<div dir="ltr"><div class="gmail_default" style="font-family:georgia,serif">Dear Wei,</div><div class="gmail_default" style="font-family:georgia,serif"><br></div><div class="gmail_default" style="font-family:georgia,serif">I tried with the options suggested by you, the configure completed with success but I have got another error in make while using <span style="font-family:arial,sans-serif;font-size:12.8000001907349px">CXXCPPFLAGS="-DMPICH_IGNORE_</span><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">CXX_SEEK -DMPICH_SKIP_MPICXX" as following</span></div><div class="gmail_default" style="font-family:georgia,serif"><span style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></span></div><div class="gmail_default" style="font-family:georgia,serif"><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">..................................................</span></div><div class="gmail_default" style="font-family:georgia,serif"><span style="font-family:arial,sans-serif;font-size:12.8000001907349px">....................................................</span></div><div class="gmail_default"><div class="gmail_default"><span style="font-size:12.8000001907349px">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;}</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px"> ^</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px"><br></span></div><div class="gmail_default"><span style="font-size:12.8000001907349px">compilation aborted for ncmpi_notyet.cpp (code 2)</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px">make[2]: *** [ncmpi_notyet.o] Error 2</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px">make[2]: Leaving directory `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src/libcxx'</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px">make[1]: *** [libcxx] Error 2</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px">make[1]: Leaving directory `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src'</span></div><div class="gmail_default"><span style="font-size:12.8000001907349px">make: *** [all] Error 2</span></div><div style="font-family:arial,sans-serif;font-size:12.8000001907349px"><br></div></div><div class="gmail_default" style="font-family:georgia,serif"><br></div><div class="gmail_default" style="font-family:georgia,serif">please find the output of make command as an attachment.</div><div class="gmail_default" style="font-family:georgia,serif"><br></div><div class="gmail_default" style="font-family:georgia,serif"><br></div><div class="gmail_default" style="font-family:georgia,serif">Sincerely</div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 29, 2015 at 12:59 PM, Wei-keng Liao <span dir="ltr"><<a href="mailto:wkliao@eecs.northwestern.edu" target="_blank">wkliao@eecs.northwestern.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Please try<br>
<br>
./configure MPICC=mpiicc MPICXX=mpiicpc MPIF77=mpiifort MPIF90=mpiifort --prefix=$RLIB \<br>
CXXCPPFLAGS="-DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX"<br>
<br>
Wei-keng<br>
<span><br>
On Jul 28, 2015, at 11:55 PM, Dhirendra Kumar wrote:<br>
<br>
> Dear Wei<br>
><br>
> Thanx for the reply. I ran the $CFLAGS command which displays the result-<br>
><br>
> -O3 -xHost -axSSE4.2 -fPIC<br>
><br>
> also I configured the parallel netcdf with the arguements suggested by you as-<br>
> ./configure MPICC=mpiicc MPICXX=mpiicpc MPIF77=mpiifort MPIF90=mpiifort --prefix=$RLIB<br>
><br>
> and while running make, I am getting the following error-<br>
><br>
</span>> /opt/intel/impi/<a href="http://4.1.0.024/intel64/bin/mpiicpc" rel="noreferrer" target="_blank">4.1.0.024/intel64/bin/mpiicpc</a> -c -O3 -xHost -axSSE4.2 -fPIC -I. -I. -I../lib -DHAVE_CONFIG_H ncmpiType.cpp<br>
> /opt/intel/impi/<a href="http://4.1.0.024/intel64/include/mpicxx.h(95)" rel="noreferrer" target="_blank">4.1.0.024/intel64/include/mpicxx.h(95)</a>: catastrophic error: #error directive: "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"<br>
<span>> #error "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"<br>
><br>
> compilation aborted for ncmpiType.cpp (code 4)<br>
> make[2]: *** [ncmpiType.o] Error 4<br>
> make[2]: Leaving directory `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src/libcxx'<br>
> make[1]: *** [libcxx] Error 2<br>
> make[1]: Leaving directory `/home/dkumar/RLIB/parallel-netcdf-1.6.1/src'<br>
> make: *** [all] Error 2<br>
><br>
> I am attaching the config.log file for your reference....Please have a look.<br>
><br>
> Thanks<br>
><br>
> Sincerely<br>
> Dhirendra<br>
><br>
><br>
</span><span>> On Tue, Jul 28, 2015 at 11:09 PM, Wei-keng Liao <<a href="mailto:wkliao@eecs.northwestern.edu" target="_blank">wkliao@eecs.northwestern.edu</a>> wrote:<br>
> Hi, Dhirendra<br>
><br>
> Could you also run this command that shows the environment CFLAGS in your settings?<br>
><br>
> echo $CFLAGS<br>
><br>
><br>
> Wei-keng<br>
><br>
> On Jul 28, 2015, at 6:43 AM, Dhirendra Kumar wrote:<br>
><br>
> > Dear All,<br>
> ><br>
</span>> > 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/<a href="http://4.1.0.024/intel64/bin-" rel="noreferrer" target="_blank">4.1.0.024/intel64/bin-</a><br>
<span>> ><br>
> > 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-<br>
> ><br>
> > ./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<br>
> ><br>
> > and I am getting the following error:<br>
</span><span>> > checking for mpicc... /opt/intel/impi/<a href="http://4.1.0.024/intel64/bin/mpicc" rel="noreferrer" target="_blank">4.1.0.024/intel64/bin/mpicc</a><br>
> > checking for gcc... /opt/intel/impi/<a href="http://4.1.0.024/intel64/bin/mpicc" rel="noreferrer" target="_blank">4.1.0.024/intel64/bin/mpicc</a><br>
</span><span>> > checking whether the C compiler works... no<br>
> > configure: error: in `/home/dkumar/RLIB/parallel-netcdf-1.6.1':<br>
> > configure: error: C compiler cannot create executables<br>
> > See `config.log' for more details<br>
> > configure: WARNING: cache variable ac_cv_env_FCFLAGS_value contains a newline<br>
> ><br>
> > 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).<br>
> ><br>
> > Any help would be appreciated. I am attaching the config.log file for the reference.<br>
> ><br>
> > Regards<br>
> > Dhirendra Kumar<br>
> ><br>
> > --<br>
> > ========================================<br>
> > Dhirendra Kumar<br>
> > UGC-JRF<br>
> > School of Environmental Sciences, JNU<br>
> > New Delhi (India)<br>
> > Contact: +91 9910778043<br>
</span>> > Alternate email: <a href="mailto:dhirendra.cub@outlook.com" target="_blank">dhirendra.cub@outlook.com</a><br>
<span>> > =========================================<br>
> > <config.log><br>
><br>
><br>
><br>
><br>
> --<br>
> ========================================<br>
> Dhirendra Kumar<br>
> UGC-JRF<br>
> School of Environmental Sciences, JNU<br>
> New Delhi (India)<br>
> Contact: +91 9910778043<br>
</span>> Alternate email: <a href="mailto:dhirendra.cub@outlook.com" target="_blank">dhirendra.cub@outlook.com</a><br>
> =========================================<br>
> <config.log><br>
<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">========================================</div><div dir="ltr">Dhirendra Kumar<div>UGC-JRF <br></div><div>School of Environmental Sciences, JNU<br></div><div>New Delhi (India)</div><div>Contact: <font face="comic sans ms, sans-serif">+91 9910778043</font></div><div>Alternate email: <a href="mailto:dhirendra.cub@outlook.com" target="_blank">dhirendra.cub@outlook.com</a></div><div>=========================================</div></div></div></div></div></div></div></div></div>
</div></div>