Richard,
I've tried to set the compilers to use mpif77, mpif90 and mpicc. I do not
believe I have the pgi compilers installed. I'm working with ubuntu 9.4 with
pretty standard compilers (gfortran, f2c, gcc, g++) installed.
I'm attaching the nm output.
Thanks for the help Richard. I'm going to try some of Ed's suggestions next
and I'll report back if there's any change in status.
Regards,
-Joe Buck
On Wed, Feb 3, 2010 at 10:25 AM, Richard Hedges <richard-hedges@xxxxxxxx>wrote:
> Howdy Joe,
>
> It looks like something like this has been encountered when trying to
> compile with the PGI compilers:
> http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg01641.html
>
> There is some discussion of the thread re. the procedure naming conventions
> for FORTRAN that may be at the heart of the problem.
>
> Do you know what the underlying compilers are?
>
> What do you get from "nm .../libnetcdf.a |grep nf_"
>
>
>
> go slugs!
>
> - Richard
>
>
> At 12:26 AM -0800 2/3/10, Joe Buck wrote:
>
> I've built mpi2 v 1.2.1 with these flags:
> CFLAGS="-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64
> -fPIC" ./configure --enable-f90 --enable-f77 --with-mpe --with-romio
> --prefix=/install/mpich2-121
>
> I then build hdf5 v1.8 with these flags:
> FC=mpif90 F77=mpif77 F90=mpif90 CC=mpicc CFLAGS="-D_LARGEFILE_SOURCE
> -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC" LIBS="-lz -lm"
> ./configure --enable-parallel --enable-fortran --prefix=/install/hdf5-1.8
> --disable-shared
>
> and everything with hdf5 checked out with "make check"
>
> Finally I configured netcdf v4.0.1 like so:
> buck@bender:/tmp/netcdf-4.0.1$ CPPFLAGS="-I/install/mpich2-121/include
> -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC"
> CFLAGS="-I/install/mpich2-121/include -D_LARGEFILE_SOURCE
> -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC" F77=mpif77 F90=mpif90
> FC=mpif90 CC=mpicc CXX=mpicxx LIBS="-lz -lm" ./configure --enable-netcdf-4
> --prefix=/install/netcdf-4.0.1 --enable-large-file-tests
> --with-hdf5=/install/hdf5-1.8 --with-zlib=/usr --enable-separate-fortran
>
>
> make works just fine but when I run "make check" I get errors when it tries
> to build fortran files that start like this:
> /bin/sh ../libtool --tag=F77 --mode=link mpif77 -I../fortran
> -I/install/hdf5-1.8/include -I/usr/include -I../libsrc4 -I../f90 -g
> -L/lib -L/install/hdf5-1.8/lib -L/usr/lib -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
> ../fortran/libnetcdff.la <http://*libnetcdff.la> -lm ../libsrc4/
> libnetcdf.la <http://*libnetcdf.la> -lhdf5_hl -lhdf5 -lz -lm
> libtool: link: mpif77 -I../fortran -I/install/hdf5-1.8/include
> -I/usr/include -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 -L/lib
> -L/install/hdf5-1.8/lib -L/usr/lib ../fortran/.libs/libnetcdff.a
> /tmp/netcdf-4.0.1/libsrc4/.libs/libnetcdf.a ../libsrc4/.libs/libnetcdf.a
> /install/hdf5-1.8/lib/libhdf5_hl.a /install/hdf5-1.8/lib/libhdf5.a -lz -lm
> test_get.o: In function `test_nf_get_var1_text':
>
> /tmp/netcdf-4.0.1/nf_test/test_get.F:25: undefined reference to `nf_open_'
> /tmp/netcdf-4.0.1/nf_test/test_get.F:34: undefined reference to
> `nf_get_var1_text_'
> /tmp/netcdf-4.0.1/nf_test/test_get.F:38: undefined reference to
> `nf_get_var1_text_'
> ....
>
> I'm attaching the entire results.
> Any ideas would be appreciated. I've tried playing with flags for a while
> and can't quite seem to get this ironed out.
> Thanks,
> -Joe Buck
>
>
> Content-Type: text/plain; charset=US-ASCII; name="mc2.txt"
> Content-Disposition: attachment; filename="mc2.txt"
> X-Attachment-Id: f_g57utkpj0
>
> Attachment converted: Macintosh HD:mc2.txt (TEXT/MSWD) (01CF155F)
> _______________________________________________
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit: http://*www.*
> unidata.ucar.edu/mailing_lists/
>
>
>
> --
>
>
>
>
> ====================================================
>
> Richard Hedges
> Customer Support and Test - File Systems Project
> Development Environment Group - Livermore Computing
> Lawrence Livermore National Laboratory
> 7000 East Avenue, MS L-557
> Livermore, CA 94551
>
> v: (925) 423-2699
> f: (925) 423-6961
> E: richard-hedges@xxxxxxxx
>
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U nf_def_compound_
U nf_def_dim_
U nf_def_enum_
U nf_def_grp_
U nf_def_opaque_
U nf_def_var_
U nf_def_var_chunking_
U nf_def_var_deflate_
U nf_def_var_endian_
U nf_def_var_fill_
U nf_def_var_fletcher32_
U nf_def_vlen_
U nf_del_att_
U nf_delete_
U nf_enddef_
U nf_free_vlen_
U nf_get_att_
U nf_get_att_double_
U nf_get_att_int1_
U nf_get_att_int2_
U nf_get_att_int_
U nf_get_att_real_
U nf_get_att_text_
U nf_get_chunk_cache_
U nf_get_var1_double_
U nf_get_var1_int1_
U nf_get_var1_int2_
U nf_get_var1_int64_
U nf_get_var1_int_
U nf_get_var1_real_
U nf_get_vara_double_
U nf_get_vara_int1_
U nf_get_vara_int2_
U nf_get_vara_int64_
U nf_get_vara_int_
U nf_get_vara_real_
U nf_get_varm_double_
U nf_get_varm_int1_
U nf_get_varm_int2_
U nf_get_varm_int64_
U nf_get_varm_int_
U nf_get_varm_real_
U nf_get_varm_text_
U nf_get_vars_
U nf_get_vars_double_
U nf_get_vars_int1_
U nf_get_vars_int2_
U nf_get_vars_int64_
U nf_get_vars_int_
U nf_get_vars_real_
U nf_get_vars_text_
U nf_inq_
U nf_inq_att_
U nf_inq_attid_
U nf_inq_attname_
U nf_inq_base_pe_
U nf_inq_compound_
U nf_inq_compound_field_
U nf_inq_compound_fielddim_sizes_
U nf_inq_compound_fieldindex_
U nf_inq_compound_fieldname_
U nf_inq_compound_fieldndims_
U nf_inq_compound_fieldoffset_
U nf_inq_compound_fieldtype_
U nf_inq_compound_name_
U nf_inq_compound_nfields_
U nf_inq_compound_size_
U nf_inq_dim_
U nf_inq_dimid_
U nf_inq_dimids_
U nf_inq_enum_
U nf_inq_enum_ident_
U nf_inq_enum_member_
U nf_inq_format_
U nf_inq_grp_ncid_
U nf_inq_grp_parent_
U nf_inq_grpname_
U nf_inq_grpname_full_
U nf_inq_grpname_len_
U nf_inq_grps_
U nf_inq_libvers_
U nf_inq_ncid_
U nf_inq_opaque_
U nf_inq_type_
U nf_inq_typeids_
U nf_inq_user_type_
U nf_inq_var_
U nf_inq_var_chunking_
U nf_inq_var_deflate_
U nf_inq_var_endian_
U nf_inq_var_fill_
U nf_inq_var_fletcher32_
U nf_inq_varid_
U nf_inq_varids_
U nf_inq_vlen_
U nf_insert_array_compound_
U nf_insert_compound_
U nf_insert_enum_
U nf_open_
U nf_open_par_
U nf_put_att_
U nf_put_att_double_
U nf_put_att_int1_
U nf_put_att_int2_
U nf_put_att_int_
U nf_put_att_real_
U nf_put_att_text_
U nf_put_var1_double_
U nf_put_var1_int1_
U nf_put_var1_int2_
U nf_put_var1_int64_
U nf_put_var1_int_
U nf_put_var1_real_
U nf_put_vara_double_
U nf_put_vara_int1_
U nf_put_vara_int2_
U nf_put_vara_int64_
U nf_put_vara_int_
U nf_put_vara_real_
U nf_put_varm_double_
U nf_put_varm_int1_
U nf_put_varm_int2_
U nf_put_varm_int64_
U nf_put_varm_int_
U nf_put_varm_real_
U nf_put_varm_text_
U nf_put_vars_
U nf_put_vars_double_
U nf_put_vars_int1_
U nf_put_vars_int2_
U nf_put_vars_int64_
U nf_put_vars_int_
U nf_put_vars_real_
U nf_put_vars_text_
U nf_redef_
U nf_rename_att_
U nf_rename_dim_
U nf_rename_var_
U nf_set_base_pe_
U nf_set_chunk_cache_
U nf_set_fill_
U nf_strerror_
U nf_sync_
U nf_var_par_access_
U nc_inq_compound_nfields
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