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



Ben,

> thanks for this email and your previous help.
> >  /usr/local/bin/nc-config --has-hdf5
> >  /usr/local/bin/nc-config --has-dap
> 
> 
> these both return yes. so I gather that the netcdf library was installed with 
> hdf5.
> 
> iâve moved on to installing the netCDF fortran library and we are again 
> running into problems.
> 
> the air quality models i hope to run are built for pgf90 as opposed to 
> gfortran. my hope is to compile netcdf-fortran-4.4.1
> with pgf90. we were able to successfully change the compiler in the Makefile 
> but then we get an error stating:
> 
> PGF90-S-0081-Illegal selector - KIND value must be non-negative 
> (module_netcdf_nc_data.F90: 175)
> 
> do you know how to work around this problem?

We don't have access to PGI C or Fortran compilers here, so don't test with 
them.
PGI provides its own guide to building netCDF Fortran with their compilers, 
though
it may be a little out of date, and shows csh rather than bash shell syntax for
setting environment variables:

  http://www.pgroup.com/resources/netcdf/netcdf411_pgi2011.htm

However, the error message you showed above indicates that the pgf90 Fortran 
compiler doesn't support the KIND (primitive data type) used in the referenced 
statement, which is a parameter named C_SIGNED_CHAR that's provided by the
ISO_C_BINDING standard intrinsic module. If a particular C type has no 
matching Fortran kind, the parameter value will be negative.

You might try to make sure the following Fortran program can be compiled 
correctly, or adjust the pgf90 configuration or flags until it does:

PROGRAM testit
USE,INTRINSIC :: ISO_C_BINDING
INTEGER(KIND=C_SIGNED_CHAR) :: j = -127_C_SIGNED_CHAR
IF(j /= -127) THEN
  PRINT *, 'Compiler does not support standard ISO_C_BINDING'
ELSE
  PRINT *, 'Success'
ENDIF
END PROGRAM testit

--Russ

> 
> On Sep 14, 2014, at 2:36 PM, Unidata netCDF Support <address@hidden> wrote:
> 
> > Ben,
> >
> >> an IT person at UBC may have done what i needed. I donât understand how, 
> >> as when i run make check the program still crashes.
> >>
> >> I want to check to see if all the programs / libraries were installed in 
> >> netCDF 4.3.2:
> >>
> >> from what i can tell here is what was installed:
> >> usr/local/bin:
> >> nc-config
> >> nccopy
> >> ncdump
> >> ncgen
> >> ncgen3
> >
> > Yes, that's all the executables installed by netCDF 4.3.2.
> >
> >> usr/local/lib
> >> libnetcdf.la
> >> libnetcdf.so
> >> libnetcdf.so.7
> >> libnetcdf.so.7.2.0
> >
> > Yup, that's all that's needed for the netCDF-C library.  However, our
> > netcdf-4.3.2 installation also has a subdirectory named pkgconfig/
> > with the file pkgconfig/netcdf.pc that gets installed if your system
> > has the pkg-config software installed (see the Wikipedia entry).  It's
> > not necessary, just a convenience for other software that depends
> > on netCDF and uses pkg-config to find out how to link with it.
> >
> >> usr/local/include
> >> netcdf.h
> >
> > Yes, that's the only include file installed.
> >
> >> is there anything else that is missing or didnât install?
> >> does anything else get installed in a parent directory?
> >
> > By default, the man page documentation is also installed in
> > /usr/local/share/man/{man1,man3} on our Linux systems.
> >
> > Just having those directories and files installed in /usr/local
> > doesn't tell you whether the libraries and utility programs were
> > built and configured right for your use.  For example, if you
> > need features of netCDF-4 such as compression and chunking,
> > then HDF5 must have bee installed and the netCDF libraries
> > must have been built with HDF5-support.  You could determine
> > this most easily by just running the program
> >
> >  /usr/local/bin/nc-config --has-hdf5
> >
> > which should output "yes", and similarly for determining whether
> > it was built with support for DAP, the data access protocol that
> > makes it possible to access netCDF data from remote DAP servers
> >
> >  /usr/local/bin/nc-config --has-dap
> >
> > should return "yes".  You can see everything supported by using --all.
> >
> > --Russ
> >
> >> On Sep 12, 2014, at 10:36 AM, Unidata netCDF Support <address@hidden> 
> >> wrote:
> >>
> >>> Ben,
> >>>
> >>>> I do have the HDF5version 1.8.13,
> >>>> I took the steps you mentioned:
> >>>>
> >>>> 1) H5DIR=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
> >>>> 2) CPPFLAGS=-I${H5DIR}/include
> >>>> 3) LDFLAGS=-L${H5DIR}/lib
> >>>>
> >>>> for
> >>>> 4) ./configure ...
> >>>> I did ./configure 
> >>>> --prefix=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/NETCDF
> >>>>
> >>>> âyet the problem persists. are there any other things that need to be 
> >>>> pointed tot he H5DIR?
> >>>
> >>> Maybe this is a simple problem with the Unix shell you are using
> >>> and setting environment variables that shell scripts like
> >>> configure can access.
> >>>
> >>> You don't have to worry about this if you set CPPFLAGS and
> >>> LDFLAGS as part of the list of arguments to configure, as
> >>> in
> >>>
> >>> ./configure --prefix=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/NETCDF 
> >>> CPPFLAGS=-I${H5DIR}/include LDFLAGS=-L${H5DIR}/lib
> >>>
> >>> In that case, the configure script sees the settings and uses
> >>> them.
> >>>
> >>> Instead, you can precede the configure command with the
> >>> environment variable settings if you are using bash, ksh,
> >>> zsh, or a similar POSIX-standard command shell, as in:
> >>>
> >>> CPPFLAGS=-I${H5DIR}/include LDFLAGS=-L${H5DIR}/lib ./configure 
> >>> --prefix=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/NETCDF
> >>>
> >>> If you set the environment variables separately from the configure
> >>> command line, they are local to that shell, so to make them
> >>> accessible to subshells such as script files like configure, you
> >>> have to explicitly export them, as in
> >>>
> >>> H5DIR=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
> >>> CPPFLAGS=-I${H5DIR}/include
> >>> LDFLAGS=-L${H5DIR}/lib
> >>> export CPPFLAGS LDFLAGS
> >>>
> >>> If you are instead using a non-POSIX shell such as csh, you
> >>> need to instead use the setenv command, as in
> >>>
> >>> setenv H5DIR /mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
> >>> setenv CPPFLAGS -I${H5DIR}/include
> >>> setenv LDFLAGS -L${H5DIR}/lib
> >>>
> >>> I hope one of those works ...
> >>>
> >>> --Russ
> >>>
> >>>> On Sep 11, 2014, at 8:12 PM, Unidata netCDF Support <address@hidden> 
> >>>> wrote:
> >>>>
> >>>>> Hi Ben,
> >>>>>
> >>>>>> sorry to bombard your with questions.
> >>>>>
> >>>>> No problem ...
> >>>>>
> >>>>>> have you had a minute to consider my last one?
> >>>>>> I have installed hdf5 into the directory:
> >>>>>>
> >>>>>> /mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
> >>>>>
> >>>>> OK, but are you sure that's HDF5 version 1.8.8 or later, preferably 
> >>>>> 1.8.13?
> >>>>> You can check by looking in the file
> >>>>>
> >>>>> /mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5/lib/libhdf5.settings
> >>>>>
> >>>>> for a line like:
> >>>>>
> >>>>>                    HDF5 Version: 1.8.13
> >>>>>
> >>>>> which identifies the installed version.  An error message you're 
> >>>>> getting when
> >>>>> trying to run the netCDF tests seems to indicate an older HDF5 version,
> >>>>> 1.8.4 (patch1), which is too old to pass the stringent tests in netCDF 
> >>>>> 4.3.2.
> >>>>>
> >>>>>>> =========================================
> >>>>>>>
> >>>>>>> netCDF 4.3.2: ncdump/test-suite.log
> >>>>>>>
> >>>>>>> =========================================
> >>>>>>>
> >>>>>>> # TOTAL: 39
> >>>>>>> # PASS:  37
> >>>>>>> # SKIP:  0
> >>>>>>> # XFAIL: 0
> >>>>>>> # FAIL:  2
> >>>>>>> # XPASS: 0
> >>>>>>> # ERROR: 0
> >>>>>>>
> >>>>>>> .. contents:: :depth: 2
> >>>>>>>
> >>>>>>> FAIL: tst_h_scalar
> >>>>>>>
> >>>>>>> ==================
> >>>>>>>
> >>>>>>> HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 
> >>>>>>> 47514256252672:
> >>>>>>> #000: ../../../src/H5T.c line 1595 in H5Tcreate(): unable to create 
> >>>>>>> type
> >>>>>
> >>>>> To build netCDF, you need to set CPPFLAGS and LDFLAGS to point to your 
> >>>>> HDF5
> >>>>> installation directories, something like
> >>>>>
> >>>>> H5DIR=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
> >>>>> CPPFLAGS=-I${H5DIR}/include  LDFLAGS=-L${H5DIR}/lib ./configure ...
> >>>>> make check
> >>>>> make install # (or sudo make install)
> >>>>>
> >>>>> --Russ
> >>>>>
> >>>>> 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
> 
> 
> 

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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