Segm fault when running HF_corrections for Si.

Concerns issues with computing quasiparticle corrections to the DFT eigenvalues - i.e., the self-energy within the GW approximation (-g n), or considering the Hartree-Fock exchange only (-x)

Moderators: Daniele Varsano, andrea.ferretti, andrea marini, myrta gruning

Segm fault when running HF_corrections for Si.

Postby plasmon » Thu Aug 23, 2018 9:47 am

Dear Yambo users,

I am trying to calculate the G0W0 calculations for Si which is an example downloaded from YAMBO website.
1)QE part
cat >scf.in<<EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Si',
outdir='./'
pseudo_dir= './',
wf_collect=.true.,
verbosity ='high',
/&end
&system
ibrav=2,
celldm(1)=10.183,
nat=2,
ntyp=1,
ecutwfc=15.0,
force_symmorphic= .true.,
nbnd=10,
/&end
&electrons
diago_full_acc=.true.,
conv_thr = 1.0d-8
/&end
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS (automatic)
4 4 4 1 1 1
EOF

cat >nsfc.in<<EOF
&control
calculation='nscf',
prefix='Si',
outdir='./'
pseudo_dir= './',
wf_collect=.true.,
verbosity ='high',
/&end
&system
ibrav=2,
celldm(1)=10.183,
nat=2,
ntyp=1,
ecutwfc=15.0,
nbnd=50,
force_symmorphic= .true.,
/&end
&electrons
diago_thr_init = 1.0d-5
/&end
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS (automatic)
12 12 12 0 0 0
EOF

2)yambo part
cat >init<<EOF
setup # [R INI] Initialization
MaxGvecs= 1200 RL # [INI] Max number of G-vectors planned to use
EOF

cat >HF_corrections<<EOF
HF_and_locXC # [R XX] Hartree-Fock Self-energy and Vxc
EXXRLvcs= 15 Ry # [XX] Exchange RL components
%QPkrange # [GW] QP generalized Kpoint/Band indices
1| 3| 1| 15|
%
%QPerange # [GW] QP generalized Kpoint/Energy indices
1| 3| 0.0|-1.0|
EOF


3)results

I run succcessfully at the init step, but failed in the HF_corrections step, with the error information,


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


<---> [01] CPU structure, Files & I/O Directories
<---> [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] Bare local and non-local Exchange-Correlation
<---> [WF] Performing Wave-Functions I/O from ./SAVE
<---> [FFT-HF/Rho] Mesh size: 14 14 14[admin:21302] *** Process received signal ***
[admin:21302] Signal: Segmentation fault (11)
[admin:21302] Signal code: (128)
[admin:21302] Failing at address: (nil)
[admin:21302] [ 0] /lib64/libpthread.so.0[0x370b60f7e0]
[admin:21302] [ 1] /usr/lib64/libblas.so.3(cdotc_+0x68)[0x2b23b6b5b508]
[admin:21302] [ 2] yambo[0x5f020f]
[admin:21302] [ 3] yambo[0x4fed6a]
[admin:21302] [ 4] yambo[0x478fb8]
[admin:21302] [ 5] yambo[0x47614b]
[admin:21302] [ 6] yambo[0x40cdf3]
[admin:21302] [ 7] yambo[0x407fdd]
[admin:21302] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd)[0x370ae1ed1d]
[admin:21302] [ 9] yambo[0x406df9]
[admin:21302] *** End of error message ***
Segmentation fault (core dumped)


Could you please tell me how to resolve this problem? Thank you!

Hao Zhang
-------------
Dr. Hao Zhang
Fudan University, Shanghai, China
http://homepage.fudan.edu.cn/zhanghao/
Dr. Hao Zhang
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/
plasmon
 
Posts: 7
Joined: Thu Aug 23, 2018 9:18 am
Location: Fudan University, Shanghai, China

Re: Segm fault when running HF_corrections for Si.

Postby Daniele Varsano » Fri Aug 24, 2018 9:27 am

Dear Hao,
thanks for filling your sgnature.
As I already suggested in the other post,
try to recompile yambo adding the following option in the configure:
./configure --enable-int-linalg --other_options

to see if there is some incompatibility in the linear algebra libraries you are linking.
If the problem persists, please post here your config.log file.

Remember to do a
make clean_all
before recompiling,


Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm


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