I compiled yambo 5.0.4 on a HPC to use nonlinear optics. Since on this HPC, I don't have internet access I downloaded all external libraries by running download_all_libs.sh on my local machine and copied the repository to the HPC.
Then I configured with
./configure --enable-memory-profile --enable-time-profile --enable-mpi --enable-dp
Here is the configure report for compiler information etc.:
As you can see, I have used gcc 9.2.0.# [VER] 5.0.4 r.19595
#
# - GENERAL CONFIGURATIONS -
#
# [SYS] linux@x86_64
# [SRC] /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4
# [BRN]
# [CMP] /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4
# [TGT] /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4
# [BIN] /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/bin
# [LIB] /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external
#
# [EDITOR] vim
# [ MAKE ] make
#
# [X] Double precision
# [X] Keep object files
# [X] Run-Time timing profile
# [X] Run-Time memory profile
#
# - SCRIPTS -
#
# [-] YDB: Yambo DataBase
# [-] YAMBOpy: Yambo Python scripts
#
# - PARALLEL SUPPORT -
#
# [X] MPI
# [-] OpenMP
#
# - LIBRARIES [E=external library; I?=internal library (c=to be compiled / f=found already compiled); X=system default; -=not used;] -
#
# > I/O: (NETCDF with large files support)
#
# [ - ] FUTILE :
#
# [ - ] YAML :
#
# [ Ic] IOTK : /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/lib/libiotk.a (QE hdf5-support)
# -I/zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/include/
# [ - ] ETSF_IO :
#
# [ Ic] NETCDF : /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/v4/serial/lib/libnetcdff.a /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/v4/serial/lib/libnetcdf.a
# -I/zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/v4/serial/include -I/zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/v4/serial/include
# [ Ic] HDF5 : /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/v4/serial/lib/libhdf5hl_fortran.a /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/v4/serial/lib/libhdf5_fortran.a /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/v4/serial/lib/libhdf5_hl.a /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/v4/serial/lib/libhdf5.a -lz -lm -ldl -lcurl
# -I/zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/v4/serial/include
#
# > MATH: (Internal FFTW3)
#
# [ Ic] FFT : /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/lib/libfftw3.a
# -I/zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/include/
# [ Ic] BLAS : /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/lib/libblas.a
# [ Ic] LAPACK : /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/lib/liblapack.a
# [ - ] SCALAPACK :
# [ - ] BLACS :
# [ - ] PETSC :
#
# [ - ] SLEPC :
#
#
# > OTHERs
#
# [ Ic] LibXC : /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/lib/libxcf90.a /zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/lib/libxc.a
# -I/zhome/academic/HLRS/tp/xgpmipi/yambo-5.0.4/lib/external/gfortran/mpif90/include
# [ E ] MPI : -L/opt/hlrs/non-spack/mpi/mpt/2.23/lib -lmpi
# -I/opt/hlrs/non-spack/mpi/mpt/2.23/include
# [ Ic] Ydriver : 1.0.0
#
# - COMPILERS -
#
# FC kind = gfortran GNU Fortran (GCC) 9.2.0
# MPI kind= HPE MPT 2.23 08/26/20 02:54:49-root
#
# [ CPP ] /opt/hlrs/non-spack/compiler/gcc/9.2.0/bin/gcc -E -P -D_HDF5_LIB -D_HDF5_IO -D_MPI -D_FFTW -D_DOUBLE -D_TIMING -D_P2Y_QEXSD_HDF5
# [ FPP ] /opt/hlrs/non-spack/compiler/gcc/9.2.0/bin/gfortran -E -P -cpp -D_HDF5_LIB -D_HDF5_IO -D_MPI -D_FFTW -D_DOUBLE -D_TIMING
# [ CC ] mpicc -O2 -D_C_US -D_FORTRAN_US
# [ FC ] mpif90 -O3 -g -mtune=native
# [ FCUF] -O0 -g -mtune=native
# [ F77 ] mpif90 -O3 -g -mtune=native
# [ F77U] -O0 -g -mtune=native
# [Cmain]
#
Afterwards, I compiled with (make 4.2.1)
make core
make nl-project
This was successful without any errors. Everything worked well except for yambo_nl where the -u option is missing. When I tried ./yambo_nl -h I got
In my case it seems that the yambo executable was compiled instead of yambo_nl, but still called yambo_nl.___ __ _____ __ __ _____ _____
| Y || _ || Y || _ \ | _ |
| | ||. | ||. ||. | / |. | |
\ _/ |. _ ||.\ / ||. _ \ |. | |
|: | |: | ||: | ||: | \|: | |
|::| |:.|:.||:.|:.||::. /|::. |
`--" `-- --"`-- --"`-----" `-----"
'A shiny pot of fun and happiness [C.D.Hogan]'
This is : yambo
Version : 5.0.4 Revision 19595 Hash 896bffc02
Configuration: MPI+HDF5_IO
Help & version:
-help (-h) <string> :<string> can be an option (e.g. -h optics)
-version :Code version & libraries
Input file & Directories:
-Input (-F) <string> :Input file
-Verbosity (-V) <string> :Input file variables verbosity (more with -h Verbosity)
-Job (-J) <string> :Job string
-Idir (-I) <string> :Input directory
-Odir (-O) <string> :I/O directory
-Cdir (-C) <string> :Communication directory
Parallel Control:
-parenv (-E) <string> :Environment Parallel Variables file
-nompi :Switch off MPI support
Initializations:
-setup (-i) :Initialization
-coulomb (-r) :Coulomb potential
Response Functions:
-optics (-o) <string> :Linear Response optical properties (more with -h optics)
-X (-d) <string> :Inverse Dielectric Matrix (more with -h X)
-dipoles (-q) :Oscillator strenghts (or dipoles)
-kernel (-k) <string> :Kernel (more with -h kernel)
Self-Energy:
-hf (-x) :Hartree-Fock
-gw0 (-p) <string> :GW approximation (more with -h gw0)
-dyson (-g) <string> :Dyson Equation solver (more with -h dyson)
-lifetimes (-l) :GoWo Quasiparticle lifetimes
Bethe-Salpeter Equation:
-Ksolver (-y) <string> :BSE solver (more with -h Ksolver)
Total Energy:
-acfdt :ACFDT Total Energy
Utilites:
-Quiet (-Q) :Quiet input file creation
-fatlog :Verbose (fatter) log(s)
-DBlist (-D) :Databases properties
-walltime <int> :Walltime (more with -h walltime)
YAMBO developers group (http://www.yambo-code.org)
I have already tried to compile different yambo versions and with different compilers but I always get the executable where the -u option is missing.
Do you have an idea what the problem could be? I am glad about any help I can get.
Best regards
Mike