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hi ed,
thanks ed. i got it compiled by setting CPPFLAGS. i use the
following information to configure the hdf src and netcdf src.
hdf installation
------------------------
./configure --enable-parallel
--with-zlib=/apps/rhel5/graphics/x86_64/intel/11.1.038/szip/lib
--prefix=/usr/rmt_share/scratch95/w/wwinthan/pnetcdf/ --disable-f90
netcdf installation
--------------------------
./configure --enable-netcdf-4
--prefix=/usr/rmt_share/scratch95/w/wwinthan/pnetcdf/netcdf-4.0.1
--with-hdf5=/usr/rmt_share/scratch95/w/wwinthan/pnetcdf/ --disable-f90
--with-zlib=/apps/rhel5/graphics/x86_64/intel/11.1.038/szip/lib
I got the following run-time error as follow
../utilities.cpp:(.text+0xf3d): undefined reference to `nc_create_par'
../utilities.cpp:(.text+0xf61): undefined reference to `nc_def_dim'
../utilities.cpp:(.text+0xf8b): undefined reference to `nc_def_dim'
../utilities.cpp:(.text+0xfba): undefined reference to `nc_def_var'
../utilities.cpp:(.text+0xfd2): undefined reference to `nc_enddef'
../utilities.cpp:(.text+0x110e): undefined reference to `nc_var_par_access'
../utilities.cpp:(.text+0x1140): undefined reference to `nc_put_vara_double'
../utilities.cpp:(.text+0x1158): undefined reference to `nc_close'
thanks
winthan
On Sat, Jan 9, 2010 at 6:13 AM, Ed Hartnett <ed@xxxxxxxxxxxxxxxx> wrote:
> winthan <keshunli@xxxxxxxxx> writes:
>
> > I used the following to configure the netcdf and hdf.�
> > ./configure
> > --prefix=/usr/rmt_share/scratch95/w/wwinthan/pnetcdf/installnetcdf
> > --enable-netcdf-4
> > --with-hdf5=/apps/rhel5/graphics/x86_64/intel/11.1.038/hdf5-1.8.3p/
> > --with-szlib=/apps/rhel5/graphics/x86_64/intel/11.1.038/hdf5-1.8.3p/
> > --disable-f90
> > i have previously installed hdf5 with parallel mode and also with szlib .
> > i attached the config.log. can you tell me what i'm missing?
> > if needed,i can also install the hdf5 and szlib again. can you help me
> > with how to configure ?
> > after i make all,i get the following error
> > make �all-recursive
> > make[1]: Entering directory
> > `/usr/rmt_share/scratch95/w/wwinthan/pnetcdf/netcdf-4.0.1'
> > Making all in fortran
> > make[2]: Entering directory
> > `/usr/rmt_share/scratch95/w/wwinthan/pnetcdf/netcdf-4.0.1/fortran'
> > make �all-am
> > make[3]: Entering directory
> > `/usr/rmt_share/scratch95/w/wwinthan/pnetcdf/netcdf-4.0.1/fortran'
> > depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> > �� � � �/bin/sh ../libtool --tag=CC � --mode=compile mpicc
> -DHAVE_CONFIG_H
> > -I. -I.. � -I../libsrc4
> > -I/apps/rhel5/graphics/x86_64/intel/11.1.038/hdf5-1.8.3p//include � �
> -g
> > -O2 -MT fort-attio.lo -MD -MP -MF $depbase.Tpo -c -o fort-attio.lo
> > fort-attio.c &&\
> > �� � � �mv -f $depbase.Tpo $depbase.Plo
> > libtool: compile: �mpicc -DHAVE_CONFIG_H -I. -I.. -I../libsrc4
> > -I/apps/rhel5/graphics/x86_64/intel/11.1.038/hdf5-1.8.3p//include -g -O2
> > -MT fort-attio.lo -MD -MP -MF .deps/fort-attio.Tpo -c fort-attio.c -o
> > fort-attio.o
> > icc: command line warning #10120: overriding '-O3' with '-O2'
> > cfortran.h(138): catastrophic error: #error directive: "cfortran.h:
> �Can't
> > find your environment among: � �- MIPS cc and f77 2.0. (e.g. Silicon
> > Graphics, DECstations, ...) � � � � - IBM AIX XL C and FORTRAN
> > Compiler/6000 Version 01.01.0000.0000 � � � � - VAX � VMS CC
> 3.1 and
> > FORTRAN 5.4. � � � � � � � � � � � � � � �
> � � � �- Alpha VMS DEC C 1.3
>
> Sorry, I couldn't quite read your output - too much gobbledy-goop. But
> when building with parallel you need to set the CPPFLAGS=-DgFortran.
>
> (If you are not using gfortran, you can also try -Df2cFortran or
> -DpgiFortran. One of these three works for almost any fortran compiler.)
>
> Also note that all component parts (HDF5, zlib, and szlib, if you are
> using it) must be built with the same C compiler command, usually
> "mpicc". Also hdf5 requires the --enable-parallel option.
>
> Good luck,
>
> Ed
> --
> Ed Hartnett -- ed@xxxxxxxxxxxxxxxx
>
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