[CP2K-user] [CP2K:19915] Re: FFTW_PLAN_TYPE PATIENT and EXHAUSTIVE not working
Léon Luntadila Lufungula
Leon.luntadilalufungula at uantwerpen.be
Fri Feb 16 09:01:04 UTC 2024
Dear Frederick,
Thanks for guiding me in solving this issue!
1) I have not yet checked if this is indeed the case but I'm quite new to
AIMD calculations and the reference manual stated that this was recommended
for long AIMD trajectories, so I assumed this would be a good option to
enable. If you could show me how to check this, I would greatly appreciate
the help! For the same calculation with the default FFTW_PLAN_TYPE ESTIMATE
I get the following timings:
-------------------------------------------------------------------------------
-
-
- T I M I N G
-
-
-
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL
TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE
MAXIMUM
CP2K 1 1.0 0.0 0.0 259198.3
259201.0
qs_mol_dyn_low 1 2.0 0.5 0.6 259198.0
259200.7
velocity_verlet 21600 3.0 4.7 5.3 259117.8
259120.7
qs_forces 21601 4.0 6.7 8.3 259054.1
259057.9
qs_energies 21601 5.0 1.3 2.0 216944.6
216962.9
scf_env_do_scf 21601 6.0 0.7 1.0 197423.7
197426.9
scf_env_do_scf_inner_loop 172819 7.0 2.9 3.7 147536.9
147542.8
rebuild_ks_matrix 194420 8.7 0.7 0.7 113213.6
113417.8
qs_ks_build_kohn_sham_matrix 194420 9.7 21.9 25.3 113212.9
113417.2
qs_ks_update_qs_env 194420 8.0 1.5 1.8 85131.3
85315.6
* pw_transfer 4104421 12.9 259.1 293.8 53272.8
54657.8*
sum_up_and_integrate 194420 10.7 158.9 210.4 54433.6
54518.3
integrate_v_rspace 194420 11.7 6.8 8.9 54274.2
54375.6
*fft_wrap_pw1pw2 3715581 14.0 41.8 46.1 52788.9
54160.2 fft_wrap_pw1pw2_200 2160221 15.4 5123.8 5554.3
50067.4 51727.8*
init_scf_loop 21601 7.0 0.6 0.8 49795.6
49797.8
qs_vxc_create 194420 10.7 4.5 5.3 49235.6
49729.8
xc_vxc_pw_create 194420 11.7 990.7 1608.7 49231.1
49725.4
qs_rho_update_rho_low 194420 8.1 0.8 0.9 44519.7
44594.7
calculate_rho_elec 194420 9.1 109.2 184.2 44518.9
44593.9
fft3d_ps 3715581 16.0 10122.9 14717.9 41927.7
43177.5
dbcsr_multiply_generic 2981151 12.6 130.7 138.3 42145.8
42708.1
prepare_preconditioner 21601 8.0 0.1 0.2 38552.7
38578.0
grid_integrate_task_list 194420 12.7 34380.1 37401.8 34380.1
37401.8
xc_pw_derive 1166520 13.7 9.8 11.0 34752.0
36587.5
make_preconditioner 21601 9.0 0.4 0.6 36451.6
36464.5
qs_scf_new_mos 172819 8.0 0.9 1.4 34340.9
34469.5
qs_scf_loop_do_ot 172819 9.0 0.8 1.0 34340.0
34468.7
make_full_all 21601 10.0 4.6 5.3 34250.9
34260.8
ot_scf_mini 172819 10.0 4.0 4.7 31468.4
31598.1
multiply_cannon 2981151 13.6 192.3 222.5 29228.9
30932.4
mp_alltoall_z22v 3715581 18.0 27949.9 30346.5 27949.9
30346.5
multiply_cannon_loop 2981151 14.6 215.7 231.9 27541.2
28832.2
xc_pw_divergence 194420 12.7 4.0 4.7 26628.5
28220.2
qs_ks_update_qs_env_forces 21601 5.0 0.1 0.2 28174.2
28195.0
xc_rho_set_and_dset_create 194420 12.7 239.1 269.1 20595.1
28022.0
ot_mini 172819 11.0 1.0 1.4 23618.8
23759.5
grid_collocate_task_list 194420 10.1 22590.9 23442.1 22590.9
23442.1
rs_pw_transfer 1987402 12.3 41.9 48.7 21225.8
22117.5
yz_to_x 993701 17.7 742.7 1149.4 19795.7
21777.5
density_rs2pw 194420 10.1 8.1 8.9 20317.1
21233.4
mp_waitall_1 ******* -4.3 17314.7 19114.1 17314.7
19114.1
multiply_cannon_multrec ******* 15.6 17135.6 18128.8 17149.2
18142.9
cp_fm_diag_elpa 64803 11.3 0.4 0.5 18118.8
18125.4
cp_fm_diag_elpa_base 64803 12.3 17919.4 18033.2 18104.5
18104.8
mp_waitany ******* 14.1 13555.6 14684.3 13555.6
14684.3
xc_functional_eval 194420 13.7 2.0 2.6 8289.8
14473.2
pbe_lda_eval 194420 14.7 8287.8 14472.3 8287.8
14472.3
2) Unfortunately, no pdbg-version was compiled on my HPC center, but I did
run a calculation with TRACE and TRACE_MASTER enabled. See attached files
for the output.
Kind regards,
Léon
On Friday 16 February 2024 at 09:36:56 UTC+1 Frederick Stein wrote:
> Dear Leon,
>
> I do not know the root of the error and I cannot suggest a solution. The
> options themself are tested within our regtest suite and we do not find any
> issues there. So, it seems to be a more complicated problem either on FFTW
> site or on CP2K site.
>
> I have two questions:
>
> 1. Did you check whether the FFT kernel actually needs an improvement?
> Check the runtime of the routines pw_transfer and those starting with
> fft_wrap_pw1pw2 (or similar).
>
> 2. Do you have a pdbg-version of CP2K available? If yes, can you run one
> of the failing tests with that one? It might also help to turn on the
> keywords TRACE and TRACE_MASTER in the GLOBAL section of your input files
> to identify the actual routine on CP2K site where the error occurs.
>
> Regards,
>
> Frederick
>
> Léon Luntadila Lufungula schrieb am Montag, 12. Februar 2024 um 10:42:16
> UTC+1:
>
>> Dear all,
>>
>> I've been running some AIMD calculations and am trying to speed up the
>> calculations a bit by playing with the FFTW_PLAN_TYPE option.
>> Unfortunately, only MEASURE and the default ESTIMATE are working. If I try
>> to set it to PATIENT (as recommended for long AIMD runs) or EXHAUSTIVE, the
>> calculation crashes almost immediately with the following error messages
>> (see also attached files):
>>
>> [PATIENT]
>>
>> ...
>>
>> corrupted double-linked list
>>
>> corrupted double-linked list (not small)
>>
>> cp2k.popt: malloc.c:4106: _int_malloc: Assertion `(unsigned long) (size)
>> >= (unsigned long) (nb)' failed.
>>
>>
>>
>> Program received signal SIGABRT: Process abort signal.
>>
>> ...
>>
>> [EXHAUSTIVE]
>>
>> ...
>>
>> malloc_consolidate(): unaligned fastbin chunk detected
>>
>> malloc_consolidate(): unaligned fastbin chunk detected
>>
>>
>>
>> Program received signal SIGABRT: Process abort signal.
>>
>>
>>
>> Backtrace for this error:
>>
>> corrupted double-linked list
>>
>>
>>
>> Program received signal SIGABRT: Process abort signal.
>>
>>
>>
>> Backtrace for this error:
>>
>> malloc_consolidate(): unaligned fastbin chunk detected
>>
>>
>>
>> Program received signal SIGABRT: Process abort signal.
>>
>>
>>
>> Backtrace for this error:
>>
>>
>>
>> Program received signal SIGABRT: Process abort signal.
>>
>>
>>
>> Backtrace for this error:
>>
>> corrupted double-linked list
>>
>> cp2k.popt: malloc.c:4106: _int_malloc: Assertion `(unsigned long) (size)
>> >= (unsigned long) (nb)' failed.
>>
>> ...
>>
>> I'm running CP2K/2023.2-foss-2022a as compiled with Easybuild by our HPC
>> centre, but the same problems appear when I try the CP2K/2022.1-foss-2022a
>> version. However, when I run it with the CP2K/7.1-intel-2020a version which
>> is also available, both EXHAUSTIVE and PATIENT seem to be working
>> properly... Is this something that can be solved in some way or will this
>> require a different compilation of CP2K, possibly with the intel toolchain
>> instead of the foss toolchain?
>>
>>
>> Kind regards,
>>
>> Léon
>>
>>
>>
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