[Paraview] PV on SGI Altix: Sgi MPI error

Tue Apr 26 06:55:43 EDT 2011

Hi George,
yes. I am in fact linking to the lmpi library.
I'll paste a part of the CMakeCache here; this may be more revealing:

//CXX compiler.
CMAKE_CXX_COMPILER:FILEPATH=/opt/app/intel/Compiler/11.1/038/bin/intel64/icpc

//Flags used by the compiler during all build types.
CMAKE_CXX_FLAGS:STRING=-I /opt/sgi/mpt/mpt-1.23/include -L 
/opt/sgi/mpt/mpt-1.23/lib  -lmpi -lmpi++abi1002

//C compiler.
CMAKE_C_COMPILER:FILEPATH=/opt/app/intel/Compiler/11.1/038/bin/intel64/icc

//Flags used by the compiler during all build types.
CMAKE_C_FLAGS:STRING=-I /opt/sgi/mpt/mpt-1.23/include -L 
/opt/sgi/mpt/mpt-1.23/lib  -lmpi

//MPI compiler. Used only to detect MPI compilation flags.
MPI_COMPILER:FILEPATH=/opt/app/intel/Compiler/11.1/038/bin/intel64/icpc

//MPI compilation flags
MPI_COMPILE_FLAGS:STRING=-I /opt/sgi/mpt/mpt-1.23/include -L 
/opt/sgi/mpt/mpt-1.23/lib  -lmpi -lmpi++abi1002

//Extra MPI libraries to link against
MPI_EXTRA_LIBRARY:STRING=/opt/sgi/mpt/mpt-1.23/lib/libmpi.so;/opt/sgi/mpt/mpt-1.23/lib/libmpi_mt.so;/opt/sgi/mpt/mpt-1.23/lib/libmpi++.so;/opt/sgi/mpt/mpt-1.23/lib/libxmpi.so

//MPI include path
MPI_INCLUDE_PATH:STRING=/opt/sgi/mpt/mpt-1.23/include/mpi++.h:/opt/sgi/mpt/mpt-1.23/include/mpi.h

//MPI library to link against
MPI_LIBRARY:FILEPATH=/opt/sgi/mpt/mpt-1.23/lib/libmpi++abi1002.so

Do you spot anything out of place? Please let me know...

Regards,
Pratik

On Tuesday 26 April 2011 03:29 PM, George Zagaris wrote:
> Hi Pratik,
>
> I did not realize that you were doing that already.
>
> The error is a link error with the library
> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so.
> So, regardless if the references are declared in the corresponding headers,
> mpi.h&  mpi++.h, they are not in the library you are linking. You can do an
> `nm /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so` and grep for a method to verify that.
>
> Is there a libmpi.so you can link to? It looks like you are linking in only the
> C++ MPI interface.
>
> Regards,
> George
>
> On Tue, Apr 26, 2011 at 1:59 AM, pratik<pratik.mallya at gmail.com>  wrote:
>    
>> On Tuesday 26 April 2011 07:54 AM, George Zagaris wrote:
>>      
>>> Hi Pratik,
>>>
>>> I am not sure if this will resolve your issue but,
>>> on some system configurations you have to link
>>> MPI with your executable using -lmpi instead of
>>> calling the mpicxx wrapper.
>>>
>>> Regards,
>>> George
>>>
>>> On Mon, Apr 25, 2011 at 9:54 PM,<paraview-request at paraview.org>    wrote:
>>>
>>>        
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>>>> Today's Topics:
>>>>
>>>>    1. PV on SGI Altix: Sgi MPI error (pratik)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Tue, 26 Apr 2011 07:24:07 +0530
>>>> From: pratik<pratik.mallya at gmail.com>
>>>> Subject: [Paraview] PV on SGI Altix: Sgi MPI error
>>>> To: paraview at paraview.org
>>>> Message-ID:<4DB625BF.5070302 at gmail.com>
>>>> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>>>>
>>>> On this system, i tried building pvserver (3.10.1)(no qt) with my local
>>>> openmpi lib and the system gcc compilers and it worked perfectly.
>>>> However, the "people incharge" insist that I use the sgi mpt libraries
>>>> for mpi.
>>>> Well, for the previous install(openmpi), i had used mpic++ instead of
>>>> g++ (i read somewhere in mailing list that it solves the errors, and it
>>>> did); for the current install i am getting the error given below. I have
>>>> also attached cmakecache.txt. can anyone please tell me what i must do?
>>>> I have given the right include and lib directories for PV, and mpi.h
>>>> does have some of these functions, so why am i getting this error?
>>>>
>>>> [  4%] Built target vtklibxml2
>>>> [  4%] Built target vtkDICOMParser
>>>> Linking CXX executable ../../../bin/ProcessShader
>>>> /opt/intel/Compiler/11.1/038/lib/intel64/libimf.so: warning: warning:
>>>> feupdateenv is not implemented and will always fail
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Topo_test'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_size'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Test_cancelled'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Finalize'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Buffer_detach'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Graph_neighbors'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Graphdims_get'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Gatherv'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_translate_ranks'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Error_string'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Wtick'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_remote_size'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Reduce_scatter'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Bsend'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_free'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Probe'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Errhandler_create'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Cart_rank'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Intercomm_create'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_DUP_FN'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_size'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Sendrecv_replace'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Graph_map'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Startall'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Testall'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_free'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Iprobe'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Error_class'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Attr_get'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_remote_group'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_intersection'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Send'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Cart_shift'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Rsend_init'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Gather'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_create_resized'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Keyval_create'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Alltoall'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Test'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_difference'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Scan'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_indexed'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Cart_create'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Cart_sub'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Address'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Allreduce'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Keyval_free'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Buffer_attach'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Testany'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Cart_map'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_size'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_range_incl'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Graph_get'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Ssend_init'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Waitsome'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Scatterv'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Recv'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Unpack'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_hindexed'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Cart_get'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Dims_create'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Isend'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Graph_neighbors_count'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Get_count'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Testsome'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Allgather'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_free'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Waitany'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Abort'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Cancel'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Waitall'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_create'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_NULL_COPY_FN'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Op_free'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Graph_create'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_vector'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Cart_coords'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Get_processor_name'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Errhandler_set'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Issend'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Wait'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Rsend'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Init'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_test_inter'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_rank'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Sendrecv'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Irsend'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_struct'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Intercomm_merge'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_get_true_extent'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Alltoallw'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_rank'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Op_create'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Cartdim_get'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Barrier'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_compare'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Allgatherv'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Irecv'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Ibsend'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Bcast'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Alltoallv'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_union'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Pcontrol'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_dup'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_compare'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Reduce'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_group'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Request_free'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Comm_split'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Attr_put'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Bsend_init'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Scatter'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_hvector'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_commit'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Errhandler_free'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Recv_init'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Ssend'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_excl'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Attr_delete'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_range_excl'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Initialized'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Pack_size'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_contiguous'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Wtime'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_NULL_DELETE_FN'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Group_incl'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Send_init'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Type_get_extent'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to
>>>> `MPI_Get_elements'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Pack'
>>>> /opt/sgi/mpt/mpt-1.23/lib/libmpi++.so: undefined reference to `MPI_Start'
>>>> make[2]: *** [bin/ProcessShader] Error 1
>>>> make[1]: ***
>>>> [VTK/Utilities/MaterialLibrary/CMakeFiles/ProcessShader.dir/all] Error 2
>>>> make: *** [all] Error 2
>>>>
>>>> pratik
>>>>
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>>>>
>>>>          
>> Hi George,
>> Did you mean to use the C++ compiler with the -lmpi flags instead of mpicxx
>> wrapper? Because that is what i have done here ( i had done that because  i
>> couldn't find an mpicxx wrapper in the installed directory for the sgi
>> mpt(1.23)...they only seem to have the mpiexec and mpirun executables in the
>> /bin directory).
>> Anyways, thanks for trying to help. If you have any other ideas, please do
>> share them. I just can't figure out why the error is showing especially when
>> all the references seem to be declared in the mpi.h and mpi++.h header files
>> provided by sgi mpt.
>>
>> Regards,
>> Pratik
>>
>>      