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[netCDF #DZV-771355]: Problem compiling with Portland PGI 10.9 (works with netcdf 4.1.1)

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  • Subject: [netCDF #DZV-771355]: Problem compiling with Portland PGI 10.9 (works with netcdf 4.1.1)
  • Date: Sat, 28 May 2011 09:16:16 -0600
> Full Name: Antonio Messina
> Email Address: address@hidden
> Organization: The Abdus Salam ICTP
> Package Version: 4.1.2
> Operating System: Linux RHEL 5.5
> Hardware: Linux x86_64
> Description of problem: Dear all,
> 
> I'm having troubles compiling netcdf 4.1.2 with pgi 10.9. The error I'm
> getting is:
> 
> make[6]: Entering directory 
> `/svn/argo/lazybuilder/build/netcdf-4.1.2_pgi%10.9/netcdf-4.1.2/udunits/lib'
> /bin/sh ../libtool --tag=CC   --mode=link 
> /opt/pgi/10.9/linux86-64/10.9/bin/pgcc  -DpgiFortran -O2 -Msignextend    -o 
> libudunits2.la -rpath /opt/netcdf/4.1.2/pgi/10.9/lib unitcore.lo converter.lo 
> formatter.lo idToUnitMap.lo unitToIdMap.lo unitAndId.lo systemMap.lo 
> prefix.lo parser.lo status.lo xml.lo error.lo ut_free_system.lo udunits-1.lo  
> -lexpat
> libtool: link: /opt/pgi/10.9/linux86-64/10.9/bin/pgcc -shared  -fpic -DPIC  
> .libs/unitcore.o .libs/converter.o .libs/formatter.o .libs/idToUnitMap.o 
> .libs/unitToIdMap.o .libs/unitAndId.o .libs/systemMap.o .libs/prefix.o 
> .libs/parser.o .libs/status.o .libs/xml.o .libs/error.o 
> .libs/ut_free_system.o .libs/udunits-1.o   /usr/lib/libexpat.so -lc  -O2   
> -Wl,-soname -Wl,libudunits2.so.0 -o .libs/libudunits2.so.0.0.0
> /usr/lib/libexpat.so: could not read symbols: File in wrong format
> make[6]: *** [libudunits2.la] Error 2
> 
> 
> It seems that it's trying to use the 32bit version of libxpat.so while
> compiling a 64bit version of the program. Moreover, if I run the following
> command from udunits/lib directory:
> 
> /opt/pgi/10.9/linux86-64/10.9/bin/pgcc -shared  -fpic -DPIC  .libs/unitcore.o 
> .libs/converter.o .libs/formatter.o .libs/idToUnitMap.o .libs/unitToIdMap.o 
> .libs/unitAndId.o .libs/systemMap.o .libs/prefix.o .libs/parser.o 
> .libs/status.o .libs/xml.o .libs/error.o .libs/ut_free_system.o 
> .libs/udunits-1.o   /usr/lib64/libexpat.so -lc  -O2   -Wl,-soname 
> -Wl,libudunits2.so.0 -o .libs/libudunits2.so.0.0.0
> 
> it compiles fine.
> 
> Please note that NetCDF 4.1.1 doesn't have this problem (using the same
> configuration/compilation flags)
> 
> I'm using the following environment variables during configuration:
> 
> export CPPFLAGS="-DpgiFortran ";
> export CFLAGS="-DpgiFortran -O2 -Msignextend ";
> export FFLAGS="-O2 ";
> 
> ./configure --prefix=/opt/netcdf/4.1.2/pgi/10.9 
> --with-hdf5=/opt/hdf5/1.8.5-patch1/gnu/4.1.2 
> --with-szip=/opt/hdf5/1.8.5-patch1/gnu/4.1.2 
> --with-szlib=/opt/hdf5/1.8.5-patch1/gnu/4.1.2 --enable-netcdf4 --with-libcf 
> --enable-logging --with-udunits --disable-cxx

The libtool command should be linking to just "libexpat.so", not 
"usr/lib/libexpat.so", as then the appropriate 64-bit library
would be found in /usr/lib64, which is in the default path for 64-bit Linux 
platforms.  You might try the latest snapshot for
netCDF 4.1.3 to see if the problem is fixed in that version:

  ftp://ftp.unidata.ucar.edu/pub/netcdf/snapshot/netcdf-4-daily.tar.gz

because our nightly test shows this is building with udunits OK on a Linux RHEL 
system:

  
http://www.unidata.ucar.edu/software/netcdf/builds/snapshot/nc_make_distcheck_out.txt

--Russ

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



Ticket Details
===================
Ticket ID: DZV-771355
Department: Support netCDF
Priority: Normal
Status: Closed