Hi Ted,
I do have an idea; I will describe what I think is going on. If you provide
the full config.log, I can confirm or reject my idea.
Lately, when this has cropped up, it is a result of the `conftest` executable
failing because of a "missing" .so, typically libnetcdf. This is often the
case on modern Linux systems when libnetcdf lives outside of '/usr'.
Specifically, the location of the shared library needs to live in the
'LD_LIBRARY_PATH' variable.
The fix is to run configure as follows:
$ LD_LIBRARY_PATH="/custom/location/lib" CPPFLAGS=<...> LDFLAGS=<...>
./configure
If you provide the config.log file, I can probably figure out the exact way you
would need to invoke configure. Although it may also be self-evident if you
take a look yourself. If config.log doesn't reveal any symptom of a missing
shared library, I will admit I'm wrong and figure out a new cause from there!
I hope this helps,
-Ward
>
> Hi,
>
> I got no response on this from the netcdfgroup mailing list, and I've run
> into it again on a system that I really need it get it working. Somehow the
> configure script (or autoconf or something else) is putting extra parentheses
> around the test variable in the conftest program: it should have (sizeof
> (off_t)), not (sizeof ((off_t))). The compilation then fails:
>
> configure:21173: mpicc -c -fPIC -I/usr/local/include
> -I/home/emansell/opt/pnetcdf161/include
> -I/home/emansell/local/netcdf4331mpi/include -fPIC conftest.c >&5
> conftest.c(101): error: expected an expression
> if (sizeof ((off_t)))
> ^
>
> compilation aborted for conftest.c (code 2)
> configure:21173: $? = 2
> configure: failed program was:
>
> Some more info from config.log is attached at the end. The netcdf-c works
> fine, obviously, since I got to this step. The hdf5 (1.8.13) files are also
> in /home/emansell/local/netcdf4331mpi. I have compile this successfully on
> other systems, but I have no clue on this issue.
>
> Any ideas?
>
> Thanks,
>
> -- Ted
>
> __________________________________________________________
> | Edward Mansell <address@hidden>
> | National Severe Storms Laboratory
> |--------------------------------------------------------------
> | "The contents of this message are mine personally and
> | do not reflect any position of the U.S. Government or NOAA."
> |--------------------------------------------------------------
>
>
> Begin forwarded message:
>
> > From: Ted Mansell <address@hidden>
> > Subject: netcdf fortran configure fail on sizeof
> > Date: August 8, 2015 at 4:03:48 PM CDT
> > To: "netcdfgroup (address@hidden)" <address@hidden>
> >
> > I'm trying to configure/compile the netcdf-fortran-4 on an AMD/Redhat Linux
> > system, and 4.2, 4.4.0, 4.4.2 all are having a problem with configure. No
> > problem with the netcdf-c (e.g., netcdf-c-4.3.1.1). It is failing on the
> > "sizeof" tests, where an extra set of parentheses is getting put around the
> > test variable (e.g., _Bool, off_t, etc.) so that the compile of conftest.c
> > fails because it has
> >
> > if (sizeof ((_Bool)))
> >
> > when it should be
> >
> > if (sizeof (_Bool))
> >
> > The netcdf-c does exactly the same test, but apparently does not add the
> > extraneous parentheses. I'm using Portland Group 10.8 (it's an older AMD
> > system: Linux alpha 2.6.18-398.el5 #1 SMP Tue Aug 12 06:26:17 EDT 2014
> > x86_64 x86_64 x86_64 GNU/Linux).
> >
> > I suppose this is some kind of autoconf issue?
> >
> > -- Ted
> >
> > __________________________________________________________
> > | Edward Mansell <address@hidden>
> > | National Severe Storms Laboratory
> > |--------------------------------------------------------------
> > | "The contents of this message are mine personally and
> > | do not reflect any position of the U.S. Government or NOAA."
> > |--------------------------------------------------------------
> >
>
> This file contains any messages produced by compilers while
> running configure, to aid debugging if configure makes a mistake.
>
> It was created by netCDF-Fortran configure 4.4.0, which was
> generated by GNU Autoconf 2.69. Invocation command line was
>
> $ ./configure --prefix=/home/emansell/local/netcdf4331mpi FC=mpif90
> F90=mpif90 CC=mpicc F77=mpif90 LDFLAGS=-L/home/emansell/opt/pnetcdf161/lib
> -L/home/emansell/local/netcdf4331mpi/lib -L/usr/local/lib
> CPPFLAGS=-I/home/emansell/opt/pnetcdf161/include
> -I/home/emansell/local/netcdf4331mpi/include -fPIC CFLAGS=-fPIC
> -I/usr/local/include FCFLAGS=-fPIC --enable-parallel-tests
>
> ## --------- ##
> ## Platform. ##
> ## --------- ##
>
> hostname = hrothgar.hpcc.ttu.edu
> uname -m = x86_64
> uname -r = 2.6.32-431.5.1.el6.x86_64
> uname -s = Linux
> uname -v = #1 SMP Wed Feb 12 00:41:43 UTC 2014
>
> /usr/bin/uname -p = unknown
> /bin/uname -X = unknown
>
> /bin/arch = x86_64
> /usr/bin/arch -k = unknown
> /usr/convex/getsysinfo = unknown
> /usr/bin/hostinfo = unknown
> /bin/machine = unknown
> /usr/bin/oslevel = unknown
> /bin/universe = unknown
>
> PATH: /lustre/work/apps/intel/composer_xe_2013.1.117/bin/intel64
> PATH: /lustre/work/apps/intel/composer_xe_2013.1.117/mpirt/bin/intel64
> PATH: /lustre/work/apps/intel/composer_xe_2013.1.117/bin/intel64
> PATH: /lustre/work/apps/intel/composer_xe_2013.1.117/bin/intel64_mic
> PATH: /lustre/work/apps/intel/composer_xe_2013.1.117/debugger/gui/intel64
> PATH: /opt/gridengine/bin/lx26-amd64
> PATH: /lustre/work/apps/openmpi/bin
> PATH: /lustre/work/apps/svn/bin
> PATH: /sbin
> PATH: /usr/sbin
> PATH: /bin
> PATH: /usr/local/bin
> PATH: /usr/bin
> PATH: /usr/X11R6/bin
> PATH: /lustre/work/apps/bin
> PATH: /home/emansell/bin
>
>
>
>
>
Ticket Details
===================
Ticket ID: JCT-681222
Department: Support netCDF
Priority: Normal
Status: Closed
NOTE: All email exchanges with Unidata User Support are recorded in the Unidata inquiry tracking system and then made publicly available through the web. If you do not want to have your interactions made available in this way, you must let us know in each email you send to us.