error for Optics: STOP signal received while in :[04] Optics

[damao4361556]

Deat YAMBO developer,

I came across a error with the usage of yambo.

I install YAMBO-4.2. Follow the tutorials for hBN,

Code: Select all

yambo
yambo -F yambo.in_IP -J Full -o c
yambo -F yambo.in_IP -J Full

but receive the error;

Code: Select all

 <---> [01] CPU structure, Files & I/O Directories
 <---> CPU-Threads:1(CPU)-24(threads)
 <---> [02] CORE Variables Setup
 <---> [02.01] Unit cells
 <---> [02.02] Symmetries
 <---> [02.03] RL shells
 <---> [02.04] K-grid lattice
 <---> [02.05] Energies [ev] & Occupations
 <---> [03] Transferred momenta grid
 <---> [04] Optics
 <---> [LA] SERIAL linear algebra
 <---> [DIP] Checking dipoles header
 <---> [X-CG] R(p) Tot o/o(of R)  :   5499   52992     100
 <---> Xo@q[1] |                                        | [000%] --(E) --(X)

[ERROR] STOP signal received while in :[04] Optics
[ERROR]Allocation of ggw%rhotw failed

the report and log files are attached.
Could anyone tell me what's the problems?

thanks

[Daniele Varsano]

Dear Eric,
can you please also post the input file of your calculation?

Best,
Daniele

[damao4361556]

Dear Eric,
can you please also post the input file of your calculation?

Hi Daniele

here it is:
&control
calculation='scf',
prefix='hBN',
restart_mode='from_scratch'
pseudo_dir = './Pseudos'
wf_collect=.true.
nstep = 200
verbosity = 'high'
/
&system
ibrav = 4,
celldm(1) = 4.716
celldm(3) = 2.582
nat= 4,
ntyp= 2,
force_symmorphic=.true.
ecutwfc = 40,
/
&electrons
electron_maxstep = 100
conv_thr = 1.0e-8
/
ATOMIC_SPECIES
B 10 B.pz-vbc.UPF
N 14 N.pz-vbc.UPF
ATOMIC_POSITIONS {crystal}
B 0.6666667 0.3333333 0.0000000
N -0.6666667 -0.3333333 0.0000000
B -0.6666667 -0.3333333 0.5000000
N 0.6666667 0.3333333 0.5000000
K_POINTS {automatic}
6 6 2 1 1 1

&control
calculation='nscf',
prefix='hBN',
pseudo_dir = './Pseudos'
nstep = 200
verbosity = 'high'
wf_collect=.true.
/
&system
ibrav = 4,
celldm(1) = 4.716
celldm(3) = 2.582
nat= 4,
ntyp= 2,
force_symmorphic=.true.
ecutwfc = 40,nbnd = 100
/
&electrons
diago_thr_init=5.0e-6,
diago_full_acc=.true.
electron_maxstep = 100,
diagonalization='david'
mixing_mode = 'plain'
mixing_beta = 0.6
conv_thr = 1.0e-8
/
ATOMIC_SPECIES
B 10 B.pz-vbc.UPF
N 14 N.pz-vbc.UPF
ATOMIC_POSITIONS {crystal}
B 0.6666667 0.3333333 0.0000000
N -0.6666667 -0.3333333 0.0000000
B -0.6666667 -0.3333333 0.5000000
N 0.6666667 0.3333333 0.5000000
K_POINTS {automatic}
6 6 2 0 0 0

thanks

[Daniele Varsano]

Dear Eric,
I was meaning your Yambo input file (yambo.in_IP).

Daniele

[damao4361556]

Dear Eric,
I was meaning your Yambo input file (yambo.in_IP).

Dear Daniele,

here it is, thanks for helps.

Code: Select all

optics                         # [R OPT] Optics
chi                            # [R CHI] Dyson equation for Chi.
X_Threads=0                    # [OPENMP/X] Number of threads for response functions
DIP_Threads=0                  # [OPENMP/X] Number of threads for dipoles
Chimod= "IP"                   # [X] IP/Hartree/ALDA/LRC/BSfxc
NGsBlkXd= 1            RL      # [Xd] Response block size
% QpntsRXd
 1 | 1 |                       # [Xd] Transferred momenta
%
% BndsRnXd
   1 | 100 |                   # [Xd] Polarization function bands
%
% EnRngeXd
  0.00000 | 10.00000 | eV      # [Xd] Energy range
%
% DmRngeXd
  0.10000 |  0.10000 | eV      # [Xd] Damping range
%
ETStpsXd= 1001                 # [Xd] Total Energy steps
% LongDrXd
 1.000000 | 0.000000 | 0.000000 |        # [Xd] [cc] Electric Field
%

[Daniele Varsano]

Dear Eric,
I can't find anything wrong in your input file. The only thing I can see is that you are using dipoles databases calculated in a previous run, which is totally fine but maybe you calculated for many G vectors and now it is causing some problem in allocation? This is just a speculation.
Can you try to remove your ndb.dipoles database from the SAVE directory, run your input and report again?
When doing so can you run by using a single thread?
X_Threads=1 # [OPENMP/X] Number of threads for response functions
DIP_Threads=1

and
export OMP_NUM_THREADS=1
in your launch script or just type it if you are running in interactive.

Best,
Daniele

[damao4361556]

Hi Daniele,

There is ndb.dip_iR_and_P type file, not sure this is what you mean ndb.dipoles. I remove ndb.dip_iR_and_P type files, also with the same error

I also try your suggestions, change the following line in the input and do export OMP_NUM_THREADS=1 in the terminal
X_Threads=1 # [OPENMP/X] Number of threads for response functions
DIP_Threads=1

But still with the error:
[ERROR] STOP signal received while in :[04] Optics
[ERROR]Allocation of ggw%rhotw failed

here is the input:

Code: Select all

optics                         # [R OPT] Optics
chi                            # [R CHI] Dyson equation for Chi.
X_Threads= 1                   # [OPENMP/X] Number of threads for response functions
DIP_Threads= 1                 # [OPENMP/X] Number of threads for dipoles
Chimod= "IP"                   # [X] IP/Hartree/ALDA/LRC/BSfxc
NGsBlkXd= 1            RL      # [Xd] Response block size
% QpntsRXd
 1 | 1 |                       # [Xd] Transferred momenta
%
% BndsRnXd
   1 | 100 |                   # [Xd] Polarization function bands
%
% EnRngeXd
  0.00000 | 10.00000 | eV      # [Xd] Energy range
%
% DmRngeXd
  0.10000 |  0.10000 | eV      # [Xd] Damping range
%
ETStpsXd= 1001                 # [Xd] Total Energy steps
% LongDrXd
 1.000000 | 0.000000 | 0.000000 |        # [Xd] [cc] Electric Field
%

The report and log files are attached.

Any ideas?

thanks

[Daniele Varsano]

Dear Eric,

we ran your input and we were not able to reproduce your problem. Everything went fine, so I do not have many suggestions to spot the problem.
You could recompile from scratch the code (after a make clean_all) adding --enable-memory-profile in the configure in order to monitor the memory required, which should be very small in your example and then check if you have some memory limit in your system (ulimit -a). At the moment I do not have further suggestions.
If you want you can also upload your config.log as we can have a look if there is something uncommon in the compilation.
Best,
Daniele

[damao4361556]

Hi Daniele,

I am thinking if it is related to the installation.
here is the command for configure, the config.log is also attached, could you please have a look at it?

Code: Select all

./configure FC=ifort F77=ifort PFC=mpif90 CC=icc \
--enable-momory-profile \
--enable-iotk --enable-netcdf --enable-time-profile \
--with-blas-libs="-L/opt/intel/composer_xe_2013.2.146/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core \
--with-netcdf-lib="-L/home/weili/soft/yambo/netcid-work/lib" --with-netcdf-include="/home/weili/soft/yambo/netcid-work/include" \
--with-blacs-libs="-L/opt/intel/composer_xe_2013.2.146/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_blacs_openmpi_lp64" \
--with-fftw-lib="-L/opt/intel/composer_xe_2013.2.146/mkl/interfaces/fftw3xf" \
--with-scalapack-libs="-L/opt/intel/composer_xe_2013.2.146/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_scalapack_lp64" \
--with-p2y-version=5.1 \
--with-iotk-path=/home/weili/soft/espresso-5.1.1/espresso-5.1.1/bin/iotk

thanks

[Daniele Varsano]

Dear Eric,
I'm not sure this is related to your problem but, please note your mpif90 comp is pointing to a gfortran compiler while you are using intel for the other compilers, it looks that finally, you ended up
to a serial compilation.
Moreover, some of the libraries you linked looks they have problems to be linked. This is not finally a problem as yambo download and recompiles them. Other options you used are obsolete.
Maybe you can try to recompile just by typing a simple
./configure
or you can specify your favorite compilers paying attention they are all Intel or gnu.

Best,
Daniele