Re: [netcdf-hdf] compiling error

• To: Ed Hartnett <ed@xxxxxxxxxxxxxxxx>
• Subject: Re: [netcdf-hdf] compiling error
• From: winthan <keshunli@xxxxxxxxx>
• Date: Wed, 13 Jan 2010 17:15:04 -0800

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 Sun, Jan 10, 2010 at 12:01 PM, winthan <keshunli@xxxxxxxxx> wrote:

> 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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    • From: winthan
  • Re: [netcdf-hdf] compiling error
    • From: Ed Hartnett
  • Re: [netcdf-hdf] compiling error
    • From: winthan