Segmentation fault Yambo 5.2/5,3 [CPU]

Deals with issues related to computation of optical spectra in reciprocal space: RPA, TDDFT, local field effects.

Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, andrea marini, Daniele Varsano, Conor Hogan

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harrier_class
Posts: 7
Joined: Tue May 13, 2025 4:27 pm

Segmentation fault Yambo 5.2/5,3 [CPU]

Post by harrier_class » Thu Apr 09, 2026 3:14 pm

Dear all,

I am trying to configure and compile Yambo 5.3 [and alos tried 5.2] on the CPU-cluster Fritz HPC [FAU, Erlangen].

(1) Compiler:
Intel Ice Lake Server


(2) Architecture:
Intel Ice Lake Server

(3) if the problems occur compiling in serial/in parallel
serial [probably also in paralle, but need to try, to be certain]

(4) the version of Yambo (revision number/major release version)
5.3 [downloaded the source code from the official git repo of Yambo and changed the branch 5.3 using git branch -a, git checkout 5.3]
5.2 [downloaded the source code from the official git repo of Yambo and changed the branch 5.2 using git branch -a, git checkout 5.2]

Further, I would like to share that the compilation was performed on the login node

Code: Select all

module purge
module load intel/2021.4.0
module load intelmpi/2021.6.0
module load mkl/2021.4.0
module load hdf5/1.10.7-impi-intel
module load netcdf-c/4.8.1
module load netcdf-fortran/4.5.3-intel


H5PFX=$(dirname $(dirname $(which h5pfc)))
NCPFX=$(nc-config --prefix)
NFFX=$(nf-config --prefix)

export CC=mpiicc
export FC=mpiifort
export CXX=mpiicpc
export PICC=mpiicc
export MPIFC=mpiifort
export MPICXX=mpiicpc

./configure \
  --enable-mpi --enable-open-mp --enable-par-linalg --enable-memory-profile \
  --with-hdf5-path="$H5PFX" \
  --with-netcdf-path="$NCPFX" \
  --with-netcdff-path="$NFFX" \
  --with-blas-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
  --with-lapack-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
  --with-scalapack-libs="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64" \
  --with-blacs-libs="-L${MKLROOT}/lib/intel64 -lmkl_blacs_intelmpi_lp64" \
  --with-fft-includedir="${MKLROOT}/include" \
  --with-fft-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl"

After the compilation, I dont get any error, but whil running the tddft calculation, I get the error:

Code: Select all

[f1254:1160487:0:1160487] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7ffed4c1cd30)
 1  /lib64/libucs.so.0(+0x2c31c) [0x1461ded3b31c]
 2  /lib64/libucs.so.0(+0x2c4ea) [0x1461ded3b4ea]
 3  /lib64/libpthread.so.0(+0x12990) [0x146275129990]
 4  /home/woody/bccc/bccc128h/software/yambo_5.2_fritz_cpu/bin/yambo() [0x5fa804]
 5  /home/woody/bccc/bccc128h/software/yambo_5.2_fritz_cpu/bin/yambo() [0x5f1619]
 6  /home/woody/bccc/bccc128h/software/yambo_5.2_fritz_cpu/bin/yambo() [0x5ec877]
 7  /home/woody/bccc/bccc128h/software/yambo_5.2_fritz_cpu/bin/yambo() [0x53cbf1]
 8  /home/woody/bccc/bccc128h/software/yambo_5.2_fritz_cpu/bin/yambo() [0x4f35a4]
 9  /home/woody/bccc/bccc128h/software/yambo_5.2_fritz_cpu/bin/yambo() [0x415ed4]
10  /home/woody/bccc/bccc128h/software/yambo_5.2_fritz_cpu/bin/yambo() [0x805fe5]
11  /home/woody/bccc/bccc128h/software/yambo_5.2_fritz_cpu/bin/yambo() [0x414a05]
12  /lib64/libc.so.6(__libc_start_main+0xe5) [0x14627120d865]
13  /home/woody/bccc/bccc128h/software/yambo_5.2_fritz_cpu/bin/yambo() [0x41482e]


Now, the strange part for me is that the TDDFT jobs are running perfectly nicely with Yambo 5.0 [also installed with the same commands]. So, I am bit perplexed about why its not working with Yambo 5.3 and 5.2


Can you help?

--
Best regards,
Vipul
Vipul Kumar Ambasta
MSc. student
Friedrich Alexander Universitaet
Erlangen (Germany)
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Davide Sangalli
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Re: Segmentation fault Yambo 5.2/5,3 [CPU]

Post by Davide Sangalli » Thu Apr 09, 2026 6:15 pm

Dear Vipul,
please provide the report of your compilation (config/report), an input file and the log file of your tddft run

Meanwhile, few remarks.

If you are using tddft in transition space, in yambo 5.3 the implementation was completely rewritten to be much more efficient. However, it is still possible to switch to the older implementation by using the following input variable

Code: Select all

FxcMode="R-def"
yambo 5.2 and previous versions always use R-def implementation

Moreover, there was a bug in the R-def implementation, which was introduced in 5.2 and fixed only in 5.4. I just pushed the fix now in 5.3
Please try to re-compile 5.3 after git pull, and test tddft with both FxcMode="G-def" and FxcMode="R-def"
Alternatively you can directly switch to 5.4. If non of this options works, you can also check the lumen fork of the yambo code: https://gitlab.com/lumen-code/lumen

Last, please also remember to check on how many threads you are running.

Best,
D.
Davide Sangalli, PhD
Piazza Leonardo Da Vinci, 32, 20133 – Milano
CNR, Istituto di Struttura della Materia (ISM)
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/
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harrier_class
Posts: 7
Joined: Tue May 13, 2025 4:27 pm

Re: Segmentation fault Yambo 5.2/5,3 [CPU]

Post by harrier_class » Fri Apr 17, 2026 2:46 pm

Dear Davide,

Thanks a lot for quick reply!

I did follow all the suggestions shared by you.

1. pulling 5.3 from the git and recompiling it and then running the input with both modes FxcMode="G-def" and FxcMode="R-def", however, I get the same error.
2. pulling 5.4 from the git and compilng it and running the input file with both modes FxcMode="G-def" and FxcMode="R-def", however, I get the same error

I also understand that it might be due to the memory issues, however, the same calculation with same threads and nodes run using Yambo 5.0. So, I think I am making some mistake either during the compilation or running the job. To give you further insight, please find the input file and log files for 5.3 and 5.4. Also, please find the compilation (config/report) for each compilation attached.

And yes, eventhough, the exact same calculations are going as desired using 5.0 branch, I am interested in using the newer versions, cause they have faster implementations and it puzzles me where I am going wrong. Would be great, if you can help me figure it out.

input file

Code: Select all

optics                           # [R] Linear Response optical properties
chi                              # [R][CHI] Dyson equation for Chi.
tddft                            # [R][K] Use TDDFT kernel
#DegFix                        # Force the code to impose the energy levels to respect their degeneracy
X_Threads=0                      # [OPENMP/X] Number of threads for response functions
Chimod= "ALDA"                   # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
FxcGRLc= 3                 Ry    # [TDDFT] XC-kernel RL size
NGsBlkXd= 3                Ry    # [Xd] Response block size
% QpntsRXd
 1 | 1 |                             # [Xd] Transferred momenta
%
% BndsRnXd
    1 |  800 |                       # [Xd] Polarization function bands
%
% EnRngeXd
  0.00000 | 10.00000 |         eV    # [Xd] Energy range
%
% DmRngeXd
 0.100000 | 0.100000 |         eV    # [Xd] Damping range
%
ETStpsXd= 100                    # [Xd] Total Energy steps
% LongDrXd
 1.000000 | 0.000000 | 0.000000 |        # [Xd] [cc] Electric Field
%
FxcMode="G-def"
config/report for Yambo 5.3

Code: Select all

#
# [VER] 5.3
#
# Legend: [E]=external library [C]=internal lib to be compiled [I]=internal lib already compiled [X]=used [-]=not used
# 
# - GENERAL CONFIGURATIONS -
# 
# [SYS] linux@x86_64
# [SRC] /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu
# [BRN] 5.3
# [CMP] /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu
# [TGT] /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu
# [BIN] /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin
# [LIB] /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/lib/external/intel/mpiifort
#
# [EDITOR] vim
# [ MAKE ] make
#
# [-] 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/GPU SUPPORT -
#
# [-] GPU support ( no_gpu )
# [E] MPI
# [X] OpenMP
# 
# - I/O -
#
# [X]: Parallel I/O (via HDF5)
# [E]: HDF5 Parallel_lib
# [E]: NETCDF Large Files Support enabled, Version 4
# 
# - LIBRARIES - 
# 
# > I/O: NETCDF Large Files Support enabled, Version 4, HDF5 Parallel_lib
#
# [C] IOTK      : -L(LIB)/lib -liotk (QE hdf5-support)
#                 -I(LIB)/include/
# [-] ETSF_IO   : 
#                 
# [E] NETCDFF   : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/intel-2021.4.0/netcdf-fortran-4.5.3-p7gftpw46fnndtrywsezbfeg2f5miy24/lib -lnetcdff
#                 -I/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/intel-2021.4.0/netcdf-fortran-4.5.3-p7gftpw46fnndtrywsezbfeg2f5miy24/include
# [E] NETCDF    : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/netcdf-c-4.8.1-dl7xq5t2pm7nvcwav4ox3w2lsqpymuhf/lib -lnetcdf
#                 -I/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/netcdf-c-4.8.1-dl7xq5t2pm7nvcwav4ox3w2lsqpymuhf/include
# [E] HDF5      : -L/apps/SPACK/0.17.1/opt/linux-almalinux8-icelake/intel-2021.4.0/hdf5-1.10.7-7i3kpe42vkt72pp5olnghymkkyarwvxl/lib -lhdf5_hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz -lm -ldl
#                 -I/apps/SPACK/0.17.1/opt/linux-almalinux8-icelake/intel-2021.4.0/hdf5-1.10.7-7i3kpe42vkt72pp5olnghymkkyarwvxl/include
#
# > MATH: (FFTW MKL) 
#
# [E] BLAS      : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl (for petsc: -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl)
# [E] LAPACK    : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl (for petsc: -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl)
# [E] SCALAPACK : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_scalapack_lp64 
# [E] BLACS     : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_blacs_intelmpi_lp64
# [E] FFT       : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl
#                 -I/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/include
# [-] PETSC     : 
#                  
# [-] SLEPC     : 
#                  
#
# > OTHERs: (devxlib tarball)
#
# [C] LibXC     : -L(LIB)/lib/ -lxcf90 -lxcf03 -lxc
#                 -I(LIB)/include
# [C] DevXlib   : -L(LIB)/no_gpu/lib -ldevXlib
#                 -I(LIB)/no_gpu/include
# [-] LibCUDA   :    
#                 
# [E] MPI       : -L/apps/SPACK/0.18.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mpi-2021.6.0-t6dnxugu5zjf26ectgs7xwbjq34ota6k/mpi/2021.6.0/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /apps/SPACK/0.18.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mpi-2021.6.0-t6dnxugu5zjf26ectgs7xwbjq34ota6k/mpi/2021.6.0/lib/release -Xlinker -rpath -Xlinker /apps/SPACK/0.18.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mpi-2021.6.0-t6dnxugu5zjf26ectgs7xwbjq34ota6k/mpi/2021.6.0/lib -lmpifort -lmpi -ldl -lrt -lpthread 
#                 -I/apps/SPACK/0.18.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mpi-2021.6.0-t6dnxugu5zjf26ectgs7xwbjq34ota6k/mpi/2021.6.0/include 
#
# - COMPILERS -
#
# FC kind = intel mpiifort for the Intel(R) MPI Library 2021.6 for Linux*
# MPI kind= Intel(R) MPI Library 2021.6 for Linux* OS
#
# [ CPP ] mpiicc -E -ansi -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP  -D_SCALAPACK   -D_OPENMP -D_TIMING     -D_P2Y_QEXSD_HDF5
# [ FPP ] fpp -free -P -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP  -D_SCALAPACK   -D_OPENMP -D_TIMING    
# [ CC  ] mpiicc -O2 -std=gnu99 -D_C_US -D_FORTRAN_US
# [ FC  ] mpiifort -assume bscc -O2 -g    -qopenmp -parallel 
# [ FCUF] -assume bscc -O0 -g   
# [ F77 ] mpiifort -assume bscc -O2 -g   
# [ F77U] -assume bscc -O0 -g   
# [Cmain] -nofor-main
#
# You can modify compilers and flags by editing the file "config/setup"
#
config/report for Yambo 5.4

Code: Select all

#
# [VER] 5.4
#
# Legend: [E]=external library [C]=internal lib to be compiled [I]=internal lib already compiled [X]=used [-]=not used
# 
# - GENERAL CONFIGURATIONS -
# 
# [SYS] linux@x86_64
# [SRC] /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu
# [BRN] 5.4
# [CMP] /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu
# [TGT] /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu
# [BIN] /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/bin
# [LIB] /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/lib/external/intel/mpiifort
#
# [EDITOR] vim
# [ MAKE ] make
#
# [-] 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/GPU SUPPORT -
#
# [-] GPU support ( no_gpu )
# [E] MPI
# [X] OpenMP
# 
# - I/O -
#
# [X]: Parallel I/O (via HDF5)
# [E]: HDF5 Parallel_lib
# [E]: NETCDF Large Files Support enabled, Version 4
# 
# - LIBRARIES - 
# 
# > I/O: NETCDF Large Files Support enabled, Version 4, HDF5 Parallel_lib
#
# [C] IOTK      : -L(LIB)/lib -liotk (QE hdf5-support)
#                 -I(LIB)/include/
# [-] ETSF_IO   : 
#                 
# [E] NETCDFF   : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/intel-2021.4.0/netcdf-fortran-4.5.3-p7gftpw46fnndtrywsezbfeg2f5miy24/lib -lnetcdff
#                 -I/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/intel-2021.4.0/netcdf-fortran-4.5.3-p7gftpw46fnndtrywsezbfeg2f5miy24/include
# [E] NETCDF    : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/netcdf-c-4.8.1-dl7xq5t2pm7nvcwav4ox3w2lsqpymuhf/lib -lnetcdf
#                 -I/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/netcdf-c-4.8.1-dl7xq5t2pm7nvcwav4ox3w2lsqpymuhf/include
# [E] HDF5      : -L/apps/SPACK/0.17.1/opt/linux-almalinux8-icelake/intel-2021.4.0/hdf5-1.10.7-7i3kpe42vkt72pp5olnghymkkyarwvxl/lib -lhdf5_hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz -lm -ldl
#                 -I/apps/SPACK/0.17.1/opt/linux-almalinux8-icelake/intel-2021.4.0/hdf5-1.10.7-7i3kpe42vkt72pp5olnghymkkyarwvxl/include
#
# > MATH: (FFTW MKL) 
#
# [E] BLAS      : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl (for petsc: -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl)
# [E] LAPACK    : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl (for petsc: -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl)
# [E] SCALAPACK : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_scalapack_lp64 
# [-] ELPA      :  
#                 
# [E] BLACS     : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_blacs_intelmpi_lp64
# [E] FFT       : -L/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl
#                 -I/apps/SPACK/0.17.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-vw4vllug36zymedwgtd6gks2r2f5ilcd/mkl/2021.4.0/include
# [-] PETSC     :  
#                  
# [-] SLEPC     :  
#                  
# [-] ChASE     : 
#                  
#
# > OTHERs: (devxlib tarball)
#
# [I] Ydiago    : (CMP)/lib/external/intel/mpiifort/lib/libydiago.a
#                 -I(CMP)/lib/external/intel/mpiifort/include/
# [C] LibXC     : -L(LIB)/lib/ -lxcf90 -lxcf03 -lxc
#                 -I(LIB)/include
# [C] DevXlib   : -L(LIB)/no_gpu/lib -ldevXlib
#                 -I(LIB)/no_gpu/include
# [-] LibCUDA   :    
#                 
# [E] MPI       : -L/apps/SPACK/0.18.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mpi-2021.6.0-t6dnxugu5zjf26ectgs7xwbjq34ota6k/mpi/2021.6.0/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /apps/SPACK/0.18.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mpi-2021.6.0-t6dnxugu5zjf26ectgs7xwbjq34ota6k/mpi/2021.6.0/lib/release -Xlinker -rpath -Xlinker /apps/SPACK/0.18.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mpi-2021.6.0-t6dnxugu5zjf26ectgs7xwbjq34ota6k/mpi/2021.6.0/lib -lmpifort -lmpi -ldl -lrt -lpthread 
#                 -I/apps/SPACK/0.18.0/opt/linux-almalinux8-icelake/gcc-8.5.0/intel-oneapi-mpi-2021.6.0-t6dnxugu5zjf26ectgs7xwbjq34ota6k/mpi/2021.6.0/include 
#
# - COMPILERS -
#
# FC kind = intel mpiifort for the Intel(R) MPI Library 2021.6 for Linux*
# MPI kind= Intel(R) MPI Library 2021.6 for Linux* OS
#
# [ CPP ] mpiicc -E -ansi -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP  -D_SCALAPACK   -D_YDIAGO   -D_OPENMP -D_TIMING     -D_P2Y_QEXSD_HDF5
# [ FPP ] fpp -free -P -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP  -D_SCALAPACK   -D_YDIAGO   -D_OPENMP -D_TIMING    
# [ CC  ] mpiicc -O2 -std=gnu99 -D_C_US -D_FORTRAN_US
# [ FC  ] mpiifort -assume bscc -O2 -g    -qopenmp -parallel 
# [ FCUF] -assume bscc -O0 -g   
# [ F77 ] mpiifort -assume bscc -O2 -g   
# [ F77U] -assume bscc -O0 -g   
# [Cmain] -nofor-main
#
# You can modify compilers and flags by editing the file "config/setup"
#

log file for my tddft run [yambo 5.3]

Code: Select all

____    ____    ___      .___  ___.  .______     ______
\   \  /   /   /   \     |   \/   |  |   _  \   /  __  \
 \   \/   /   /  ^  \    |  \  /  |  |  |_)  | |  |  |  |
  \_    _/   /  /_\  \   |  |\/|  |  |   _  <  |  |  |  |
    |  |    /  _____  \  |  |  |  |  |  |_)  | |  `--"  |
    |__|   /__/     \__\ |__|  |__|  |______/   \______/



 <---> P1: [01] MPI/OPENMP structure, Files & I/O Directories
 <---> P1-f0101.nhr.fau.de: MPI Cores-Threads   : 16(CPU)-18(threads)
 <---> P1-f0101.nhr.fau.de: [02] CORE Variables Setup
 <---> P1-f0101.nhr.fau.de: [02.01] Unit cells
 <---> P1-f0101.nhr.fau.de: [02.02] Symmetries
 <---> P1-f0101.nhr.fau.de: [02.03] Reciprocal space
 <---> P1-f0101.nhr.fau.de: [02.04] K-grid lattice
 <---> P1-f0101.nhr.fau.de: [02.05] Energies & Occupations
 <---> P1-f0101.nhr.fau.de: [03] Transferred momenta grid and indexing
 <---> P1-f0101.nhr.fau.de: [04] Dipoles
 <---> P1-f0101.nhr.fau.de: [04.01] Setup: observables and procedures
 <---> P1-f0101.nhr.fau.de: [PARALLEL DIPOLES for K(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <---> P1-f0101.nhr.fau.de: [PARALLEL DIPOLES for CON bands on 4 CPU] Loaded/Total (Percentual):57/228(25%)
 <---> P1-f0101.nhr.fau.de: [PARALLEL DIPOLES for VAL bands on 4 CPU] Loaded/Total (Percentual):143/572(25%)
 <02s> P1-f0101.nhr.fau.de: [DIP] Database not correct or missing. To be computed
 <02s> P1-f0101.nhr.fau.de: [x,Vnl] computed using 2624 projectors
 <02s> P1-f0101.nhr.fau.de: [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
 <03s> P1-f0101.nhr.fau.de: R V P [g-space] |                                        | [000%] --(E) --(X)
 <03s> P1-f0101.nhr.fau.de: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):200/800(25%)
 <03s> P1-f0101.nhr.fau.de: [MEMORY] Alloc WF%c( 291.8170 [Mb]) TOTAL:  480.4430 [Mb] (traced)  96.11200 [Mb] (memstat)
 <03s> P1-f0101.nhr.fau.de: [MEMORY] Alloc wf_disk( 208.6490 [Mb]) TOTAL:  692.0140 [Mb] (traced)  96.11200 [Mb] (memstat)
 <04s> P1-f0101.nhr.fau.de: [MEMORY]  Free wf_disk( 208.6490 [Mb]) TOTAL:  483.3650 [Mb] (traced)  96.24400 [Mb] (memstat)
 <45s> P1-f0101.nhr.fau.de: R V P [g-space] |#                                       | [002%] 41s(E) 27m-48s(X)
 <50s> P1-f0101.nhr.fau.de: R V P [g-space] |####################################### | [097%] 46s(E) 47s(X)
 <50s> P1-f0101.nhr.fau.de: R V P [g-space] |########################################| [100%] 46s(E) 46s(X)
 <50s> P1-f0101.nhr.fau.de: [MEMORY]  Free WF%c( 291.8170 [Mb]) TOTAL:  188.6320 [Mb] (traced)  96.24400 [Mb] (memstat)
 <51s> P1-f0101.nhr.fau.de: [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.
 <51s> P1-f0101.nhr.fau.de: [WARNING] In case H contains other non local terms, these are neglected
 <51s> P1-f0101.nhr.fau.de: [05] Optics
 <51s> P1-f0101.nhr.fau.de: [PARALLEL Response_G_space for K(bz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <51s> P1-f0101.nhr.fau.de: [PARALLEL Response_G_space for Q(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <51s> P1-f0101.nhr.fau.de: [PARALLEL Response_G_space for G-vectors on 2 CPU]
 <51s> P1-f0101.nhr.fau.de: [PARALLEL Response_G_space for K-q(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <51s> P1-f0101.nhr.fau.de: [LA@Response_G_space] PARALLEL linear algebra uses a 2x2 SLK grid (4 cpu)
 <51s> P1-f0101.nhr.fau.de: [PARALLEL Response_G_space for K(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <51s> P1-f0101.nhr.fau.de: [PARALLEL Response_G_space for CON bands on 4 CPU] Loaded/Total (Percentual):57/228(25%)
 <51s> P1-f0101.nhr.fau.de: [PARALLEL Response_G_space for VAL bands on 2 CPU] Loaded/Total (Percentual):286/572(50%)
 <51s> P1-f0101.nhr.fau.de: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):286/572(50%)
 <51s> P1-f0101.nhr.fau.de: [MEMORY] Alloc WF%c( 828.1840 [Mb]) TOTAL:  912.8360 [Mb] (traced)  97.33600 [Mb] (memstat)
 <51s> P1-f0101.nhr.fau.de: [FFT-Rho] Mesh size:   81   44  104
 <51s> P1-f0101.nhr.fau.de: [MEMORY] Alloc wf_disk( 417.2980 [Mb]) TOTAL:  1.335928 [Gb] (traced)  97.33600 [Mb] (memstat)
 <53s> P1-f0101.nhr.fau.de: [MEMORY]  Free wf_disk( 417.2980 [Mb]) TOTAL:  918.6300 [Mb] (traced)  97.85200 [Mb] (memstat)
 <53s> P1-f0101.nhr.fau.de: [xc] Functional : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 <53s> P1-f0101.nhr.fau.de: [xc] LIBXC used to calculate xc functional

and the corresponding error [yambo 5.3 again]

Code: Select all

[f0104:641514:0:641514] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x80015d298a90)
[f0101:1757892:0:1757892] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x8005d6e6fd80)
[f0104:641516:0:641516] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7fff2e0aedc0)
==== backtrace (tid: 641514) ====
 0  /lib64/libucs.so.0(ucs_handle_error+0x2dc) [0x15112db4413c]
 1  /lib64/libucs.so.0(+0x2c31c) [0x15112db4431c]
 2  /lib64/libucs.so.0(+0x2c4ea) [0x15112db444ea]
 3  /lib64/libpthread.so.0(+0x12990) [0x1511c3f32990]
==== backtrace (tid: 641516) ====
 4  /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin/yambo() [0x5fd3d7]
 5  /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin/yambo() [0x5f4334]
 6  /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin/yambo() [0x5ef517]
 7  /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin/yambo() [0x53a2d6]
 8  /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin/yambo() [0x4f003c]
 9  /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin/yambo() [0x4158eb]
10  /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin/yambo() [0x7de575]
11  /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin/yambo() [0x7dd365]
12  /lib64/libc.so.6(__libc_start_main+0xe5) [0x1511c0016865]
13  /home/woody/bccc/bccc128h/software/yambo_5.3_fritz_cpu/bin/yambo() [0x41442e]


log file for my tddft run [yambo 5.4]

Code: Select all

___    ____    ___      .___  ___.  .______     ______
\   \  /   /   /   \     |   \/   |  |   _  \   /  __  \
 \   \/   /   /  ^  \    |  \  /  |  |  |_)  | |  |  |  |
  \_    _/   /  /_\  \   |  |\/|  |  |   _  <  |  |  |  |
    |  |    /  _____  \  |  |  |  |  |  |_)  | |  `--"  |
    |__|   /__/     \__\ |__|  |__|  |______/   \______/



 <---> P1: [01] MPI/OPENMP structure, Files & I/O Directories
 <---> P1-f0220.nhr.fau.de: MPI Cores-Threads   : 16(CPU)-18(threads)
 <---> P1-f0220.nhr.fau.de: [02] CORE Variables Setup
 <---> P1-f0220.nhr.fau.de: [02.01] Unit cells
 <---> P1-f0220.nhr.fau.de: [02.02] Symmetries
 <---> P1-f0220.nhr.fau.de: [02.03] Reciprocal space
 <---> P1-f0220.nhr.fau.de: [02.04] K-grid lattice
 <---> P1-f0220.nhr.fau.de: [02.05] Energies & Occupations
 <---> P1-f0220.nhr.fau.de: [03] Transferred momenta grid and indexing
 <---> P1-f0220.nhr.fau.de: [04] Dipoles
 <---> P1-f0220.nhr.fau.de: [04.01] Setup: observables and procedures
 <---> P1-f0220.nhr.fau.de: [PARALLEL DIPOLES for K(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <---> P1-f0220.nhr.fau.de: [PARALLEL DIPOLES for CON bands on 4 CPU] Loaded/Total (Percentual):57/228(25%)
 <---> P1-f0220.nhr.fau.de: [PARALLEL DIPOLES for VAL bands on 4 CPU] Loaded/Total (Percentual):143/572(25%)
 <02s> P1-f0220.nhr.fau.de: [DIP] Database not correct or missing. To be computed
 <02s> P1-f0220.nhr.fau.de: [x,Vnl] computed using 2624 projectors
 <02s> P1-f0220.nhr.fau.de: [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
 <03s> P1-f0220.nhr.fau.de: R V P [g-space] |                                        | [000%] --(E) --(X)
 <03s> P1-f0220.nhr.fau.de: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):200/800(25%)
 <03s> P1-f0220.nhr.fau.de: [MEMORY] Alloc WF%c( 291.8170 [Mb]) TOTAL:  480.4430 [Mb] (traced)  96.08800 [Mb] (memstat)
 <04s> P1-f0220.nhr.fau.de: [MEMORY] Alloc wf_disk( 208.6490 [Mb]) TOTAL:  692.0140 [Mb] (traced)  96.08800 [Mb] (memstat)
 <06s> P1-f0220.nhr.fau.de: [MEMORY]  Free wf_disk( 208.6490 [Mb]) TOTAL:  483.3650 [Mb] (traced)  96.61200 [Mb] (memstat)
 <48s> P1-f0220.nhr.fau.de: R V P [g-space] |#                                       | [002%] 44s(E) 29m-37s(X)
 <53s> P1-f0220.nhr.fau.de: R V P [g-space] |########################################| [100%] 49s(E) 49s(X)
 <53s> P1-f0220.nhr.fau.de: [MEMORY]  Free WF%c( 291.8170 [Mb]) TOTAL:  188.6320 [Mb] (traced)  96.61200 [Mb] (memstat)
 <56s> P1-f0220.nhr.fau.de: [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.
 <56s> P1-f0220.nhr.fau.de: [WARNING] In case H contains other non local terms, these are neglected
 <56s> P1-f0220.nhr.fau.de: [05] Optics
 <56s> P1-f0220.nhr.fau.de: [PARALLEL Response_G_space for K(bz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <56s> P1-f0220.nhr.fau.de: [PARALLEL Response_G_space for Q(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <56s> P1-f0220.nhr.fau.de: [PARALLEL Response_G_space for G-vectors on 2 CPU]
 <56s> P1-f0220.nhr.fau.de: [PARALLEL Response_G_space for K-q(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <56s> P1-f0220.nhr.fau.de: [LA@Response_G_space] PARALLEL linear algebra uses a 2x2 SLK grid (4 cpu)
 <56s> P1-f0220.nhr.fau.de: [PARALLEL Response_G_space for K(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <56s> P1-f0220.nhr.fau.de: [PARALLEL Response_G_space for CON bands on 4 CPU] Loaded/Total (Percentual):57/228(25%)
 <56s> P1-f0220.nhr.fau.de: [PARALLEL Response_G_space for VAL bands on 2 CPU] Loaded/Total (Percentual):286/572(50%)
 <57s> P1-f0220.nhr.fau.de: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):286/572(50%)
 <57s> P1-f0220.nhr.fau.de: [MEMORY] Alloc WF%c( 828.1840 [Mb]) TOTAL:  912.8360 [Mb] (traced)  97.12000 [Mb] (memstat)
 <57s> P1-f0220.nhr.fau.de: [FFT-Rho] Mesh size:   81   44  104
 <57s> P1-f0220.nhr.fau.de: [MEMORY] Alloc wf_disk( 417.2980 [Mb]) TOTAL:  1.335928 [Gb] (traced)  97.12000 [Mb] (memstat)
 <58s> P1-f0220.nhr.fau.de: [MEMORY]  Free wf_disk( 417.2980 [Mb]) TOTAL:  918.6300 [Mb] (traced)  97.68000 [Mb] (memstat)
 <58s> P1-f0220.nhr.fau.de: [xc] Functional : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 <58s> P1-f0220.nhr.fau.de: [xc] LIBXC used to calculate xc functional
~
and the respective error [yambo 5.4]

Code: Select all

[f0262:1861049:0:1861049] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7fff1adea0e0)
[f0220:2697938:0:2697938] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x8000a07969a0)
[f0229:1089873:0:1089873] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7ffe5ba43360)
[f0253:3124991:0:3124991] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x8003e2db9f50)
[f0262:1861050:0:1861050] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x800384e7a140)
[f0262:1861051:0:1861051] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x8000d3353860)
[f0262:1861048:0:1861048] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7fffa97a23d0)
[f0220:2697936:0:2697936] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x80023b8acc00)
[f0220:2697937:0:2697937] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7ffc9abff100)
[f0229:1089872:0:1089872] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x800133f50890)
==== backtrace (tid:1861048) ====
==== backtrace (tid:1861050) ====
 0  /lib64/libucs.so.0(ucs_handle_error+0x2dc) [0x15064141913c]
 1  /lib64/libucs.so.0(+0x2c31c) [0x15064141931c]
 2  /lib64/libucs.so.0(+0x2c4ea) [0x1506414194ea]
 3  /lib64/libpthread.so.0(+0x12990) [0x1506d7807990]
 4  /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/bin/yambo() [0x616f97]
 5  /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/bin/yambo() [0x60def4]
 6  /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/bin/yambo() [0x6090d7]
 7  /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/bin/yambo() [0x54d8c6]
 8  /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/bin/yambo() [0x50389f]
 9  /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/bin/yambo() [0x41652b]
10  /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/bin/yambo() [0x802025]
11  /home/woody/bccc/bccc128h/software/yambo_5.4_fritz_cpu/bin/yambo() [0x800e25]
12  /lib64/libc.so.6(__libc_start_main+0xe5) [0x1506d38eb865
--
Thanks and best regards,
Vipul
Vipul Kumar Ambasta
MSc. student
Friedrich Alexander Universitaet
Erlangen (Germany)
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User avatar
Davide Sangalli
Posts: 680
Joined: Tue May 29, 2012 4:49 pm
Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
Contact:
Contact Davide Sangalli

Re: Segmentation fault Yambo 5.2/5,3 [CPU]

Post by Davide Sangalli » Fri Apr 17, 2026 3:11 pm

Ok, then I'm not sure about what is going on.

Can you also add the log of the succesfull run with 5.0, and the report (r-jobanme) of the three runs ?

Best,
D.
Davide Sangalli, PhD
Piazza Leonardo Da Vinci, 32, 20133 – Milano
CNR, Istituto di Struttura della Materia (ISM)
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/
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harrier_class
Posts: 7
Joined: Tue May 13, 2025 4:27 pm

Re: Segmentation fault Yambo 5.2/5,3 [CPU]

Post by harrier_class » Fri Apr 17, 2026 3:53 pm

Dear Davide,

Thanks for your prompt reply.

Sure, please find the requested files attached.

log file from the successful yambo 5.0

Code: Select all


  __ __  ____ ___ ___ ____   ___
 |  |  |/    |   |   |    \ /   \
 |  |  |  o  | _   _ |  o  )     |
 |  ~  |     |  \_/  |     |  O  |
 |___, |  _  |   |   |  O  |     |
 |     |  |  |   |   |     |     |
 |____/|__|__|___|___|_____|\___/


 <---> P6: [01] MPI/OPENMP structure, Files & I/O Directories
 <---> P6-f0154.nhr.fau.de: MPI Cores-Threads   : 16(CPU)-18(threads)
 <---> P6-f0154.nhr.fau.de: [02] CORE Variables Setup
 <---> P6-f0154.nhr.fau.de: [02.01] Unit cells
 <---> P6-f0154.nhr.fau.de: [02.02] Symmetries
 <---> P6-f0154.nhr.fau.de: [02.03] Reciprocal space
 <---> P6-f0154.nhr.fau.de: [02.04] K-grid lattice
 <---> P6-f0154.nhr.fau.de: [02.05] Energies & Occupations
 <---> P6-f0154.nhr.fau.de: [03] Transferred momenta grid and indexing
 <---> P6-f0154.nhr.fau.de: [04] Dipoles
 <---> P6-f0154.nhr.fau.de: DIPOLES parallel ENVIRONMENT is incomplete. Switching to defaults
 <---> P6-f0154.nhr.fau.de: [PARALLEL DIPOLES for K(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <---> P6-f0154.nhr.fau.de: [PARALLEL DIPOLES for CON bands on 4 CPU] Loaded/Total (Percentual):57/228(25%)
 <---> P6-f0154.nhr.fau.de: [PARALLEL DIPOLES for VAL bands on 4 CPU] Loaded/Total (Percentual):143/572(25%)
 <---> P6-f0154.nhr.fau.de: [DIP] Checking dipoles header
 <02s> P6-f0154.nhr.fau.de: [WARNING][DIP] Database not correct or missing. To be computed
 <02s> P6-f0154.nhr.fau.de: [x,Vnl] computed using 2624 projectors
 <02s> P6-f0154.nhr.fau.de: [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
 <03s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |                                        | [000%] --(E) --(X)
 <03s> P6-f0154.nhr.fau.de: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):200/800(25%)
 <01m-33s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#                                       | [002%] 01m-29s(E) 59m-52s(X)
 <02m-45s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |##                                      | [005%] 02m-42s(E) 54m-01s(X)
 <03m-58s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |###                                     | [007%] 03m-54s(E) 52m-05s(X)
 <05m-10s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |####                                    | [010%] 05m-07s(E) 51m-06s(X)
 <06m-22s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#####                                   | [012%] 06m-19s(E) 50m-32s(X)
 <07m-35s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |######                                  | [015%] 07m-31s(E) 50m-09s(X)
 <08m-47s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#######                                 | [017%] 08m-43s(E) 49m-52s(X)
 <09m-59s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |########                                | [020%] 09m-56s(E) 49m-39s(X)
 <11m-11s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#########                               | [022%] 11m-08s(E) 49m-29s(X)
 <12m-24s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |##########                              | [025%] 12m-20s(E) 49m-22s(X)
 <13m-36s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |###########                             | [027%] 13m-32s(E) 49m-15s(X)
 <14m-48s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |############                            | [030%] 14m-45s(E) 49m-10s(X)
 <16m-01s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#############                           | [032%] 15m-57s(E) 49m-05s(X)
 <17m-13s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |##############                          | [035%] 17m-09s(E) 49m-01s(X)
 <18m-25s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |###############                         | [037%] 18m-21s(E) 48m-58s(X)
 <19m-37s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |################                        | [040%] 19m-34s(E) 48m-55s(X)
 <20m-50s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#################                       | [042%] 20m-46s(E) 48m-52s(X)
 <22m-02s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |##################                      | [045%] 21m-58s(E) 48m-50s(X)
 <23m-14s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |###################                     | [047%] 23m-11s(E) 48m-48s(X)
 <24m-26s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |####################                    | [050%] 24m-23s(E) 48m-46s(X)
 <25m-39s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#####################                   | [052%] 25m-35s(E) 48m-44s(X)
 <26m-51s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |######################                  | [055%] 26m-48s(E) 48m-43s(X)
 <28m-03s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#######################                 | [057%] 28m-00s(E) 48m-41s(X)
 <29m-15s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |########################                | [060%] 29m-12s(E) 48m-40s(X)
 <30m-28s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#########################               | [062%] 30m-24s(E) 48m-39s(X)
 <31m-40s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |##########################              | [065%] 31m-37s(E) 48m-38s(X)
 <32m-52s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |###########################             | [067%] 32m-49s(E) 48m-37s(X)
 <34m-05s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |############################            | [070%] 34m-01s(E) 48m-36s(X)
 <35m-17s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#############################           | [072%] 35m-14s(E) 48m-36s(X)
 <36m-30s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |##############################          | [075%] 36m-26s(E) 48m-35s(X)
 <37m-42s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |###############################         | [077%] 37m-39s(E) 48m-34s(X)
 <38m-55s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |################################        | [080%] 38m-51s(E) 48m-34s(X)
 <40m-07s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#################################       | [082%] 40m-03s(E) 48m-33s(X)
 <41m-19s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |##################################      | [085%] 41m-16s(E) 48m-33s(X)
 <42m-32s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |###################################     | [087%] 42m-28s(E) 48m-32s(X)
 <43m-44s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |####################################    | [090%] 43m-40s(E) 48m-32s(X)
 <44m-56s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |#####################################   | [092%] 44m-53s(E) 48m-31s(X)
 <46m-09s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |######################################  | [095%] 46m-05s(E) 48m-31s(X)
 <47m-21s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |####################################### | [097%] 47m-18s(E) 48m-30s(X)
 <48m-34s> P6-f0154.nhr.fau.de: Dipoles: P, V and iR (T) |########################################| [100%] 48m-30s(E) 48m-30s(X)
 <51m-40s> P6-f0154.nhr.fau.de: [DIP] Checking dipoles header
 <51m-40s> P6-f0154.nhr.fau.de: [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.
 <51m-40s> P6-f0154.nhr.fau.de: [WARNING] In case H contains other non local terms, these are neglected
 <51m-40s> P6-f0154.nhr.fau.de: [05] Optics
 <51m-40s> P6-f0154.nhr.fau.de: Response_G_space parallel ENVIRONMENT is incomplete. Switching to defaults
 <51m-40s> P6-f0154.nhr.fau.de: [PARALLEL Response_G_space for K(bz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <51m-40s> P6-f0154.nhr.fau.de: [PARALLEL Response_G_space for Q(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <51m-40s> P6-f0154.nhr.fau.de: [PARALLEL Response_G_space for K-q(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <51m-40s> P6-f0154.nhr.fau.de: [LA@Response_G_space] PARALLEL linear algebra uses a 4x4 SLK grid (16 cpu)
 <51m-40s> P6-f0154.nhr.fau.de: [PARALLEL Response_G_space for K(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <51m-40s> P6-f0154.nhr.fau.de: [PARALLEL Response_G_space for CON bands on 2 CPU] Loaded/Total (Percentual):114/228(50%)
 <51m-40s> P6-f0154.nhr.fau.de: [PARALLEL Response_G_space for VAL bands on 2 CPU] Loaded/Total (Percentual):286/572(50%)
 <52m-56s> P6-f0154.nhr.fau.de: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):286/572(50%)
 <52m-56s> P6-f0154.nhr.fau.de: [FFT-Rho] Mesh size:   81   44  104
 <53m-00s> P6-f0154.nhr.fau.de: [xc] Functional : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 <53m-00s> P6-f0154.nhr.fau.de: [xc] LIBXC used to calculate xc functional
 <53m-01s> P6-f0154.nhr.fau.de: [WARNING] Fxc not coded for GGA. Using LDA part only of the functional
 <53m-01s> P6-f0154.nhr.fau.de: [WARNING] Fxc not coded for GGA. Using LDA part only of the functional
 <53m-02s> P6-f0154.nhr.fau.de: [PARALLEL distribution for RL vectors(X) on 4 CPU] Loaded/Total (Percentual):1057077/7667361(14%)
 <53m-02s> P6-f0154.nhr.fau.de: [DIP] Checking dipoles header
 <53m-02s> P6-f0154.nhr.fau.de: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):800/800(100%)
 <53m-02s> P6-f0154.nhr.fau.de: [FFT-X] Mesh size:   81   44  104
 <53m-06s> P6-f0154.nhr.fau.de: [X-CG] R(p) Tot o/o(of R):   15194   32604     100
 <53m-06s> P6-f0154.nhr.fau.de: [X] Upper matrix triangle filled
 <53m-06s> P6-f0154.nhr.fau.de: Xo@q[1] |                                        | [000%] --(E) --(X)
 <53m-18s> P6-f0154.nhr.fau.de: Xo@q[1] |#                                       | [002%] 12s(E) 07m-42s(X)
 <53m-30s> P6-f0154.nhr.fau.de: Xo@q[1] |##                                      | [005%] 24s(E) 07m-55s(X)
 <53m-43s> P6-f0154.nhr.fau.de: Xo@q[1] |###                                     | [007%] 36s(E) 07m-58s(X)
 <53m-54s> P6-f0154.nhr.fau.de: Xo@q[1] |####                                    | [010%] 48s(E) 07m-58s(X)
 <54m-07s> P6-f0154.nhr.fau.de: Xo@q[1] |#####                                   | [012%] 01m-00s(E) 08m-00s(X)
 <54m-19s> P6-f0154.nhr.fau.de: Xo@q[1] |######                                  | [015%] 01m-12s(E) 08m-01s(X)
 <54m-31s> P6-f0154.nhr.fau.de: Xo@q[1] |#######                                 | [017%] 01m-24s(E) 08m-01s(X)
 <54m-43s> P6-f0154.nhr.fau.de: Xo@q[1] |########                                | [020%] 01m-36s(E) 08m-02s(X)
 <54m-55s> P6-f0154.nhr.fau.de: Xo@q[1] |#########                               | [022%] 01m-48s(E) 08m-02s(X)
 <55m-07s> P6-f0154.nhr.fau.de: Xo@q[1] |##########                              | [025%] 02m-00s(E) 08m-02s(X)
 <55m-20s> P6-f0154.nhr.fau.de: Xo@q[1] |###########                             | [027%] 02m-13s(E) 08m-04s(X)
 <55m-32s> P6-f0154.nhr.fau.de: Xo@q[1] |############                            | [030%] 02m-25s(E) 08m-04s(X)
 <55m-44s> P6-f0154.nhr.fau.de: Xo@q[1] |#############                           | [032%] 02m-37s(E) 08m-04s(X)
 <55m-56s> P6-f0154.nhr.fau.de: Xo@q[1] |##############                          | [035%] 02m-49s(E) 08m-04s(X)
 <56m-08s> P6-f0154.nhr.fau.de: Xo@q[1] |###############                         | [037%] 03m-01s(E) 08m-04s(X)
 <56m-20s> P6-f0154.nhr.fau.de: Xo@q[1] |################                        | [040%] 03m-14s(E) 08m-04s(X)
 <56m-32s> P6-f0154.nhr.fau.de: Xo@q[1] |#################                       | [042%] 03m-26s(E) 08m-04s(X)
 <56m-45s> P6-f0154.nhr.fau.de: Xo@q[1] |##################                      | [045%] 03m-38s(E) 08m-04s(X)
 <56m-57s> P6-f0154.nhr.fau.de: Xo@q[1] |###################                     | [047%] 03m-50s(E) 08m-04s(X)
 <57m-09s> P6-f0154.nhr.fau.de: Xo@q[1] |####################                    | [050%] 04m-02s(E) 08m-05s(X)
 <57m-22s> P6-f0154.nhr.fau.de: Xo@q[1] |#####################                   | [052%] 04m-15s(E) 08m-05s(X)
 <57m-34s> P6-f0154.nhr.fau.de: Xo@q[1] |######################                  | [055%] 04m-27s(E) 08m-05s(X)
 <57m-46s> P6-f0154.nhr.fau.de: Xo@q[1] |#######################                 | [057%] 04m-39s(E) 08m-05s(X)
 <57m-58s> P6-f0154.nhr.fau.de: Xo@q[1] |########################                | [060%] 04m-51s(E) 08m-05s(X)
 <58m-10s> P6-f0154.nhr.fau.de: Xo@q[1] |#########################               | [062%] 05m-04s(E) 08m-06s(X)
 <58m-23s> P6-f0154.nhr.fau.de: Xo@q[1] |##########################              | [065%] 05m-16s(E) 08m-06s(X)
 <58m-35s> P6-f0154.nhr.fau.de: Xo@q[1] |###########################             | [067%] 05m-28s(E) 08m-06s(X)
 <58m-47s> P6-f0154.nhr.fau.de: Xo@q[1] |############################            | [070%] 05m-40s(E) 08m-06s(X)
 <58m-59s> P6-f0154.nhr.fau.de: Xo@q[1] |#############################           | [072%] 05m-52s(E) 08m-06s(X)
 <59m-11s> P6-f0154.nhr.fau.de: Xo@q[1] |##############################          | [075%] 06m-04s(E) 08m-06s(X)
 <59m-24s> P6-f0154.nhr.fau.de: Xo@q[1] |###############################         | [077%] 06m-17s(E) 08m-06s(X)
 <59m-36s> P6-f0154.nhr.fau.de: Xo@q[1] |################################        | [080%] 06m-29s(E) 08m-06s(X)
 <59m-48s> P6-f0154.nhr.fau.de: Xo@q[1] |#################################       | [082%] 06m-41s(E) 08m-06s(X)
 <01h-00m> P6-f0154.nhr.fau.de: Xo@q[1] |##################################      | [085%] 06m-53s(E) 08m-06s(X)
 <01h-00m> P6-f0154.nhr.fau.de: Xo@q[1] |###################################     | [087%] 07m-05s(E) 08m-06s(X)
 <01h-00m> P6-f0154.nhr.fau.de: Xo@q[1] |####################################    | [090%] 07m-18s(E) 08m-06s(X)
 <01h-00m> P6-f0154.nhr.fau.de: Xo@q[1] |#####################################   | [092%] 07m-30s(E) 08m-06s(X)
 <01h-00m> P6-f0154.nhr.fau.de: Xo@q[1] |######################################  | [095%] 07m-42s(E) 08m-06s(X)
 <01h-01m> P6-f0154.nhr.fau.de: Xo@q[1] |####################################### | [097%] 07m-54s(E) 08m-06s(X)
 <01h-01m> P6-f0154.nhr.fau.de: Xo@q[1] |########################################| [100%] 08m-06s(E) 08m-06s(X)
 <01h-04m> P6-f0154.nhr.fau.de: [PARALLEL distribution for X Frequencies on 1 CPU] Loaded/Total (Percentual):100/100(100%)
 <01h-04m> P6-f0154.nhr.fau.de: X@q[1] |                                        | [000%] --(E) --(X)
 <01h-04m> P6-f0154.nhr.fau.de: X@q[1] |#########                               | [023%] 05s(E) 21s(X)
 <01h-04m> P6-f0154.nhr.fau.de: X@q[1] |###################                     | [048%] 10s(E) 21s(X)
 <01h-04m> P6-f0154.nhr.fau.de: X@q[1] |#############################           | [073%] 15s(E) 20s(X)
 <01h-04m> P6-f0154.nhr.fau.de: X@q[1] |####################################### | [098%] 20s(E) 20s(X)
 <01h-04m> P6-f0154.nhr.fau.de: X@q[1] |########################################| [100%] 20s(E) 20s(X)
 <01h-04m> P6-f0154.nhr.fau.de: [PARALLEL distribution for RL vectors(X) on 4 CPU] Loaded/Total (Percentual):1916148/7667361(25%)
 <01h-04m> P6-f0154.nhr.fau.de: [06] Timing Overview
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                      io_ATMPROJ_pwscf :      0.0000s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                            io_COL_CUT :      0.0000s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                                 io_HF :      0.0000s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                          io_KB_abinit :      0.0000s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                                  io_X :      0.0001s CPU (  4 calls,   0.014 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]               IO_and_Messaging_switch :      0.0001s CPU (  8 calls,   0.010 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                                 io_BS :      0.0003s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                        io_Double_Grid :      0.0004s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                          PP_uspp_init :      0.0007s CPU (  3 calls,   0.240 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                              io_QINDX :      0.0167s CPU (  2 calls,   8.373 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                            io_DIPOLES :      0.0508s CPU (  5 calls,  10.162 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                             FFT_setup :      0.0979s CPU (  2 calls,  48.952 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                           io_KB_pwscf :      0.0985s CPU (  3 calls,  32.822 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                               io_GROT :      0.0986s CPU (  2 calls,  49.276 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                MATRIX transfer (NONE) :      0.2411s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                           io_fragment :      0.3512s CPU (  8 calls,  43.896 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]     MATRIX transfer (X_G_X_redux_2_1) :      0.3972s CPU (100 calls,   3.972 msec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                   XC_potential_driver :      1.3267s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]     MATRIX transfer (X_G_X_redux_1_1) :      1.9245s CPU (100 calls,   0.019 sec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                             X (REDUX) :      2.0551s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                       PARALLEL_M_by_M :      2.5593s CPU (100 calls,   0.026 sec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                                 io_WF :      6.6599s CPU ( 13 calls,   0.512 sec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                           WF_load_FFT :      9.5755s CPU (  3 calls,   3.192 sec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                   PARALLEL_lin_system :     15.4870s CPU (100 calls,   0.155 sec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                        LINEAR ALGEBRA :     15.4877s CPU (100 calls,   0.155 sec avg)
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                         X (procedure) :     68.1044s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                        eval_G_minus_G :     75.4370s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                            Xo (REDUX) :    125.3631s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                        Xo (procedure) :    498.5217s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                     DIPOLE_transverse :      48m-31s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]                               Dipoles :      51m-38s CPU
 <01h-04m> P6-f0154.nhr.fau.de: [07] Game Over & Game summary
 <01h-04m> P6-f0154.nhr.fau.de: [TIMING]            [Time-Profile]: 01h-04m


r-optics file [Successful 5.0]

Code: Select all

                                                                          
     **    **    **     ****     ****  ******     *******                 
    //**  **    ****   /**/**   **/** /*////**   **/////**                
     //****    **//**  /**//** ** /** /*   /**  **     //**               
      //**    **  //** /** //***  /** /******  /**      /**               
       /**   **********/**  //*   /** /*//// **/**      /**               
       /**  /**//////**/**   /    /** /*    /**//**     **                
       /**  /**     /**/**        /** /*******  //*******                 
       //   //      // //         //  ///////    ///////                  
                                                                          
          Version 5.0.4 Revision 19598 Hash 20b2ffa04                     
                         Branch is 5.0                                    
                 MPI+OpenMP+SLK+HDF5_IO Build                             
                   http://www.yambo-code.org                              
 
 03/25/2026 at 16:11 yambo @ f0153.nhr.fau.de
 ==================================================

 Cores-Threads       : 16(CPU)-18(threads)
 MPI Cores           :  16
 Threads per core    :  18
 Threads total       :  288
 Nodes Computing     :   4
 Nodes IO            :  1

 Fragmented WFs      : yes
 CORE databases      : .
 Additional I/O      : .
 Communications      : .
 Input file          : yambo.in_ALDA
 Report file         : ./r_optics_chi_tddft_03
 Verbose log/report  : no
 Log files           : ./LOG

 Precision           : SINGLE
  
 [RD./SAVE//ns.db1]--------------------------------------------------------------
  Bands                                            :   800
  K-points                                         :  1
  G-vectors                                        :  1494439 [RL space]
  Components                                       :  186763 [wavefunctions]
  Symmetries                                       :  2 [spatial]
  Spinor components                                :  1
  Spin polarizations                               :  1
  Temperature                                      :  0.025852 [eV]
  Electrons                                        :   1144.00   
  WF G-vectors                                     :  186763
  Max atoms/species                                :  224
  No. of atom species                              :  3
  Exact exchange fraction in XC                    :  0.000000
  Exact exchange screening in XC                   :  0.000000
  Magnetic symmetries                              : no
 - S/N 000735 ---------------------------------------------- v.05.00.04 r.19598 -

 [02] CORE Variables Setup
 =========================


  [02.01] Unit cells
  ==================

***removed, as do not wish to upload the structure on internet*** let me know if you need this

  [02.02] Symmetries
  ==================

  Inversion symmetry    : yes
  Spatial inversion     : yes
  Inversion index       :  2
  K-space Time-reversal : no
  Magnetic symmetries   : no
  Group table correct   : yes
  Symmetries units      :  [cc]

   [S 1]:   1.00000      0.00000     0.474319E-8   0.00000      1.00000      0.00000    -0.948637E-8   0.00000      1.00000   
   [S 2]:  -1.00000      0.00000    -0.474319E-8   0.00000     -1.00000      0.00000     0.948637E-8   0.00000     -1.00000   

  [02.03] Reciprocal space
  ========================

  nG shells         :  262100
  nG charge         :  1494439
  nG WFs            :  186763
  nC WFs            :  186763
  G-vecs. in first 80 shells:  [ Number ]
    1   3   5   7   9  11  13  15  17
    19   23   25   29   33   35   39   41   43
    47   49   53   57   59   63   65   69   71
    75   77   81   83   87   91   93   95   97
    99  103  107  109  113  115  117  121  125
   127  129  133  137  141  143  147  151  155
   159  163  167  171  175  177  179  181  185
   187  189  193  195  199  201  205  207  209
   211  215  219  223  225  229  231  235
  ...
  Shell energy in first 80 shells:  [ mHa ]
    0.00000   9.80940  15.51580  21.61848  29.03190  39.23758  47.33998  52.81564  62.06318
   62.16679  62.62503  64.45917  68.33143  74.43412  79.28600  81.84754  86.47394  88.28455
    92.0532   92.6803  100.1556  114.8788  114.9205  114.9824  116.1276  117.2748  128.1075
   132.1016  138.3315  139.2896  139.6422  141.1002  145.4959  156.6395  156.9503  157.6393
   160.5717  167.7361  168.9432  172.5880  180.9232  187.2930  189.3599  191.1471  192.4578
   194.5664  201.1200  209.4551  209.7660  210.4550  211.2625  213.3873  221.0719  225.4036
   226.7783  232.8810  240.1086  240.2944  242.1756  242.2172  243.2354  245.2349  247.3820
   248.2527  248.6671  250.5001  252.1120  253.9356  257.8367  258.6025  261.2870  270.2311
   272.8889  273.3257  273.4293  275.7217  279.2843  290.5486  292.0569  295.0328
  ...

  [02.04] K-grid lattice
  ======================

  Compatible Grid is   : 0D
  K lattice UC volume  :  0.007928 [a.u.]

  [02.05] Energies & Occupations
  ==============================

  [X] === General ===
  [X] Electronic Temperature                        :  0.258606E-1   300.100    [eV K]
  [X] Bosonic    Temperature                        :  0.258606E-1   300.100    [eV K]
  [X] Finite Temperature mode                       : yes
  [X] El. density                                   :  0.24675E+24 [cm-3]
  [X] Fermi Level                                   :  1.165298 [eV]

  [X] === Gaps and Widths ===
  [X] Conduction Band Min                           :  0.698940 [eV]
  [X] Valence Band Max                              : -0.699258 [eV]
  [X] Filled Bands                                  :   572
  [X] Empty Bands                                   :   573   800
  [X] Direct Gap                                    :  1.398198 [eV]
  [X] Direct Gap localized at k-point               :  1
   
   

 [03] Transferred momenta grid and indexing
 ==========================================

 [RD./SAVE//ndb.kindx]-----------------------------------------------------------
  Fragmentation                                    : no
  Polarization last K                              :  1
  QP states                                        :  1  1
  X grid is uniform                                : yes
  Grids                                            : X S
  BS scattering                                    : no
  COLL scattering                                  : no
  Sigma scattering                                 : yes
  X scattering                                     : yes
 - S/N 000735 ---------------------------------------------- v.05.00.04 r.19598 -

 IBZ Q-points :  1
 BZ  Q-points :  1

 K/Q-points units:
 rlu = crystal or reduced units; cc = cartesian coordinates; iku = interal k-units

 Q [1]:  0.000000  0.000000  0.000000 [rlu]

 [04] Dipoles
 ============


 [WARNING][DIP] Database not correct or missing. To be computed
 [RD./SAVE//ns.kb_pp_pwscf]------------------------------------------------------
  Fragmentation                                    : yes
 - S/N 000735 ---------------------------------------------- v.05.00.04 r.19598 -

 [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
 [WF-Oscillators/G space/Transverse up loader] Normalization (few states)  min/max  :  0.91027E-10   1.0000    

 [WR./SAVE//ndb.dipoles]---------------------------------------------------------
  Brillouin Zone Q/K grids (IBZ/BZ)                :  1  1  1  1
  RL vectors                                       :  186763 [WF]
  Fragmentation                                    : yes
  Electronic Temperature                           :  300.1000 [K]
  Bosonic    Temperature                           :  300.1000 [K]
  DIP band range                                   :     1   800
  DIP band range limits                            :   572   573
  DIP e/h energy range                             : -1.000000 -1.000000 [eV]
  RL vectors in the sum                            :  186763
  [r,Vnl] included                                 : yes
  Bands ordered                                    : yes
  Direct v evaluation                              : no
  Approach used                                    : G-space v
  Dipoles computed                                 : R V P
  Wavefunctions                                    : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 - S/N 000735 ---------------------------------------------- v.05.00.04 r.19598 -

 [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.

 [WARNING] In case H contains other non local terms, these are neglected

 Timing [Min/Max/Average]: 51m-38s/51m-38s/51m-38s

 [05] Optics
 ===========

 [SLK-Inversion]  Pools        :  1
 [SLK-Inversion]  BLACS grid   :   4   4

 [FFT-Rho] Mesh size:   81   44  104

 [xc] Functional : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 [xc] LIBXC used to calculate xc functional
  PP Number of Atomic Species                      :  3
  NLCC RL compoments                               :  1494439
 - S/N 000735 ---------------------------------------------- v.05.00.04 r.19598 -

 [WARNING] Fxc not coded for GGA. Using LDA part only of the functional

 [WARNING] Fxc not coded for GGA. Using LDA part only of the functional
 [RD./SAVE//ndb.dipoles]---------------------------------------------------------
  Brillouin Zone Q/K grids (IBZ/BZ)                :  1  1  1  1
  RL vectors                                       :  186763 [WF]
  Fragmentation                                    : yes
  Electronic Temperature                           :  300.1000 [K]
  Bosonic    Temperature                           :  300.1000 [K]
  DIP band range                                   :     1   800
  DIP band range limits                            :   572   573
  DIP e/h energy range                             : -1.000000 -1.000000 [eV]
  RL vectors in the sum                            :  186763
  [r,Vnl] included                                 : yes
  Bands ordered                                    : yes
  Direct v evaluation                              : no
  Approach used                                    : G-space v
  Dipoles computed                                 : R V P
  Wavefunctions                                    : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 - S/N 000735 ---------------------------------------------- v.05.00.04 r.19598 -
 [FFT-X] Mesh size:   81   44  104

 [X-CG] R(p) Tot o/o(of R):   19156   32604     100

 Timing [Min/Max/Average]: 13m-00s/13m-00s/13m-00s

 [06] Timing Overview
 ====================

 Clock: global (MAX - min (if any spread is present) clocks)
                       io_ATMPROJ_pwscf :      0.0004s P1 [MAX]      0.0000s P2 [min]
                             io_COL_CUT :      0.0009s P10 [MAX]      0.0000s P5 [min]
                           io_KB_abinit :      0.0004s P1 [MAX]      0.0000s P11 [min]
                                  io_HF :      0.0015s P12 [MAX]      0.0000s P6 [min]
                                   io_X :      0.0029s P10 (  4 calls,   0.726 msec avg) [MAX]      0.0001s P6 (  4 calls,   0.014 msec avg) [min]
                IO_and_Messaging_switch :      0.0001s P1 (  8 calls,   0.010 msec avg) [MAX]      0.0001s P8 (  8 calls,   0.010 msec avg) [min]
                           PP_uspp_init :      0.1378s P8 (  3 calls,  45.946 msec avg) [MAX]      0.0001s P13 (  3 calls,   0.034 msec avg) [min]
                                  io_BS :      0.0006s P10 [MAX]      0.0002s P9 [min]
                         io_Double_Grid :      0.0008s P12 [MAX]      0.0004s P16 [min]
                               io_QINDX :      0.0248s P10 (  2 calls,  12.376 msec avg) [MAX]      0.0149s P5 (  2 calls,   7.430 msec avg) [min]
                             io_DIPOLES :      0.0890s P1 (  6 calls,  14.827 msec avg) [MAX]      0.0446s P2 (  5 calls,   8.919 msec avg) [min]
                                io_GROT :      0.1238s P13 (  2 calls,  61.903 msec avg) [MAX]      0.0870s P7 (  2 calls,  43.493 msec avg) [min]
                            io_KB_pwscf :      0.1008s P7 (  3 calls,  33.612 msec avg) [MAX]      0.0899s P13 (  3 calls,  29.975 msec avg) [min]
                              FFT_setup :      0.1152s P10 (  2 calls,  57.585 msec avg) [MAX]      0.0928s P3 (  2 calls,  46.389 msec avg) [min]
                            io_fragment :      0.9927s P10 (  8 calls, 124.089 msec avg) [MAX]      0.1501s P9 (  7 calls,  21.437 msec avg) [min]
      MATRIX transfer (X_G_X_redux_2_1) :      1.5442s P13 (100 calls,   0.015 msec avg) [MAX]      0.1529s P2 (100 calls,   1.529 msec avg) [min]
                 MATRIX transfer (NONE) :      0.2501s P15 [MAX]      0.2349s P1 [min]
                    XC_potential_driver :      1.3267s P6 [MAX]      0.2734s P9 [min]
                             Xo (REDUX) :    150.3123s P16 [MAX]      0.4280s P3 [min]
      MATRIX transfer (X_G_X_redux_1_1) :      2.5124s P13 (100 calls,   0.025 sec avg) [MAX]      1.5884s P3 (100 calls,   0.016 sec avg) [min]
                        PARALLEL_M_by_M :      2.8910s P8 (100 calls,   0.029 sec avg) [MAX]      1.9608s P13 (100 calls,   0.020 sec avg) [min]
                              X (REDUX) :      2.0632s P13 [MAX]      2.0448s P1 [min]
                                  io_WF :      8.7860s P7 ( 12 calls,   0.732 sec avg) [MAX]      5.0032s P12 ( 12 calls,   0.417 sec avg) [min]
                            WF_load_FFT :     11.8459s P7 (  3 calls,   3.949 sec avg) [MAX]      7.9898s P12 (  3 calls,   2.663 sec avg) [min]
                    PARALLEL_lin_system :     15.7679s P4 (100 calls,   0.158 sec avg) [MAX]     15.3342s P13 (100 calls,   0.153 sec avg) [min]
                         LINEAR ALGEBRA :     15.7684s P4 (100 calls,   0.158 sec avg) [MAX]     15.3349s P13 (100 calls,   0.153 sec avg) [min]
                          X (procedure) :     68.5123s P3 [MAX]     20.7154s P15 [min]
                         eval_G_minus_G :     77.8107s P12 [MAX]     73.4818s P8 [min]
                         Xo (procedure) :      11m-10s P13 [MAX]    483.9968s P8 [min]
                      DIPOLE_transverse :      51m-37s P4 [MAX]      48m-31s P6 [min]
                                Dipoles :      51m-38s P1 [MAX]      51m-38s P16 [min]

 [07] Game Over & Game summary
 =============================

 03/25/2026 at 16:11 yambo @ f0153.nhr.fau.de [start]
 03/25/2026 at 17:16                          [end]

 Timing   [Min/Max/Average]: 01h-04m/01h-04m/01h-04m
             [Time-Profile]: 01h-04m

 .-ACKNOWLEDGMENT
 |
 | The users of YAMBO have little formal obligations with respect to
 | the YAMBO group (those specified in the GNU General Public
 | License, http://www.gnu.org/copyleft/gpl.txt). However, it is
 | common practice in the scientific literature, to acknowledge the
 | efforts of people that have made the research possible. In this
 | spirit, please find below the reference we kindly ask you to use
 | in order to acknowledge YAMBO
 |
 | Many-body perturbation theory calculations using the yambo code
 | D. Sangalli, A. Ferretti, H. Miranda, C. Attaccalite, I. Marri, E. Cannuccia, P. Melo,
 | M Marsili, F Paleari, A Marrazzo, G Prandini, P Bonfà, M O Atambo, F Affinito,
 | M Palummo, A Molina-Sánchez, C Hogan, M Grüning, D Varsano and A Marini.
 | J. Phys.: Condens. Matter 31, 325902 (2019).
 |
 | Yambo: An ab initio tool for excited state calculations
 | A. Marini, C. Hogan, M. Grüning, D. Varsano
 | Computer Physics Communications 180, 1392 (2009).
 |
  
 .-Input file  yambo.in_ALDA
 | optics                           # [R] Linear Response optical properties
 | chi                              # [R][CHI] Dyson equation for Chi.
 | tddft                            # [R][K] Use TDDFT kernel
 | ElecTemp= 0.025861         eV    # Electronic Temperature
 | BoseTemp= 0.025861         eV    # Bosonic Temperature
 | X_CPU= "4.2.2.1.1"               # [PARALLEL] CPUs for each role
 | X_ROLEs= "g.v.c.k.q"             # [PARALLEL] CPUs roles (q,g,k,c,v)
 | X_nCPU_LinAlg_INV= 16            # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
 | X_Threads= 18                    # [OPENMP/X] Number of threads for response functions
 | DIP_CPU= "4.4.1"                 # [PARALLEL] CPUs for each role
 | DIP_ROLEs= "v.c.k"               # [PARALLEL] CPUs roles (k,c,v)
 | DIP_Threads= 18                  # [OPENMP/X] Number of threads for dipoles
 | Chimod= "ALDA"                   # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
 | FxcGRLc= 3                 Ry    # [TDDFT] XC-kernel RL size
 | NGsBlkXd= 3                Ry    # [Xd] Response block size
 | % QpntsRXd
 |  1 | 1 |                             # [Xd] Transferred momenta
 | %
 | % BndsRnXd
 |     1 |  800 |                       # [Xd] Polarization function bands
 | %
 | GrFnTpXd= "R"                    # [Xd] Green`s function (T)ordered,(R)etarded,(r)senant,(a)ntiresonant [T, R, r, Ta, Ra]
 | % EnRngeXd
 |   0.00000 | 10.00000 |         eV    # [Xd] Energy range
 | %
 | % DmRngeXd
 |  0.100000 | 0.100000 |         eV    # [Xd] Damping range
 | %
 | ETStpsXd= 100                    # [Xd] Total Energy steps
 | % LongDrXd
 |  0.100000E-4 |  0.00000    |  0.00000    # [Xd] [cc] Electric Field
 | %
 | DipComputed= "R V P"             # [DIP] [default R P V; extra P2 Spin Orb]
r-optics file Yambo 5.3

Code: Select all

                                                                          
     __  __   ________   ___ __ __    _______   ______                    
    /_/\/_/\ /_______/\ /__//_//_/\ /_______/\ /_____/\                   
    \ \ \ \ \\::: _  \ \\::\| \| \ \\::: _  \ \\:::_ \ \                  
     \:\_\ \ \\::(_)  \ \\:.      \ \\::(_)  \/_\:\ \ \ \                 
      \::::_\/ \:: __  \ \\:.\-/\  \ \\::  _  \ \\:\ \ \ \                
        \::\ \  \:.\ \  \ \\. \  \  \ \\::(_)  \ \\:\_\ \ \               
         \__\/   \__\/\__\/ \__\/ \__\/ \_______\/ \_____\/               
                                                                          
                                                                          
    Version 5.3.0 Revision 23936 Hash (prev commit) 6e050e3697            
                         Branch is 5.3                                    
               MPI+OpenMP+SLK+HDF5_MPI_IO Build                           
                   http://www.yambo-code.eu                               
 
 04/17/2026 at 15:24 yambo @ f0101.nhr.fau.de
 ==================================================

 Cores-Threads       : 16(CPU)-18(threads)
 MPI Cores           :  16
 Threads per core    :  18
 Threads total       :  288
 Nodes Computing     :   4
 Nodes IO            :  1

 Fragmented WFs      : yes
 CORE databases      : .
 Additional I/O      : .
 Communications      : .
 Input file          : yambo.in_ALDA
 Report file         : ./r_optics_chi_tddft_03
 Verbose log/report  : no
 Log files           : ./LOG

 Precision           : SINGLE
  
 [RD./SAVE//ns.db1]--------------------------------------------------------------
  Bands                                            :   800
  K-points                                         :  1
  G-vectors                                        :  1494439 [RL space]
  Components                                       :  186763 [wavefunctions]
  Symmetries                                       :  2 [spatial]
  Spinor components                                :  1
  Spin polarizations                               :  1
  Temperature                                      :  0.025852 [eV]
  Electrons                                        :   1144.00   
  WF G-vectors                                     :  186763
  Max atoms/species                                :  224
  No. of atom species                              :  3
  Exact exchange fraction in XC                    :  0.000000
  Exact exchange screening in XC                   :  0.000000
  Magnetic symmetries                              : no
 - S/N 006477 ---------------------------------------------- v.05.03.00 r.23936 -

 [02] CORE Variables Setup
 =========================


  [02.01] Unit cells
  ==================

***removed, as do not wish to upload the structure on internet*** let me know if you need this

   

  [02.02] Symmetries
  ==================

  Inversion symmetry    : yes
  Spatial inversion     : yes
  Inversion index       :  2
  K-space Time-reversal : no
  Magnetic symmetries   : no
  Group table correct   : yes
  Symmetries units      :  [cc]

   [S 1]:   1.00000      0.00000     0.474319E-8   0.00000      1.00000      0.00000    -0.948637E-8   0.00000      1.00000   
   [S 2]:  -1.00000      0.00000    -0.474319E-8   0.00000     -1.00000      0.00000     0.948637E-8   0.00000     -1.00000   

  [02.03] Reciprocal space
  ========================

  nG shells         :  262122
  nG charge         :  1494439
  nG WFs            :  186763
  nC WFs            :  186763
  G-vecs. in first 80 shells:  [ Number ]
    1   3   5   7   9  11  13  15  17
    19   23   25   29   33   35   39   41   43
    47   49   53   57   59   63   65   69   71
    75   77   81   83   87   91   93   95   97
    99  103  107  109  113  115  117  121  125
   127  129  133  137  141  143  147  151  155
   159  163  167  171  175  177  179  181  185
   187  189  193  195  199  201  205  207  209
   211  215  219  223  225  229  231  235
  ...
  Shell energy in first 80 shells:  [ mHa ]
    0.00000   9.80940  15.51580  21.61848  29.03190  39.23758  47.33998  52.81564  62.06318
   62.16679  62.62503  64.45917  68.33143  74.43412  79.28600  81.84754  86.47394  88.28455
    92.0532   92.6803  100.1556  114.8788  114.9205  114.9824  116.1276  117.2748  128.1075
   132.1016  138.3315  139.2896  139.6422  141.1002  145.4959  156.6395  156.9503  157.6393
   160.5717  167.7361  168.9432  172.5880  180.9232  187.2930  189.3599  191.1471  192.4578
   194.5664  201.1200  209.4551  209.7660  210.4550  211.2625  213.3873  221.0719  225.4036
   226.7783  232.8810  240.1086  240.2944  242.1756  242.2172  243.2354  245.2349  247.3820
   248.2527  248.6671  250.5001  252.1120  253.9356  257.8367  258.6025  261.2870  270.2311
   272.8889  273.3257  273.4293  275.7217  279.2843  290.5486  292.0569  295.0328
  ...

  [02.04] K-grid lattice
  ======================

  Compatible Grid is   : 0D
  K lattice UC volume  :  0.007928 [a.u.]

  [02.05] Energies & Occupations
  ==============================

  [X] === General ===
  [X] Electronic Temperature                        :  0.258606E-1   300.100    [eV K]
  [X] Bosonic    Temperature                        :  0.258606E-1   300.100    [eV K]
  [X] Finite Temperature mode                       : yes
  [X] El. density                                   :  0.24675E+24 [cm-3]
  [X] Fermi Level                                   :  1.165298 [eV]

  [X] === Gaps and Widths ===
  [X] Conduction Band Min                           :  0.698940 [eV]
  [X] Valence Band Max                              : -0.699258 [eV]
  [X] Filled Bands                                  :   572
  [X] Empty Bands                                   :   573   800
  [X] Direct Gap                                    :  1.398198 [eV]
  [X] Direct Gap localized at k                     :  1
   
   

 [03] Transferred momenta grid and indexing
 ==========================================

 [RD./SAVE//ndb.kindx]-----------------------------------------------------------
  Fragmentation                                    : no
  Polarization last K ( bz)                        :  1
  Polarization last K (ibz)                        :  1
  QP states                                        :  1  1
  X grid is uniform                                : yes
  Grids (string)                                   :  X S
  Grids (int-vector)                               :  1  0  0  1
 - S/N 006477 ---------------------------------------------- v.05.03.00 r.23936 -

 IBZ Q-points                                      :  1
 BZ  Q-points                                      :  1

 K/Q-points units:
 rlu = crystal or reduced units; cc = cartesian coordinates; iku = interal k-units

 Q [1]          [rlu]:  0.000000  0.000000  0.000000

 [04] Dipoles
 ============


  [04.01] Setup: observables and procedures
  =========================================

  [RD./SAVE//ns.kb_pp_pwscf]------------------------------------------------------
   Fragmentation                                    : yes
  - S/N 006477 ---------------------------------------------- v.05.03.00 r.23936 -

  [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
  [WF-Oscillators/G space/Transverse up loader] Normalization (few states)  min/max  :  0.91027E-10   1.0000    

  [WR./SAVE//ndb.dipoles]---------------------------------------------------------
   Brillouin Zone Q/K grids (IBZ/BZ)                :  1  1  1  1
   RL vectors                                       :  186763 [WF]
   Fragmentation                                    : yes
   Electronic Temperature                           :  300.1000 [K]
   Bosonic    Temperature                           :  300.1000 [K]
   DIP band range                                   :     1   800
   DIP band range limits                            :   572   573
   DIP e/h energy range                             : -1.000000 -1.000000 [eV]
   RL vectors in the sum                            :  186763
   [r,Vnl] included                                 : yes
   Bands ordered                                    : yes
   Direct v evaluation                              : no
   Approach used                                    : G-space v
   Dipoles computed                                 : R V P [G-space]
   Wavefunctions                                    : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
  - S/N 006477 ---------------------------------------------- v.05.03.00 r.23936 -

  [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.

  [WARNING] In case H contains other non local terms, these are neglected

 Timing [Min/Max/Average]: 50s/50s/50s

 [05] Optics
 ===========

 [SLK-Inversion]  Pools        :   4
 [SLK-Inversion]  BLACS grid   :  2  2

 [xc] Functional : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 [xc] LIBXC used to calculate xc functional
  PP Number of Atomic Species                      :  3
  NLCC RL compoments                               :  1494439
 - S/N 006477 ---------------------------------------------- v.05.03.00 r.23936 -

Yambo 5.4 r-optics file

Code: Select all

                                                                          
     __  __   ________   ___ __ __    _______   ______                    
    /_/\/_/\ /_______/\ /__//_//_/\ /_______/\ /_____/\                   
    \ \ \ \ \\::: _  \ \\::\| \| \ \\::: _  \ \\:::_ \ \                  
     \:\_\ \ \\::(_)  \ \\:.      \ \\::(_)  \/_\:\ \ \ \                 
      \::::_\/ \:: __  \ \\:.\-/\  \ \\::  _  \ \\:\ \ \ \                
        \::\ \  \:.\ \  \ \\. \  \  \ \\::(_)  \ \\:\_\ \ \               
         \__\/   \__\/\__\/ \__\/ \__\/ \_______\/ \_____\/               
                                                                          
                                                                          
    Version 5.4.0 Revision 24143 Hash (prev commit) 77ed66f02             
                         Branch is 5.4                                    
               MPI+OpenMP+SLK+HDF5_MPI_IO Build                           
                   http://www.yambo-code.eu                               
 
 04/17/2026 at 15:35 yambo @ f0220.nhr.fau.de
 ==================================================

 Cores-Threads       : 16(CPU)-18(threads)
 MPI Cores           :  16
 Threads per core    :  18
 Threads total       :  288
 Nodes Computing     :   4
 Nodes IO            :  1

 Fragmented WFs      : yes
 CORE databases      : .
 Additional I/O      : .
 Communications      : .
 Input file          : yambo.in_ALDA
 Report file         : ./r_optics_chi_tddft_04
 Verbose log/report  : no
 Log files           : ./LOG

 Precision           : SINGLE
  
 [RD./SAVE//ns.db1]--------------------------------------------------------------
  Bands                                            :   800
  K-points                                         :  1
  G-vectors                                        :  1494439 [RL space]
  Components                                       :  186763 [wavefunctions]
  Symmetries                                       :  2 [spatial]
  Spinor components                                :  1
  Spin polarizations                               :  1
  Temperature                                      :  0.025852 [eV]
  Electrons                                        :   1144.00   
  WF G-vectors                                     :  186763
  Max atoms/species                                :  224
  No. of atom species                              :  3
  Exact exchange fraction in XC                    :  0.000000
  Exact exchange screening in XC                   :  0.000000
  Magnetic symmetries                              : no
 - S/N 009529 ---------------------------------------------- v.05.04.00 r.24143 -

 [02] CORE Variables Setup
 =========================

***removed, as do not wish to upload the structure on internet*** let me know if you need this

  [02.02] Symmetries
  ==================

  Inversion symmetry    : yes
  Spatial inversion     : yes
  Inversion index       :  2
  K-space Time-reversal : no
  Magnetic symmetries   : no
  Group table correct   : yes
  Symmetries units      :  [cc]

   [S 1]:   1.00000      0.00000     0.474319E-8   0.00000      1.00000      0.00000    -0.948637E-8   0.00000      1.00000   
   [S 2]:  -1.00000      0.00000    -0.474319E-8   0.00000     -1.00000      0.00000     0.948637E-8   0.00000     -1.00000   

  [02.03] Reciprocal space
  ========================

  nG shells         :  262122
  nG charge         :  1494439
  nG WFs            :  186763
  nC WFs            :  186763
  G-vecs. in first 80 shells:  [ Number ]
    1   3   5   7   9  11  13  15  17
    19   23   25   29   33   35   39   41   43
    47   49   53   57   59   63   65   69   71
    75   77   81   83   87   91   93   95   97
    99  103  107  109  113  115  117  121  125
   127  129  133  137  141  143  147  151  155
   159  163  167  171  175  177  179  181  185
   187  189  193  195  199  201  205  207  209
   211  215  219  223  225  229  231  235
  ...
  Shell energy in first 80 shells:  [ mHa ]
    0.00000   9.80940  15.51580  21.61848  29.03190  39.23758  47.33998  52.81564  62.06318
   62.16679  62.62503  64.45917  68.33143  74.43412  79.28600  81.84754  86.47394  88.28455
    92.0532   92.6803  100.1556  114.8788  114.9205  114.9824  116.1276  117.2748  128.1075
   132.1016  138.3315  139.2896  139.6422  141.1002  145.4959  156.6395  156.9503  157.6393
   160.5717  167.7361  168.9432  172.5880  180.9232  187.2930  189.3599  191.1471  192.4578
   194.5664  201.1200  209.4551  209.7660  210.4550  211.2625  213.3873  221.0719  225.4036
   226.7783  232.8810  240.1086  240.2944  242.1756  242.2172  243.2354  245.2349  247.3820
   248.2527  248.6671  250.5001  252.1120  253.9356  257.8367  258.6025  261.2870  270.2311
   272.8889  273.3257  273.4293  275.7217  279.2843  290.5486  292.0569  295.0328
  ...

  [02.04] K-grid lattice
  ======================

  Compatible Grid is   : 0D
  K lattice UC volume  :  0.007928 [a.u.]

  [02.05] Energies & Occupations
  ==============================

  [X] === General ===
  [X] Electronic Temperature                        :  0.258606E-1   300.100    [eV K]
  [X] Bosonic    Temperature                        :  0.258606E-1   300.100    [eV K]
  [X] Finite Temperature mode                       : yes
  [X] El. density                                   :  0.24675E+24 [cm-3]
  [X] Fermi Level                                   :  1.165298 [eV]

  [X] === Gaps and Widths ===
  [X] Conduction Band Min                           :  0.698940 [eV]
  [X] Valence Band Max                              : -0.699258 [eV]
  [X] Filled Bands                                  :   572
  [X] Empty Bands                                   :   573   800
  [X] Direct Gap                                    :  1.398198 [eV]
  [X] Direct Gap localized at k                     :  1
   
   

 [03] Transferred momenta grid and indexing
 ==========================================

 [RD./SAVE//ndb.kindx]-----------------------------------------------------------
  Fragmentation                                    : no
  Polarization last K ( bz)                        :  1
  Polarization last K (ibz)                        :  1
  QP states                                        :  1  1
  X grid is uniform                                : yes
  Grids (string)                                   :  X S
  Grids (int-vector)                               :  1  0  0  1
 - S/N 009529 ---------------------------------------------- v.05.04.00 r.24143 -

 IBZ Q-points                                      :  1
 BZ  Q-points                                      :  1

 K/Q-points units:
 rlu = crystal or reduced units; cc = cartesian coordinates; iku = interal k-units

 Q [1]          [rlu]:  0.000000  0.000000  0.000000

 [04] Dipoles
 ============


  [04.01] Setup: observables and procedures
  =========================================

  [RD./SAVE//ns.kb_pp_pwscf]------------------------------------------------------
   Fragmentation                                    : yes
  - S/N 009529 ---------------------------------------------- v.05.04.00 r.24143 -

  [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
  [WF-Oscillators/G space/Transverse up loader] Normalization (few states)  min/max  :  0.91027E-10   1.0000    

  [WR./SAVE//ndb.dipoles]---------------------------------------------------------
   Brillouin Zone Q/K grids (IBZ/BZ)                :  1  1  1  1
   RL vectors                                       :  186763 [WF]
   Fragmentation                                    : yes
   Electronic Temperature                           :  300.1000 [K]
   Bosonic    Temperature                           :  300.1000 [K]
   DIP band range                                   :     1   800
   DIP band range limits                            :   572   573
   DIP e/h energy range                             : -1.000000 -1.000000 [eV]
   RL vectors in the sum                            :  186763
   [r,Vnl] included                                 : yes
   Bands ordered                                    : yes
   Direct v evaluation                              : no
   Approach used                                    : G-space v
   Dipoles computed                                 : R V P [G-space]
   Wavefunctions                                    : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
  - S/N 009529 ---------------------------------------------- v.05.04.00 r.24143 -

  [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.

  [WARNING] In case H contains other non local terms, these are neglected

 Timing [Min/Max/Average]: 55s/55s/55s

 [05] Optics
 ===========

 [SLK-Inversion]  Pools        :   4
 [SLK-Inversion]  BLACS grid   :  2  2

 [xc] Functional : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 [xc] LIBXC used to calculate xc functional
  PP Number of Atomic Species                      :  3
  NLCC RL compoments                               :  1494439
 - S/N 009529 ---------------------------------------------- v.05.04.00 r.24143 -

Thanks a lot.

--
Best regards,
Vipul
Vipul Kumar Ambasta
MSc. student
Friedrich Alexander Universitaet
Erlangen (Germany)
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User avatar
Davide Sangalli
Posts: 680
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Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
Contact:
Contact Davide Sangalli

Re: Segmentation fault Yambo 5.2/5,3 [CPU]

Post by Davide Sangalli » Fri Apr 17, 2026 6:01 pm

Ok, from the reports and the log, I'd say the reason is the different default parallelization, which in turn requires more memory

Please add to your input file

Code: Select all

X_CPU= "4.2.2.1.1"               # [PARALLEL] CPUs for each role
X_ROLEs= "g.v.c.k.q"             # [PARALLEL] CPUs roles (q,g,k,c,v)
X_nCPU_LinAlg_INV= 16            # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)

Note, you are running on 16 MPI tasks and 18 threads, for a total of 288 cores. Is this wanted?
I'd say this is not very efficient

To control the number of threads you can set

Code: Select all

export OMP_NUM_THREADS=1
(or any other number of threads you like, in your submission script.

Best,
D.
Davide Sangalli, PhD
Piazza Leonardo Da Vinci, 32, 20133 – Milano
CNR, Istituto di Struttura della Materia (ISM)
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/
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harrier_class
Posts: 7
Joined: Tue May 13, 2025 4:27 pm

Re: Segmentation fault Yambo 5.2/5,3 [CPU]

Post by harrier_class » Mon Apr 20, 2026 1:37 pm

Dear Davide,

Thanks for your prompt reply.

I tried your suggestions. Unfortunately, I get the same error.

Please find the LOG file attached: [run on Yambo 5.4]

Code: Select all

  
 __   __  _______  __   __  _______  _______
|  | |  ||   _   ||  |_|  ||  _    ||       |
|  |_|  ||  |_|  ||       || |_|   ||   _   |
|       ||       ||       ||       ||  | |  |
|_     _||       ||       ||  _   | |  |_|  |
  |   |  |   _   || ||_|| || |_|   ||       |
  |___|  |__| |__||_|   |_||_______||_______|


 <---> P1: [01] MPI/OPENMP structure, Files & I/O Directories
 <---> P1-f0147.nhr.fau.de: MPI Cores-Threads   : 288(CPU)-1(threads)
 <---> P1-f0147.nhr.fau.de: MPI Cores-Threads   : X(environment)-4.2.2.1.1(CPUs)-g.v.c.k.q(ROLEs)
 <---> P1-f0147.nhr.fau.de: [02] CORE Variables Setup
 <---> P1-f0147.nhr.fau.de: [02.01] Unit cells
 <02s> P1-f0147.nhr.fau.de: [02.02] Symmetries
 <02s> P1-f0147.nhr.fau.de: [02.03] Reciprocal space
 <02s> P1-f0147.nhr.fau.de: [02.04] K-grid lattice
 <02s> P1-f0147.nhr.fau.de: [02.05] Energies & Occupations
 <02s> P1-f0147.nhr.fau.de: [03] Transferred momenta grid and indexing
 <02s> P1-f0147.nhr.fau.de: [04] Dipoles
 <02s> P1-f0147.nhr.fau.de: [04.01] Setup: observables and procedures
 <02s> P1-f0147.nhr.fau.de: [PARALLEL DIPOLES for K(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <02s> P1-f0147.nhr.fau.de: [PARALLEL DIPOLES for CON bands on 12 CPU] Loaded/Total (Percentual):19/228(8%)
 <02s> P1-f0147.nhr.fau.de: [PARALLEL DIPOLES for VAL bands on 24 CPU] Loaded/Total (Percentual):24/572(4%)
 <02s> P1-f0147.nhr.fau.de: [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.
 <02s> P1-f0147.nhr.fau.de: [WARNING] In case H contains other non local terms, these are neglected
 <02s> P1-f0147.nhr.fau.de: [05] Optics
 <02s> P1-f0147.nhr.fau.de: [PARALLEL Response_G_space for K(bz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <02s> P1-f0147.nhr.fau.de: [PARALLEL Response_G_space for Q(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <02s> P1-f0147.nhr.fau.de: [PARALLEL Response_G_space for G-vectors on 6 CPU]
 <02s> P1-f0147.nhr.fau.de: [PARALLEL Response_G_space for K-q(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <02s> P1-f0147.nhr.fau.de: [LA@Response_G_space] PARALLEL linear algebra uses a 4x4 SLK grid (16 cpu)
 <02s> P1-f0147.nhr.fau.de: [PARALLEL Response_G_space for K(ibz) on 1 CPU] Loaded/Total (Percentual):1/1(100%)
 <02s> P1-f0147.nhr.fau.de: [PARALLEL Response_G_space for CON bands on 12 CPU] Loaded/Total (Percentual):19/228(8%)
 <02s> P1-f0147.nhr.fau.de: [PARALLEL Response_G_space for VAL bands on 4 CPU] Loaded/Total (Percentual):143/572(25%)
 <03s> P1-f0147.nhr.fau.de: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):143/572(25%)
 <03s> P1-f0147.nhr.fau.de: [MEMORY] Alloc WF%c( 414.0920 [Mb]) TOTAL:  498.7310 [Mb] (traced)  60.88400 [Mb] (memstat)
 <03s> P1-f0147.nhr.fau.de: [FFT-Rho] Mesh size:   81   44  104
 <03s> P1-f0147.nhr.fau.de: [MEMORY] Alloc wf_disk( 208.6490 [Mb]) TOTAL:  713.1740 [Mb] (traced)  60.88400 [Mb] (memstat)
 <06s> P1-f0147.nhr.fau.de: [MEMORY]  Free wf_disk( 208.6490 [Mb]) TOTAL:  504.5250 [Mb] (traced)  60.88400 [Mb] (memstat)
 <26s> P1-f0147.nhr.fau.de: [xc] Functional : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 <26s> P1-f0147.nhr.fau.de: [xc] LIBXC used to calculate xc functional
About the OMP_NUM_THREADS, yes first I tried with less OMP paralleziation, however, despite beiong slow, I had to go with higher values of OMP_NUM_THREASDS, just because otherwise it goes OOM very quickly.

However, now, I again I tried with OMP_NUM_THREADS =1, and I get the same error. Can you help me debug it?


--
Best regards,
Vipul
Vipul Kumar Ambasta
MSc. student
Friedrich Alexander Universitaet
Erlangen (Germany)
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User avatar
Davide Sangalli
Posts: 680
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Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
Contact:
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Re: Segmentation fault Yambo 5.2/5,3 [CPU]

Post by Davide Sangalli » Mon Apr 20, 2026 10:40 pm

Just to be sure. In the last log you both set the parallelization, and change the number of threads.

I'd first just change the parallelization, and then eventually the number of threads.

Best,
D.
Davide Sangalli, PhD
Piazza Leonardo Da Vinci, 32, 20133 – Milano
CNR, Istituto di Struttura della Materia (ISM)
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/
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harrier_class
Posts: 7
Joined: Tue May 13, 2025 4:27 pm

Re: Segmentation fault Yambo 5.2/5,3 [CPU]

Post by harrier_class » Wed Apr 22, 2026 12:13 pm

Dear Davide,

Thanks for your prompt reply. Yes, I did in the same was as you suggested: first changing only the parallelization and then both parallelization and number of threads. I get the same error.

--
Best regards,
Vipul
Vipul Kumar Ambasta
MSc. student
Friedrich Alexander Universitaet
Erlangen (Germany)
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