compiling yambo with netcdf+hdf5

[jjmm1974]

Dear all

I know that this topic has been posted several times, but I have been unable to find any solution to my problem.

I have compiled and installed netcdf-4.3.2 + hdf5 with:

export CFLAGS="-fPIC -I/usr/local/hdf5-1.8.12/include -I/usr/local/include"
export LDFLAGS="-L/usr/local/hdf5-1.8.12/lib -L/usr/local/lib"
export LIBS="-lnetcdf -lhdf5_hl -lhdf5 -lz -lm -lcurl"
CC=icc ./configure --prefix="/usr/local/netcdf-4.3.2"
make chek install

The testing was successful. Then I installed the Fortran library as:

export FCFLAGS="-fPIC -I/usr/local/hdf5-1.8.12/include -I/usr/local/include"
export LDFLAGS="-L/usr/local/hdf5-1.8.12/lib -L/usr/local/lib"
export LIBS="-lnetcdf"
CC=icc FC=ifort ./configure --prefix="/usr/local/netcdf-4.3.2"
make check install

and, again, everything looked fine. The static and shared libraries libnetcdf.* and libnetcdff.* where under /usr/local/netcdf-4.3.2/lib.

Then I tried to install Yambo. I got the distribution via svn, and made (not quite elegant, sorry):

FC=ifort CC=icc ./configure --enable-netcdf-hdf5 --enable-netcdf-LFS --with-netcdf-lib=/usr/local/netcdf-4.3.2/lib --with-netcdf-include=/usr/local/netcdf-4.3.2/include --with-netcdf-link='-lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lcurl -lz' --with-iotk='/share/apps/espresso-5.0.2/iotk' --with-p2y=5.0.2
--with-blas="-L/opt/intel/mkl/lib/intel64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" \
--with-lapack="-L/opt/intel/mkl/lib/intel64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" \
--with-blacs="-L/opt/intel/mkl/lib/intel64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" \
--with-scalapack="-L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_lp64" \
--with-fftw=/usr/local/lib --with-fftw-lib=-lfftw3

After configuring, I did:

make yambo interfaces

but it stopped with the message:

... [LOTS OF SUCCESSFUL LIBRARIES MADE]...

>>>[Linking yambo]<<<
make[1]: Entering directory `/home/bloch/Desktop/yambo/stable/driver'
ld: cannot find -lhdf5_hl
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/home/bloch/Desktop/yambo/stable/driver'
make: *** [yambo] Error 2

I attach config.log file for reference. It seems to me that, for some strange reason, the hdl5* libraries are not found despite they are there.

I would appreciate any kind of help, and I apologize if this is dummy... It is just my desperation!

Thanks in advance

Juan J. Meléndez
Department of Physics
University of Extremadura

[Daniele Varsano]

Dear Juan,
from the config.log I can see that the hdf5 are not seen. It looks me that the path to the hdf5 libs is missing. You can try to add to the netcdf-link=
something like "-L/usr/local/hdf5-1.8.12/lib -lhdf5_hl -lhdf5 etc. etc." and similarly the include directory.
Anyway I'm not used to work with the hdf5, as I'm happy with old releases of netcdf (3-6-3)(3.4.0) which use to compile easily.

Best,
Daniele

[jjmm1974]

Dear Daniele:

Thanks a lot for your quick response. I tried with:

--with-netcdf-link='-lnetcdff -lnetcdf -lcurl -lz -L/usr/local/hdf5-1.8.12/lib -I/usr/local/hdf5-1.8.12/include -lhdf5_hl -lhdf5'

(everything else unchanged), but still failed. I think I'll give a chance to older netcdf versions...

Take care

Juanjo

[jjmm1974]

It worked with netcdf-3.6.3! Thanks a lot, Daniele