gcc / icc confliict with pnetcdf 1.7.0

[Wei-keng Liao]

Hi, Carl

I must apologize for misspelling your name.
Please excuse my such ignorance.

Wei-keng

On Apr 17, 2016, at 6:56 PM, Wei-keng Liao wrote:

> Hi, Carol
> 
> ncoffsets is a sequential program developed to be compiled by a non-MPI
> compiler (default gcc) so it can run on the machine PnetCDF is built.
> In a cross-compile environment, this means ncoffsets can be run on the
> build machine (eg. login node).
> 
> As for using gcc to compile ncoffsets utility tool, I think in your
> case, "unset CPATH" is the right solution. Otherwise, you probably will
> see the same error message when compiling a C program that includes the
> header file inttypes.h.
> 
> My understanding of autotools is that message you got simply says your
> icc is compatible to gcc for the features required by autotools. So you
> can ignore that message.
> 
> I think you are safe to use icc based MPI compiler.
> I use icc 16.0.0 for testing PnetCDF.
> 
> Wei-keng
> 
> On Apr 17, 2016, at 3:30 PM, Carl Ponder wrote:
> 
>> I'm building pnetcdf 1.7.0 using the Intel 15.0 compiler and ran into this error:
>> make -w -C ncoffsets
>> make[3]: Entering directory `/cm/extra/apps/PNetCDF/1.7.0/Intel-15.0_OpenMPI-1.10.2_CUDA-7.5/distro/src/utils/ncoffsets'
>> /usr/bin/gcc -o ncoffsets ncoffsets.c
>> In file included from /usr/include/inttypes.h:27:0,
>>                 from ncoffsets.c:16:
>> /cm/shared/apps/intel/composer_xe/2015.5.223/compiler/include/stdint.h:43:54: error: missing binary operator before token "("
>>     defined(__has_include_next) && __has_include_next(<stdint.h>)
>>                                                      ^
>> /cm/shared/apps/intel/composer_xe/2015.5.223/compiler/include/stdint.h:292:1: error: unknown type name ‘uint__INTPTR_WIDTH___t’
>> typedef __uintn_t(__INTPTR_WIDTH__) uintptr_t;
>> ^
>> make[3]: *** [ncoffsets] Error 1
>> make[3]: Leaving directory `/cm/extra/apps/PNetCDF/1.7.0/Intel-15.0_OpenMPI-1.10.2_CUDA-7.5/distro/src/utils/ncoffsets'
>> I think the problem is that gcc is trying to use the Intel versions of the header-files, but the question is "why?".
>> My workaround is to use
>> unset CPATH
>> after I've loaded all my environment modules.
>> But a key question is why gcc is being invoked when I've made these settings
>> export  CC=/cm/shared/apps/intel/composer_xe/2015.5.223/bin/intel64/icc
>> export CXX=/cm/shared/apps/intel/composer_xe/2015.5.223/bin/intel64/icpc
>> export F77=/cm/shared/apps/intel/composer_xe/2015.5.223/bin/intel64/ifort
>> export F90=/cm/shared/apps/intel/composer_xe/2015.5.223/bin/intel64/ifort
>> export  FC=/cm/shared/apps/intel/composer_xe/2015.5.223/bin/intel64/ifort
>> 
>> export  MPICC=/cm/extra/apps/OpenMPI/1.10.2/Intel-15.0_CUDA-7.5_HWLoc-1.11.2/bin/mpicc
>> export MPICXX=/cm/extra/apps/OpenMPI/1.10.2/Intel-15.0_CUDA-7.5_HWLoc-1.11.2/bin/mpicxx
>> export MPIF77=/cm/extra/apps/OpenMPI/1.10.2/Intel-15.0_CUDA-7.5_HWLoc-1.11.2/bin/mpif77
>> export MPIF90=/cm/extra/apps/OpenMPI/1.10.2/Intel-15.0_CUDA-7.5_HWLoc-1.11.2/bin/mpif90
>> During the configure phase I see these messages (excerpted):
>> checking for gcc... /cm/extra/apps/OpenMPI/1.10.2/Intel-15.0_CUDA-7.5_HWLoc-1.11.2/bin/mpicc
>> checking whether the C compiler works... yes
>> checking whether we are using the GNU C compiler... yes
>> checking whether we are using the GNU C++ compiler... yes
>> checking whether we are using the GNU Fortran 77 compiler... no
>> The OpenMPI in this case had been built on top of the Intel compilers.
>> I've seen messages like this when I've built other utilities, so either
>> 	• I really am falling through to the GCC compilers, or
>> 	• Both icc & gcc look identical to the version of autotools on the system I'm using. Do the tests really make them look identical?
>> On the flipside, I don't get these messages when I use the PGI compilers.
>> But gcc is used to build the ncoffsets in this case as well, it just doesn't fail.
>> Thanks,
>> 
>>                      Carl Ponder
>> 
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