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[netCDF #XCL-692194]: /lib/libhdf5.so: file not recognized: File format not recognized

> Hi Ed,
> 
> It has been a long time since we last spoke, I hope all is well. I am
> trying to compile netcdf-4.1.1 on some new x_86-64 nodes running SUSE.
> Here is my environment:
> 
> CC=icc -g -fPIC
> CXX=icpc -g -fPIC
> FC=ifort -g -fPIC
> F77=ifort -g -fPIC
> F90=ifort -g -fPIC
> 
> LDFLAGS=-L/pphome/pem/tools/hdf5-1.8.5-patch1/lib   #Note I had to set
> this so hdfflush could be found.... never had to do that before
> 
> So the configure script seems to work
> 
> ./configure --prefix=/pphome/pem/tools/netcdf-4.0.1/install_dir
> --with-zlib=/pphome/pem/tools/zlib-1.2.5/install_dir
> --with-hdf5=/pphome/pem/tools/hdf5-1.8.5-patch1/install_dir
> --enable-netcdf-4 --enable-dap
> --with-curl=/pphome/pem/tools/curl-7.21.1/install_dir
> 
> then when I try a gmake, it exits on this error
> 
> gmake[2]: Entering directory `/pphome/pem/tools/netcdf-4.1.1/ncgen3'
> /bin/sh ../libtool --tag=CC   --mode=link icc -g -fPIC  -g -O2
> -L/pphome/pem/tools/hdf5-1.8.5-patch1/install_dir/lib
> -L/pphome/pem/tools/zlib-1.2.5/install_dir/lib
> -L/pphome/pem/tools/curl-7.21.1/install_dir/lib -lcurl
> -L/pphome/pem/tools/hdf5-1.8.5-patch1/install_dir/lib
> -L/pphome/pem/tools/netcdf-4.0.1/install_dir/lib
> -L/pphome/pem/tools/curl-7.21.1/install_dir/lib
> -L/pphome/pem/tools/libssh2-1.2.7/install_dir/lib
> -L/pphome/pem/tools/openssl-1.0.0a/install_dir/lib64
> -L/pphome/pem/tools/zlib-1.2.5/install_dir/lib
> -L/pphome/pem/tools/libssh2-1.2.7/install_dir/lib
> -L/pphome/pem/tools/libidn-1.19/install_dir/lib
> -L/pphome/pem/tools/hdf5-1.8.5-patch1/lib -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: icc -g -fPIC -g -O2 -o ncgen3 main.o load.o escapes.o
> getfill.o init.o genlib.o ncgentab.o
> -L/pphome/pem/tools/hdf5-1.8.5-patch1/install_dir/lib
> -L/pphome/pem/tools/zlib-1.2.5/install_dir/lib
> -L/pphome/pem/tools/curl-7.21.1/install_dir/lib
> -L/pphome/pem/tools/netcdf-4.0.1/install_dir/lib
> -L/pphome/pem/tools/libssh2-1.2.7/install_dir/lib
> -L/pphome/pem/tools/openssl-1.0.0a/install_dir/lib64
> -L/pphome/pem/tools/libidn-1.19/install_dir/lib
> -L/pphome/pem/tools/hdf5-1.8.5-patch1/lib ../libsrc4/.libs/libnetcdf.a
> /pphome/pem/tools/curl-7.21.1/install_dir/lib/libcurl.so -ldl
> /pphome/pem/tools/libidn-1.19/install_dir/lib/libidn.so
> /pphome/pem/tools/libssh2-1.2.7/install_dir/lib/libssh2.so -lrt -lssl
> -lcrypto
> /pphome/pem/tools/hdf5-1.8.5-patch1/install_dir/lib/libhdf5_hl.so
> /pphome/pem/tools/hdf5-1.8.5-patch1/install_dir/lib/libhdf5.so -lz -lm
> -Wl,-rpath -Wl,/pphome/pem/tools/curl-7.21.1/install_dir/lib -Wl,-rpath
> -Wl,/pphome/pem/tools/libidn-1.19/install_dir/lib -Wl,-rpath
> -Wl,/pphome/pem/tools/libssh2-1.2.7/install_dir/lib -Wl,-rpath
> -Wl,/pphome/pem/tools/hdf5-1.8.5-patch1/install_dir/lib -Wl,-rpath
> -Wl,/pphome/pem/tools/curl-7.21.1/install_dir/lib -Wl,-rpath
> -Wl,/pphome/pem/tools/libidn-1.19/install_dir/lib -Wl,-rpath
> -Wl,/pphome/pem/tools/libssh2-1.2.7/install_dir/lib -Wl,-rpath
> -Wl,/pphome/pem/tools/hdf5-1.8.5-patch1/install_dir/lib
> /pphome/pem/tools/hdf5-1.8.5-patch1/install_dir/lib/libhdf5.so: file not
> recognized: File format not recognized
> gmake[2]: *** [ncgen3] Error 1
> gmake[2]: Leaving directory `/pphome/pem/tools/netcdf-4.1.1/ncgen3'
> gmake[1]: *** [all-recursive] Error 1
> gmake[1]: Leaving directory `/pphome/pem/tools/netcdf-4.1.1'
> gmake: *** [all] Error 2
> 
> 
> So I am not sure what is going on. Could this be caused by using
> different versions of libtool? In the past I never had to set LDFLAGS
> when compiling on all our other platforms, I must be doing something
> wrong then. And I actually built netcdf-4.0.1 just fine as I usually did
> a few days ago and now I cannot figure out why this is happening. Have
> you seen this kind of error before?
> 
> Thanks,
> Paida
> 
> 
> 

Howdy Paida!

It was good to talk to you at the HDF5 workshop!

In answer to your question above, it may have to do with shared vs. static libra
ries. I would suggest getting the HDF5-1.8.5-patch1 release, and the netCDF dail
y snapshot, and building them both as shared libraries (the default).

Thanks,

Ed

Ticket Details
===================
Ticket ID: XCL-692194
Department: Support netCDF
Priority: Critical
Status: Closed