Configure error: with Intel MPI compilers.
Rob Latham
robl at mcs.anl.gov
Wed Jul 29 09:43:24 CDT 2015
On 07/29/2015 05:56 AM, Dhirendra Kumar wrote:
> Dear Wei,
>
> I tried with the options suggested by you, the configure completed with
> success but I have got another error in make while using
> CXXCPPFLAGS="-DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX" as following
This annoying problem comes up from time to time. You can probably find
this in the archives, but Wei-keng also wrote up something. It might be
in your 1.6.1 release tarball:
http://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/README.INTEL
That will tell you how to get rid of these unpleasant errors.
==rob
>
> ..................................................
> ....................................................
> ncmpi_iget_varm_string(int ncid, int varid, const MPI_Offset *startp,
> const MPI_Offset *countp, const MPI_Offset *stridep, const MPI_Offset *
> imapp, char **ip, int *req){printf("%s not implemented\n",__func__);
> return NC_EINVAL;}
>
>
> ^
>
> compilation aborted for ncmpi_notyet.cpp (code 2)
> make[2]: *** [ncmpi_notyet.o] Error 2
> make[2]: Leaving directory
> `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src/libcxx'
> make[1]: *** [libcxx] Error 2
> make[1]: Leaving directory `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src'
> make: *** [all] Error 2
>
>
> please find the output of make command as an attachment.
>
>
> Sincerely
>
> On Wed, Jul 29, 2015 at 12:59 PM, Wei-keng Liao
> <wkliao at eecs.northwestern.edu <mailto:wkliao at eecs.northwestern.edu>> wrote:
>
> Please try
>
> ./configure MPICC=mpiicc MPICXX=mpiicpc MPIF77=mpiifort
> MPIF90=mpiifort --prefix=$RLIB \
> CXXCPPFLAGS="-DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX"
>
> Wei-keng
>
> On Jul 28, 2015, at 11:55 PM, Dhirendra Kumar wrote:
>
> > Dear Wei
> >
> > Thanx for the reply. I ran the $CFLAGS command which displays the result-
> >
> > -O3 -xHost -axSSE4.2 -fPIC
> >
> > also I configured the parallel netcdf with the arguements suggested by you as-
> > ./configure MPICC=mpiicc MPICXX=mpiicpc MPIF77=mpiifort MPIF90=mpiifort --prefix=$RLIB
> >
> > and while running make, I am getting the following error-
> >
> > /opt/intel/impi/4.1.0.024/intel64/bin/mpiicpc
> <http://4.1.0.024/intel64/bin/mpiicpc> -c -O3 -xHost -axSSE4.2 -fPIC
> -I. -I. -I../lib -DHAVE_CONFIG_H ncmpiType.cpp
> > /opt/intel/impi/4.1.0.024/intel64/include/mpicxx.h(95)
> <http://4.1.0.024/intel64/include/mpicxx.h(95)>: catastrophic error:
> #error directive: "SEEK_SET is #defined but must not be for the C++
> binding of MPI. Include mpi.h before stdio.h"
> > #error "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
> >
> > compilation aborted for ncmpiType.cpp (code 4)
> > make[2]: *** [ncmpiType.o] Error 4
> > make[2]: Leaving directory `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src/libcxx'
> > make[1]: *** [libcxx] Error 2
> > make[1]: Leaving directory `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src'
> > make: *** [all] Error 2
> >
> > I am attaching the config.log file for your reference....Please have a look.
> >
> > Thanks
> >
> > Sincerely
> > Dhirendra
> >
> >
> > On Tue, Jul 28, 2015 at 11:09 PM, Wei-keng Liao <wkliao at eecs.northwestern.edu <mailto:wkliao at eecs.northwestern.edu>>
> wrote:
> > Hi, Dhirendra
> >
> > Could you also run this command that shows the environment CFLAGS in your settings?
> >
> > echo $CFLAGS
> >
> >
> > Wei-keng
> >
> > On Jul 28, 2015, at 6:43 AM, Dhirendra Kumar wrote:
> >
> > > Dear All,
> > >
> > > I am trying to compile parallel-netcdf-1.6.1 on a linux
> cluster. I have a preinstalled Intel MPI library and thus I have
> intel compilers wrapped as mpiicc, mpiicpc and mpiifort in the
> directory /opt/intel/impi/4.1.0.024/intel64/bin-
> <http://4.1.0.024/intel64/bin->
> > >
> > > I have successfully installed the HDF5 library using the above compilers and I wish to build the netcdf-4.3.3.1 with parallel support. Before doing that as I came to know that I need to install the pnetcdf library so tried I with the following configure options-
> > >
> > > ./configure CC=mpiicc CXX=mpiicpc FC=mpiifort --prefix=/export/home/dkumar/RLIB CPPFLAGS=-I/export/home/dkumar/RLIB/include LDFLAGS=-L/export/home/dkumar/RLIB/lib
> > >
> > > and I am getting the following error:
> > > checking for mpicc... /opt/intel/impi/4.1.0.024/intel64/bin/mpicc <http://4.1.0.024/intel64/bin/mpicc>
> > > checking for gcc... /opt/intel/impi/4.1.0.024/intel64/bin/mpicc <http://4.1.0.024/intel64/bin/mpicc>
> > > checking whether the C compiler works... no
> > > configure: error: in `/home/dkumar/RLIB/parallel-netcdf-1.6.1':
> > > configure: error: C compiler cannot create executables
> > > See `config.log' for more details
> > > configure: WARNING: cache variable ac_cv_env_FCFLAGS_value contains a newline
> > >
> > > I am not able to figure out what went wrong, but I think the configure script could not identify the mpicc (i.e. mpiicc is not being used for compiling).
> > >
> > > Any help would be appreciated. I am attaching the config.log file for the reference.
> > >
> > > Regards
> > > Dhirendra Kumar
> > >
> > > --
> > > ========================================
> > > Dhirendra Kumar
> > > UGC-JRF
> > > School of Environmental Sciences, JNU
> > > New Delhi (India)
> > > Contact: +91 9910778043
> > > Alternate email: dhirendra.cub at outlook.com
> <mailto:dhirendra.cub at outlook.com>
> > > =========================================
> > > <config.log>
> >
> >
> >
> >
> > --
> > ========================================
> > Dhirendra Kumar
> > UGC-JRF
> > School of Environmental Sciences, JNU
> > New Delhi (India)
> > Contact: +91 9910778043
> > Alternate email: dhirendra.cub at outlook.com
> <mailto:dhirendra.cub at outlook.com>
> > =========================================
> > <config.log>
>
>
>
>
> --
> ========================================
> Dhirendra Kumar
> UGC-JRF
> School of Environmental Sciences, JNU
> New Delhi (India)
> Contact: +91 9910778043
> Alternate email: dhirendra.cub at outlook.com
> <mailto:dhirendra.cub at outlook.com>
> =========================================
--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA
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