[netcdfgroup] nf90_open problem - perhaps installation problem

• To: netCDF Mail List <netcdfgroup@xxxxxxxxxxxxxxxx>
• Subject: [netcdfgroup] nf90_open problem - perhaps installation problem
• From: Daniel Packman <pack@xxxxxxxx>
• Date: Wed, 20 Oct 2010 11:16:43 -0600

In converting a program from netcdf2 to netcdf4, I have encountered
an error in the nf90_open. It returns -36 which nf90_strerror says is
"Invalid argument". The 3 arguments certainly look valid, so perhaps
this is an installation issue.

I want to install netcdf4/hdf5 into their own directory and want to leave
other versions of netcdf4 and hdf5 untouched. I suspect that libtool
is the culprit here and is insisting that netcdf4 link to another version
of hdf5. In any case, I'd appreciate any hints to install an isolated
netcdf4/hdf5 and comments on my configure scripts:

To install hdf5 on an x86_64 machine, I set FC=/usr/bin/f95 and did
./configure --with-szlib=/usr/local/lib --enable-fortran --prefix=/foo

I then installed hdf4.1.1 keeping FC defined as above and did
./configure --with-hdf5=/foo --prefix=/foo --enable-netcdf4 
--with-zlib=/usr/local --with-szlib=/usr/local

This build fails on linking ncgen3 with the following:
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  
-L/exports/glusterfs/hdf5-1.8.5-patch1/lib -L/usr/local/lib -L/usr/local/lib  
-L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err 
-lidn -lssl -lcrypto -lz    -o ncgen3 main.o load.o escapes.o getfill.o init.o 
genlib.o ncgentab.o ../libsrc4/libnetcdf.la  -lhdf5_hl -lhdf5 -lz  -lm 
libtool: link: gcc -g -O2 -o ncgen3 main.o load.o escapes.o getfill.o init.o 
genlib.o ncgentab.o  -L/foo/lib -L/usr/local/lib -L/usr/kerberos/lib64 
../libsrc4/.libs/libnetcdf.a 
-L/usr/local/TOOLKIT5.2.15/szip/linux64/szip-2.1/lib -lcurl -ldl -lgssapi_krb5 
-lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto 
/usr/local/TOOLKIT5.2.15/hdf5/linux64/hdf5-1.6.7/lib/libhdf5_hl.so 
/usr/lib64/.libs/libhdf5.so 
/usr/local/TOOLKIT5.2.16_gcc4.1.2_fix/szip/linux64/szip-2.1/lib/libsz.a 
/exports/glusterfs/hdf5-1.8.5-patch1/lib/libhdf5_hl.so -L/usr/local/lib/lib 
/foo/lib/libhdf5.so /usr/local/lib/libsz.so -lz -lm -Wl,-rpath 
-Wl,/usr/local/TOOLKIT5.2.15/hdf5/linux64/hdf5-1.6.7/lib -Wl,-rpath 
-Wl,/usr/lib64/.libs -Wl,-rpath -Wl,/foo/lib -Wl,-rpath 
-Wl,/usr/local/TOOLKIT5.2.15/hdf5/linux64/hdf5-1.6.7/lib -Wl,-rpath 
-Wl,/exports/glusterfs/hdf5-1.8.5-patch1/lib

gcc: /usr/local/TOOLKIT5.2.15/hdf5/linux64/hdf5-1.6.7/lib/libhdf5_hl.so: No 
such file or directory
gcc: /usr/lib64/.libs/libhdf5.so: No such file or directory

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