[netCDF #TRL-392354]: netcdf-4 build fails

Hello,

> Hi!
> 
> Per Jansson, PhD student, physical oceanography at UiT, Norway, here.
> 
> (On a brand new workstation with ubuntu 14.04 LTS.)
> 
> I'm trying to build netcdf-4.3.2 C-libraries with support for parallel and 
> netcdf-4, but ran into problems;
> 
> I have successfully installed hdf5 (1.8.13) (make check install-->ok). like 
> this;
> export LD_LIBRARYS_PATH="/home/per/local/lib /usr/local/lib"
> export CPPFLAGS="-I/home/per/local/include"

I don't know if it is relevant, but LD_LIBRARYS_PATH should, I believe, be:

LD_LIBRARY_PATH="/home/per/local/lib:/usr/local/lib"

I have not seen 'LD_LIBRARYS_PATH' before, and a google search is not showing 
me any information about it.  Section 3.3.1 of the following document describes 
how to use LD_LIBRARY_PATH.

http://tldp.org/HOWTO/Program-Library-HOWTO/shared-libraries.html

> export LDFLAGS="-L/home/per/local/lib"
> export LIBS="-lz -ldl"
> export CC=mpicc
> ./configure --prefix=/home/per/local/ -with-zlib=/home/per/local 
> -enable-parallel

Unless this is a typo in the email, I believe you should use 
'--enable-parallel', with two dashes, not '-enable-parallel', as you have 
above.  What is happening is that configure is not finding parallel symbols in 
libhdf5, and so 'USE_PARALLEL' is not being defined.  As a result, MPI_Comm is 
being defined in ncdispatch.h; this is guarded by an "#ifndef USE_PARALLEL" 
block.  Looking at the config.log file you provided, it confirms that no 
parallel symbols are found.

Can you confirm that libhdf5 actually built with parallel functionality?

Thanks,

-Ward

> make check
> make install
> 
> Then I try to build the netcdf-4.3.2 C-libraries like this;
> export LD_LIBRARYS_PATH="/home/per/local/lib /usr/local/lib"

Again, I'm not sure if it is relevant, but this should be changed as described 
above.

> export CPPFLAGS="-I/home/per/local/include"
> export LDFLAGS="-L/home/per/local/lib"
> export LIBS="-lz -ldl"
> export CC=mpicc
> ./configure --prefix=/home/per/local --enable-netcdf-4 
> --enable-parallel-tests --disable-shared --disable-dap


> so far ok
> make check
> produces; (this is end-bit of the output...)
> ============================================================================
> Testsuite summary for netCDF 4.3.2
> ============================================================================
> # TOTAL: 26
> # PASS:  26
> # SKIP:  0
> # XFAIL: 0
> # FAIL:  0
> # XPASS: 0
> # ERROR: 0
> ============================================================================
> make[3]: Leaving directory `/home/per/software/netcdf-4.3.2/h5_test'
> make[2]: Leaving directory `/home/per/software/netcdf-4.3.2/h5_test'
> make[1]: Leaving directory `/home/per/software/netcdf-4.3.2/h5_test'
> Making check in libdispatch
> make[1]: Entering directory `/home/per/software/netcdf-4.3.2/libdispatch'
> make[1]: Nothing to be done for `check'.
> make[1]: Leaving directory `/home/per/software/netcdf-4.3.2/libdispatch'
> Making check in libsrc
> make[1]: Entering directory `/home/per/software/netcdf-4.3.2/libsrc'
> make[1]: Nothing to be done for `check'.
> make[1]: Leaving directory `/home/per/software/netcdf-4.3.2/libsrc'
> Making check in libsrc4
> make[1]: Entering directory `/home/per/software/netcdf-4.3.2/libsrc4'
> /bin/bash ../libtool  --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H -I. 
> -I..  -I../include    -I/home/per/local/include  -g -O2 -MT 
> libnetcdf4_la-nc4attr.lo -MD -MP -MF .deps/libnetcdf4_la-nc4attr.Tpo -c -o 
> libnetcdf4_la-nc4attr.lo `test -f 'nc4attr.c' || echo './'`nc4attr.c
> libtool: compile:  mpicc -DHAVE_CONFIG_H -I. -I.. -I../include 
> -I/home/per/local/include -g -O2 -MT libnetcdf4_la-nc4attr.lo -MD -MP -MF 
> .deps/libnetcdf4_la-nc4attr.Tpo -c nc4attr.c -o libnetcdf4_la-nc4attr.o
> In file included from nc4dispatch.h:15:0,
> from nc4attr.c:17:
> ../include/ncdispatch.h:90:13: error: conflicting types for 'MPI_Comm'
> typedef int MPI_Comm;
> ^
> In file included from /home/per/local/include/H5public.h:61:0,
> from /home/per/local/include/hdf5.h:24,
> from ../include/nc4internal.h:18,
> from nc4attr.c:15:
> /home/per/local/include/mpi.h:324:37: note: previous declaration of 
> 'MPI_Comm' was here
> typedef struct ompi_communicator_t *MPI_Comm;
> ^
> In file included from nc4dispatch.h:15:0,
> from nc4attr.c:17:
> ../include/ncdispatch.h:91:13: error: conflicting types for 'MPI_Info'
> typedef int MPI_Info;
> ^
> In file included from /home/per/local/include/H5public.h:61:0,
> from /home/per/local/include/hdf5.h:24,
> from ../include/nc4internal.h:18,
> from nc4attr.c:15:
> /home/per/local/include/mpi.h:331:29: note: previous declaration of 
> 'MPI_Info' was here
> typedef struct ompi_info_t *MPI_Info;
> ^
> In file included from nc4dispatch.h:15:0,
> from nc4attr.c:17:
> ../include/ncdispatch.h:92:0: warning: "MPI_COMM_WORLD" redefined [enabled by 
> default]
> #define MPI_COMM_WORLD 0
> ^
> In file included from /home/per/local/include/H5public.h:61:0,
> from /home/per/local/include/hdf5.h:24,
> from ../include/nc4internal.h:18,
> from nc4attr.c:15:
> /home/per/local/include/mpi.h:1016:0: note: this is the location of the 
> previous definition
> #define MPI_COMM_WORLD OMPI_PREDEFINED_GLOBAL( MPI_Comm, ompi_mpi_comm_world)
> ^
> In file included from nc4dispatch.h:15:0,
> from nc4attr.c:17:
> ../include/ncdispatch.h:93:0: warning: "MPI_INFO_NULL" redefined [enabled by 
> default]
> #define MPI_INFO_NULL 0
> ^
> In file included from /home/per/local/include/H5public.h:61:0,
> from /home/per/local/include/hdf5.h:24,
> from ../include/nc4internal.h:18,
> from nc4attr.c:15:
> /home/per/local/include/mpi.h:743:0: note: this is the location of the 
> previous definition
> #define MPI_INFO_NULL OMPI_PREDEFINED_GLOBAL(MPI_Info, ompi_mpi_info_null)
> ^
> make[1]: *** [libnetcdf4_la-nc4attr.lo] Error 1
> make[1]: Leaving directory `/home/per/software/netcdf-4.3.2/libsrc4'
> make: *** [check-recursive] Error 1
> per@per-HP-Z620-Workstation:~/software/netcdf-4.3.2$
> 
> What is happening? If it's any help, I have attached the config.log file...
> I need the netcdf-4 to be able to install netcdf-fortran-4.4.0, which I need 
> to install ROMS (regional Ocean Model System).
> 
> 
> Best regards!
> Per
> 
> 

Ticket Details
===================
Ticket ID: TRL-392354
Department: Support netCDF
Priority: Normal
Status: Closed