Segmentation fault on sigma.cplx.x

nelsyeung's picture
Submitted by nelsyeung on Fri, 11/03/2017 - 08:32

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Dear all,

I'm getting segmentation fault when running sigma.cplx.x.
The system is MoS2 monolayer (3 atoms).
Below are the files kgrid.in, epsilon.inp, sigma.inp and sigma.out.
The sigma.out file is produced with debug mode (i.e., compiled with DEBUGFLAG = -DDEBUG -DVERBOSE).
Version: BerkeleyGW branch 1.2.x revision 7090

kgrid.in
---------------------------------------------------------------
12 12 1
0.0 0.0 0.0
0.0 0.0 0.0

3.169000000 0.000000000 0.000000000
-1.584500000 2.744434504 0.000000000
0.000000000 0.000000000 20.000000000
3
1 1.5845 0.9148 3.0810
2 0.0000 1.8296 1.5158
2 0.0000 1.8296 4.6461
32 32 216
.false.
---------------------------------------------------------------kgrid.in

epsilon.inp
---------------------------------------------------------------
number_bands 299
epsilon_cutoff 35.0
cell_slab_truncation

begin qpoints
0.001 0.0 0.0 1.0 1
0.000000000 0.083333333 0.000000000 1.0 0
0.000000000 0.166666667 0.000000000 1.0 0
0.000000000 0.250000000 0.000000000 1.0 0
0.000000000 0.333333333 0.000000000 1.0 0
0.000000000 0.416666667 0.000000000 1.0 0
0.000000000 0.500000000 0.000000000 1.0 0
0.000000000 0.583333333 0.000000000 1.0 0
0.000000000 0.666666667 0.000000000 1.0 0
0.000000000 0.750000000 0.000000000 1.0 0
0.000000000 0.833333333 0.000000000 1.0 0
0.000000000 0.916666667 0.000000000 1.0 0
0.083333333 0.083333333 0.000000000 1.0 0
0.083333333 0.166666667 0.000000000 1.0 0
0.083333333 0.250000000 0.000000000 1.0 0
0.083333333 0.333333333 0.000000000 1.0 0
0.083333333 0.416666667 0.000000000 1.0 0
0.083333333 0.500000000 0.000000000 1.0 0
0.083333333 0.583333333 0.000000000 1.0 0
0.083333333 0.666666667 0.000000000 1.0 0
0.083333333 0.750000000 0.000000000 1.0 0
0.166666667 0.166666667 0.000000000 1.0 0
0.166666667 0.250000000 0.000000000 1.0 0
0.166666667 0.333333333 0.000000000 1.0 0
0.166666667 0.416666667 0.000000000 1.0 0
0.166666667 0.500000000 0.000000000 1.0 0
0.166666667 0.583333333 0.000000000 1.0 0
0.250000000 0.250000000 0.000000000 1.0 0
0.250000000 0.333333333 0.000000000 1.0 0
0.250000000 0.416666667 0.000000000 1.0 0
0.333333333 0.333333333 0.000000000 1.0 0
end
---------------------------------------------------------------epsilon.inp

sigma.inp
---------------------------------------------------------------
number_bands 299
band_index_min 1
band_index_max 44
cell_slab_truncation
screening_semiconductor

begin kpoints
0.000000000 0.000000000 0.000000000 1.0
0.000000000 0.083333333 0.000000000 1.0
0.000000000 0.166666667 0.000000000 1.0
0.000000000 0.250000000 0.000000000 1.0
0.000000000 0.333333333 0.000000000 1.0
0.000000000 0.416666667 0.000000000 1.0
0.000000000 0.500000000 0.000000000 1.0
0.000000000 0.583333333 0.000000000 1.0
0.000000000 0.666666667 0.000000000 1.0
0.000000000 0.750000000 0.000000000 1.0
0.000000000 0.833333333 0.000000000 1.0
0.000000000 0.916666667 0.000000000 1.0
0.083333333 0.083333333 0.000000000 1.0
0.083333333 0.166666667 0.000000000 1.0
0.083333333 0.250000000 0.000000000 1.0
0.083333333 0.333333333 0.000000000 1.0
0.083333333 0.416666667 0.000000000 1.0
0.083333333 0.500000000 0.000000000 1.0
0.083333333 0.583333333 0.000000000 1.0
0.083333333 0.666666667 0.000000000 1.0
0.083333333 0.750000000 0.000000000 1.0
0.166666667 0.166666667 0.000000000 1.0
0.166666667 0.250000000 0.000000000 1.0
0.166666667 0.333333333 0.000000000 1.0
0.166666667 0.416666667 0.000000000 1.0
0.166666667 0.500000000 0.000000000 1.0
0.166666667 0.583333333 0.000000000 1.0
0.250000000 0.250000000 0.000000000 1.0
0.250000000 0.333333333 0.000000000 1.0
0.250000000 0.416666667 0.000000000 1.0
0.333333333 0.333333333 0.000000000 1.0
end
---------------------------------------------------------------sigma.inp

sigma.out
-------------------------------------------------------------------------------------------------------
================================================================================
12:15:40 Dealing with k = 0.000000 0.000000 0.000000 1 / 31
================================================================================

Reading vxc.dat
Number of q-points in the irreducible BZ(k) (nrq): 31

¦ ¦ q-point rq (irr. BZ) #eq/fBZ
----------------------------- -------
0.000000 0.000000 0.000000 1
0.000000 0.083333 0.000000 3
0.000000 0.166667 0.000000 3
0.000000 0.250000 0.000000 3
0.000000 0.333333 0.000000 3
0.000000 0.416667 0.000000 3
0.000000 0.500000 0.000000 3
0.000000 0.583333 0.000000 3
0.000000 0.666667 0.000000 3
0.000000 0.750000 0.000000 3
0.000000 0.833333 0.000000 3
0.000000 0.916667 0.000000 3
0.083333 0.083333 0.000000 6
0.083333 0.166667 0.000000 6
0.083333 0.250000 0.000000 6
0.083333 0.333333 0.000000 6
0.083333 0.416667 0.000000 6
0.083333 0.500000 0.000000 6
0.083333 0.583333 0.000000 6
0.083333 0.666667 0.000000 6
0.083333 0.750000 0.000000 6
0.166667 0.166667 0.000000 6
0.166667 0.250000 0.000000 6
0.166667 0.333333 0.000000 6
0.166667 0.416667 0.000000 6
0.166667 0.500000 0.000000 6
0.166667 0.583333 0.000000 6
0.250000 0.250000 0.000000 6
0.250000 0.333333 0.000000 6
0.250000 0.416667 0.000000 6
0.333333 0.333333 0.000000 2

Started calculating Sigma with 1364 block(s) at 12:15:40.

¦qpoint 1 out of 31

Reading Eps Back
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sigma.cplx.x 00000000012BD521 tbk_trace_stack_i Unknown Unknown
sigma.cplx.x 00000000012BB65B tbk_string_stack_ Unknown Unknown
sigma.cplx.x 0000000001188624 Unknown Unknown Unknown
sigma.cplx.x 0000000001188436 Unknown Unknown Unknown
sigma.cplx.x 00000000011288A9 Unknown Unknown Unknown
sigma.cplx.x 00000000011303B6 Unknown Unknown Unknown
libpthread-2.17.s 00007F530A185370 Unknown Unknown Unknown
sigma.cplx.x 00000000004BB628 Unknown Unknown Unknown
...
-------------------------------------------------------------------------------------------------------sigma.out

I would appreciate if anyone can help me.

Thank you very much,
Nelson

nelsyeung's picture

Submitted by nelsyeung on Thu, 11/09/2017 - 01:00

I realised that I didn't compile with OpenMP properly, but after fixing that I'm getting a segmentation fault just after the printing of "- Debug flags: ". This, however, seems to be some inconsistencies with our facilities, as submitting the job with a PBS script instead of a sbatch script works. No idea why, but I guess this problem is solved.