Yambo with netdf

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? Problems in GPU architectures? This is the place to look.

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If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
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Stephan
Posts: 62
Joined: Thu Jan 15, 2015 12:48 pm

Yambo with netdf

Post by Stephan » Tue Jan 20, 2015 3:21 pm

Hello,

I really need some help. I want to compile yambo with netcdf support.
Netcdf-C and netcdf-fortran I installed with success
For configuration I use

sudo ./configure --with-iotk='/home/pi1/Desktop/Simulation/espresso-5.1.1/S3DE/iotk' --with-p2y='5.0' --with-netcdf-lib='/usr/local/lib' --with-netcdf-include='/usr/local/include' --with-netcdf-link='-lnetcdf -lnetcdff' --with-fftw=/usr/local/fftw-3.3.4/.libs --enable-netcdf-LFS

In the mentioned files I find:
/usr/local/lib$ ls libnetcdf
libnetcdf.a libnetcdff.so.6 libnetcdf.so.7
libnetcdff.a libnetcdff.so.6.0.1 libnetcdf.so.7.2.0
libnetcdff.la libnetcdf.la
libnetcdff.so libnetcdf.so

and

/usr/local/include$ ls
curl gcc32dbg netcdf.mod
fftw3.f gcc32dbgpthr netcdf_nc_data.mod
fftw3.f03 gcc32pthr netcdf_nc_interfaces.mod
fftw3.h netcdf_f03.mod netcdf_nf_data.mod
fftw3l.f03 netcdf_fortv2_c_interfaces.mod netcdf_nf_interfaces.mod
fftw3q.f03 netcdf.h typesizes.mod
gcc32 netcdf.inc

Configuration leads to the following result:

checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking whether lstat correctly handles trailing slash... yes
checking whether stat accepts an empty string... no
checking whether make sets $(MAKE)... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for vim... vim
checking for GNU make... make
checking for ar... ar
checking /home/pi1/Desktop/Simulation/espresso-5.1.1/S3DE/iotk IOTK library... yes
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking if the current OS is supported... yes
configure: WIDESETUP: using build_os="linux"
configure: WIDESETUP: using F90SUFFIX=".f90"
configure: WIDESETUP: using AR="ar"
configure: WIDESETUP: using AR_FLAGS="-ru"
checking for Fortran flag to compile .f90 files... none
checking for gfortran version... unknown
checking for specific gfortran flags... -O3 -mtune=native
checking for specific gcc flags... -g -O2
checking for specific unoptimized flags... -O0 -mtune=native
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking for external C routine (test) naming scheme... test_
checking for Fortran flag needed to accept free-form source... none
checking fortran 90 modules inclusion flag... -I
configure: testing preprocessor gcc -E -P
checking if precompiler works on C source... yes
checking if precompiler works on F90 source... yes
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking if Fortran 77 compiler gfortran works... yes
checking for mpif90... mpif90
checking for MPI_Init... yes
checking for a working mpif.h... yes
checking for mpicc... mpicc
checking for a working mpi.h... yes
checking for FFTW... yes
checking for NetCDF in /usr/local/lib... yes
checking the configuration of the LIBXC internal library... yes
configure: creating ./config.status
config.status: creating config/setup
config.status: creating config/Makefile
config.status: creating config/report
config.status: creating src/wf_and_fft/sgfft.F
config.status: creating sbin/make_makefile.sh
config.status: creating sbin/make_message.pl
config.status: creating sbin/objects_debug.sh
config.status: creating driver/codever.h
config.status: creating driver/editor.h
config.status: creating src/external_c/.objects

#
# [VER] 3.4.1 r.3187
#
# [SYS] linux@x86_64
# [SRC] /home/pi1/Desktop/Simulation/yambo-3.4.1
# [BIN] /home/pi1/Desktop/Simulation/yambo-3.4.1/bin
# [FFT] FFTW Fast Fourier transform
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [ ] OpenMP
# [X] PW (5.0) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [X X] NETCDF/HDF5/Large Files
# [XX ] Built-in BLAS/LAPACK/LOCAL
#
# [ CPP ] gcc -E -P
# [ C ] gcc -g -O2 -D_C_US -D_FORTRAN_US
# [MPICC] mpicc -g -O2 -D_C_US -D_FORTRAN_US
# [ F90 ] gfortran -O3 -mtune=native
# [MPIF ] mpif90 -O3 -mtune=native
# [ F77 ] gfortran -O3 -mtune=native
# [Cmain]
# [NoOpt] -O0 -mtune=native
#
# [ MAKE ] make
# [EDITOR] vim

when I type make yambo install I receive the following error message
...
...
/home/pi1/netcdf-fortran-4.4.1/fortran/nf_varsio.F90:843: undefined reference to `nc_get_vars_float'
/home/pi1/Desktop/Simulation/yambo-3.4.1/lib/libnetcdff.a(nf_varsio.o): In function `nf_get_vars_double_':
/home/pi1/netcdf-fortran-4.4.1/fortran/nf_varsio.F90:877: undefined reference to `nc_inq_varndims'
/home/pi1/netcdf-fortran-4.4.1/fortran/nf_varsio.F90:896: undefined reference to `nc_get_vars_double'
/home/pi1/Desktop/Simulation/yambo-3.4.1/lib/libnetcdff.a(nf_varsio.o): In function `nf_get_vars_':
/home/pi1/netcdf-fortran-4.4.1/fortran/nf_varsio.F90:932: undefined reference to `nc_inq_varndims'
/home/pi1/netcdf-fortran-4.4.1/fortran/nf_varsio.F90:951: undefined reference to `nc_get_vars'
collect2: ld returned 1 exit status
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/home/pi1/Desktop/Simulation/yambo-3.4.1/driver'
make: *** [yambo] Error 2

what is missing?
I am trying to install yambo-3-4-1 I installed netcdf-c-4.3.2 and netcdf-fortran-4.4.1

Please help I'm becoming mad..

Best regards
Stephan
config.log
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Stephan Ludwig
1. phyical institute
University Stuttgart
Germany

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