[netCDF #OTC-268927]: compile errors netcdf 4.1.2

Hi Basil,

> I have compiled parallel netcdf 4.1.2 using xlf and xlc compilers on 
> bluegene/P  and os linux suse. The compilation was successful and I got all 
> the libraries, include files and executables (as for as I know). However, 
> "make check" showed the following errors:
> 
> ================================================
> 2 of 25 tests failed
> Please report to address@hidden
> ================================================
> make[2]: *** [check-TESTS] Error 1
> make[2]: Leaving directory 
> `/gpfs/home/basitali/netcdf413_hdf186_zlib125/netcdf-4.1.2/h5_test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory 
> `/gpfs/home/basitali/netcdf413_hdf186_zlib125/netcdf-4.1.2/h5_test'
> make: *** [check-recursive] Error 1
> 
> The makecheck.log file is attached for your review. I am wondering if these 
> errors would have any effect on the parrallel make of netcdf? If yes what I 
> could do to get rid of these errors. I used the following configure command 
> for compiling netcdf 4.1.2
> 
> ./configure --prefix=/home/basitali/netCDF_4.1.2 CC=mpixlc CXX=mpixlcxx 
> FC=mpixlf90 F77=mpixlf90 CFLAGS="-I/home/basitali/netCDF_4.1.2/include 
> -DIBMR2Fortran -I/opt/share/zlib/1.2.5/bgp-ibm/include 
> -I/opt/share/hdf5/1.8.9/bgp-ibm/include" 
> LIBS="-L/home/basitali/netCDF_4.1.2/lib -L/opt/share/zlib/1.2.5/bgp-ibm/lib 
> -L/opt/share/hdf5/1.8.9/bgp-ibm/lib -lnetcdf -lm -lhdf5_hl -lhdf5_fortran 
> -lhdf5 -lz -lm" FFLAGS="-g -I/home/basitali/netCDF_4.1.2/include" 
> FCFLAGS="-I/home/basitali/netCDF_4.1.2/include -DIBMR2Fortran 
> -I/opt/share/zlib/1.2.5/bgp-ibm/include 
> -I/opt/share/hdf5/1.8.9/bgp-ibm/include" 
> FLIBS="-L/home/basitali/netCDF_4.1.2/lib -lnetcdff 
> -L/opt/share/zlib/1.2.5/bgp-ibm/lib -L/opt/share/hdf5/1.8.9/bgp-ibm/lib 
> -lnetcdf -lm -lhdf5_hl -lhdf5_fortran -lhdf5 -lz -lm" 
> CXXFLAGS="-DIBMR2Fortran -I/home/basitali/netCDF_4.1.2/include 
> -I/opt/share/zlib/1.2.5/bgp-ibm/include 
> -I/opt/share/hdf5/1.8.9/bgp-ibm/include" CPPFLAGS="-DIBMR2Fortran 
> -I/home/basitali/netCDF_4.1.2/include -I/opt
 /share/zlib/1.2.5/bgp-ibm/include -I/opt/share/hdf5/1.8.9/bgp-ibm/include" 
--enable-parallel --with-zlib=/opt/share/zlib/1.2.5/bgp-ibm  
--with-hdf5=/opt/share/hdf5/1.8.9/bgp-ibm --enable-pnetcdf 
--with-pnetcdf=/home/basitali/pnetcdf -disable-dap --disable-shared

I'm guessing the problem may be that you're encountering a bug in the 4.1.2 
version of netCDF, 
from this entry in the netCDF 4.1.3 RELEASE_NOTES:

                Fix bug that prevents netCDF-4/HDF5 files created with
                netCDF-4.1.2 from being read by earlier versions of
                netCDF or HDF5 versions before 1.8.7.
                [NCF-23]
                https://www.unidata.ucar.edu/jira/browse/NCF-23

I may be wrong about that, but the error message in the file you attached 
indicated a failure
to open an HDF5 file, as described in the bug web page ...

> Please advise.

My advice would be to try either the 4.1.3 version of netCDF or the more recent 
4.2.1.1 C-netCDF and
the 4.2 Fortran-netCDF releases, building the C library first and then the 
Fortran library, following
the instructions here:

  For 4.1.3:
     http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install/
  For 4.2.1.1:
     http://www.unidata.ucar.edu/software/netcdf/docs/building.html

Sorry, but we lost our parallel-netCDF expertise when the developer got lured 
away last year, so
I can't answer the question about the parallel make.  I also see you're not 
setting the environment
variables MPICC, MPIFC, and MPIF77, as recommended in a address@hidden mailing 
list,
but I'm not sure if that's a problem:

  http://lists.mcs.anl.gov/pipermail/parallel-netcdf/2011-June/001193.html

--Russ

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: OTC-268927
Department: Support netCDF
Priority: Normal
Status: Closed