[Paraview] PV on SGI Altix: Sgi MPI error

Tue Apr 26 01:59:02 EDT 2011

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:
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>>    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