Configure error: with Intel MPI compilers.

Wed Jul 29 10:36:35 CDT 2015

Dhirendra,

This is the script I used to build pnetcdf 1.6.1 with Intel MPI v4.X and
v5.X.

-------------
#!/bin/bash

BASE=/home/Craig.Tierney/apps/pnetcdf/
# Set the parallel directory for testing, Home is not good for this

PDIR=/lfs3/jetmgmt/Craig.Tierney

CVER=15.0.3.187

#IMPIVER=4.1.3.049
IMPIVER=5.0.3.048

CSVER=$(echo $CVER | cut -f1 -d.)
MPISVER=$(echo $IMPIVER | cut -f1 -d.)

module load newdefaults
module load intel/$CVER
module load impi/$IMPIVER

module list
icc --version
ifort --version

export MPIF90=mpiifort
export MPIF77=mpiifort
export MPICC=mpiicc
export MPICXX=mpiicpc

if [ $MPISVER -lt 5 ]; then
export CXXFLAGS="-DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX"
fi

make distclean
./configure --prefix=$BASE/1.6.1-intel$CVER-impi$MPISVER

make -j8
make testing TEST_OUTDIR=$PDIR
make ptest TEST_MPIRUN="mpiexec.hydra -np NP" TEST_OUTDIR=$PDIR

make install
-------------

Craig

On Wed, Jul 29, 2015 at 8:50 AM, Wei-keng Liao <wkliao at eecs.northwestern.edu
> wrote:

> 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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