Yambo Community Forum

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.
Thanking you

Sincerely
Barnali Bhattacharya
Ph.D student
Assam university
India

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. Thanking you.


Sincerely

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

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: 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