Re: [netcdfgroup] issue compiling netcdf4 with mpi

• To: Joe Buck <jbbuck@xxxxxxxxx>
• Subject: Re: [netcdfgroup] issue compiling netcdf4 with mpi
• From: Richard Hedges <richard-hedges@xxxxxxxx>
• Date: Wed, 3 Feb 2010 10:25:52 -0800

Howdy Joe,

http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg01641.html

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/<http://*libnetcdff.la>libnetcdff.la -lm ../libsrc4/<http://*libnetcdf.la>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

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--



====================================================

Richard Hedges
Customer Support and Test - File Systems Project
Development Environment Group - Livermore Computing
Lawrence Livermore National Laboratory
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• References:
  • [netcdfgroup] issue compiling netcdf4 with mpi
    • From: Joe Buck