build bash error

[mashinde]

Hi frds,

I update my svn to 471M, Now i am compiling building bash again but it gives me following error.....
..
...
..
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DGFORTRAN -D'ROOT_DIR="/home/mahesh/ROMS/src"' -DRMED16 -D'HEADER="rmed16.h"' -D'ROMS_HEADER="/home/mahesh/ROMS/src/Projects/rmed16/rmed16.h"' -DNestedGrids=1 -D'ANALYTICAL_DIR="/home/mahesh/ROMS/src/Projects/rmed16"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="471M"' -IROMS/Include -I/home/mahesh/ROMS/src/Projects/rmed16 -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/home/mahesh/ROMS/src/Projects/rmed16 -IMaster -ICompilers -D'HEADER_DIR="/home/mahesh/ROMS/src/Projects/rmed16"' Master/master.F > /home/mahesh/ROMS/src/Projects/rmed16/Build/master.f90
rm -f -r /home/mahesh/make_macros.mk
cd /home/mahesh/ROMS/src/Projects/rmed16/Build; -c -frepack-arrays -O3 -ffast-math mod_kinds.f90
/bin/sh: -c: not found
make: *** [/home/mahesh/ROMS/src/Projects/rmed16/Build/mod_kinds.o] Error 127
make: *** Waiting for unfinished jobs....
ROMS/Bin/cpp_clean /home/mahesh/ROMS/src/Projects/rmed16/Build/master.f90


anybody knows the solution of it.?

Thanks in advance.

[jcwarner]

looks like u are missing a compiler name, like mpif90 or something.
it needs
mpif90 (or pgf90 or ifort ...) -c (compile only) -O3 ....

[mashinde]

Hi,

I am using mpi to build exe file...but it gives following error.....


/usr/bin/gfortran -frepack-arrays -g -fbounds-check /home/mahesh/ROMS/src/Projects/rmed16/Build/esmf_roms.o /home/mahesh/ROMS/src/Projects/rmed16/Build/master.o /home/mahesh/ROMS/src/Projects/rmed16/Build/ocean_control.o /home/mahesh/ROMS/src/Projects/rmed16/Build/ocean_coupler.o /home/mahesh/ROMS/src/Projects/rmed16/Build/propagator.o /home/mahesh/ROMS/src/Projects/rmed16/Build/roms_export.o /home/mahesh/ROMS/src/Projects/rmed16/Build/roms_import.o -o /home/mahesh/ROMS/src/Projects/rmed16/oceanG /home/mahesh/ROMS/src/Projects/rmed16/Build/libNLM.a /home/mahesh/ROMS/src/Projects/rmed16/Build/libNLM_bio.a /home/mahesh/ROMS/src/Projects/rmed16/Build/libNLM_sed.a /home/mahesh/ROMS/src/Projects/rmed16/Build/libANA.a /home/mahesh/ROMS/src/Projects/rmed16/Build/libUTIL.a /home/mahesh/ROMS/src/Projects/rmed16/Build/libMODS.a -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -lz -lcurl -Wl,-Bsymbolic-functions -lidn -lssl -lcrypto -lldap -lrt -L/usr/lib -g -O2 -Wl,-Bsymbolic-functions -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lgssapi_krb5 -lssl -lcrypto -lz
/usr/local/netcdf4/lib/libnetcdf.a(nc4file.o): In function `nc_check_for_hdf5':
/usr/local/netcdf-4.0.1/libsrc4/nc4file.c:141: undefined reference to `MPI_File_open'
/usr/local/netcdf-4.0.1/libsrc4/nc4file.c:144: undefined reference to `MPI_File_read'
/usr/local/netcdf-4.0.1/libsrc4/nc4file.c:147: undefined reference to `MPI_File_close'
/usr/local/netcdf4/lib/libhdf5.a(H5AC.o): In function `H5AC_flush':
H5AC.c:(.text+0x1e32): undefined reference to `MPI_Barrier'
H5AC.c:(.text+0x1e54): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5AC.o): In function `H5AC_broadcast_clean_list':
H5AC.c:(.text+0x6dde): undefined reference to `MPI_Bcast'
H5AC.c:(.text+0x6e00): undefined reference to `MPI_Error_string'
H5AC.c:(.text+0x729f): undefined reference to `MPI_Bcast'
H5AC.c:(.text+0x72c1): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5AC.o): In function `H5AC_propagate_flushed_and_still_clean_entries_list':
H5AC.c:(.text+0x9103): undefined reference to `MPI_Barrier'
H5AC.c:(.text+0x9125): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5AC.o): In function `H5AC_receive_and_apply_clean_list':
H5AC.c:(.text+0x9588): undefined reference to `MPI_Bcast'
H5AC.c:(.text+0x95aa): undefined reference to `MPI_Error_string'
H5AC.c:(.text+0x981a): undefined reference to `MPI_Bcast'
H5AC.c:(.text+0x983c): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Dmpio.o): In function `H5D_mpio_opt_possible':
H5Dmpio.c:(.text+0x6a4): undefined reference to `MPI_Allreduce'
H5Dmpio.c:(.text+0x6c6): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Dmpio.o): In function `H5D_mpio_get_min_chunk':
H5Dmpio.c:(.text+0xc44): undefined reference to `MPI_Allreduce'
H5Dmpio.c:(.text+0xc66): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Dmpio.o): In function `H5D_mpio_get_sum_chunk':
H5Dmpio.c:(.text+0xda4): undefined reference to `MPI_Allreduce'
H5Dmpio.c:(.text+0xdc6): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Dmpio.o): In function `H5D_inter_collective_io':
H5Dmpio.c:(.text+0x32dd): undefined reference to `MPI_Type_free'
H5Dmpio.c:(.text+0x32ff): undefined reference to `MPI_Error_string'
H5Dmpio.c:(.text+0x33e1): undefined reference to `MPI_Type_free'
H5Dmpio.c:(.text+0x3403): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Dmpio.o): In function `H5D_obtain_mpio_mode':
H5Dmpio.c:(.text+0x3bcf): undefined reference to `MPI_Gather'
H5Dmpio.c:(.text+0x3bfa): undefined reference to `MPI_Error_string'
H5Dmpio.c:(.text+0x3ff7): undefined reference to `MPI_Bcast'
H5Dmpio.c:(.text+0x4022): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Eint.o): In function `H5E_walk1_cb':
H5Eint.c:(.text+0x25a): undefined reference to `MPI_Initialized'
H5Eint.c:(.text+0x277): undefined reference to `MPI_Comm_rank'
/usr/local/netcdf4/lib/libhdf5.a(H5Eint.o): In function `H5E_walk2_cb':
H5Eint.c:(.text+0x5b1): undefined reference to `MPI_Initialized'
H5Eint.c:(.text+0x5ce): undefined reference to `MPI_Comm_rank'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpi.o): In function `H5FD_mpi_comm_info_dup':
H5FDmpi.c:(.text+0x433): undefined reference to `MPI_Comm_dup'
H5FDmpi.c:(.text+0x455): undefined reference to `MPI_Error_string'
H5FDmpi.c:(.text+0x53f): undefined reference to `MPI_Info_dup'
H5FDmpi.c:(.text+0x561): undefined reference to `MPI_Error_string'
H5FDmpi.c:(.text+0x666): undefined reference to `MPI_Comm_free'
H5FDmpi.c:(.text+0x67b): undefined reference to `MPI_Info_free'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpi.o): In function `H5FD_mpi_comm_info_free':
H5FDmpi.c:(.text+0x754): undefined reference to `MPI_Comm_free'
H5FDmpi.c:(.text+0x76c): undefined reference to `MPI_Info_free'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpio.o): In function `H5Pget_fapl_mpio':
H5FDmpio.c:(.text+0x886): undefined reference to `MPI_Comm_dup'
H5FDmpio.c:(.text+0x8a8): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x9a7): undefined reference to `MPI_Info_dup'
H5FDmpio.c:(.text+0x9c9): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0xace): undefined reference to `MPI_Comm_free'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpio.o): In function `H5FD_mpio_open':
H5FDmpio.c:(.text+0x2aaf): undefined reference to `MPI_File_open'
H5FDmpio.c:(.text+0x2ada): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x2bc8): undefined reference to `MPI_Comm_rank'
H5FDmpio.c:(.text+0x2bf3): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x2cd6): undefined reference to `MPI_Comm_size'
H5FDmpio.c:(.text+0x2d01): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x2f08): undefined reference to `MPI_File_get_size'
H5FDmpio.c:(.text+0x2f33): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x3028): undefined reference to `MPI_Bcast'
H5FDmpio.c:(.text+0x3053): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x3154): undefined reference to `MPI_File_set_size'
H5FDmpio.c:(.text+0x317f): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x325a): undefined reference to `MPI_Barrier'
H5FDmpio.c:(.text+0x3285): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x33a5): undefined reference to `MPI_File_close'
H5FDmpio.c:(.text+0x33c0): undefined reference to `MPI_Comm_free'
H5FDmpio.c:(.text+0x33db): undefined reference to `MPI_Info_free'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpio.o): In function `H5FD_mpio_close':
H5FDmpio.c:(.text+0x34ea): undefined reference to `MPI_File_close'
H5FDmpio.c:(.text+0x350c): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpio.o): In function `H5FD_mpio_read':
H5FDmpio.c:(.text+0x40a5): undefined reference to `MPI_File_set_view'
H5FDmpio.c:(.text+0x40d0): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x421f): undefined reference to `MPI_File_read_at_all'
H5FDmpio.c:(.text+0x424a): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x4358): undefined reference to `MPI_File_read_at'
H5FDmpio.c:(.text+0x4383): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x4488): undefined reference to `MPI_File_set_view'
H5FDmpio.c:(.text+0x44b3): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x45c1): undefined reference to `MPI_File_read_at'
H5FDmpio.c:(.text+0x45ec): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x46d4): undefined reference to `MPI_Get_elements'
H5FDmpio.c:(.text+0x46ff): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x47e4): undefined reference to `MPI_Type_size'
H5FDmpio.c:(.text+0x480f): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpio.o): In function `H5FD_mpio_write':
H5FDmpio.c:(.text+0x4f1f): undefined reference to `MPI_File_set_view'
H5FDmpio.c:(.text+0x4f4a): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x50ba): undefined reference to `MPI_File_write_at_all'
H5FDmpio.c:(.text+0x50e5): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x51f3): undefined reference to `MPI_File_write_at'
H5FDmpio.c:(.text+0x521e): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x5323): undefined reference to `MPI_File_set_view'
H5FDmpio.c:(.text+0x534e): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x545c): undefined reference to `MPI_File_write_at'
H5FDmpio.c:(.text+0x5487): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x556f): undefined reference to `MPI_Get_elements'
H5FDmpio.c:(.text+0x559a): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x567f): undefined reference to `MPI_Type_size'
H5FDmpio.c:(.text+0x56aa): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpio.o): In function `H5FD_mpio_flush':
H5FDmpio.c:(.text+0x5951): undefined reference to `MPI_File_sync'
H5FDmpio.c:(.text+0x5973): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpio.o): In function `H5FD_mpio_truncate':
H5FDmpio.c:(.text+0x5c02): undefined reference to `MPI_File_set_size'
H5FDmpio.c:(.text+0x5c24): undefined reference to `MPI_Error_string'
H5FDmpio.c:(.text+0x5cff): undefined reference to `MPI_Barrier'
H5FDmpio.c:(.text+0x5d21): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpiposix.o): In function `H5Pget_fapl_mpiposix':
H5FDmpiposix.c:(.text+0x7ed): undefined reference to `MPI_Comm_dup'
H5FDmpiposix.c:(.text+0x80f): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpiposix.o): In function `H5FD_mpiposix_fapl_get':
H5FDmpiposix.c:(.text+0xa9f): undefined reference to `MPI_Comm_dup'
H5FDmpiposix.c:(.text+0xac1): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpiposix.o): In function `H5FD_mpiposix_fapl_copy':
H5FDmpiposix.c:(.text+0xd70): undefined reference to `MPI_Comm_dup'
H5FDmpiposix.c:(.text+0xd92): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpiposix.o): In function `H5FD_mpiposix_fapl_free':
H5FDmpiposix.c:(.text+0xf80): undefined reference to `MPI_Comm_free'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpiposix.o): In function `H5FD_mpiposix_open':
H5FDmpiposix.c:(.text+0x13e0): undefined reference to `MPI_Comm_dup'
H5FDmpiposix.c:(.text+0x140b): undefined reference to `MPI_Error_string'
H5FDmpiposix.c:(.text+0x14f1): undefined reference to `MPI_Comm_rank'
H5FDmpiposix.c:(.text+0x151c): undefined reference to `MPI_Error_string'
H5FDmpiposix.c:(.text+0x1602): undefined reference to `MPI_Comm_size'
H5FDmpiposix.c:(.text+0x162d): undefined reference to `MPI_Error_string'
H5FDmpiposix.c:(.text+0x17c4): undefined reference to `MPI_Bcast'
H5FDmpiposix.c:(.text+0x17ef): undefined reference to `MPI_Error_string'
H5FDmpiposix.c:(.text+0x1b1a): undefined reference to `MPI_Bcast'
H5FDmpiposix.c:(.text+0x1b45): undefined reference to `MPI_Error_string'
H5FDmpiposix.c:(.text+0x1dde): undefined reference to `MPI_Comm_free'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpiposix.o): In function `H5FD_mpiposix_close':
H5FDmpiposix.c:(.text+0x1f7a): undefined reference to `MPI_Barrier'
H5FDmpiposix.c:(.text+0x1f88): undefined reference to `MPI_Comm_free'
/usr/local/netcdf4/lib/libhdf5.a(H5FDmpiposix.o): In function `H5FD_mpiposix_truncate':
H5FDmpiposix.c:(.text+0x34ac): undefined reference to `MPI_Barrier'
H5FDmpiposix.c:(.text+0x34ce): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Smpio.o): In function `H5S_mpio_hyper_type':
H5Smpio.c:(.text+0x8d1): undefined reference to `MPI_Type_contiguous'
H5Smpio.c:(.text+0x8fc): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0xa8d): undefined reference to `MPI_Type_vector'
H5Smpio.c:(.text+0xaa1): undefined reference to `MPI_Type_free'
H5Smpio.c:(.text+0xac5): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0xc1f): undefined reference to `MPI_Type_extent'
H5Smpio.c:(.text+0xc4a): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0xdc2): undefined reference to `MPI_Type_struct'
H5Smpio.c:(.text+0xdd6): undefined reference to `MPI_Type_free'
H5Smpio.c:(.text+0xdfa): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0xf07): undefined reference to `MPI_Type_commit'
H5Smpio.c:(.text+0xf32): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Smpio.o): In function `H5S_mpio_span_hyper_type':
H5Smpio.c:(.text+0x1281): undefined reference to `MPI_Type_commit'
H5Smpio.c:(.text+0x12a3): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Smpio.o): In function `H5S_obtain_datatype':
H5Smpio.c:(.text+0x151a): undefined reference to `MPI_Type_contiguous'
H5Smpio.c:(.text+0x1545): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0x1623): undefined reference to `MPI_Type_commit'
H5Smpio.c:(.text+0x164e): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0x17b4): undefined reference to `MPI_Type_hindexed'
H5Smpio.c:(.text+0x17df): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0x1a76): undefined reference to `MPI_Type_commit'
H5Smpio.c:(.text+0x1aa1): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0x1bc0): undefined reference to `MPI_Type_hvector'
H5Smpio.c:(.text+0x1beb): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0x1cc9): undefined reference to `MPI_Type_commit'
H5Smpio.c:(.text+0x1cf4): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0x1dd2): undefined reference to `MPI_Type_free'
H5Smpio.c:(.text+0x1dfd): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0x1f3d): undefined reference to `MPI_Type_struct'
H5Smpio.c:(.text+0x1f68): undefined reference to `MPI_Error_string'
H5Smpio.c:(.text+0x2084): undefined reference to `MPI_Type_free'
H5Smpio.c:(.text+0x20af): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Dchunk.o): In function `H5D_chunk_allocate':
H5Dchunk.c:(.text+0xa926): undefined reference to `MPI_Barrier'
H5Dchunk.c:(.text+0xa951): undefined reference to `MPI_Error_string'
/usr/local/netcdf4/lib/libhdf5.a(H5Dcontig.o): In function `H5D_contig_fill':
H5Dcontig.c:(.text+0xd1b): undefined reference to `MPI_Barrier'
H5Dcontig.c:(.text+0xd46): undefined reference to `MPI_Error_string'
collect2: ld returned 1 exit status

anybody knows the answer....


thanks in advance

[kate]

You need to link to the mpi library. This is usually accomplished through compiling with a script called mpif90 (for mpich). You need to find out how mpi jobs are compiled and linked on your system.

Did you set USE_MPIF90 = on?

[mashinde]

Hi...

problem solved......


Thanks !