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@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)
