[netCDF #GKD-688075]: netcdf-fortran-4.2 icc build error

Chris,

The error messages you are seeing, such as:

> netcdf_f.h(15): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, 
> int *chunksizesp);
> ^

all indicate that the macro "EXTERNL" is not being expanded properly,
perhaps because of a problem referencing the header file in which it
is defined.

Please check that this file, that should have been installed when you
ran "make install" for the netCDF C library, exists and is readable:

  
/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/netcdf-4.2_intel_mpt/include/netcdf.h

Then check that the following statements appear in that file about
lines 395-399:

#else
#define MSC_EXTRA
#endif  /* defined(DLL_NETCDF) */

# define EXTERNL MSC_EXTRA extern

Also, I see that your invocation of "icc" has "-DDLL_EXPORT" specified
on the command line, defining that macro.  That seems wrong for a
Linux platform, as I believe it's only intended for a Windows system.
It may be that definition is causing "EXTERNL" to get the wrong
definition.  For a Linux system, I think it should just get defined as
"extern". 

Did you explicitly include "-DDLL_EXPORT" in CPPFLAGS or some other
environment variable that would get included when "icc" is invoked?
This is just a guess, but otherwise, I don't know why the "EXTERNL"
macro isn't getting correctly defined in netcdf.h.

--Russ

> I downloaded and installed the netcdf-4.2 C package and successfully 
> configured it and built it.  All "make check" tests for it passed.  I have 
> downloaded the netcdf-fortran-4.2 and am trying to get it to build, but it 
> won't.  It configures fine, but icc gives me fatal compiler errors during 
> "make check".  I've searched for other reports and haven't found any.  I 
> apologize if this has already been reported, and solved, but I can't find 
> reference to it.
> 
> I am building on an SGI ICE system running Redhat 6 using the Intel v12.0.4 
> compiler with SGI's MPT version of MPI.  Am I looking at a compiler bug?  I 
> tried icc v11.1 and had the same problem.
> 
> [Christopher.W.Harrop@r15i1n7 netcdf-fortran-4.2]$ ./configure CC=icc 
> CXX=icpc F77=ifort F90=ifort FC=ifort --with-pic --enable-parallel-tests 
> --disable-shared CPPFLAGS="-I$HDF4/include 
> -I/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/hdf5-1.8.9_intel/include
>  -I$SZIP/include 
> -I/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/netcdf-4.2_intel_mpt/include"
>  LDFLAGS="-L$HDF4/lib 
> -L/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/hdf5-1.8.9_intel/lib
>  -L$SZIP/lib 
> -L/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/netcdf-4.2_intel_mpt/lib"
>  LIBS="-lmpi -lmfhdf -ldf -lhdf5_hl -lhdf5 -lsz -lnetcdf" 
> --prefix=/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/netcdf-4.2_intel_mpt
>           configure: netCDF-Fortran 4.2
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking target system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> configure: checking user options
> checking whether extra valgrind tests should be run... no
> checking whether parallel IO tests should be run... yes
> checking whether netCDF extra tests should be run (developers only)... no
> checking whether F90 API is desired... yes
> checking whether fortran type sizes should be checked... yes
> checking whether large file (> 2GB) tests should be run... no
> checking whether benchmaks should be run (experimental)... no
> checking where to put large temp files if large file tests are run... .
> configure: finding C compiler
> checking for gcc... icc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether icc accepts -g... yes
> checking for icc option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of icc... gcc3
> checking whether icc and cc understand -c and -o together... yes
> checking for an ANSI C-conforming const... yes
> configure: finding Fortran compiler (will not be used if Fortran API is not 
> desired)
> checking whether we are using the GNU Fortran compiler... no
> checking whether ifort accepts -g... yes
> checking whether we are using the GNU Fortran 77 compiler... no
> checking whether ifort accepts -g... yes
> configure: setting up Fortran 90
> checking what FC is set to... ifort
> checking for Fortran flag to compile .f90 files... none
> checking fortran 90 modules inclusion flag... -I
> configure: setting up libtool
> checking how to print strings... printf
> checking for a sed that does not truncate output... /bin/sed
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for fgrep... /bin/grep -F
> checking for ld used by icc... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
> checking the name lister (/usr/bin/nm -B) interface... BSD nm
> checking whether ln -s works... yes
> checking the maximum length of command line arguments... 98304000
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... yes
> checking for /usr/bin/ld option to reload object files... -r
> checking for objdump... objdump
> checking how to recognize dependent libraries... pass_all
> checking for ar... ar
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm -B output from icc object... ok
> checking how to run the C preprocessor... icc -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking for dlfcn.h... yes
> checking for objdir... .libs
> checking if icc supports -fno-rtti -fno-exceptions... yes
> checking for icc option to produce PIC... -fPIC -DPIC
> checking if icc PIC flag -fPIC -DPIC works... yes
> checking if icc static flag -static works... no
> checking if icc supports -c -o file.o... yes
> checking if icc supports -c -o file.o... (cached) yes
> checking whether the icc linker (/usr/bin/ld -m elf_x86_64) supports shared 
> libraries... yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for ifort option to produce PIC... -fPIC
> checking if ifort PIC flag -fPIC works... yes
> checking if ifort static flag -static works... no
> checking if ifort supports -c -o file.o... yes
> checking if ifort supports -c -o file.o... (cached) yes
> checking whether the ifort linker (/usr/bin/ld -m elf_x86_64) supports shared 
> libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for ifort option to produce PIC... -fPIC
> checking if ifort PIC flag -fPIC works... yes
> checking if ifort static flag -static works... no
> checking if ifort supports -c -o file.o... yes
> checking if ifort supports -c -o file.o... (cached) yes
> checking whether the ifort linker (/usr/bin/ld -m elf_x86_64) supports shared 
> libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> configure: finding other utilities
> configure: trying to set fortran flags for this platform
> checking what FC is set to... ifort
> checking for special C compiler options needed for large files... no
> checking for _FILE_OFFSET_BITS value needed for large files... no
> configure: displaying some results
> checking for /usr/bin/nm... /usr/bin/nm -B
> checking nm flags...
> checking for C-equivalent to Fortran routine "SUB"... sub_
> checking for Fortran "byte"... yes
> checking for Fortran "integer*2"... yes
> checking if Fortran "byte" is C "signed char"... yes
> checking if Fortran "byte" is C "short"... no
> checking if Fortran "byte" is C "int"... no
> checking if Fortran "byte" is C "long"... no
> checking if Fortran "integer*2" is C "short"... yes
> checking if Fortran "integer*2" is C "int"... no
> checking if Fortran "integer*2" is C "long"... no
> checking if Fortran "integer" is C "int"... yes
> checking if Fortran "real" is C "float"... yes
> checking if Fortran "doubleprecision" is C "double"... yes
> checking for Fortran-equivalent to netCDF "byte"... byte
> checking for Fortran-equivalent to netCDF "short"... integer*2
> checking if Fortran 90 compiler capitalizes .mod filenames... no
> checking whether extra example tests should be run... no
> checking whether a win32 DLL is desired... no
> configure: checking types, headers, and functions
> checking netcdf.h usability... yes
> checking netcdf.h presence... yes
> checking for netcdf.h... yes
> checking for library containing nc_open... no
> checking for nc_def_opaque... no
> checking for nccreate... no
> checking for nc_set_log_level... no
> checking for oc_open... no
> checking for nc_use_parallel_enabled... no
> checking netCDF v2 API present... no
> checking netCDF-4 present... no
> checking for stdlib.h... (cached) yes
> checking for sys/types.h... (cached) yes
> checking sys/param.h usability... yes
> checking sys/param.h presence... yes
> checking for sys/param.h... yes
> checking for dirent.h that defines DIR... yes
> checking for library containing opendir... none required
> checking for ANSI C header files... (cached) yes
> checking for sys/wait.h that is POSIX.1 compatible... yes
> checking whether time.h and sys/time.h may both be included... yes
> checking locale.h usability... yes
> checking locale.h presence... yes
> checking for locale.h... yes
> checking stdio.h usability... yes
> checking stdio.h presence... yes
> checking for stdio.h... yes
> checking stdarg.h usability... yes
> checking stdarg.h presence... yes
> checking for stdarg.h... yes
> checking errno.h usability... yes
> checking errno.h presence... yes
> checking for errno.h... yes
> checking ctype.h usability... yes
> checking ctype.h presence... yes
> checking for ctype.h... yes
> checking fcntl.h usability... yes
> checking fcntl.h presence... yes
> checking for fcntl.h... yes
> checking malloc.h usability... yes
> checking malloc.h presence... yes
> checking for malloc.h... yes
> checking for stdlib.h... (cached) yes
> checking for string.h... (cached) yes
> checking for strings.h... (cached) yes
> checking for unistd.h... (cached) yes
> checking for sys/stat.h... (cached) yes
> checking getopt.h usability... yes
> checking getopt.h presence... yes
> checking for getopt.h... yes
> checking sys/time.h usability... yes
> checking sys/time.h presence... yes
> checking for sys/time.h... yes
> checking sys/resource.h usability... yes
> checking sys/resource.h presence... yes
> checking for sys/resource.h... yes
> checking for vprintf... yes
> checking for _doprnt... no
> checking for stdbool.h that conforms to C99... yes
> checking for _Bool... yes
> checking for working alloca.h... yes
> checking for alloca... yes
> checking for size_t... yes
> checking for off_t... yes
> checking for ssize_t... yes
> checking for ptrdiff_t... yes
> checking for uchar... no
> checking for longlong... no
> checking whether char is unsigned... no
> checking size of short... 2
> checking size of int... 4
> checking size of long... 8
> checking size of float... 4
> checking size of double... 8
> checking size of off_t... 8
> checking size of size_t... 8
> configure: generating header files and makefiles
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating nf-config
> config.status: creating netcdf-fortran.pc
> config.status: creating man4/Makefile
> config.status: creating fortran/Makefile
> config.status: creating nf_test/Makefile
> config.status: creating f90/Makefile
> config.status: creating examples/Makefile
> config.status: creating examples/F90/Makefile
> config.status: creating examples/F77/Makefile
> config.status: creating config.h
> config.status: creating fortran/nfconfig1.inc
> config.status: executing depfiles commands
> config.status: executing libtool commands
> [Christopher.W.Harrop@r15i1n7 netcdf-fortran-4.2]$ make check
> Making check in f90
> make[1]: Entering directory 
> `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/build/netcdf-fortran-4.2/f90'
> ifort  -g -c -o typeSizes.o  typeSizes.f90
> make  check-am
> make[2]: Entering directory 
> `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/build/netcdf-fortran-4.2/f90'
> /bin/sh ../libtool --tag=FC   --mode=compile ifort  -g -c -o typeSizes.lo  
> typeSizes.f90
> libtool: compile:  ifort -g -c typeSizes.f90  -fPIC -o typeSizes.o
> /bin/sh ../libtool --tag=FC   --mode=compile ifort  -g -c -o netcdf.lo  
> netcdf.f90
> libtool: compile:  ifort -g -c netcdf.f90  -fPIC -o netcdf.o
> /bin/sh ../libtool --tag=FC   --mode=link ifort  -g  
> -L/apps/hdf4/4.2.7-intel-12.0.4.191/lib 
> -L/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/hdf5-1.8.9_intel/lib
>  -L/apps/szip/2.1-intel-12.0.4.191/lib 
> -L/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/netcdf-4.2_intel_mpt/lib
>  -o libnetcdff90.la  typeSizes.lo  netcdf.lo  -lmpi -lmfhdf -ldf -lhdf5_hl 
> -lhdf5 -lsz -lnetcdf
> libtool: link: ar cru .libs/libnetcdff90.a  typeSizes.o netcdf.o
> libtool: link: ranlib .libs/libnetcdff90.a
> libtool: link: ( cd ".libs" && rm -f "libnetcdff90.la" && ln -s 
> "../libnetcdff90.la" "libnetcdff90.la" )
> make[2]: Leaving directory 
> `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/build/netcdf-fortran-4.2/f90'
> make[1]: Leaving directory 
> `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/build/netcdf-fortran-4.2/f90'
> Making check in fortran
> make[1]: Entering directory 
> `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/build/netcdf-fortran-4.2/fortran'
> echo '!     NetCDF-3.' > netcdf.inc
> cat ../fortran/netcdf3.inc >> netcdf.inc
> make  check-am
> make[2]: Entering directory 
> `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/build/netcdf-fortran-4.2/fortran'
> depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> /bin/sh ../libtool --tag=CC   --mode=compile icc -DHAVE_CONFIG_H -I. -I..  
> -DDLL_EXPORT  -I/apps/hdf4/4.2.7-intel-12.0.4.191/include 
> -I/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/hdf5-1.8.9_intel/include
>  -I/apps/szip/2.1-intel-12.0.4.191/include 
> -I/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/netcdf-4.2_intel_mpt/include
>   -g -O2 -MT fort-attio.lo -MD -MP -MF $depbase.Tpo -c -o fort-attio.lo 
> fort-attio.c &&\
> mv -f $depbase.Tpo $depbase.Plo
> libtool: compile:  icc -DHAVE_CONFIG_H -I. -I.. -DDLL_EXPORT 
> -I/apps/hdf4/4.2.7-intel-12.0.4.191/include 
> -I/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/hdf5-1.8.9_intel/include
>  -I/apps/szip/2.1-intel-12.0.4.191/include 
> -I/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/netcdf-4.2_intel_mpt/include
>  -g -O2 -MT fort-attio.lo -MD -MP -MF .deps/fort-attio.Tpo -c fort-attio.c  
> -fPIC -DPIC -o fort-attio.o
> netcdf_f.h(15): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, 
> int *chunksizesp);
> ^
> 
> netcdf_f.h(15): error: expected a ";"
> EXTERNL int nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, 
> int *chunksizesp);
> ^
> 
> netcdf_f.h(17): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(17): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(20): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(20): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(24): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(24): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(28): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(28): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(31): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(31): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(34): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(34): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(37): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(37): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(42): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(42): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(45): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(45): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(48): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(48): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(51): warning #12: parsing restarts here after previous syntax error
> int ndims, int *dim_sizesp);
> ^
> 
> netcdf_f.h(53): warning #77: this declaration has no storage class or type 
> specifier
> EXTERNL int
> ^
> 
> netcdf_f.h(53): error: expected a ";"
> EXTERNL int
> ^
> 
> netcdf_f.h(56): warning #12: parsing restarts here after previous syntax error
> int *dim_sizesp);
> ^
> 
> compilation aborted for fort-attio.c (code 2)
> make[2]: *** [fort-attio.lo] Error 1
> make[2]: Leaving directory 
> `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/build/netcdf-fortran-4.2/fortran'
> make[1]: *** [check] Error 2
> make[1]: Leaving directory 
> `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/opt/build/netcdf-fortran-4.2/fortran'
> make: *** [check-recursive] Error 1
> [Christopher.W.Harrop@r15i1n7 netcdf-fortran-4.2]$
> 
> Thanks,
> 
> Chris
> 
> -----------------------------------------------------------------------------------------------------------
> Christopher W. Harrop                               email: address@hidden
> Global Systems Division                                                       
>    voice: (303) 497-6808
> NOAA Earth System Research Laboratory                               fax: 
> (303) 497-7259
> 325 Broadway R/GSD2
> Boulder, CO 80303
> 
> 
> 
> 
> 

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



Ticket Details
===================
Ticket ID: GKD-688075
Department: Support netCDF
Priority: Normal
Status: Closed