Yambo installation

[barnali]

Respected Sir (Daniele Varsano)

I am trying to install YAMBO-3.4.1 in a HPC machine. For this I am configured with the command

./configure FC=ifort --with-blas="-L/opt/intel/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-lapack="-L/opt/intel/mkl/lib/intel64 -lmkl_lapack95_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-blacs="-L/opt/intel/mkl/lib/intel64 -lmkl_blacs_ilp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-scalapack="-L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-fftw="-L/opt/intel/mkl/lib/intel64" --with-fftw-lib="-lmkl_core -lmkl_intel_lp64 -lfftw3xc_intel -lmkl_sequential" CC=icc MPICC=mpiicc F77=ifort --with-iotk=/home1/barnali/espresso-5.1.2/S3DE/iotk --with-p2y=5.1.2

But I met the error following error--------
.........................................................................................
checking how to get verbose linking output from ifort... -v
checking for Fortran libraries of ifort... -L/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/ -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
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 icc -E -ansi
checking if precompiler works on C source... yes
checking if precompiler works on F90 source... no
configure: error: Found precompiler problems in processing the F90/C source.
..............................................................................................................................
But when I have given the command

./configure FC=ifort --with-blas="-L/opt/intel/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-lapack="-L/opt/intel/mkl/lib/intel64 -lmkl_lapack95_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-blacs="-L/opt/intel/mkl/lib/intel64 -lmkl_blacs_ilp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-scalapack="-L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-fftw="-L/opt/intel/mkl/lib/intel64" --with-fftw-lib="-lmkl_core -lmkl_intel_lp64 -lfftw3xc_intel -lmkl_sequential" CC=icc MPICC=mpiicc F77=ifort --with-iotk=/home1/barnali/espresso-5.1.2/S3DE/iotk --with-p2y=5.1.2 FC="mpiifort" LIBS="-O2 -fPIC" FCFLAGS="-O2 -fPIC"

The error becomes-
.............................................................................................................
checking for FFTW... no
checking for blacs_set in -L/opt/intel/mkl/lib/intel64 -lmkl_blacs_ilp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential... yes
checking for pcheev in -L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential... yes
checking the configuration of the LIBXC internal library... no
configure: error: can't configure LIBXC
...........................................................................

Could you please guide me to solve this problem? I am waiting for your kind response.
Here I have attached the config1.log and config2.log for details information.

config1.log

config.log

Thanking you

Sincerely
Barnali Bhattacharya
Ph.D student
Assam university
India

[barnali]

Respected sir,

Now I am trying with yambo-4.0.1-rev.89 and configured successfully with the following command-

./configure FC=ifort --with-blas="-L/opt/intel/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-lapack="-L/opt/intel/mkl/lib/intel64 -lmkl_lapack95_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-blacs="-L/opt/intel/mkl/lib/intel64 -lmkl_blacs_ilp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-scalapack="-L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" --with-fftw="-L/opt/intel/mkl/lib/intel64" --with-fftw-lib="-lmkl_core -lmkl_intel_lp64 -lfftw3xc_intel -lmkl_sequential" CC=icc MPICC=mpiicc F77=ifort --with-iotk=/home1/barnali/espresso-5.1.2/S3DE/iotk --with-p2y=5.1.2 FC="mpiifort" LIBS="-O2 -fPIC" FCFLAGS="-O2 -fPIC"

Then I have given the command "make interfaces" for compiling yambo and p2y, but get the following error-
...............................................................................................
>>>[Linking a2y]<<<
make[1]: Entering directory `/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/interfaces/a2y'
defs_datatypes.F hdr_io.F a2y_KSS_file_name.F a2y_i.F a2y_db1.F a2y_wf.F
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libint_modules.a(mod_xc2y.o): In function `mod_xc2y_mp_xc_yamboid2kind_':
mod_xc2y.f90:(.text+0x601): undefined reference to `xc_f90_func_init_'
mod_xc2y.f90:(.text+0x60b): undefined reference to `xc_f90_info_kind_'
mod_xc2y.f90:(.text+0x61a): undefined reference to `xc_f90_func_end_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libio.a(io_elemental.o): In function `io_elemental_':
io_elemental.f90:(.text+0x14f): undefined reference to `netcdf_mp_nf90_redef_'
io_elemental.f90:(.text+0x263): undefined reference to `netcdf_mp_nf90_def_var_manydims_'
io_elemental.f90:(.text+0x2db): undefined reference to `netcdf_mp_nf90_def_var_onedim_'
io_elemental.f90:(.text+0x32f): undefined reference to `netcdf_mp_nf90_def_var_onedim_'
io_elemental.f90:(.text+0x35b): undefined reference to `netcdf_mp_nf90_enddef_'
io_elemental.f90:(.text+0xa62): undefined reference to `netcdf_mp_nf90_inq_varid_'
io_elemental.f90:(.text+0xb9b): undefined reference to `netcdf_mp_nf90_put_var_fourbyteint_'
io_elemental.f90:(.text+0xcdf): undefined reference to `netcdf_mp_nf90_get_var_fourbyteint_'
io_elemental.f90:(.text+0xf1a): undefined reference to `netcdf_mp_nf90_put_var_1d_fourbyteint_'
io_elemental.f90:(.text+0x1445): undefined reference to `netcdf_mp_nf90_get_var_1d_fourbyteint_'
io_elemental.f90:(.text+0x1b1c): undefined reference to `netcdf_mp_nf90_put_var_fourbytereal_'
io_elemental.f90:(.text+0x1c7b): undefined reference to `netcdf_mp_nf90_get_var_fourbytereal_'
io_elemental.f90:(.text+0x1f06): undefined reference to `netcdf_mp_nf90_put_var_1d_fourbytereal_'
io_elemental.f90:(.text+0x27e6): undefined reference to `netcdf_mp_nf90_get_var_1d_fourbytereal_'
io_elemental.f90:(.text+0x30a5): undefined reference to `netcdf_mp_nf90_put_var_fourbyteint_'
io_elemental.f90:(.text+0x3224): undefined reference to `netcdf_mp_nf90_get_var_fourbyteint_'
io_elemental.f90:(.text+0x3548): undefined reference to `netcdf_mp_nf90_put_var_1d_text_'
io_elemental.f90:(.text+0x371c): undefined reference to `netcdf_mp_nf90_get_var_1d_text_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libio.a(io_bulk.o): In function `io_bulk_':
io_bulk.f90:(.text+0x1a28): undefined reference to `netcdf_mp_nf90_redef_'
io_bulk.f90:(.text+0x1bb9): undefined reference to `netcdf_mp_nf90_def_var_manydims_'
io_bulk.f90:(.text+0x1c5b): undefined reference to `netcdf_mp_nf90_def_var_manydims_'
io_bulk.f90:(.text+0x1c87): undefined reference to `netcdf_mp_nf90_enddef_'
io_bulk.f90:(.text+0x1cd5): undefined reference to `netcdf_mp_nf90_inq_varid_'
io_bulk.f90:(.text+0x1d89): undefined reference to `netcdf_mp_nf90_put_var_fourbyteint_'
io_bulk.f90:(.text+0x1e30): undefined reference to `netcdf_mp_nf90_get_var_fourbyteint_'
io_bulk.f90:(.text+0x1eed): undefined reference to `netcdf_mp_nf90_put_var_1d_fourbyteint_'
io_bulk.f90:(.text+0x1fa9): undefined reference to `netcdf_mp_nf90_get_var_1d_fourbyteint_'
io_bulk.f90:(.text+0x2077): undefined reference to `netcdf_mp_nf90_put_var_2d_fourbyteint_'
io_bulk.f90:(.text+0x2133): undefined reference to `netcdf_mp_nf90_get_var_2d_fourbyteint_'
io_bulk.f90:(.text+0x2212): undefined reference to `netcdf_mp_nf90_put_var_3d_fourbyteint_'
io_bulk.f90:(.text+0x22cf): undefined reference to `netcdf_mp_nf90_get_var_3d_fourbyteint_'
io_bulk.f90:(.text+0x23c1): undefined reference to `netcdf_mp_nf90_put_var_1d_onebyteint_'
io_bulk.f90:(.text+0x247e): undefined reference to `netcdf_mp_nf90_get_var_1d_onebyteint_'
io_bulk.f90:(.text+0x2506): undefined reference to `netcdf_mp_nf90_put_var_3d_onebyteint_'
io_bulk.f90:(.text+0x2572): undefined reference to `netcdf_mp_nf90_get_var_3d_onebyteint_'
io_bulk.f90:(.text+0x265a): undefined reference to `netcdf_mp_nf90_put_var_fourbytereal_'
io_bulk.f90:(.text+0x2702): undefined reference to `netcdf_mp_nf90_get_var_fourbytereal_'
io_bulk.f90:(.text+0x27c2): undefined reference to `netcdf_mp_nf90_put_var_1d_fourbytereal_'
io_bulk.f90:(.text+0x287f): undefined reference to `netcdf_mp_nf90_get_var_1d_fourbytereal_'
io_bulk.f90:(.text+0x2907): undefined reference to `netcdf_mp_nf90_put_var_2d_fourbytereal_'
io_bulk.f90:(.text+0x2973): undefined reference to `netcdf_mp_nf90_get_var_2d_fourbytereal_'
io_bulk.f90:(.text+0x2a0d): undefined reference to `netcdf_mp_nf90_put_var_3d_fourbytereal_'
io_bulk.f90:(.text+0x2a79): undefined reference to `netcdf_mp_nf90_get_var_3d_fourbytereal_'
io_bulk.f90:(.text+0x6528): undefined reference to `netcdf_mp_nf90_put_var_3d_onebyteint_'
io_bulk.f90:(.text+0x65cd): undefined reference to `netcdf_mp_nf90_put_var_2d_fourbytereal_'
io_bulk.f90:(.text+0x666c): undefined reference to `netcdf_mp_nf90_put_var_3d_fourbytereal_'
io_bulk.f90:(.text+0x6711): undefined reference to `netcdf_mp_nf90_get_var_3d_fourbytereal_'
io_bulk.f90:(.text+0x67b6): undefined reference to `netcdf_mp_nf90_get_var_2d_fourbytereal_'
io_bulk.f90:(.text+0x685b): undefined reference to `netcdf_mp_nf90_get_var_3d_onebyteint_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libmodules.a(mod_IO.o): In function `io_m_mp_io_connect_':
mod_IO.f90:(.text+0x10d4): undefined reference to `netcdf_mp_nf90_create_'
mod_IO.f90:(.text+0x10fc): undefined reference to `netcdf_mp_nf90_enddef_'
mod_IO.f90:(.text+0x1863): undefined reference to `netcdf_mp_nf90_open_'
mod_IO.f90:(.text+0x19ab): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x1a9b): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x1b95): undefined reference to `netcdf_mp_nf90_open_'
mod_IO.f90:(.text+0x1bf8): undefined reference to `netcdf_mp_nf90_create_'
mod_IO.f90:(.text+0x1c20): undefined reference to `netcdf_mp_nf90_enddef_'
mod_IO.f90:(.text+0x1cd4): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x1dd4): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x1ec4): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x1fba): undefined reference to `netcdf_mp_nf90_strerror_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libmodules.a(mod_IO.o): In function `io_m_mp_io_disconnect_':
mod_IO.f90:(.text+0x2c53): undefined reference to `netcdf_mp_nf90_close_'
mod_IO.f90:(.text+0x2ec0): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x2f64): undefined reference to `netcdf_mp_nf90_inquire_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libmodules.a(mod_IO.o): In function `io_m_mp_file_is_open_':
mod_IO.f90:(.text+0x3e56): undefined reference to `netcdf_mp_nf90_inquire_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libmodules.a(mod_IO.o): In function `io_m_mp_netcdf_call_':
mod_IO.f90:(.text+0x3f53): undefined reference to `netcdf_mp_nf90_strerror_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libmodules.a(mod_IO.o): In function `io_m_mp_netcdf_dim_':
mod_IO.f90:(.text+0x4093): undefined reference to `netcdf_mp_nf90_inq_dimid_'
mod_IO.f90:(.text+0x40b5): undefined reference to `netcdf_mp_nf90_def_dim_'
mod_IO.f90:(.text+0x414c): undefined reference to `netcdf_mp_nf90_strerror_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libmodules.a(mod_IO.o): In function `io_m_mp_variable_is_found_':
mod_IO.f90:(.text+0x41f4): undefined reference to `netcdf_mp_nf90_inq_varid_'
mod_IO.f90:(.text+0x4208): undefined reference to `netcdf_mp_nf90_inq_varid_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libmodules.a(mod_xc_functionals.o): In function `xc_functionals_mp_xc_setup_fnctl_':
mod_xc_functionals.f90:(.text+0x10f): undefined reference to `xc_f90_func_init_'
mod_xc_functionals.f90:(.text+0x125): undefined reference to `xc_f90_info_name_'
mod_xc_functionals.f90:(.text+0x12f): undefined reference to `xc_f90_info_family_'
mod_xc_functionals.f90:(.text+0x140): undefined reference to `xc_f90_info_kind_'
mod_xc_functionals.f90:(.text+0x15f): undefined reference to `xc_f90_info_flags_'
mod_xc_functionals.f90:(.text+0x1a0): undefined reference to `xc_f90_func_init_'
mod_xc_functionals.f90:(.text+0x1b3): undefined reference to `xc_f90_info_name_'
mod_xc_functionals.f90:(.text+0x1bd): undefined reference to `xc_f90_info_family_'
mod_xc_functionals.f90:(.text+0x1ca): undefined reference to `xc_f90_info_kind_'
mod_xc_functionals.f90:(.text+0x1e0): undefined reference to `xc_f90_info_flags_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libmodules.a(mod_xc_functionals.o): In function `xc_functionals_mp_xc_setup_hyb_':
mod_xc_functionals.f90:(.text+0x360): undefined reference to `xc_f90_hyb_gga_xc_pbeh_set_par_'
mod_xc_functionals.f90:(.text+0x3ae): undefined reference to `xc_f90_hyb_gga_xc_hse_set_par_'
/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/lib/libmodules.a(mod_xc_functionals.o): In function `xc_functionals_mp_xc_string_':
mod_xc_functionals.f90:(.text+0x69e): undefined reference to `xc_f90_func_init_'
mod_xc_functionals.f90:(.text+0x6b2): undefined reference to `xc_f90_info_name_'
mod_xc_functionals.f90:(.text+0x6bc): undefined reference to `xc_f90_info_family_'
mod_xc_functionals.f90:(.text+0x6cc): undefined reference to `xc_f90_info_kind_'
mod_xc_functionals.f90:(.text+0x6ef): undefined reference to `xc_f90_info_flags_'
mod_xc_functionals.f90:(.text+0x72f): undefined reference to `xc_f90_func_init_'
mod_xc_functionals.f90:(.text+0x743): undefined reference to `xc_f90_info_name_'
mod_xc_functionals.f90:(.text+0x74d): undefined reference to `xc_f90_info_family_'
mod_xc_functionals.f90:(.text+0x75d): undefined reference to `xc_f90_info_kind_'
mod_xc_functionals.f90:(.text+0x780): undefined reference to `xc_f90_info_flags_'
make[1]: *** [a2y] Error 1
make[1]: Leaving directory `/home1/barnali/espresso-5.1.2/yambo-4.0.1-rev.89/interfaces/a2y'
make: *** [interfaces] Error 2
...........................................................................................................................................................
Why this error appeared? Do I miss anything?
Could you please guide me to fix this problem? Here I have attached the config.log.

config.log

Thanking you.


Sincerely

Barnali Bhattacharya
Ph.D student, Physics Department
Assam University, India.

[andrea.ferretti]

Dear Barnali,

concerning v4.0.1, please note the most of the flags you are specifying to ./configure have a name that is out-dated
(run ./configure --help to see the current names).
Because of this, the configure command should complain about undefined flags (please try to sort them out one by one).
Remember to do a make clean_all before trying again with a different set of flags.

Concerning 3.4.1, something minimal like this works in my case for intel+linux X86_64:

Code: Select all

	./configure \
	--with-blas="-lmkl_intel_lp64  -lmkl_sequential -lmkl_core" \
	--with-lapack=" -lmkl_intel_lp64  -lmkl_sequential -lmkl_core" \
	--with-iotk="/home/ferretti/espresso-5.2.0/iotk" \
	PFC="mpif90" \
	FC="mpif90" \
	F90="mpif90" \
	F77="ifort" \
	CC="icc" \
	LDFLAGS="-nofor_main"

in any case, if you browse the forum, there should be plenty of suggestions about compilation of 3.4.1.
You can also have a look here:
http://www.yambo-code.org/download/compiling.php

Andrea