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Subject: [OMPI users] Problem installing Dalton with OpenMPI over PelicanHPC
From: Silviu Groza (silviugroza_at_[hidden])
Date: 2009-05-12 11:13:54


Dear all,
I am trying to install Dalton quantum chemistry program with OpenMPI over PelicanHPC, but it ends with an error.
PelicanHPC comes with both LAM and OpenMPI preinstalled. The version of OpenMPI is "OMPI_VERSION "1.2.7rc2"" (from version.h).
The wrappers that I use are mpif77.openmpi and mpicc.openmpicc.
Bellow, you can see the "link" and "include" of the wrappers:

++++++++++++++++++++++++++++++++++++++

pelican:/# mpicc.openmpi -show
gcc -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include -pthread -L/usr/lib/openmpi/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

pelican:/# mpif77.openmpi -show
gfortran -I/usr/lib/openmpi/include -pthread -L/usr/lib/openmpi/lib -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

pelican:/# mpif77.openmpi -v
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 4.3.2-1.1' --with-bugurl=file:///usr/share/doc/gcc-4.3/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.3 --program-suffix=-4.3 --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-mpfr --enable-cld --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.3.2 (Debian 4.3.2-1.1)

+++++++++++++++++++++++++++++++++++++

The Makefile.conf of Dalton is:

++++++++++++++++++++++++++++++++++++++

ARCH        = linux
#
#
CPPFLAGS      = -DVAR_G77 -DSYS_LINUX -DVAR_MFDS -DVAR_SPLITFILES -D'INSTALL_WRKMEM=60000000' -D'INSTALL_BASDIR="/root/Fig/dalton-2.0/basis/"' -DVAR_MPI -DIMPLICIT_NONE
F77           = mpif77.openmpi
CC            = mpicc.openmpi
RM            = rm -f
FFLAGS        = -march=x86-64 -O3 -ffast-math -fexpensive-optimizations -funroll-loops -fno-range-check -fsecond-underscore
SAFEFFLAGS    = -march=x86-64 -O3 -ffast-math -fexpensive-optimizations -funroll-loops -fno-range-check -fsecond-underscore
CFLAGS        = -march=x86-64 -O3 -ffast-math -fexpensive-optimizations -funroll-loops -std=c99 -DRESTRICT=restrict
INCLUDES      = -I../include
LIBS          = -L/usr/lib -llapack -lblas
INSTALLDIR    = /root/Fig/dalton-2.0/bin
PDPACK_EXTRAS = linpack.o eispack.o
GP_EXTRAS     =
AR            = ar
ARFLAGS       = rvs
# flags for ftnchek on Dalton /hjaaj
CHEKFLAGS  = -nopure -nopretty -nocommon -nousage -noarray -notruncation -quiet  -noargumants -arguments=number  -usage=var-unitialized
# -usage=var-unitialized:arg-const-modified:arg-alias
# -usage=var-unitialized:var-set-unused:arg-unused:arg-const-modified:arg-alias
#
default : linuxparallel.x
#
# Parallel initialization
#
MPI_INCLUDE_DIR = -I/usr/lib/openmpi/include
MPI_LIB_PATH    = -L/usr/lib/openmpi/lib
MPI_LIB         = -lmpi
#
#
# Suffix rules
# hjaaj Oct 04: .g is a "cheat" suffix, for debugging.
#               'make x.g' will create x.o from x.F or x.c with -g debug flag set.
#
..SUFFIXES : .F .o .c .i .g

..F.o:
    $(F77) $(INCLUDES) $(CPPFLAGS) $(FFLAGS) -c $*.F

..F.g:
    $(F77) $(INCLUDES) $(CPPFLAGS) $(FFLAGS) -g -c $*.F

..c.o:
    $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -c $*.c

..c.g:
    $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -g -c $*.c

..F.i:
    $(F77) $(INCLUDES) $(CPPFLAGS) -E $*.F > $*.i

++++++++++++++++++++++++++++++++++++

"make" command gives me the error:

+++++++++++++++++++++++++++++++++++++++

---------------> Linking sequential dalton.x ...
mpif77.openmpi -march=x86-64 -O3 -ffast-math -fexpensive-optimizations -funroll-loops -fno-range-check -fsecond-underscore \
        -o /root/Fig/dalton-2.0/bin/dalton.x abacus/dalton.o cc/crayio.o abacus/linux_mem_allo.o \
        abacus/herpar.o eri/eri2par.o amfi/amfi.o amfi/symtra..o gp/mpi_dummy.o -Labacus -labacus -Lrsp -lrsp -Lsirius -lsirius -labacus -Leri -leri -Ldensfit -ldensfit -Lcc  -lcc -Ldft -ldft -Lgp -lgp -Lpdpack -lpdpack -L/usr/lib -llapack -lblas
dft/libdft.a(general.o): In function `mpi_sync_data':
general.c:(.text+0x78): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0xc3): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0xdc): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0xff): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0x122): undefined reference to `ompi_mpi_comm_world'
dft/libdft.a(general.o):general.c:(.text+0x136): more undefined references to `ompi_mpi_comm_world' follow
dft/libdft.a(general.o): In function `dft_cslave__':
general.c:(.text+0x44e): undefined reference to `ompi_mpi_int'
dft/libdft.a(general.o): In function `dft_wake_slaves':
general.c:(.text+0x485): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0x4e7): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0x4ee): undefined reference to `ompi_mpi_int'
general.c:(.text+0x507): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0x50e): undefined reference to `ompi_mpi_int'
general.c:(.text+0x528): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0x52f): undefined reference to `ompi_mpi_int'
dft/libdft.a(general.o): In function `dftfuncsync_':
general.c:(.text+0x13d1): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0x13d6): undefined reference to `ompi_mpi_int'
general.c:(.text+0x140c): undefined reference to `ompi_mpi_comm_world'
general.c:(.text+0x1411): undefined reference to `ompi_mpi_char'
dft/libdft.a(grid-gen.o): In function `grid_generate':
grid-gen.c:(.text+0x6bc1): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x6bc6): undefined reference to `ompi_mpi_int'
grid-gen.c:(.text+0x6c00): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x6c10): undefined reference to `ompi_mpi_int'
grid-gen.c:(.text+0x6c2d): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x6c38): undefined reference to `ompi_mpi_double'
grid-gen.c:(.text+0x6c5c): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x6c67): undefined reference to `ompi_mpi_double'
grid-gen.c:(.text+0x6c8a): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x6c95): undefined reference to `ompi_mpi_double'
grid-gen.c:(.text+0x6cbb): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x6cc6): undefined reference to `ompi_mpi_int'
dft/libdft.a(grid-gen.o): In function `grid_open':
grid-gen.c:(.text+0x7c7d): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x7c8c): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x7cfe): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x7d03): undefined reference to `ompi_mpi_double'
grid-gen.c:(.text+0x7d26): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x7d2d): undefined reference to `ompi_mpi_int'
grid-gen.c:(.text+0x7f71): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x7f7e): undefined reference to `ompi_mpi_int'
grid-gen.c:(.text+0x8001): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x83cc): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x83d7): undefined reference to `ompi_mpi_int'
grid-gen.c:(.text+0x8410): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x841b): undefined reference to `ompi_mpi_int'
grid-gen.c:(.text+0x8449): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x8454): undefined reference to `ompi_mpi_double'
grid-gen.c:(.text+0x847c): undefined reference to `ompi_mpi_double'
grid-gen.c:(.text+0x848d): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x84af): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x84ba): undefined reference to `ompi_mpi_double'
grid-gen.c:(.text+0x84df): undefined reference to `ompi_mpi_comm_world'
grid-gen.c:(.text+0x84ea): undefined reference to `ompi_mpi_int'
dft/libdft.a(prop-eval.o): In function `dft_lin_respf__':
prop-eval.c:(.text+0x3e6c): undefined reference to `ompi_mpi_comm_world'
prop-eval.c:(.text+0x3e71): undefined reference to `ompi_mpi_int'
prop-eval.c:(.text+0x41c1): undefined reference to `ompi_mpi_op_sum'
prop-eval.c:(.text+0x41c6): undefined reference to `ompi_mpi_double'
prop-eval.c:(.text+0x41ce): undefined reference to `ompi_mpi_comm_world'
prop-eval.c:(.text+0x45f7): undefined reference to `ompi_mpi_op_sum'
prop-eval.c:(.text+0x45fc): undefined reference to `ompi_mpi_double'
prop-eval.c:(.text+0x460a): undefined reference to `ompi_mpi_comm_world'
dft/libdft.a(prop-eval.o): In function `dft_lin_respab__':
prop-eval.c:(.text+0x9ebb): undefined reference to `ompi_mpi_int'
prop-eval.c:(.text+0x9ec1): undefined reference to `ompi_mpi_comm_world'
dft/libdft.a(prop-eval.o): In function `dft_lin_resp_':
prop-eval.c:(.text+0xa882): undefined reference to `ompi_mpi_comm_world'
prop-eval.c:(.text+0xa887): undefined reference to `ompi_mpi_int'
dft/libdft.a(prop-eval.o):(.data+0x10): undefined reference to `ompi_mpi_double'
dft/libdft.a(prop-eval.o):(.data+0x28): undefined reference to `ompi_mpi_double'
dft/libdft.a(prop-eval.o):(.data+0x40): undefined reference to `ompi_mpi_int'
dft/libdft.a(prop-eval.o):(.data+0x58): undefined reference to `ompi_mpi_int'
dft/libdft.a(quad-fast.o): In function `dftqrcf_':
quad-fast.c:(.text+0x354): undefined reference to `ompi_mpi_op_sum'
quad-fast.c:(.text+0x359): undefined reference to `ompi_mpi_double'
quad-fast.c:(.text+0x364): undefined reference to `ompi_mpi_comm_world'
dft/libdft.a(quad-fast.o):(.data+0x10): undefined reference to `ompi_mpi_double'
dft/libdft.a(quad-fast.o):(.data+0x28): undefined reference to `ompi_mpi_double'
dft/libdft.a(quad-fast.o):(.data+0x40): undefined reference to `ompi_mpi_double'
dft/libdft.a(quad-fast.o):(.data+0x58): undefined reference to `ompi_mpi_int'
dft/libdft.a(quad-fast.o):(.data+0x70): undefined reference to `ompi_mpi_int'
dft/libdft.a(quad-fast.o):(.data+0x88): undefined reference to `ompi_mpi_int'
dft/libdft.a(quad-fast.o):(.data+0xa0): undefined reference to `ompi_mpi_int'
dft/libdft.a(quad-fast.o):(.data+0xb8): undefined reference to `ompi_mpi_int'
dft/libdft.a(quad-fast.o):(.rodata+0x30): more undefined references to `ompi_mpi_int' follow
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_group'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_view'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_sync'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_amode'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Pack_external'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_iwrite_at'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Status_set_elements'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_status_ignore'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Add_error_class'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_type_extent'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_delete'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_FORTRAN_BOTTOM'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_all_begin'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_at_all_end'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_bottom'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_fortran_argv_f2c'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_mpi_param_check'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_FORTRAN_IN_PLACE'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_ordered'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_request_null'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_set_errhandler'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_attr_get_fortran_mpi2'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_statuses_ignore'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_all_begin'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_ordered_begin'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Pack_external_size'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_bottom_'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_set_atomicity'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_iwrite'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_errhandler_invoke'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_fortran_string_f2c'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_all_end'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_seek'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_at_all_begin'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_at_all_begin'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_FORTRAN_ARGV_NULL'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_at_all'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_atomicity'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_ordered_end'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_open'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Win_unlock'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_in_place'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_status_ignore_'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_all'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_ordered_begin'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_statuses_ignore_'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Type_create_indexed_block'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Grequest_complete'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Unpack_external'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_errcodes_ignore'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_in_place_'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_c2f'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_iwrite_shared'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_attr_get_fortran_mpi1'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_attr_set_fortran_mpi2'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_mpi_finalized'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_at'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_ordered'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_FORTRAN_STATUS_IGNORE'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Win_test'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_fortran_multiple_argvs_f2c'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_errhandler'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_errcode_intern_lastused'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_f2c'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_iread_at'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_mpi_initialized'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_iread'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_create_errhandler'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_mpi_file_null'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_set_info'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_shared'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_argv_null_'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_attr_create_keyval'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_at_all'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_preallocate'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_iread_shared'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_FORTRAN_ERRCODES_IGNORE'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_close'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Register_datarep'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_FORTRAN_STATUSES_IGNORE'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_at'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_set_size'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_errcodes_ignore_'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Type_create_f90_real'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_shared'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_attr_set_fortran_mpi1'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_ordered_end'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_mpi_datatype_null'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_info'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_set_view'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Win_lock'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Request_get_status'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_argv_null'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_read_all_end'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_call_errhandler'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Add_error_string'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_errcodes_intern'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_position'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_size'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_all'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_byte_offset'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_ddt_match_size'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_FORTRAN_ARGVS_NULL'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Comm_call_errhandler'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_argvs_null'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_get_position_shared'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_mpi_errors_are_fatal_comm_handler'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_fortran_string_c2f'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_File_write_at_all_end'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Type_create_f90_integer'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Type_create_f90_complex'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Status_set_cancelled'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Win_call_errhandler'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Add_error_code'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_fortran_argvs_null_'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_Grequest_start'
collect2: ld returned 1 exit status
make: *** [linux.x] Error 1
pelican:~/Fig/dalton-2.0# 

+++++++++++++++++++++++++++++++++++

I think that there is some sort of mixing LAM with OpenMPI libraries.
I don't know what am I doing wrong.
Thank you