[QE-users] erratic segfault in neb.x

[Pietro Davide Delugas]

Ok
I will have a look at it in the develop version.
does this happen only when you use neb.x with environ or even in cases 
when you are not using environ,
the segmentation is always at the same point or changes from time to time ?
does it happen only on Marconi  ?


On 02/12/2019 03:08 PM, Giuseppe Mattioli wrote:
>
> Dear All
> I'm using version 6.3-backports patched with Environ-1.0 on 
> marconi at cineca. neb.x runs often without problems, but it sometimes 
> stops with segfault, with no apparent reason but the usage (or the 
> lack of usage) of the INTERMEDIATE_IMAGE card. I can provide further 
> details, if required. The pseudopotentials are taken from the sg15 
> ONCV library, regenerated by Lorenzo Paulatto with the 
> pseudowavefunctions in order to perform lda_plus_u calculations.
>
> For example, this input runs smoothly to completion.
>
> export FILE="neb1-int"
> export INPFILE=$FILE-1.inp
> export OUTFILE=$FILE-1.out
> echo " $FILE"
> echo " $INPFILE"
> echo " $OUTFILE"
>
> cat > $INPFILE << EOF
> BEGIN
> BEGIN_PATH_INPUT
>  &PATH
>   restart_mode      = 'from_scratch'
>   string_method     = 'neb',
>   nstep_path        = 999,
>   ds                = 2.D0,
>   opt_scheme        = "broyden",
>   num_of_images     = 10,
>   k_max             = 0.3D0,
>   k_min             = 0.2D0,
>   CI_scheme         = "auto",
>   path_thr          = 0.1D0,
>  /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
>  &control
>     calculation = 'relax'
>     restart_mode='from_scratch',
>     prefix='$FILE',
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/',
>     tprnfor=.true.,
>     nstep=999,
>     disk_io='low',
>     max_seconds=1750,
>  /
>  &system
>     ibrav=1, celldm(1)=20.0000,
>     nat=5, ntyp=2, tot_charge=-1.0,
>     ecutwfc=80.0,
>     occupations='smearing', degauss=0.01,
>     nspin=2,
>     starting_magnetization(1)=0.01,
>     vdw_corr='grimme-d3',
>     lda_plus_u=.true.,
>     Hubbard_U(1)=3.5,
>  /
>  &electrons
>     diagonalization='david',
>     mixing_mode='plain'
>     mixing_beta=0.1
>     conv_thr=1.0d-6
>     electron_maxstep=100
>     scf_must_converge=.false.,
>  /
>  &ions
>     ion_dynamics='bfgs'
>  /
> ATOMIC_SPECIES
> O    15.999    O_ONCV_PBE-1.0.UPF
> H     1.008    H_ONCV_PBE-1.0.UPF
> K_POINTS {gamma}
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS {angstrom}
> O        4.455702089   2.212044072   3.611730009
> H        5.090393412   2.499936581   4.262397225
> O        2.270203543   3.193235686   4.044718451
> H        3.308435164   2.764849675   3.850959602
> H        2.215855793   4.058643985   3.647644713
> INTERMEDIATE_IMAGE
> ATOMIC_POSITIONS {angstrom}
> O          4.45570        2.21204        3.61173
> H          5.09039        2.49994        4.26240
> O          2.27020        3.19324        4.04472
> H          3.42650        2.77458        3.83417
> H          2.21586        4.05864        3.64764
> LAST_IMAGE
> ATOMIC_POSITIONS {angstrom}
> O        4.600629464   2.152014485   3.601034260
> H        5.218013126   2.475466817   4.252935018
> O        2.416588332   3.145598027   4.054390916
> H        3.610759008   2.629944672   3.805624086
> H        2.335480069   3.991125998   3.620425719
> END_POSITIONS
> END_ENGINE_INPUT
> END
> EOF
> $PARA_PREFIX $ESPRESSO/neb.x -environ -ni 2 -inp $INPFILE >> $OUTFILE
>
> If you simply drop the INTERMEDIATE_IMAGE lines (coordinates included, 
> of course) from the input with everything else untouched, then neb.x 
> stops without complaining during the first iteration, and slurm.out says
>
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image              PC                Routine Line        Source
> neb.x              0000000000D57E84  Unknown Unknown  Unknown
> libpthread-2.17.s  00002B1713218370  Unknown Unknown  Unknown
> neb.x              0000000000D1C520  Unknown Unknown  Unknown
> neb.x              0000000000D30482  Unknown Unknown  Unknown
> neb.x              0000000000D27AB0  Unknown Unknown  Unknown
> neb.x              0000000000CDEF1A  Unknown Unknown  Unknown
> neb.x              00000000008A22A8  qes_libs_module_m 1325  qes_libs.f90
> neb.x              000000000057B8E3  pw_restart_new_mp 498  
> pw_restart_new.f90
> neb.x              0000000000577BE9  punch_ 73  punch.f90
> neb.x              0000000000438481  compute_scf_IP_do 325  
> compute_scf.f90
> neb.x              00000000004369A6  compute_scf_ 140  compute_scf.f90
> neb.x              000000000040ECC2  path_base_mp_sear 828  path_base.f90
> neb.x              00000000004072AD  MAIN__ 105  neb.f90
> neb.x              0000000000406E5E  Unknown Unknown  Unknown
> libc-2.17.so       00002B1713748B35  __libc_start_main Unknown  Unknown
> neb.x              0000000000406D69  Unknown Unknown  Unknown
>
> The same is randomly happening for different (and more sensible, this 
> is only an example) calculations.
> Is anybody able to suggest improvements for this situation?
> Thank you in advance
> Giuseppe
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
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