Segmentation fault

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Segmentation fault

Postby ramieor » Wed Apr 06, 2016 11:08 am

Dear VASP community,

I really appreciate the help provided by you for the people who are having trouble with VASP. I am a beginner in this field. I have successfully compiled VASP using intel 2016 and ran many jobs without any problems. However, in one simple case I am getting segmentation fault and I cannot get over it. Here is my INCAR file:

System = singlepoint
ISMEAR = -1; SIGMA = 0.1;
IBRION=2; ISIF=2 ; NSW=200
NCORE= 8
LREAL= Auto

The POSCAR looks like this:

singlepoint
1.00000000000000
19.96416780462500 0.0000135395080124 0.0000000000000000
0.0000078181802728 9.71580339157950520600 0.0000000000000000
0.0000000000000000 0.0000000000000000 19.9889240840472837
C
64
Direct
0.0158599100328659 0.0288117987603237 0.5850000000000009
0.0158342910477269 0.2787941584217910 0.5850000000000009
......
.....

The KPOINT file is:

K-Points Comment
0 0 = automatic generation of k-points
Monkhorst M use Monkhorst Pack
1 1 1 grid 7x7x7
0 0 0 shift (usually 0 0 0)

I am using the PAW_PBE pseudopotential.
I am also using the ulimit -s unlimited command. I tried to run this using 16 cores or just 1 core. I tried to run it with a recompiled VASP with intel 2015. BUt no matter what I try I am always getting a segmentation fault (always at the fourth step of the calculation). I have copies the output file bellow.

Any help, advise, clue will be highly appreciated!

Thanks a lot,
Obaidur

--------------------------------------------------------------------------------
Intel Composer XE / Intel Parallel Studio XE
--------------------------------------------------------------------------------
Version: 2016.

The installation directory is:
/vegas/apps/compiler/intel/compilers_and_libraries_2016/linux

For documentation see:
- file:///vegas/apps/compiler/intel/documentation_2016/en/ps2016/getstart_clus_l.htm
- https://software.intel.com/en-us/intel- ... umentation

Alternatively to loading this module, source the following file:
. /vegas/apps/compiler/intel/compilers_and_libraries_2016/linux/bin/compilervars.sh intel64

Setting the following environment variables:
CC = icc
CXX = icpc
CPP = icc -E
CXXCPP = icpc -E
ICCROOT = /vegas/apps/compiler/intel/compilers_and_libraries_2016/linux
MKLROOT = /vegas/apps/compiler/intel/compilers_and_libraries_2016/linux/mkl
TBBROOT = /vegas/apps/compiler/intel/compilers_and_libraries_2016/linux/tbb
IPPROOT = /vegas/apps/compiler/intel/compilers_and_libraries_2016/linux/ipp

Attention: Loads many Intel libraries as well, but not the Intel MPI module
Load the Intel MPI library separately (impi)
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Intel MPI (impi) - Message parsing interface library
--------------------------------------------------------------------------------
Version: 5.1.1

Defaults to use the following setting:
- I_MPI_FABRICS = shm:ofa
- I_MPI_FALLBACK = 0
- I_MPI_DEBUG = 0

For documentation see:
- /vegas/apps/compiler/intel/impi/5.1.1.109/doc
- https://software.intel.com/en-us/intel- ... umentation

Setting the following environment variables:
- MPIROOT = /vegas/apps/compiler/intel/impi/5.1.1.109
- I_MPI_ROOT = /vegas/apps/compiler/intel/impi/5.1.1.109

This modulefile connects Intel MPI with SLURM. Thus, MPI applications are
started by SLURM automatically, e.g. via srun command:
srun -n20 ./mympibin
If that is not what you want, unload this modulefile and and load the MPI
settings via following command:
source /vegas/apps/compiler/intel/impi/5.1.1.109/bin64/mpivars.sh
--------------------------------------------------------------------------------
Starting at Wed Apr 6 11:03:57 CEST 2016
Running on hosts: aria20
Running on 1 nodes.
Running on 16 processors.
Current working directory is /vegas/scratch/zosi3692/all-stretch/uniaxial-x/graphene-done/temp/step67
running on 16 total cores
distrk: each k-point on 16 cores, 1 groups
distr: one band on 8 cores, 2 groups
using from now: INCAR
vasp.5.4.1 05Feb16 (build Apr 05 2016 17:56:59) complex

POSCAR found type information on POSCAR C
POSCAR found : 1 types and 64 ions
scaLAPACK will be used
LDA part: xc-table for Pade appr. of Perdew
POSCAR, INCAR and KPOINTS ok, starting setup
WARNING: small aliasing (wrap around) errors must be expected
FFT: planning ...
WAVECAR not read
entering main loop
N E dE d eps ncg rms rms(c)
DAV: 1 0.209695635525E+04 0.20970E+04 -0.78117E+04 372 0.921E+02
DAV: 2 -0.674816956833E+02 -0.21644E+04 -0.20426E+04 480 0.238E+02
DAV: 3 -0.554603870272E+03 -0.48712E+03 -0.48387E+03 408 0.120E+02
DAV: 4 -0.576910760779E+03 -0.22307E+02 -0.21995E+02 392 0.322E+01
DAV: 5 -0.577639906812E+03 -0.72915E+00 -0.72477E+00 424 0.506E+00forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
vasp 0000000001510235 Unknown Unknown Unknown
vasp 000000000150DFF7 Unknown Unknown Unknown
vasp 000000000148E244 Unknown Unknown Unknown
vasp 000000000148E056 Unknown Unknown Unknown
vasp 000000000142FB86 Unknown Unknown Unknown
vasp 0000000001435900 Unknown Unknown Unknown
libpthread.so.0 00002B6809073130 Unknown Unknown Unknown
vasp 00000000006E3170 Unknown Unknown Unknown
vasp 00000000008A3943 Unknown Unknown Unknown
vasp 000000000089B88D Unknown Unknown Unknown
vasp 0000000000D261F4 Unknown Unknown Unknown
vasp 000000000129E679 MAIN__ 2872 main.F
vasp 00000000004093BE Unknown Unknown Unknown
libc.so.6 00002B68095A3AF5 Unknown Unknown Unknown
vasp 00000000004092C9 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
.............
...............
(more lines like these)
..............
...........
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
vasp 0000000001510235 Unknown Unknown Unknown
vasp 000000000150DFF7 Unknown Unknown Unknown
vasp 000000000148E244 Unknown Unknown Unknown
vasp 000000000148E056 Unknown Unknown Unknown
vasp 000000000142FB86 Unknown Unknown Unknown
vasp 0000000001435900 Unknown Unknown Unknown
libpthread.so.0 00002AC50AA21130 Unknown Unknown Unknown
vasp 00000000006E3170 Unknown Unknown Unknown
vasp 00000000008A3943 Unknown Unknown Unknown
vasp 000000000089B88D Unknown Unknown Unknown
vasp 0000000000D261F4 Unknown Unknown Unknown
vasp 000000000129E679 MAIN__ 2872 main.F
vasp 00000000004093BE Unknown Unknown Unknown
libc.so.6 00002AC50AF51AF5 Unknown Unknown Unknown
vasp 00000000004092C9 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
vasp 0000000001510235 Unknown Unknown Unknown
vasp 000000000150DFF7 Unknown Unknown Unknown
vasp 000000000148E244 Unknown Unknown Unknown
vasp 000000000148E056 Unknown Unknown Unknown
vasp 000000000142FB86 Unknown Unknown Unknown
vasp 0000000001435900 Unknown Unknown Unknown
libpthread.so.0 00002B9D9F702130 Unknown Unknown Unknown
vasp 00000000006E3170 Unknown Unknown Unknown
vasp 00000000008A3943 Unknown Unknown Unknown
vasp 000000000089B88D Unknown Unknown Unknown
vasp 0000000000D261F4 Unknown Unknown Unknown
vasp 000000000129E679 MAIN__ 2872 main.F
vasp 00000000004093BE Unknown Unknown Unknown
libc.so.6 00002B9D9FC32AF5 Unknown Unknown Unknown
vasp 00000000004092C9 Unknown Unknown Unknown
srun: error: aria20: tasks 0-15: Exited with exit code 174
srun: Terminating job step 868087.0
Finished at Wed Apr 6 11:04:17 CEST 2016
ramieor
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Posts: 1
Joined: Tue Apr 05, 2016 6:14 pm

Re: Segmentation fault

Postby admin » Tue Apr 12, 2016 1:10 pm

Can you display your POSCAR?
admin
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Joined: Tue Aug 03, 2004 8:18 am


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