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Subject: Re: [OMPI users] open-mpi error
From: Markus Stiller (pge08fjv_at_[hidden])
Date: 2011-11-26 12:22:17


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_at_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-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On
>>> Behalf Of Markus Stiller
>>> Sent: 24 November 2011 20:41
>>> To:users_at_[hidden]
>>> 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_at_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
>>> users_at_[hidden]
>>> 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
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
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