[QE-users] segfault with HSE06
Fabrizio Ferrari
ferrariruffino.fz at gmail.com
Tue Jul 9 13:40:10 CEST 2019
Yes!
Il mar 9 lug 2019, 13:39 Michal Krompiec <michal.krompiec at gmail.com> ha
scritto:
> Hi Fabrizio,
> Thanks. Do you mean replacing this: (lines 466-475)
> IF(DoLoc) then
> !$omp parallel do collapse(3) default(shared)
> firstprivate(npol,nrxxs,nkqs,ibnd_buff_start,ibnd_buff_end)
> private(ir,ibnd,ikq,ipol)
> DO ikq=1,SIZE(locbuff,3)
> DO ibnd=1, x_nbnd_occ
> DO ir=1,nrxxs*npol
> locbuff(ir,ibnd,ikq)=0.0_DP
> ENDDO
> ENDDO
> ENDDO
> ELSE
>
> with the following:
>
> IF(DoLoc) then
> IF(gamma_only) then
> !$omp parallel do collapse(3) default(shared)
> firstprivate(npol,nrxxs,nkqs,ibnd_buff_start,ibnd_buff_end)
> private(ir,ibnd,ikq,ipol)
> DO ikq=1,SIZE(locbuff,3)
> DO ibnd=1, x_nbnd_occ
> DO ir=1,nrxxs*npol
> locbuff(ir,ibnd,ikq)=0.0_DP
> ENDDO
> ENDDO
> ENDDO
> END IF
> ELSE
>
> ?
>
> On Tue, 9 Jul 2019 at 11:37, Fabrizio Ferrari <ferrariruffino.fz at gmail.com>
> wrote:
>
>> Hello,
>> if you put the loop at line 467 of PW/src/exx.f90 inside an
>> 'IF(gamma_only)', the segfault should disappear. I'm just checking if that
>> is the only fix needed.
>>
>> Fabrizio
>>
>> On Tue, Jul 9, 2019 at 12:27 PM Michal Krompiec <
>> michal.krompiec at gmail.com> wrote:
>>
>>> I got a similar segfault using a fresh installation of QE 6.4.1, on a
>>> different HPC, this time with Intel 2018 compilers and ELPA, with the same
>>> input file and pseudos (SG15) as previously.
>>> I noticed that my molecule is a bit too high in the simulation cell (vs.
>>> the potential added by assume_isolated), but increasing the size of the
>>> cell in the Z direction changed nothing.
>>> Switching off assume_isolated also didn't help.
>>>
>>> from stdout:
>>>
>>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>>> Image PC Routine Line
>>> Source
>>> pw.x 00000000056A6D8D Unknown Unknown
>>> Unknown
>>> libpthread-2.17.s 00002AC70727E5E0 Unknown Unknown
>>> Unknown
>>> pw.x 00000000005B3618 Unknown Unknown
>>> Unknown
>>> pw.x 00000000005AE060 Unknown Unknown
>>> Unknown
>>> pw.x 000000000040ADFD Unknown Unknown
>>> Unknown
>>> pw.x 000000000059D83D Unknown Unknown
>>> Unknown
>>> pw.x 00000000004086C9 Unknown Unknown
>>> Unknown
>>> pw.x 000000000040851E Unknown Unknown
>>> Unknown
>>> libc-2.17.so 00002AC7077AEC05 __libc_start_main Unknown
>>> Unknown
>>> pw.x 0000000000408429 Unknown Unknown
>>> Unknown
>>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>>>
>>> Last few lines of the log file:
>>>
>>> convergence has been achieved in 9 iterations
>>>
>>> Using localization algorithm with threshold: 0.50D-02
>>>
>>> Using ACE for calculation of exact exchange
>>>
>>> EXX grid: 1427071 G-vectors FFT dimensions: ( 90, 90, 375)
>>>
>>> NBands = 15 nks = 1 nkqs = 9
>>> Canonical Orbitals
>>>
>>> Any suggestions?
>>>
>>> Thanks,
>>> Michal
>>>
>>>
>>> On Mon, 8 Jul 2019 at 13:27, Michal Krompiec <michal.krompiec at gmail.com>
>>> wrote:
>>>
>>>> Hello,
>>>> I'm getting a segmentation fault when trying to run a HSE06 SCF
>>>> calculation in QE 6.4rc (built with gcc and OpenMPI). I got the same result
>>>> regardless of number of OMP threads (1-2) or MPI processes, it is also not
>>>> because I'm running out of memory. Increasing OMP_STACK_SIZE didn't help.
>>>> I'm using SG15 norm-conserving pseudopotentials.
>>>> This is the error message:
>>>>
>>>> Program received signal SIGSEGV: Segmentation fault - invalid memory
>>>> reference.
>>>>
>>>> Backtrace for this error:
>>>>
>>>> Backtrace for this error:
>>>> #0 0x2ba41caf6607 in ???
>>>> #1 0x2ba41caf586d in ???
>>>> #2 0x2ba41d9d5fdf in ???
>>>> #1 0x2ba41caf586d in ???
>>>> #2 0x2ba41d9d5fdf in ???
>>>> #3 0x481031 in __exx_MOD_exxinit._omp_fn.41
>>>> at
>>>> /home/hpcadmin/Cluster-packages/Apps/QE/q-e-qe-6.4-rc/PW/src/exx.f90:471
>>>>
>>>>
>>>> And this is the input file:
>>>> &CONTROL
>>>> nstep = 150
>>>> prefix = 'pz'
>>>> calculation = 'scf'
>>>> /
>>>> &SYSTEM
>>>> ecutwfc = 60
>>>> ecutrho = 240
>>>> occupations = 'smearing'
>>>> degauss = 0.03
>>>> smearing = 'marzari-vanderbilt'
>>>> assume_isolated = '2D'
>>>> ntyp = 3
>>>> nat = 10
>>>> ibrav = 0
>>>> vdw_corr='dft-d3'
>>>> nosym = .true.
>>>> input_dft = 'hse'
>>>> localization_thr = 0.005
>>>>
>>>> /
>>>> &ELECTRONS
>>>> electron_maxstep = 1000
>>>> mixing_mode = 'plain'
>>>> mixing_beta = 0.3
>>>> mixing_ndim = 10
>>>> /
>>>> &IONS
>>>> ion_dynamics = 'bfgs'
>>>> /
>>>>
>>>> ATOMIC_SPECIES
>>>> H 1 H_ONCV_PBE-1.0.upf
>>>> C 12 C_ONCV_PBE-1.0.upf
>>>> N 14 N_ONCV_PBE-1.0.upf
>>>>
>>>> K_POINTS automatic
>>>> 3 3 1 0 0 0
>>>>
>>>> CELL_PARAMETERS angstrom
>>>> 9.45000000000000 0.00000000000000 0.0
>>>> 0.00000000000000 8.90954544295050 0.0
>>>> 0.00000000000000 0.00000000000000 40.0
>>>>
>>>> ATOMIC_POSITIONS angstrom
>>>> N 3.220157348 4.070243213 7.161850862
>>>> C 2.057591707 4.250681378 7.817575738
>>>> C 4.333273229 4.171146830 7.913403134
>>>> C 2.009345068 4.525337360 9.193044239
>>>> C 4.285082283 4.446195607 9.288766365
>>>> N 3.122476937 4.626559339 9.944547282
>>>> H 1.139008253 4.174089393 7.227702259
>>>> H 5.290517910 4.028527369 7.402554504
>>>> H 1.052120461 4.668162403 9.703968061
>>>> H 5.203598139 4.523590493 9.878655120
>>>>
>>>>
>>>> I would be grateful for any suggestions. In the meantime, we are
>>>> upgrading to 6.4.1 to see if this helps.
>>>>
>>>> Best regards,
>>>>
>>>> Michal Krompiec
>>>>
>>>> Merck KGaA, Darmstadt, Germany & University of Southampton
>>>>
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>>
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>
> _______________________________________________
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