[netCDF #FYY-183264]: netcdf4.1.1 with hdf5-1.8.4-patch1

Violeta,

> unfortunately it does not work. Here are the output files  for
> netcdf-4.1.1
> 
> 
> 
> I amd using szip-2.1,  zlib-1.2.5, hdf5-1.8.5-patch1,  netcdf-4.1.1

The error message appears to indicate the HDF5-1.8.6 is being used, rather than
1.8.5-patch1:

> *** Tests successful!
> PASS: tst_h_atts3
> HDF5-DIAG: Error detected in HDF5 (1.8.6) thread 0:
>   #000: H5Ddeprec.c line 169 in H5Dcreate1(): unable to create dataset
>     major: Dataset
>     minor: Unable to initialize object

Is it possible there are multiple installations of HDF5, and you are linking to 
the HDF5-1.8.6
library?  We have reported a problem with the combination of netCDF-4.1.1 and 
HDF5-1.8.6
as well as possible workarounds here:

  
http://www.unidata.ucar.edu/software/netcdf/docs/known_problems.html#incompat-411-186

We don't have ifort available on our MacOS X test platform, so can't duplicate 
the problem you
are seeing, but our daily snapshot passes all tests using the cc compiler 
that's part of the Xcode
developer tools with gfortran or g95.

> For HDF5 configure:
> ./configure --prefix=/usr/local/hdf5 --disable-shared --enable-
> fortran --with-zlib=/usr/local --with-szlib=/usr/local/szip

We don't use "--enable-fortran" with our HDF5 build, because the netCDF-4 
library makes no use
of the HDF5 Fortran API.  Instead the netCDF Fortran API is implemented on top 
of the netCDF C library.
But I doubt if that is relevant to the problem you are seeing.

> For netcdf4 configure:
> ./configure --prefix=/usr/local/hdf5 --disable-shared --enable-
> fortran --with-zlib=/usr/local --with-szlib=/usr/local/szip /
> --enable-netcdf4 --enable-fortran --with-zlib=/usr/local --with-
> szlib=/usr/local/szip --with-hdf5=/usr/loca/hdf5 /
> --enable-separate-fortran
> 
> My .profile:
> PATH=$PATH:$HOME:/usr/bin:/usr/local:/Applications/itt/idl/idl82/bin:/
> Applications/TeX:/opt/local/bin:~/scripts
> export CC=gcc
> export F9X=ifort
> export CXX=g++
> export FC=ifort
> export F77=ifort
> export F90=ifort
> export HDF5_DIR=/usr/local/hdf5
> export HDF5_LIB_DIR=/usr/local/lib
> export HDF5DIR=/usr/local/hdf5
> export NETCDF4_DIR=/usr/local/netcdf4
> export FCFLAGS='-O3'
> export FFLAGS='-O3'
> export CFLAGS='-O3'
> export CXXFLAGS='-O3 '
> export MACOSX_DEPLOYMENT_TARGET=10.5
> export LDFLAGS='-O3 '
> export DYLD_LIBRARY_PATH=/usr/local/lib:/usr/local/hdf5/:/usr/local/
> netcdf4:/usr/local/szip/lib:${DYLD_LIBRARY_PATH}
> 
> the ifort is /opt/intel/Compiler/11.0/054/bin/ia32/ifort
> 
> I did try with different compile flags like '-O3 -xN -ip -no-prec-div
> -static' as per Intel advice but no change.

We do have successful tests of our daily snapshot with ifort 10.1 on a linux 
platform, 
using no extra flags, just

  CC=icc CFLAGS="-g -O2" FC=ifort FCFLAGS=-g F77=ifort FFLAGS=-g 

--Russ

> On Mar 15, 2011, at 4:58 PM, Unidata netCDF Support wrote:
> 
> > Hi Violeta,
> >
> >> I am tryind to install netsdf4 on and Mac OS X 10.5.8 with Intel
> >> FORTRAN compiles ifort version 11.0.
> >>
> >> The "make check" fails 1 out of 59 tests. Here it is attached the
> >> make.out.txt t file with the output.
> >  ...
> >> *** testing long string variable...ok.
> >> *** Tests successful!
> >> PASS: tst_strings
> >> HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
> >>   #000: H5O.c line 676 in H5Oget_info_by_idx(): group not found
> >>     major: Symbol table
> >>     minor: Object not found
> >>   #001: H5Gloc.c line 578 in H5G_loc_find_by_idx(): can't find object
> >>     major: Symbol table
> >>     minor: Object not found
> >  ...
> >> ================================================
> >> 1 of 59 tests failed
> >> Please report to address@hidden
> >> ================================================
> >> make[2]: *** [check-TESTS] Error 1
> >
> > This looks like a problem that was fixed in HDF5-1.8.5-patch1.
> > Could you
> > please try installing that version instead of HDF5-1.8.4-patch1 and
> > let
> > us know if the problem persists?  Note, please don't use the later
> > release
> > 1.8.6 of HDF5, which has an incompatibility with netCDF 4.1.1 that
> > we don't
> > have a fix for yet.
> >
> > I hope this works.
> >
> > --Russ
> >
> >
> >
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: FYY-183264
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> >
> 
> 
> 

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



Ticket Details
===================
Ticket ID: FYY-183264
Department: Support netCDF
Priority: Normal
Status: Closed