I see you are running this via "sudo". Unfortunately, that has a peculiar behavior - it resets the environmental variables to something appropriate for root. So I suspect that the library path is not correct as far as mpirun is concerned.
You can check it easily enough - just do "sudo printenv". When I set my ld_library_path and then do that, my envar setting is gone. My suggestion would be to avoid running this as root. Change the permissions on the OMPI binary directory so the tools can be executed by anyone, and then just run mpirun directly. That should fix the problem. On Nov 26, 2011, at 10:22 AM, Markus Stiller wrote: > Hi Castain, > >> You have some major problems with confused installations of MPIs. First, you >> cannot compile an application against>MPICH and expect to run it with OMPI - >> the two are not binary compatible. You need to compile against the >> MPI>installation you intend to run against. > > I did this, sry i didnt tell this. > I tried mpich and openmpi, and of course for each case i compiled againt > mpich and opem mpi > >> Second, your errors appear to be because you are not pointing your library >> path at the OMPI installation, and so the>libraries are not being found. You >> need to set LD_LIBRARY_PATH to include the path to where you installed >> OMPI.>Based on the configure line you give, that would mean ensuring that >> /opt/mpirun/lib was in that envar. Likewise,>/opt/mpirun/bin needs to be in >> your PATH. > > hmm....i installed openmpi in the std location, changed the variables to this > and this works now.... > > But now i have the same problem again (the problem why i wrote u in the first > place): > > markus@linux-6wa6:/media/808CCB178CCB069E/MD Simulations/Test Simu1> sudo > mpirun -n 4 ./DLPOLY.Z > root's password: > [linux-6wa6:05565] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file > runtime/orte_init.c at line 125 > -------------------------------------------------------------------------- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > orte_ess_base_select failed > --> Returned value Not found (-13) instead of ORTE_SUCCESS > -------------------------------------------------------------------------- > [linux-6wa6:05565] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file > orterun.c at line 543 > > > > What can i do with this? > Thx, > Markus > > On 11/25/2011 03:42 AM, Ralph Castain wrote: >> Hi Markus >> >> You have some major problems with confused installations of MPIs. First, you >> cannot compile an application against MPICH and expect to run it with OMPI - >> the two are not binary compatible. You need to compile against the MPI >> installation you intend to run against. >> >> Second, your errors appear to be because you are not pointing your library >> path at the OMPI installation, and so the libraries are not being found. You >> need to set LD_LIBRARY_PATH to include the path to where you installed OMPI. >> Based on the configure line you give, that would mean ensuring that >> /opt/mpirun/lib was in that envar. Likewise, /opt/mpirun/bin needs to be in >> your PATH. >> >> Once you have those correctly set, and build your app against the >> appropriate mpicc, you should be able to run. >> >> BTW: your last message indicates that you built against an old LAM MPI, so >> you appear to have some pretty old software laying around. Perhaps cleaning >> out some of the old MPI installations would help. >> >> >> On Nov 24, 2011, at 4:32 PM, Markus Stiller wrote: >> >>> On 11/24/2011 10:08 PM, MM wrote: >>>> Hi >>>> >>>> I get the same error while linking against home built 1.5.4 openmpi libs on >>>> win32. >>>> I didn't get this error against the prebuilt libs. >>>> >>>> I see you use Suse. There probably is a openmpi.rpm or openmpi.dpkg already >>>> available for Suse which contains the libraries and you could link against >>>> those and that may work >>>> >>>> MM >>>> >>>> -----Original Message----- >>>> From:users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On >>>> Behalf Of Markus Stiller >>>> Sent: 24 November 2011 20:41 >>>> To:us...@open-mpi.org >>>> Subject: [OMPI users] open-mpi error >>>> >>>> Hello, >>>> >>>> i have some problem with mpi, i looked in the FAQ and google already but i >>>> couldnt find a solution. >>>> >>>> To build mpi i used this: >>>> shell$ ./configure --prefix=/opt/mpirun >>>> <...lots of output...> >>>> shell$ make all install >>>> >>>> Worked fine so far. I am using dlpoly, and this makefile: >>>> $(MAKE) LD="mpif90 -o" LDFLAGS="-O3" \ >>>> FC="mpif90 -c" FCFLAGS="-O3" \ >>>> EX=$(EX) BINROOT=$(BINROOT) $(TYPE) >>>> >>>> This worked fine too, >>>> the problem occurs when i want to run a job with >>>> mpiexec -n 4 ./DLPOLY.Z or >>>> mpirun -n 4 ./DLPOLY.z >>>> >>>> I get this error: >>>> -------------------------------------------------------------------------- >>>> [linux-6wa6:02927] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file >>>> orterun.c at line 543 markus@linux-6wa6:/media/808CCB178CCB069E/MD >>>> Simulations/Test Simu1> sudo mpiexec -n 4 ./DLPOLY.Z [linux-6wa6:03731] >>>> [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c >>>> at >>>> line 125 >>>> -------------------------------------------------------------------------- >>>> It looks like orte_init failed for some reason; your parallel process is >>>> likely to abort. There are many reasons that a parallel process can fail >>>> during orte_init; some of which are due to configuration or environment >>>> problems. This failure appears to be an internal failure; here's some >>>> additional information (which may only be relevant to an Open MPI >>>> developer): >>>> >>>> orte_ess_base_select failed >>>> --> Returned value Not found (-13) instead of ORTE_SUCCESS >>>> -------------------------------------------------------------------------- >>>> [linux-6wa6:03731] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file >>>> orterun.c at line 543 >>>> >>>> >>>> Some Informations: >>>> I use Open MPI 1.4.4, Suse 64bit, AMD quadcore >>>> >>>> make check gives: >>>> make: *** No rule to make target `check'. Stop. >>>> I attached the ompi_info. >>>> >>>> Thx alot for your help, >>>> >>>> regards, >>>> Markus >>>> >>>> >>>> _______________________________________________ >>>> users mailing list >>>> us...@open-mpi.org >>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>> >>> Now i made open mpi new, but now im ggetting stuff like this: >>> >>> .................. >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_base_param_find' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `asc_parse' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_base_param_register_string' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_base_param_register_int' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lampanic' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_thread_self' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_debug_close' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_CONVERSION_FN_NULL' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_read_at_all' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `sfh_sock_set_buf_size' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `blktype' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_preallocate' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `ao_init' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_mutex_destroy' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_iread_shared' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `al_init' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `stoi' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_base_hostmap' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_FORTRAN_ERRCODES_IGNORE' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_close' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `al_next' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_Register_datarep' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_FORTRAN_STATUSES_IGNORE' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `nid_parse' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `mpi_fortran_bottom__' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_write_at' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_set_size' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `al_append' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `nid_free' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `terror' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_perror' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_Type_create_f90_real' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_write_shared' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `ompi_attr_set_fortran_mpi1' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_register_objects' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_write' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_base_param_lookup_string' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `next_prime' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `show_help' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lt_dlclose' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_write_ordered_end' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_rtrnamepub' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `ompi_mpi_datatype_null' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_get_info' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `ah_expand' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_cr_verbose' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_arr_find' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `bfiselect' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_set_view' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_rtrnamedel' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_mutex_lock' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `bfiprobe' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_gethostname' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_Win_lock' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_mkcoll' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_Request_get_status' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `mpi_fortran_argv_null' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `mpi_conversion_fn_null__' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `ompi_attr_create_keyval_fint' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `ah_init' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_read_all_end' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `_kio' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `asc_environment' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_mkpt' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_mp_finalize' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_base_module_find' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_call_errhandler' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_Add_error_string' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_kexit' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_arr_size' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `ompi_errcodes_intern' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_get_position' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `kexit' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `show_help_file' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_get_size' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `kpause' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_write_all' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_trpoint' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_get_byte_offset' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_mutex_init' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_getpid' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `ompi_ddt_match_size' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_FORTRAN_ARGVS_NULL' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_Comm_call_errhandler' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `ompi_mpi_comm_world' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `mpi_fortran_argvs_null' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_arr_remove' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_did' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `mrev4' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `rpdoom' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_get_position_shared' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `ompi_mpi_errors_are_fatal_comm_handler' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `_lam_signal' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `ompi_fortran_string_c2f' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_reset_pid_cache' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `bfselect' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_base_open' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_File_write_at_all_end' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_base_close' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lt_dlsym' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_ssi_base_set_verbose' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_arr_init' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_Type_create_f90_integer' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `ompi_registered_datareps' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `rw' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_Type_create_f90_complex' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_Status_set_cancelled' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `getroute' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_deregister_object' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `ldogetlinks' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `MPI_Win_call_errhandler' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_strncpy' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_Add_error_code' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `microsleep' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `asc_run' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_mutex_unlock' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `ah_free' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `kinit' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `lam_thread_create' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_Grequest_start' >>> /usr/local/lib64/libmpi_f77.so: undefined reference to >>> `mpi_fortran_status_ignore__' >>> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined >>> reference to `kenter' >>> collect2: ld returned 1 exit status >>> make[1]: *** [master] Error 1 >>> make[1]: Leaving directory `/home/markus/Downloads/dl_poly_4.02/source' >>> make: *** [hpc] Error 2 >>> >>> Whats wrong here? >>> How can i tell this where to find these things? >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
