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Subject: [OMPI users] Compiling an OpenMPI application with intel compilers
From: Stephen J. Barr (stephenjbarr_at_[hidden])
Date: 2012-08-12 00:33:16

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Hello,

I have the latest OpenMPI on linux which I compiled with the Intel compiler
suite. I am trying to compile an OpenMPI application. My particular
application uses RInside and RcppEigen. If I comment out the openMPI parts
of my code, the compile string is:

icpc -I/usr/share/R/include -I/usr/lib/R/site-library/Rcpp/include
-I/usr/local/lib/R/site-library/RInside/include -O3 -pipe -g -Wall
 -I/usr/local/lib/R/site-library/RcppEigen/include
sjb_simple_smle_with_Rinside.cpp -L/usr/lib/R/lib -lR -lblas -llapack
-L/usr/lib/R/site-library/Rcpp/lib -lRcpp
-Wl,-rpath,/usr/lib/R/site-library/Rcpp/lib
-L/usr/local/lib/R/site-library/RInside/lib -lRInside
-Wl,-rpath,/usr/local/lib/R/site-library/RInside/lib -o
sjb_simple_smle_with_Rinside

Thus, I tried to compile with mpic++ using:

mpic++ -I/usr/share/R/include -I/usr/lib/R/site-library/Rcpp/include
-I/usr/local/lib/R/site-library/RInside/include -O3 -pipe -g -Wall
 -I/usr/local/lib/R/site-library/RcppEigen/include
sjb_simple_smle_with_Rinside.cpp -L/usr/lib/R/lib -lR -lblas -llapack
-L/usr/lib/R/site-library/Rcpp/lib -lRcpp
-Wl,-rpath,/usr/lib/R/site-library/Rcpp/lib
-L/usr/local/lib/R/site-library/RInside/lib -lRInside
-Wl,-rpath,/usr/local/lib/R/site-library/RInside/lib -o
sjb_simple_smle_with_Rinside

If I uncomment
#include "mpi.h"

and try to compile, I get the errors below. Is there any trick to compiling
OpenMPI applications with the Intel compilers?

Thanks,
Stephen

COMPILE ERROR:

stevejb_at_ursamajor:~/Projects/big_data_sim_mle/simple_smle/R_inside_version$
mpic++ -I/usr/share/R/include -I/usr/lib/R/site-library/Rcpp/include
-I/usr/local/lib/R/site-library/RInside/include -O3 -pipe -g -Wall
-I/usr/local/lib/R/site-library/RcppEigen/include
sjb_simple_smle_with_Rinside.cpp -L/usr/lib/R/lib -lR -lblas -llapack
-L/usr/lib/R/site-library/Rcpp/lib -lRcpp
-Wl,-rpath,/usr/lib/R/site-library/Rcpp/lib
-L/usr/local/lib/R/site-library/RInside/lib -lRInside
-Wl,-rpath,/usr/local/lib/R/site-library/RInside/lib -o
sjb_simple_smle_with_Rinside -shared-intel -I/usr/local/include -pthread
-L/usr/local/lib -lmpi_cxx -lmpi -ldl -lm -Wl,--export-dynamic -lrt -lnsl
-lutil
/usr/local/include/openmpi/ompi/mpi/cxx/datatype.h(142): error: expected a
type specifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/datatype.h(142): error: expected a
")"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/datatype.h(142): error: expected an
identifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/datatype.h(142): error: "virtual"
is not allowed
    virtual void Free();
    ^

/usr/local/include/openmpi/ompi/mpi/cxx/datatype.h(142): error: expected a
";"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/op.h(48): error: expected a type
specifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/op.h(48): error: expected a ")"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/op.h(48): error: expected an
identifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/op.h(48): error: "virtual" is not
allowed
    virtual void Free();
    ^

/usr/local/include/openmpi/ompi/mpi/cxx/op.h(48): error: expected a ";"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/request.h(96): error: expected a
type specifier
    virtual void Free(void);
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/request.h(96): error: expected a ")"
    virtual void Free(void);
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/request.h(96): error: expected an
identifier
    virtual void Free(void);
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/request.h(96): error: "virtual" is
not allowed
    virtual void Free(void);
    ^

/usr/local/include/openmpi/ompi/mpi/cxx/request.h(96): error: expected a ";"
    virtual void Free(void);
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/group.h(111): error: expected a
type specifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/group.h(111): error: expected a ")"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/group.h(111): error: expected an
identifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/group.h(111): error: "virtual" is
not allowed
    virtual void Free();
    ^

/usr/local/include/openmpi/ompi/mpi/cxx/group.h(111): error: expected a ";"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/comm.h(264): error: expected a type
specifier
    virtual void Free(void);
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/comm.h(264): error: expected a ")"
    virtual void Free(void);
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/comm.h(264): error: expected an
identifier
    virtual void Free(void);
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/comm.h(264): error: "virtual" is
not allowed
    virtual void Free(void);
    ^

/usr/local/include/openmpi/ompi/mpi/cxx/comm.h(264): error: expected a ";"
    virtual void Free(void);
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/win.h(118): error: expected a type
specifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/win.h(118): error: expected a ")"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/win.h(118): error: expected an
identifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/win.h(118): error: "virtual" is not
allowed
    virtual void Free();
    ^

/usr/local/include/openmpi/ompi/mpi/cxx/win.h(118): error: expected a ";"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/errhandler.h(59): error: expected a
type specifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/errhandler.h(59): error: expected a
")"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/errhandler.h(59): error: expected
an identifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/errhandler.h(59): error: "virtual"
is not allowed
    virtual void Free();
    ^

/usr/local/include/openmpi/ompi/mpi/cxx/errhandler.h(59): error: expected a
";"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/info.h(84): error: expected a type
specifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/info.h(84): error: expected a ")"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/info.h(84): error: expected an
identifier
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/info.h(84): error: "virtual" is not
allowed
    virtual void Free();
    ^

/usr/local/include/openmpi/ompi/mpi/cxx/info.h(84): error: expected a ";"
    virtual void Free();
                 ^

/usr/local/include/openmpi/ompi/mpi/cxx/request_inln.h(39): error: expected
an identifier
  MPI::Request::Free()
                ^

/usr/local/include/openmpi/ompi/mpi/cxx/request_inln.h(38): error: inline
specifier allowed on function declarations only
  inline void
  ^

/usr/local/include/openmpi/ompi/mpi/cxx/request_inln.h(39): error:
incomplete type is not allowed
  MPI::Request::Free()
                ^

/usr/local/include/openmpi/ompi/mpi/cxx/request_inln.h(39): error: a
nonstatic member reference must be relative to a specific object
  MPI::Request::Free()
                ^

/usr/local/include/openmpi/ompi/mpi/cxx/request_inln.h(39): error: expected
an expression
  MPI::Request::Free()
                ^

/usr/local/include/openmpi/ompi/mpi/cxx/request_inln.h(39): error: expected
a ")"
  MPI::Request::Free()
                ^

/usr/local/include/openmpi/ompi/mpi/cxx/request_inln.h(40): error: expected
a ";"
  {
  ^

/usr/local/include/openmpi/ompi/mpi/cxx/op_inln.h(123): error: identifier
"ompi_op_set_cxx_callback" is undefined
      ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func);
      ^

/usr/local/include/openmpi/ompi/mpi/cxx/op_inln.h(128): error: expected an
identifier
  MPI::Op::Free()
           ^

/usr/local/include/openmpi/ompi/mpi/cxx/op_inln.h(127): error: inline
specifier allowed on function declarations only
  inline void
  ^

/usr/local/include/openmpi/ompi/mpi/cxx/op_inln.h(128): error: incomplete
type is not allowed
  MPI::Op::Free()
           ^

/usr/local/include/openmpi/ompi/mpi/cxx/op_inln.h(128): error: a nonstatic
member reference must be relative to a specific object
  MPI::Op::Free()
           ^

/usr/local/include/openmpi/ompi/mpi/cxx/op_inln.h(128): error: expected an
expression
  MPI::Op::Free()
           ^

/usr/local/include/openmpi/ompi/mpi/cxx/op_inln.h(128): error: expected a
")"
  MPI::Op::Free()
           ^

/usr/local/include/openmpi/ompi/mpi/cxx/op_inln.h(129): error: expected a
";"
  {
  ^

sjb_simple_smle_with_Rinside.cpp(35): warning #12: parsing restarts here
after previous syntax error
  using namespace Rcpp;
                      ^

sjb_simple_smle_with_Rinside.cpp(77): error: identifier "as" is undefined
    const Map<MatrixXd> Xmat(as<Map<MatrixXd> >(Xmat_sexp));
                             ^

sjb_simple_smle_with_Rinside.cpp(77): error: type name is not allowed
    const Map<MatrixXd> Xmat(as<Map<MatrixXd> >(Xmat_sexp));
                                ^

sjb_simple_smle_with_Rinside.cpp(80): error: type name is not allowed
    const Map<MatrixXd> Ymat(as<Map<MatrixXd> >(Ymat_sexp));
                                ^

sjb_simple_smle_with_Rinside.cpp(87): error: type name is not allowed
    const Map<MatrixXd> ua(as<Map<MatrixXd> >(ua_sexp));
                              ^

sjb_simple_smle_with_Rinside.cpp(89): error: type name is not allowed
    const Map<MatrixXd> ub(as<Map<MatrixXd> >(ub_sexp));
                              ^

sjb_simple_smle_with_Rinside.cpp(98): error: type name is not allowed
    const Map<VectorXd> start_vector(as<Map<VectorXd> >(start_sexp));
                                        ^

compilation aborted for sjb_simple_smle_with_Rinside.cpp (code 2)

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