Hello,
I'm trying to compile NetCDF v4.0.1 to run the ROMS model
(http://www.myroms.org) in a parallel configuration.
What I've done so far is to install MPICH2 with the configuration
./configure --enable-f90 --with-mpe --with-romio --prefix=/usr/local
and HDF5 (v1.8.3) with the options:
CC=mpicc LIBS="-lm -lz" CPPFLAGS="-DpgiFortran" ./configure
--enable-parallel --enable-fortran --prefix=/usr/local
(I believe the "LIBS" options are not necessary here but they don't
hurt). A 'make check' works nicely here.
I have the intel fortran compiler installed (v11.0). When I compile
netcdf v4.0.1 with:
CC=mpicc CPPFLAGS="-DpgiFortran" LIBS="-lm -lz -lhdf5" ./configure
--enable-netcdf-4 --prefix=/usr/local
using 'make check', the the build fails with the output I've pasted
below. It looks like the HDF5 libraries were compiled without the
necessary MPI support, but my understanding is that the
'--enable-parallel' flag should do this. Am I missing something?
Best Regards,
Carlos
libtool: link: ifort -I../fortran -I../libsrc4 -I../f90 -g -o nf_test
test_get.o test_put.o nf_error.o nf_test.o test_read.o test_write.o
util.o fortlib.o ../libsrc4/.libs/libnetcdf.a -lhdf5_hl -lm -lz -lhdf5
../libsrc4/.libs/libnetcdf.a(nc4file.o): In function `nc_check_for_hdf5':
/home/cmoffat/Sandbox/netcdf-4.0.1/libsrc4/nc4file.c:141: undefined
reference to `MPI_File_open'
/home/cmoffat/Sandbox/netcdf-4.0.1/libsrc4/nc4file.c:144: undefined
reference to `MPI_File_read'
/home/cmoffat/Sandbox/netcdf-4.0.1/libsrc4/nc4file.c:147: undefined
reference to `MPI_File_close'
/usr/local/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/lib/libhdf5.a(H5FDmpiposix.o): In function
`H5FD_mpiposix_fapl_free':
H5FDmpiposix.c:(.text+0xf80): undefined reference to `MPI_Comm_free'
/usr/local/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/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/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/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/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/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/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/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'
make[2]: *** [nf_test] Error 1
make[2]: Leaving directory `/home/cmoffat/Sandbox/netcdf-4.0.1/nf_test'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/cmoffat/Sandbox/netcdf-4.0.1/nf_test'
make: *** [check-recursive] Error 1
