[QE-users] erratic segfault in neb.x
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Tue Feb 12 15:44:45 CET 2019
Thank you Pietro
I need a couple of hours to answer all your questions...
Best
Giuseppe
Pietro Davide Delugas <pdelugas at sissa.it> ha scritto:
> 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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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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