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[netCDF #FAC-106953]: netcdf 4.1.1 configure problem on 64 bit linux

Hi Mark,

Thanks for reporting the fix you found.  We'll file your response
where it can be found by others searching for a workaround for this 


> I resolved this issue by removing the "-static" option in the
> environmental flags (also took out "-no-prec-dev").
> (instead of what Intel talks about
> http://www.intel.com/support/performancetools/sb/CS-027812.htm)
> This enables the configuration to look for either static or shared
> libraries.
> And I needed to force netcdf 4.1 to look in the /usr/lib64 directory for
> system libraries on my 64-bit linux machine (otherwise it only looks in
> /usr/lib).
> I used:
> CFLAGS=-O3 -xT -ip
> CXXFLAGS=-O3 -xT -ip
> FFLAGS=-O3 -xT -ip
> LDFLAGS=-L/usr/lib64
> FORTRAN=ifort
> F77=ifort
> FC=ifort
> FORTC=ifort
> CC=icc
> F90=ifort
> F9X=ifort
> CXX=icpc
> CPP=icc -E
> CXXCPP=icpc -E
> ./configure --with-hdf5=/usr/local/hdf5 --with-zlib=/usr --enable-hdf4
> --with-hdf4=/usr/local --disable-dap
> mark

> Hello netCDF Support,
> I'm trying to install netCDF 4.1.1 with both hdf4 and hdf5. But it won't
> get past checking for hdf5 libraries even though they exist.  It finds
> the hdf5 include files but not the hdf5 libraries.  I get:
> "configure: error: Can't find or link to the hdf5 library. Configure
> with --disable-netcdf-4 or see config.log for errors."
> It looks like it'll configure if I don't enable-hdf4, but I need both
> hdf4 and 5.
> And I noticed that where it fails, "checking for H5Fflush in -lhdf5", it
> can't find compatible libm.a, libz.a. It seems to be only looking in
> /usr/lib instead of /usr/lib64. And it can't find -ljpeg even though
> /usr/lib64/libjpeg.so exists.
> ld: skipping incompatible /usr/lib/libm.a when searching for -lm
> ld: skipping incompatible /usr/lib/libz.a when searching for -lz
> ld: cannot find -ljpeg
> I've attached the config.log file.
> Here's my setup:
> CentOS release 5.5 64-bit
> Linux 2.6.18-194.26.1.el5 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
> Processors - Intel(R) Xeon(R) CPU E5345  @ 2.33GHz
> HDF4 - version hdf-4.2.5 (located in /usr/local)
> ./configure --disable-netcdf
> HDF5 - version hdf5-1.8.5-patch1 (located in /usr/local/hdf5)
> ./configure --prefix=/usr/local/hdf5 --enable-fortran --enable-cxx
> --with-zlib=/usr
> ifort v11.1 - Intel Fortran 64 v11.1 Build 20100414 (l_cprof_p_11.1.072)
> icc v11.1 - Intel C 64 v11.1 Build 20100414 (l_cproc_p_11.1.072)
> zlib-1.2.3-3.x86_64
> libjpeg-6b-37.x86_64
> # based on
> http://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-netcdf-with-the-intel-compilers/
> setenv FORTRAN ifort
> setenv F77 ifort
> setenv FC ifort
> setenv FORTC ifort
> setenv F90 ifort
> setenv F9X ifort
> setenv CC icc
> setenv CXX icpc
> setenv CFLAGS '-O3 -xT -ip -no-prec-div -static'
> setenv CXXFLAGS '-O3 -xT -ip -no-prec-div -static'
> setenv FFLAGS '-O3 -xT -ip -no-prec-div -static'
> setenv CPP 'icc -E'
> setenv CXXCPP 'icpc -E'
> My configure statement:
> ./configure --with-hdf5=/usr/local/hdf5 --with-zlib=/usr --enable-hdf4
> --with-hdf4=/usr/local
> Am I using incorrect flags? Is netCDF 4.1.1 compatible with hdf-4.2.5
> and hdf5-1.8.5-patch1?

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu

Ticket Details
Ticket ID: FAC-106953
Department: Support netCDF
Priority: Critical
Status: Closed

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