error in installation. NETCDF?

[giacsport]

Dear All,
I am trying to install yambo code in my 64bit cluster.

The configuration path I use is this

./configure --with-iotk='/home/giacomo/src/espresso-5.0/iotk/' --with-p2y=4.0 --with-p2y=5.0 --enable-dp --with-mpi FC=ifort --with-netcdf-include=/usr/local/octopus-3.2.0/include/ --with-netcdf-lib=/usr/local/octopus-3.2.0/


The compilation is ok (no error messages). Then when I give the "make yambo interfaces" I get this error message:

>>>[Linking yambo]<<<
make[1]: Entering directory `/misc/home/giacomo/src/yambo-3.2.5/driver'

/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-ocinternal.o): In function `ocopen':
ocinternal.c:(.text+0x7e4): undefined reference to `curl_version_info'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-http.o): In function `ocfetchhttpcode':
http.c:(.text+0x11): undefined reference to `curl_easy_getinfo'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-http.o): In function `ocsetcurlproperties':
http.c:(.text+0xe3): undefined reference to `curl_easy_strerror'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-http.o): In function `ocfetchlastmodified':
http.c:(.text+0x1bc): undefined reference to `curl_easy_setopt'
http.c:(.text+0x1cd): undefined reference to `curl_easy_strerror'
http.c:(.text+0x211): undefined reference to `curl_easy_setopt'
http.c:(.text+0x225): undefined reference to `curl_easy_setopt'
http.c:(.text+0x239): undefined reference to `curl_easy_setopt'
http.c:(.text+0x24d): undefined reference to `curl_easy_setopt'
http.c:(.text+0x261): undefined reference to `curl_easy_setopt'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-http.o):http.c:(.text+0x275): more undefined references to `curl_easy_setopt' follow
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-http.o): In function `ocfetchlastmodified':
http.c:(.text+0x27d): undefined reference to `curl_easy_perform'
http.c:(.text+0x29e): undefined reference to `curl_easy_getinfo'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-http.o): In function `ocfetchurl_file':
http.c:(.text+0x2fc): undefined reference to `curl_easy_setopt'
http.c:(.text+0x30d): undefined reference to `curl_easy_strerror'
http.c:(.text+0x360): undefined reference to `curl_easy_setopt'
http.c:(.text+0x374): undefined reference to `curl_easy_setopt'
http.c:(.text+0x38a): undefined reference to `curl_easy_setopt'
http.c:(.text+0x39f): undefined reference to `curl_easy_perform'
http.c:(.text+0x3cf): undefined reference to `curl_easy_getinfo'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-http.o): In function `occurlopen':
http.c:(.text+0x417): undefined reference to `curl_easy_init'
http.c:(.text+0x433): undefined reference to `curl_easy_setopt'
http.c:(.text+0x453): undefined reference to `curl_easy_setopt'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-http.o): In function `ocfetchurl':
http.c:(.text+0x4d7): undefined reference to `curl_easy_setopt'
http.c:(.text+0x4e8): undefined reference to `curl_easy_strerror'
http.c:(.text+0x532): undefined reference to `curl_easy_setopt'
http.c:(.text+0x546): undefined reference to `curl_easy_setopt'
http.c:(.text+0x55c): undefined reference to `curl_easy_setopt'
http.c:(.text+0x564): undefined reference to `curl_easy_perform'
http.c:(.text+0x589): undefined reference to `curl_easy_getinfo'
http.c:(.text+0x5c6): undefined reference to `curl_easy_strerror'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-http.o): In function `occurlclose':
http.c:(.text+0x3e6): undefined reference to `curl_easy_cleanup'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-curlfunctions.o): In function `set_verify':
curlfunctions.c:(.text+0x1e): undefined reference to `curl_easy_setopt'
curlfunctions.c:(.text+0x3b): undefined reference to `curl_easy_setopt'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-curlfunctions.o): In function `set_cookies':
curlfunctions.c:(.text+0x5f): undefined reference to `curl_easy_setopt'
curlfunctions.c:(.text+0x7e): undefined reference to `curl_easy_setopt'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-curlfunctions.o): In function `set_proxy':
curlfunctions.c:(.text+0xb9): undefined reference to `curl_easy_setopt'
/home/giacomo/src/yambo-3.2.5/lib/libnetcdf.a(liboc_la-curlfunctions.o):curlfunctions.c:(.text+0xeb): more undefined references to `curl_easy_setopt' follow
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/misc/home/giacomo/src/yambo-3.2.5/driver'
make: *** [yambo] Error 2
[giacomo@princeps yambo-3.2.5]$

If I properly understand I think that here the problem is represented by my NETCDF.
Could anyone kindly help me in fixing this my error.

I attach also the confog.log file

Very best regards,
Giacomo


------------------
Giacomo Giorgi,
University of Tokyo

[Daniele Varsano]

Dear Giacomo,
a possible reason of your problem is that yambo and netcdf are compiled with different compilers.
I can see that you linked the necdf from the octopus software, you can try to download the
netcdf alone and compile them.

Cheers,

Daniele

[giacsport]

Thanks Daniele for the kind and quick reply.

Allow me another question and excuse me if it can be silly. I am not a very good programmer....

I compiled and installed the netcdf 3.6.2 with ifort.

I passed all the tests (make check)

Now in the netcdf directory I have these files and dirs

acinclude.m4 config.guess config.log configure cxx f90 install-sh ltmain.sh Makefile.in ncdump nc_test RELEASE_NOTES
aclocal.m4 config.h config.status configure.ac depcomp fortran libsrc Makefile man ncgen nf_test stamp-h1
compile config.h.in config.sub COPYRIGHT examples INSTALL libtool Makefile.am missing nctest README VERSION


I think that "libsrc" is the library directory to be link as "-with--netcdf-lib=/home/giacomo/src/netcdf-3.6.2/libsrc/".
but what about the path for "-with--netcdf-include"? I don't see any directory "include" here.

Could you help me?

Best,
Giacomo

[Daniele Varsano]

Dear Giacomo,

I think that "libsrc" is the library directory to be link as "-with--netcdf-lib=/home/giacomo/src/netcdf-3.6.2/libsrc/".
but what about the path for "-with--netcdf-include"? I don't see any directory "include" here.

I think that libsrc contain the source files, and it is not the right directory. Tipically you should have a lib directory containing:
libnetcdf.a libnetcdf.la libnetcdf_c++.a libnetcdf_c++.la pkgconfig
and an include directory containing:
NETCDF.mod TYPESIZES.mod ncvalues.h netcdf.h netcdf.hh netcdf.inc netcdfcpp.h

After the netcdf compilation, may be you should type make install.
I hope that this is the problem, otherwise check where the above files are placed.

Cheers,

Daniele

[kahvazi.m]

Dear developers

I am a new yambo user and very glad of using yambo. I use QE 4.1 for
my calculatiouns .I want a calculat the optical properties of compound semiconductor
with yambo code, but I am a bigginner to use a yambo code because I'm a new
user yambo. I'm trying to install yambo code on opensuse 11, but I can not install (or link) netcdf library.
my installation procedure is:
linux-4cwd:/usr/local/codes # ls
mpich2-1.4 yambo
linux-4cwd:/usr/local/codes # cd yambo/
linux-4cwd:/usr/local/codes/yambo # ls
ndb.BS_diago_Q01 ns.db1
ndb.BS_Q1 ns.wf
ndb.dipoles ns.wf_fragments_1_1
ndb.em1s SiH4_NETCDF_databases_and_reference_files.zip
ndb.gops yambo-3.2.5
ndb.Haydock_restart yambo-3.2.5-rev.26.tar.gz
ndb.kindx
linux-4cwd:/usr/local/codes/yambo # cd yambo-3.2.5/
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5 # ls
bin config configure driver lib src
ChangeLog config.log COPYING include Makefile ypp
commit.msg config.status doc interfaces sbin
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5 # ./configure
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 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... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for vim... vim
checking for GNU make... make
checking for ar... ar
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 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/i586-suse-linux/4.3 -L/usr/lib/gcc/i586-suse-linux/4.3/../../../../i586-suse-linux/lib -L/usr/lib/gcc/i586-suse-linux/4.3/../../.. -lgfortranbegin -lgfortran -lm
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... no
checking for mpxlf90... no
checking for mpxlf... no
checking for mpf90... no
checking for mpxlf95... no
checking for mpxlf_r... no
checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
checking for a working mpif.h... no
checking for a working mpi.h... no
checking for a working mpi module... no
configure: WARNING: could not compile a FORTRAN mpi test program. YAMBO serial only.
checking for FFTW... no
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] 3.2.5 r.1015
#
# [SYS] linux@i686
# [SRC] /usr/local/codes/yambo/yambo-3.2.5
# [BIN] /usr/local/codes/yambo/yambo-3.2.5/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [ ] MPI
# [ ] PW (4.0) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [ ] LibXC
# [ ] 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]
# [ F90 ] gfortran -O3 -mtune=native
# [MPIF ]
# [ F77 ] gfortran -O3 -mtune=native
# [Cmain]
# [NoOpt] -O0 -mtune=native
#
# [ MAKE ] make
# [EDITOR] vim
#
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5 # make yambo

>>>[Making slatec]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/lib/slatec'
ar: creating libslatec.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/lib/slatec'

>>>[Making blas]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/lib/blas'
ar: creating libblas.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/lib/blas'

>>>[Making lapack]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/lib/lapack'
ar: creating liblapack.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/lib/lapack'

>>>[Making external_c]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/external_c'
ar: creating libexternal_c.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/external_c'

>>>[Making modules]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/modules'
ar: creating libmodules.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/modules'

>>>[Making xc_functionals]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/xc_functionals'
ar: creating libxc_functionals.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/xc_functionals'

>>>[Making parser]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/parser'
ar: creating libparser.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/parser'

>>>[Making communicate]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/communicate'
ar: creating libcommunicate.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/communicate'

>>>[Making common]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/common'
ar: creating libcommon.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/common'

>>>[Making io]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/io'
ar: creating libio.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/io'

>>>[Making wf_and_fft]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/wf_and_fft'
sgfft.F ar: creating libwf_and_fft.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/wf_and_fft'

>>>[Making coulomb]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/coulomb'
ar: creating libcoulomb.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/coulomb'

>>>[Making bz_ops]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/bz_ops'
ar: creating libbz_ops.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/bz_ops'

>>>[Making qp_ctl]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/qp_ctl'
ar: creating libqp_ctl.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/qp_ctl'

>>>[Making setup]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/setup'
ar: creating libsetup.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/setup'

>>>[Making interface]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/interface'
ar: creating libinterface.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/interface'

>>>[Making tddft]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/tddft'
ar: creating libtddft.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/tddft'

>>>[Making pol_function]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/pol_function'
ar: creating libpol_function.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/pol_function'

>>>[Making qp]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/qp'
ar: creating libqp.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/qp'

>>>[Making bse]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/bse'
ar: creating libbse.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/bse'

>>>[Linking yambo]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/driver'

make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/driver'

linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5 # make yambo interfaces

>>>[Making slatec]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/lib/slatec'
ar: creating libslatec.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/lib/slatec'

>>>[Making blas]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/lib/blas'
ar: creating libblas.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/lib/blas'

>>>[Making lapack]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/lib/lapack'
ar: creating liblapack.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/lib/lapack'

>>>[Making external_c]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/external_c'
ar: creating libexternal_c.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/external_c'

>>>[Making modules]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/modules'
ar: creating libmodules.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/modules'

>>>[Making xc_functionals]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/xc_functionals'
ar: creating libxc_functionals.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/xc_functionals'

>>>[Making parser]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/parser'
ar: creating libparser.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/parser'

>>>[Making communicate]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/communicate'
ar: creating libcommunicate.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/communicate'

>>>[Making common]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/common'
ar: creating libcommon.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/common'

>>>[Making io]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/io'
ar: creating libio.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/io'

>>>[Making wf_and_fft]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/wf_and_fft'
ar: creating libwf_and_fft.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/wf_and_fft'

>>>[Making coulomb]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/coulomb'
ar: creating libcoulomb.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/coulomb'

>>>[Making bz_ops]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/bz_ops'
ar: creating libbz_ops.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/bz_ops'

>>>[Making qp_ctl]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/qp_ctl'
ar: creating libqp_ctl.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/qp_ctl'

>>>[Making setup]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/setup'
ar: creating libsetup.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/setup'

>>>[Making interface]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/interface'
ar: creating libinterface.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/interface'

>>>[Making tddft]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/tddft'
ar: creating libtddft.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/tddft'

>>>[Making pol_function]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/pol_function'
ar: creating libpol_function.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/pol_function'

>>>[Making qp]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/qp'
ar: creating libqp.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/qp'

>>>[Making bse]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/bse'
ar: creating libbse.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/bse'

>>>[Linking yambo]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/driver'

make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/driver'


>>>[Making external_c]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/external_c'
ar: creating libexternal_c.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/external_c'

>>>[Making modules]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/modules'
ar: creating libmodules.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/modules'

>>>[Making parser]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/parser'
ar: creating libparser.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/parser'

>>>[Making communicate]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/communicate'
ar: creating libcommunicate.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/communicate'

>>>[Making common]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/common'
ar: creating libcommon.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/common'

>>>[Making io]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/io'
ar: creating libio.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/io'

>>>[Making bz_ops]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/src/bz_ops'
ar: creating libbz_ops.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/src/bz_ops'

>>>[Making int_modules]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/interfaces/int_modules'
ar: creating libint_modules.a
make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/interfaces/int_modules'

>>>[Linking a2y]<<<
make[1]: Entering directory `/usr/local/codes/yambo/yambo-3.2.5/interfaces/a2y'

make[1]: Leaving directory `/usr/local/codes/yambo/yambo-3.2.5/interfaces/a2y'

linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5 # ls
bin config configure driver lib src
ChangeLog config.log COPYING include Makefile ypp
commit.msg config.status doc interfaces sbin
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5 # cd doc
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc # ls
QuickGuidedTour.pdf README sample
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc # cd sample/
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc/sample # ls
bulk_silicon
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc/sample # cd bulk_silicon/
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc/sample/bulk_silicon # ls
experiment.dat README SAVE
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc/sample/bulk_silicon # cd SAVE/linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc/sample/bulk_silicon/SAVE # ls
database_DB1_NETCDF_format.gz database_WF_NETCDF_format.gz gunzip
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc/sample/bulk_silicon/SAVE # gunzip database_DB1_NETCDF_format.gz

gzip: database_DB1_NETCDF_format.gz: unexpected end of file
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc/sample/bulk_silicon/SAVE # ncgen -o ns.db1 database_DB1_NETCDF_format
bash: ncgen: command not found
linux-4cwd:/usr/local/codes/yambo/yambo-3.2.5/doc/sample/bulk_silicon/SAVE #


please guide me in simple languge. Do I have the wrong installation?
Do you need internet connection to install netcdf library?
How to install yambo codes on the Linux operating system is easier?
I've read almost all educational site yambo but so far I have not managed to install and running it.
please help me with patience and simply get.

thanks in advance.
motahare kahvazi.

[Daniele Varsano]

Dear Mothare,
first let me ask to fill up your signature with your affiliation, it is a rule of the forum.

Next, from the summary of the configure, you can see that you did not link the mpi (parallel compilation),
netcdf, and PW support (which you need for interfacing yambo with qe). HAve a look at the checkboxes.
# [ ] MPI
# [ ] PW (4.0) support
# [ ] NETCDF/HDF5/Large Files

These should be crossed with an X.


In order to link them you have to set up properly your configure command.
Type configure -h in order to have suggestion of the command to use.
For example you have to run the configure as:
the command you need are:
for linking to QE:
--with-iotk=
--with-p2y=
for linkng the netcdf
--with-netcdf-include
--with-netcdf-lib=
--with-netcdf-link=

For instance have a look to the confgure command in this post:
viewtopic.php?f=1&t=401#p2305

and put your directory where iotk, netcdf are.
If you do not have the necdf installed you have to download and compile it.

If you have problems, please post the error and upload the config.log file.

Cheers,

Daniele