Configure error: with Intel MPI compilers.
Wei-keng Liao
wkliao at eecs.northwestern.edu
Wed Jul 29 09:50:20 CDT 2015
Hi, Dhirendra
The errors you are seeing have been reported by Craig Tierney. This is due to an older version of Intel compiler. A fix of this error has been added to the project repo and will appear in the next release of PnetCDF.
If you would like to try the latest under development codes, please see the instructions at the bottom of PnetCDF download page: http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/Download
Or if you do not need C++, you can add "-disable-cxx" to your configure command line, i.e.
./configure MPICC=mpiicc MPICXX=mpiicpc MPIF77=mpiifort MPIF90=mpiifort --prefix=$RLIB \
CXXCPPFLAGS="-DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX" --disable-cxx
Wei-keng
On Jul 29, 2015, at 5:56 AM, Dhirendra Kumar wrote:
> Dear Wei,
>
> I tried with the options suggested by you, the configure completed with success but I have got another error in make while using CXXCPPFLAGS="-DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX" as following
>
> ..................................................
> ....................................................
> ncmpi_iget_varm_string(int ncid, int varid, const MPI_Offset *startp, const MPI_Offset *countp, const MPI_Offset *stridep, const MPI_Offset * imapp, char **ip, int *req){printf("%s not implemented\n",__func__); return NC_EINVAL;}
> ^
>
> compilation aborted for ncmpi_notyet.cpp (code 2)
> make[2]: *** [ncmpi_notyet.o] Error 2
> make[2]: Leaving directory `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src/libcxx'
> make[1]: *** [libcxx] Error 2
> make[1]: Leaving directory `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src'
> make: *** [all] Error 2
>
>
> please find the output of make command as an attachment.
>
>
> Sincerely
>
> On Wed, Jul 29, 2015 at 12:59 PM, Wei-keng Liao <wkliao at eecs.northwestern.edu> wrote:
> Please try
>
> ./configure MPICC=mpiicc MPICXX=mpiicpc MPIF77=mpiifort MPIF90=mpiifort --prefix=$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 -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): 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> 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-
> > >
> > > 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
> > > checking for gcc... /opt/intel/impi/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
> > > =========================================
> > > <config.log>
> >
> >
> >
> >
> > --
> > ========================================
> > Dhirendra Kumar
> > UGC-JRF
> > School of Environmental Sciences, JNU
> > New Delhi (India)
> > Contact: +91 9910778043
> > Alternate email: 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
> =========================================
> <results.txt>
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