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[netCDF #FLE-841916]: Testsuite summary for netCDF 4.3.2



Ben,

> OK I was able to install the latest version of HDF5.
> thanks for your help with that.
> 
> because iâm on a server I couldnât put it in the use/local directory, 
> other people were worried that by updating netCDF and related applications i 
> would stop their WRF and MEGAN models from working.
> 
> /home/bweinste/WORK/MEGAN/MEGANv2.10/local
> 
> this is my version of  user/local

Right, that's fine, I was just using /usr/local as an example for how to
specify the install directory, you could use anything and it doesn't have 
to end with "/local".

Once you have the HDF5 libraries installed as shared libraries (the 
default) in someplace that the dynamic loader (ld.so on Linux) doesn't
look for shared libraries, you may need to add the lib location to the
directories that get searched.  This is specified using the 
LD_LIBRARY_PATH environment variable (or DYLD_LIBRARY_PATH on OSX),
for example:

  
LD_LIBRARY_PATH=/home/bweinste/WORK/MEGAN/MEGANv2.10/local/lib:$LD_LIBRARY_PATH
  export LD_LIBRARY_PATH

See if setting and exporting that environment variable fixes the problem
you're seeing.

--Russ

> I went to configure netCDF 4.3.2 to the same series of directories by 
> entering:
> ./configure --prefix=/mnt/data/bweinste/MEGAN/MEGANv2.10/local
> 
> that seemed to work ok. but when i typed in: $ make check install it failed 
> again. I got the following message in the log:
> 
> =========================================
> netCDF 4.3.2: ncgen3/test-suite.log
> =========================================
> 
> # TOTAL: 2
> # PASS:  0
> # SKIP:  0
> # XFAIL: 0
> # FAIL:  2
> # XPASS: 0
> # ERROR: 0
> 
> .. contents:: :depth: 2
> 
> FAIL: run_tests.sh
> ==================
> 
> *** Testing ncgen3.
> *** creating classic file c0.nc from c0.cdl...
> /home/bweinste/WORK/MEGAN/MEGANv2.10/local/NETCDF/netcdf-4.3.2/ncgen3/.libs/lt-ncgen3:
>  error while loading shared libraries: libnetcdf.so.7: cannot open shared 
> object file: No such file or directory
> 
> 
> FAIL: run_nc4_tests.sh
> ======================
> *** Testing ncgen3 for netCDF-4.
> *** creating netCDF-4 file c0_4.nc from c0.cdl...
> /home/bweinste/WORK/MEGAN/MEGANv2.10/local/NETCDF/netcdf-4.3.2/ncgen3/.libs/lt-ncgen3:
>  error while loading shared libraries: libnetcdf.so.7: cannot open shared 
> object file: No such file or directory
> 
> 
> can you help me interpret the cause of this failure? is it because i need to 
> install everything in the usr/bin/local directories? is it because I tried to 
> install it before and it doesnât like to overwrite some files?
> cheers,
> 
> -ben
> 
> 
> On Sep 9, 2014, at 4:54 PM, Unidata netCDF Support <address@hidden> wrote:
> 
> > Ben,
> >
> >> when i download it, should i put it in the same directory as the netcdf 
> >> library?
> >>
> >> for example, if iâm putting the netCDF library in
> >>
> >> /mnt/data/bweinste/MEGAN/MEGANv2.10/lib/NETCDF
> >>
> >> should i also put the HDF5 in the NETCDF directory?
> >
> > It depends on whether you are downloading the pre-built binary HDF5 library 
> > or
> > downloading the source to build and install yourself.
> >
> > For the pre-built binaries, you can install HDF5 in the same directories as 
> > netCDF.  For
> > example, if netCDF is installed in /usr/local (in the subdirectories lib, 
> > include, bin,
> > and share of /usr/local), then HDF5 binaries can be installed in the same 
> > directories.
> >
> > If you're building from source, don't download the HDF5 sources into the 
> > same directory
> > as  the netCDF sources!  But you can make sure they're installed in the 
> > same directories
> > by specifying the same parent directory with the --prefix option to the 
> > configure script,
> > for example --prefix=/usr/local .  If you build with CMake instead of 
> > configure, you
> > can do the analogous thing by specifying the same install parent directory.
> >
> > We recommend just building from the sources as a normal user (not as root), 
> > but
> > then running "make install" as root or with "sudo make install", to get 
> > things installed
> > where they belong.
> >
> > --Russ
> >
> >> iâm working on a server and one concern other people have is that if i 
> >> install any updates it will stop their models from working. thus iâm 
> >> trying to keep all my stuff contained
> >>
> >> cheers and thanks for the support
> >>
> >> Ben
> >>
> >> On Sep 9, 2014, at 2:14 PM, Unidata netCDF Support <address@hidden> wrote:
> >>
> >>> Ben,
> >>>
> >>>> thanks for getting back to me last week.
> >>>> Can you tell me where I can get the updated version of HDF5?
> >>>>
> >>>> iâve looked on your website and canât seem to find that.
> >>>
> >>> We've got a source release here:
> >>>
> >>> ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/hdf5-1.8.13.tar.gz
> >>>
> >>> but a better place would be the The HDF Group site where we got it
> >>> from:
> >>>
> >>> http://www.hdfgroup.org/HDF5/release/obtain5.html
> >>>
> >>> If you don't see a pre-built binary distribution for your platform,
> >>> get the source code release under the "All Platforms" link.
> >>>
> >>> --Russ
> >>>
> >>>> Ben
> >>>>
> >>>>
> >>>> On Sep 5, 2014, at 12:17 PM, Unidata netCDF Support <address@hidden> 
> >>>> wrote:
> >>>>
> >>>>> Hi Ben,
> >>>>>
> >>>>> You have to use a more recent version of HDF5, 1.8.8 or later, with 
> >>>>> netCDF
> >>>>> 4.3.
> >>>>> ?2?
> >>>>> .
> >>>>>
> >>>>> There was a bug in HDF5-1.8.7
> >>>>> ?that the
> >>>>> current netCDF version
> >>>>> ? detects
> >>>>> when built with
> >>>>> ?that version (or earlier) of HDF5.
> >>>>>
> >>>>> ?Your "make check" should work
> >>>>> fine with HDF5 versions 1.8.8 and later. If you have to rebuild HDF5 
> >>>>> from
> >>>>> source anyway, I
> >>>>> ? ?
> >>>>> would recommend just using the latest version 1.8.1
> >>>>> ?3?
> >>>>> , as that's what
> >>>>> ? ?
> >>>>> we've done the most testing with.
> >>>>>
> >>>>> --Russ
> >>>>>
> >>>>>
> >>>>> address@hidden> wrote:
> >>>>>
> >>>>>> New Ticket: Testsuite summary for netCDF 4.3.2
> >>>>>>
> >>>>>> To whom it may concern,
> >>>>>>
> >>>>>> i tried to install netCDF 4.3.2 and had the following issue:
> >>>>>>
> >>>>>>
> >>>>>> ============================================================================
> >>>>>> Testsuite summary for netCDF 4.3.2
> >>>>>>
> >>>>>> ============================================================================
> >>>>>> # TOTAL: 39
> >>>>>> # PASS:  37
> >>>>>> # SKIP:  0
> >>>>>> # XFAIL: 0
> >>>>>> # FAIL:  2
> >>>>>> # XPASS: 0
> >>>>>> # ERROR: 0
> >>>>>>
> >>>>>> ============================================================================
> >>>>>> See ncdump/test-suite.log
> >>>>>> Please report to address@hidden
> >>>>>>
> >>>>>> ============================================================================
> >>>>>>
> >>>>>> the failures were as follows:
> >>>>>>
> >>>>>> FAIL: tst_h_scalar
> >>>>>> FAIL: tst_h_scalar.sh
> >>>>>>
> >>>>>> is this a big problem? is there a way to correct these? does this mean
> >>>>>> that netCDF will not work properly? Iâm fairly new to the netCDF 
> >>>>>> library
> >>>>>> and am unsure what this means. I installed netCDF as instructed by an 
> >>>>>> air
> >>>>>> quality model, MEGAN (the model of emissions of gases and aerosols from
> >>>>>> nature).
> >>>>>>
> >>>>>> any assistance is appreciated.
> >>>>>>
> >>>>>> Ben Weinstein,
> >>>>>> student at the University of British Columbia
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Ticket Details
> >>>>>> ===================
> >>>>>> Ticket ID: FLE-841916
> >>>>>> Department: Support netCDF
> >>>>>> Priority: Normal
> >>>>>> Status: Open
> >>>>>> Link:
> >>>>>> https://www.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=viewticket&ticketid=24407
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Ticket Details
> >>>>> ===================
> >>>>> Ticket ID: FLE-841916
> >>>>> Department: Support netCDF
> >>>>> Priority: Normal
> >>>>> Status: Closed
> >>>>
> >>>>
> >>> Russ Rew                                         UCAR Unidata Program
> >>> address@hidden                      http://www.unidata.ucar.edu
> >>>
> >>>
> >>>
> >>> Ticket Details
> >>> ===================
> >>> Ticket ID: FLE-841916
> >>> Department: Support netCDF
> >>> Priority: Normal
> >>> Status: Closed
> >>
> >>
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: FLE-841916
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: FLE-841916
Department: Support netCDF
Priority: Normal
Status: Closed


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