o
    [ 50%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/ContigSearchEntry.cpp.o
    [ 51%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/VirtualKmerColor.cpp.o
    [ 52%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/DistributionWriter.cpp.o
    [ 53%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/ColoredPeakFinder.cpp.o
    [ 53%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/QualityCaller.cpp.o
    [ 54%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/SearchDirectory.cpp.o
    [ 55%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/Scaffolder.cpp.o
    [ 56%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/SummarizedLink.cpp.o
    [ 57%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/ScaffoldingAlgorithm.cpp.o
    [ 57%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/ScaffoldingVertex.cpp.o
    [ 58%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/ScaffoldingEdge.cpp.o
    [ 59%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/ScaffoldingLink.cpp.o
    [ 60%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GeneOntology/KeyEncoder.cpp.o
    [ 60%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GeneOntology/GeneOntology.cpp.o
    [ 61%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp.o
    [ 62%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GenomeNeighbourhood/NeighbourPair.cpp.o
    [ 63%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GenomeNeighbourhood/Neighbour.cpp.o
    [ 64%] Building CXX object CMakeFiles/Ray.dir/code/plugin_PhylogenyViewer/GenomeToTaxonLoader.cpp.o
    [ 64%] Building CXX object CMakeFiles/Ray.dir/code/plugin_PhylogenyViewer/PhylogenyViewer.cpp.o
    [ 65%] Building CXX object CMakeFiles/Ray.dir/code/plugin_PhylogenyViewer/PhylogeneticTreeLoader.cpp.o
    [ 66%] Building CXX object CMakeFiles/Ray.dir/code/plugin_PhylogenyViewer/TaxonNameLoader.cpp.o
    [ 67%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/MasterModeExecutor.cpp.o
    [ 67%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/MessageTagHandler.cpp.o
    [ 68%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/SlaveModeHandler.cpp.o
    [ 69%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/MasterModeHandler.cpp.o
    [ 70%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/SlaveModeExecutor.cpp.o
    [ 71%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/MessageTagExecutor.cpp.o
    [ 71%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/master_modes.cpp.o
    [ 72%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/ComputeCore.cpp.o
    [ 73%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/slave_modes.cpp.o
    [ 74%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/OperatingSystem.cpp.o
    [ 75%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/statistics.cpp.o
    [ 75%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationExperimental.cpp.o
    [ 76%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationKautz.cpp.o
    [ 77%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/ConnectionGraph.cpp.o
    [ 78%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementation.cpp.o
    [ 78%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationGroup.cpp.o
    [ 79%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationComplete.cpp.o
    [ 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

    Leave a comment:


  • seb567
    replied
    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.


    Originally posted by Saratoga View Post
    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

    Leave a comment:


  • Saratoga
    replied
    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

    Leave a comment:


  • seb567
    replied
    What is the output of this:

    Code:
    mpicxx -showme:compile
    Code:
    mpicxx -showme:link
    Code:
    ompi_info -a|head
    Code:
    ompi_info -a|grep compiler

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




    Originally posted by Saratoga View Post
    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

    Leave a comment:


  • seb567
    replied
    Where did it seg fault exactly ?

    Originally posted by Saratoga View Post
    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!

    Leave a comment:


  • Saratoga
    replied
    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!

    Leave a comment:


  • Saratoga
    replied
    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

    Leave a comment:


  • seb567
    replied
    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





    Originally posted by Saratoga View Post
    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

    Leave a comment:


  • seb567
    replied
    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


    Originally posted by Saratoga View Post
    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

    Leave a comment:


  • Saratoga
    replied
    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

    Leave a comment:

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 07:20 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
33 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
37 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
41 views
0 likes
Last Post seqadmin  
Working...
X