segment fault (bug?) in ABINIT v6.4.2

chen · Post by **chen** » Sun Jan 23, 2011 9:07 pm

The code crashes in the first iteration, no problem with ABINIT 6.0.3

here is the messages from the crash

ITER STEP NUMBER 1
vtorho : nnsclo_now= 2, note that nnsclo,dbl_nnsclo,istep= 0 0 1
**** In vtorho for isppol= 1
starting lobpcg, with nblockbd,mpi_enreg%nproc_band 22 2
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libblas.so.3 00002B4A063DC6F5 Unknown Unknown Unknown
libblas.so.3 00002B4A063DC6C1 Unknown Unknown Unknown
libblas.so.3 00002B4A05EFDE25 Unknown Unknown Unknown
libblas.so.3 00002B4A06633049 Unknown Unknown Unknown
abinit 00000000006C18C3 Unknown Unknown Unknown
abinit 00000000006971A7 Unknown Unknown Unknown
abinit 00000000005F5C2E Unknown Unknown Unknown
abinit 00000000005C5D5F Unknown Unknown Unknown
abinit 0000000000509FF0 Unknown Unknown Unknown
abinit 00000000004264E9 Unknown Unknown Unknown
abinit 0000000000416748 Unknown Unknown Unknown
abinit 000000000040AD5A Unknown Unknown Unknown
abinit 0000000000406592 Unknown Unknown Unknown
libc.so.6 00002B4A0937F994 Unknown Unknown Unknown
abinit 00000000004064B9 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libblas.so.3 00002B5B203706F5 Unknown Unknown Unknown
libblas.so.3 00002B5B203706C1 Unknown Unknown Unknown
libblas.so.3 00002B5B1FE91E25 Unknown Unknown Unknown
libblas.so.3 00002B5B205C7049 Unknown Unknown Unknown
abinit 00000000006C18C3 Unknown Unknown Unknown
abinit 00000000006971A7 Unknown Unknown Unknown
abinit 00000000005F5C2E Unknown Unknown Unknown
abinit 00000000005C5D5F Unknown Unknown Unknown
abinit 0000000000509FF0 Unknown Unknown Unknown
abinit 00000000004264E9 Unknown Unknown Unknown
abinit 0000000000416748 Unknown Unknown Unknown
abinit 000000000040AD5A Unknown Unknown Unknown

and the input is as

Code: Select all

# input for a BCC K
#============================

chkprim 0

#=====================
# spin related
nsppol  2
spinat
  0 0 4
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0

  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0
  0 0 0

  0 0 0
  0 0 0
  0 0 0
   0 0 0
   0 0 0
   0 0 0
   0 0 0
   0 0 0
   0 0 0
   0 0 0

   0 0 0
   0 0 0
   0 0 0
   0 0 0
   0 0 0
   0 0 0

 occopt   3
 tsmear   0.1 eV
 nsym     1

 accesswff   1  # mpi-IO
 nline      10
 iscf        7
 npulayit    4
 diemixmag  -4.0
 prtwf       1
 prtden      0

 nband       44
 #---------------------------------
 # parallel
 paral_kgb 1   # parallel activated over kpt, fft and bands, contain spin
 npkpt    20   # CPUs for kpt
 npfft     1   # CPUs for fft
 npband    2   # CPUs for bands
 wfoptalg 14   # Locally Optimal Block Preconditioned Conjugate Gradient (lobpcg) method of Knyazev.
 nloalg    4
fftalg    401
intxc     0
fft_opt_lob  2
istwfk    200*1

#------------ fix atom positions ---------
#natfix    36
#iatfix    2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 3

#-------- cell optimizatoin -------
#optcell 0
#ionmov  3
#tolmxf  1.0d-4
#ntime   50

#============ below are in terms of Angstrom ===========
# K surface 3x3x1 10 Angstrom Vacc
acell  3*1.0 angstrom
rprim
   7.949999999999999      -7.949999999999998       7.950000000000000
   7.949999999999999      -7.949999999999998      -7.949999999999998
   15.021067811865478      15.021067811865478       0.000000000000000

ntypat 2
znucl  26  19   # K
natom  37
typat  1  36*2
xcart
### Cartesian coordinates (bohr)
  3.28778025355234E+01  2.83171187844130E+00 -4.36387110966763E-03 ## <------ Fe atom
  5.00777425210000E+00 -5.00777425210000E+00 -8.43769498715119E-15
  1.00155485040000E+01 -1.00155485040000E+01 -5.00777425210000E+00
  1.50233227560000E+01 -1.50233227560000E+01 -1.00155485040000E+01
  1.00155485040000E+01 -1.00155485040000E+01  5.00777425210000E+00 1.00155485040000E+01 -1.00155485040000E+01  5.00777425210000E+00
 1.50233227560000E+01 -1.50233227560000E+01 -4.44089209850063E-15
 2.00310970090000E+01 -2.00310970090000E+01 -5.00777425210000E+00
 1.50233227560000E+01 -1.50233227560000E+01  1.00155485040000E+01
 2.00310970090000E+01 -2.00310970090000E+01  5.00777425210000E+00
 2.50388712610000E+01 -2.50388712610000E+01 -7.10542735760100E-15
 5.00777425210000E+00  5.00777425210000E+00 -6.00932910260000E-15
 1.00155485040000E+01  9.76996261670138E-15 -5.00777425210000E+00
 1.50233227560000E+01 -5.00777425210000E+00 -1.00155485040000E+01
 1.00155485040000E+01  7.10542735760100E-15  5.00777425210000E+00
 1.50233227560000E+01 -5.00777425210000E+00 -4.44089209850063E-15
 2.00310970090000E+01 -1.00155485040000E+01 -5.00777425210000E+00
 1.50233227560000E+01 -5.00777425210000E+00  1.00155485040000E+01
 2.00310970090000E+01 -1.00155485040000E+01  5.00777425210000E+00
 2.50388712610000E+01 -1.50233227560000E+01 -3.55271367880050E-15
 1.50233227560000E+01  5.00777425210000E+00  4.44089209850063E-16
 2.00310970090000E+01 -8.88178419700125E-15 -5.00777425210000E+00
 2.50388712610000E+01 -5.00777425210000E+00 -1.00155485040000E+01
 2.00310970090000E+01 -7.10542735760100E-15  5.00777425210000E+00
 2.50388712610000E+01 -5.00777425210000E+00 -1.77635683940025E-15
 3.00466455130000E+01 -1.00155485040000E+01 -5.00777425210000E+00
 2.50388712610000E+01 -5.00777425210000E+00  1.00155485040000E+01
 3.00466455130000E+01 -1.00155485040000E+01  5.00777425210000E+00
 3.50544197650000E+01 -1.50233227560000E+01 -3.55271367880050E-15
 1.50233227560000E+01  1.50233227560000E+01  0.00000000000000E+00
 2.00310970090000E+01  1.00155485040000E+01 -5.00777425210000E+00
 2.50388712610000E+01  5.00777425210000E+00 -1.00155485040000E+01
 2.00310970090000E+01  1.00155485040000E+01  5.00777425210000E+00
 2.50388712610000E+01  5.00777425210000E+00  2.66453525910038E-15
 3.00466455130000E+01 -1.77635683940025E-15 -5.00777425210000E+00
 2.50388712610000E+01  5.00777425210000E+00  1.00155485040000E+01
 3.00466455130000E+01 -1.77635683940025E-15  5.00777425210000E+00
 3.50544197650000E+01 -5.00777425210000E+00  7.10542735760100E-15
ecut  1200 eV

ixc    11 #pbe
kptopt 1
ngkpt
 4 4 1
nshiftk
  1
shiftk
  0 0 0

nstep   150             # Maximal number of SCF cycles
tolvrs  1e-2
diemix  0.5
diemac  100000.0        # Although this is not mandatory, it is worth to

Alain_Jacques · Post by **Alain_Jacques** » Mon Jan 24, 2011 11:12 am

Dear Chen,

It looks like that libblas crashes. Did you compile Abinit with an external BLAS/LAPACK? You can check this in config.log and config.dump. If this is your case, try to re- configure/compile with --disable-linalg option.
Would you be so kind to provide more info about the binary (compiled on what? output of ldd abinit, ...)

Kind regards,

Alain

chen · Post by **chen** » Fri Jan 28, 2011 11:20 pm

Hi Alain,

this is what I did for the configure

./configure FC=mpif90 CC=mpicc --enable-mpi-io --enable-mpi

it is on Intel Nehalem with OpenMPI.

chen

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