Re: Subfind took too much time to run

From: Weiguang Cui <cuiweiguang_at_gmail.com>
Date: Wed, 11 Aug 2021 09:46:05 +0100

Hi Volker,

Yes, `ErrTolTheta` is set to 0.5 which is just slightly small than the
proposed value in the document. But I really doubt that is the cause.

I can understand that the two massive halos, even treated with separated
tasks, can be costly. I suppose this is seen from
"SUBFIND: Processing overall took (total time=1482.26 sec)"

But there is about 2.5ks time difference to this line:
"SUBFIND: Finished with SUBFIND. (total time=4092.76 sec)"
Which should be reposeful for this cost? I can not see any significant cost
listed between the two lines. Maybe I am wrong in interpreting this and
they are not in sequence.
Thanks.

Best,
Weiguang

-------------------------------------------
https://weiguangcui.github.io/


On Tue, Aug 10, 2021 at 6:50 PM Volker Springel <
vspringel_at_mpa-garching.mpg.de> wrote:

>
> Hi Weiguang,
>
> No, the code has decided to treat the two biggest halos with 2 tasks each
> (because they don't fit on a single processor with their ~6 million
> particles), all the other tasks are used to process the 8913146 halos that
> are smaller. Only for halos that are treated with multiple tasks you see
> the "root-task" messages.
>
> The gravitational unbinding of highly resolved halos can take quite a bit
> of time... it might be that you have set a quite small value of
> ErrTolTheta, which would slow it down unnecessarily.
>
> Regards,
> Volker
>
>
> > On 7. Aug 2021, at 21:42, Weiguang Cui <cuiweiguang_at_gmail.com> wrote:
> >
> > Dear all,
> >
> > I understand that this simulation (2048^3 particles) is large to run, is
> it normal that the SUBFIND takes about 4ks to complete? It seems that there
> are only two tasks to run subfind. Are there some options in SUBFIND that I
> did set not correctly?
> >
> > ```
> > SUBFIND: We now execute a parallel version of SUBFIND.
> > SUBFIND: Previous subhalo catalogue had approximately a size
> 2.76992e+09, and the summed squared subhalo size was 1.16758e+14
> > SUBFIND: Number of FOF halos treated with collective SubFind algorithm =
> 2
> > SUBFIND: Number of processors used in different partitions for the
> collective SubFind code = 4
> > SUBFIND: (The adopted size-limit for the collective algorithm was
> 5965232 particles, for threshold size factor 0.6)
> > SUBFIND: The other 8913146 FOF halos are treated in parallel with serial
> code
> > SUBFIND: subfind_distribute_groups() took 0.044987 sec
> > SUBFIND: particle balance=1.23335
> > SUBFIND: subfind_exchange() took 20.5998 sec
> > SUBFIND: particle balance for processing=1
> > SUBFIND: root-task=2: Collectively doing halo 1 of length 6001658 on
> 2 processors.
> > SUBFIND: root-task=0: Collectively doing halo 0 of length 6318694 on
> 2 processors.
> > SUBFIND: subdomain decomposition took 5.28067 sec
> > SUBFIND: serial subfind subdomain decomposition took 4.50761 sec
> > SUBFIND: root-task=2: total number of subhalo coll_candidates=2858
> > SUBFIND: root-task=2: number of subhalo candidates small enough to be
> done with one cpu: 2858. (Largest size 234093)
> > SUBFIND: root-task=0: total number of subhalo coll_candidates=3148
> > SUBFIND: root-task=0: number of subhalo candidates small enough to be
> done with one cpu: 3148. (Largest size 1116065)
> > SUBFIND: root-task=2: bringing the independent ones back took 1.43275 sec
> > SUBFIND: root-task=2: the collective unbinding of remaining halos took
> 728.107 sec
> > SUBFIND: root-task=2: found 2312 bound substructures in FoF group of
> length 6001658
> > SUBFIND: root-task=2: Collective processing of halo 1 took 1212.43
> > SUBFIND: root-task=0: bringing the independent ones back took 1.69057 sec
> > SUBFIND: root-task=0: the collective unbinding of remaining halos took
> 893.829 sec
> > SUBFIND: root-task=0: found 2642 bound substructures in FoF group of
> length 6318694
> > SUBFIND: subfind_hbt_single_group() processing for Ngroups=1 took
> 1459.14 sec
> > SUBFIND: root-task=0: Collective processing of halo 0 took 1473.2
> > SUBFIND: Processing overall took (total time=1482.26 sec)
> > ALLOCATE: Changing to MaxPart = 17425843
> > ALLOCATE: Changing to MaxPartSph = 0
> > SUBFIND: subfind_exchange() (for return to original CPU) took 26.0112
> sec
> > TREE: Full tree construction for all particles. (presently
> allocated=3948.2 MB)
> > GRAVTREE: Tree construction done. took 71.5354 sec
> <numnodes>=1.90281e+06 NTopnodes=70545 NTopleaves=61727
> tree-build-scalability=0.962969
> > SUBFIND: SO iteration 1: need to repeat for 7848033 halo centers.
> (took 0.309375 sec)
> > SUBFIND: SO iteration 2: need to repeat for 7848033 halo centers.
> (took 0.2519 sec)
> > SUBFIND: SO iteration 3: need to repeat for 7848033 halo centers.
> (took 0.268218 sec)
> > SUBFIND: SO iteration 4: need to repeat for 7848033 halo centers.
> (took 0.266999 sec)
> > SUBFIND: SO iteration 5: need to repeat for 7848033 halo centers.
> (took 0.288053 sec)
> > SUBFIND: SO iteration 6: need to repeat for 7848033 halo centers.
> (took 0.266823 sec)
> > SUBFIND: SO iteration 7: need to repeat for 7848033 halo centers.
> (took 0.264547 sec)
> > SUBFIND: SO iteration 8: need to repeat for 7848033 halo centers.
> (took 0.263144 sec)
> > SUBFIND: SO iteration 9: need to repeat for 7848033 halo centers.
> (took 0.256196 sec)
> > SUBFIND: SO iteration 10: need to repeat for 7848033 halo centers.
> (took 0.264536 sec)
> > SUBFIND: SO iteration 11: need to repeat for 7848033 halo centers.
> (took 0.257483 sec)
> > SUBFIND: SO iteration 12: need to repeat for 7848033 halo centers.
> (took 0.25124 sec)
> > SUBFIND: SO iteration 13: need to repeat for 7848033 halo centers.
> (took 0.261861 sec)
> > SUBFIND: SO iteration 14: need to repeat for 7848033 halo centers.
> (took 0.257919 sec)
> > SUBFIND: SO iteration 15: need to repeat for 7848030 halo centers.
> (took 0.268111 sec)
> > SUBFIND: SO iteration 16: need to repeat for 38913 halo centers.
> (took 0.259465 sec)
> > SUBFIND: SO iteration 17: need to repeat for 37 halo centers.
> (took 0.0242081 sec)
> > SUBFIND: SO iteration 1: need to repeat for 7848033 halo centers.
> (took 0.264944 sec)
> > SUBFIND: SO iteration 2: need to repeat for 7848033 halo centers.
> (took 0.237437 sec)
> > SUBFIND: SO iteration 3: need to repeat for 7848033 halo centers.
> (took 0.257997 sec)
> > SUBFIND: SO iteration 4: need to repeat for 7848033 halo centers.
> (took 0.263542 sec)
> > SUBFIND: SO iteration 5: need to repeat for 7848033 halo centers.
> (took 0.268112 sec)
> > SUBFIND: SO iteration 6: need to repeat for 7848033 halo centers.
> (took 0.254724 sec)
> > SUBFIND: SO iteration 7: need to repeat for 7848033 halo centers.
> (took 0.268252 sec)
> > SUBFIND: SO iteration 8: need to repeat for 7848033 halo centers.
> (took 0.25666 sec)
> > SUBFIND: SO iteration 9: need to repeat for 7848033 halo centers.
> (took 0.272972 sec)
> > SUBFIND: SO iteration 10: need to repeat for 7848033 halo centers.
> (took 0.251183 sec)
> > SUBFIND: SO iteration 11: need to repeat for 7848033 halo centers.
> (took 0.265267 sec)
> > SUBFIND: SO iteration 12: need to repeat for 7848033 halo centers.
> (took 0.257801 sec)
> > SUBFIND: SO iteration 13: need to repeat for 7848033 halo centers.
> (took 0.269823 sec)
> > SUBFIND: SO iteration 14: need to repeat for 7848033 halo centers.
> (took 0.265494 sec)
> > SUBFIND: SO iteration 15: need to repeat for 7848030 halo centers.
> (took 0.247782 sec)
> > SUBFIND: SO iteration 16: need to repeat for 36428 halo centers.
> (took 0.259644 sec)
> > SUBFIND: SO iteration 17: need to repeat for 35 halo centers.
> (took 0.019228 sec)
> > SUBFIND: SO iteration 1: need to repeat for 7848033 halo centers.
> (took 0.265704 sec)
> > SUBFIND: SO iteration 2: need to repeat for 7848033 halo centers.
> (took 0.229607 sec)
> > SUBFIND: SO iteration 3: need to repeat for 7848033 halo centers.
> (took 0.254473 sec)
> > SUBFIND: SO iteration 4: need to repeat for 7848033 halo centers.
> (took 0.25696 sec)
> > SUBFIND: SO iteration 5: need to repeat for 7848033 halo centers.
> (took 0.26164 sec)
> > SUBFIND: SO iteration 6: need to repeat for 7848033 halo centers.
> (took 0.25506 sec)
> > SUBFIND: SO iteration 7: need to repeat for 7848033 halo centers.
> (took 0.240955 sec)
> > SUBFIND: SO iteration 8: need to repeat for 7848033 halo centers.
> (took 0.260188 sec)
> > SUBFIND: SO iteration 9: need to repeat for 7848033 halo centers.
> (took 0.248877 sec)
> > SUBFIND: SO iteration 10: need to repeat for 7848033 halo centers.
> (took 0.256545 sec)
> > SUBFIND: SO iteration 11: need to repeat for 7848033 halo centers.
> (took 0.25118 sec)
> > SUBFIND: SO iteration 12: need to repeat for 7848033 halo centers.
> (took 0.25854 sec)
> > SUBFIND: SO iteration 13: need to repeat for 7848033 halo centers.
> (took 0.246834 sec)
> > SUBFIND: SO iteration 14: need to repeat for 7848033 halo centers.
> (took 0.27007 sec)
> > SUBFIND: SO iteration 15: need to repeat for 7848033 halo centers.
> (took 0.258597 sec)
> > SUBFIND: SO iteration 16: need to repeat for 122350 halo centers.
> (took 0.248988 sec)
> > SUBFIND: SO iteration 17: need to repeat for 181 halo centers.
> (took 0.0358 sec)
> > SUBFIND: SO iteration 1: need to repeat for 7848033 halo centers.
> (took 0.269485 sec)
> > SUBFIND: SO iteration 2: need to repeat for 7848033 halo centers.
> (took 0.228188 sec)
> > SUBFIND: SO iteration 3: need to repeat for 7848033 halo centers.
> (took 0.234185 sec)
> > SUBFIND: SO iteration 4: need to repeat for 7848033 halo centers.
> (took 0.229443 sec)
> > SUBFIND: SO iteration 5: need to repeat for 7848033 halo centers.
> (took 0.224041 sec)
> > SUBFIND: SO iteration 6: need to repeat for 7848033 halo centers.
> (took 0.232641 sec)
> > SUBFIND: SO iteration 7: need to repeat for 7848033 halo centers.
> (took 0.230443 sec)
> > SUBFIND: SO iteration 8: need to repeat for 7848033 halo centers.
> (took 0.219413 sec)
> > SUBFIND: SO iteration 9: need to repeat for 7848033 halo centers.
> (took 0.220803 sec)
> > SUBFIND: SO iteration 10: need to repeat for 7848033 halo centers.
> (took 0.237108 sec)
> > SUBFIND: SO iteration 11: need to repeat for 7848033 halo centers.
> (took 0.232947 sec)
> > SUBFIND: SO iteration 12: need to repeat for 7848033 halo centers.
> (took 0.240728 sec)
> > SUBFIND: SO iteration 13: need to repeat for 7848033 halo centers.
> (took 0.228163 sec)
> > SUBFIND: SO iteration 14: need to repeat for 7848033 halo centers.
> (took 0.221182 sec)
> > SUBFIND: SO iteration 15: need to repeat for 7848033 halo centers.
> (took 0.224345 sec)
> > SUBFIND: SO iteration 16: need to repeat for 6272558 halo centers.
> (took 0.226659 sec)
> > SUBFIND: SO iteration 17: need to repeat for 46051 halo centers.
> (took 0.188434 sec)
> > SUBFIND: SO iteration 18: need to repeat for 52 halo centers.
> (took 0.01652 sec)
> > SUBFIND: determining spherical overdensity masses took 16.475 sec
> > SUBFIND: assembled and ordered groups and subhalos (took 5.52871 sec)
> > FOF/SUBFIND: writing group catalogue file:
> './snaps//groups_026/fof_subhalo_tab_026.0' (file 1 of 32)
> > FOF/SUBFIND: writing group catalogue block 0 (GroupLen)...
> > FOF/SUBFIND: writing group catalogue block 1 (GroupMass)..
> > FOF/SUBFIND: writing group catalogue block 2 (GroupPos)...
> > FOF/SUBFIND: writing group catalogue block 3 (GroupVel)...
> > FOF/SUBFIND: writing group catalogue block 4 (GroupLenType)...
> > FOF/SUBFIND: writing group catalogue block 5 (GroupOffsetType)...
> > FOF/SUBFIND: writing group catalogue block 6 (GroupMassType)...
> > FOF/SUBFIND: writing group catalogue block 7 (GroupAscale)...
> > FOF/SUBFIND: writing group catalogue block 9 (Group_M_Mean200)...
> > FOF/SUBFIND: writing group catalogue block 10 (Group_R_Mean200)...
> > FOF/SUBFIND: writing group catalogue block 11 (Group_M_Crit200)..
> > FOF/SUBFIND: writing group catalogue block 12 (Group_R_Crit200)...
> > FOF/SUBFIND: writing group catalogue block 13 (Group_M_Crit500)...
> > FOF/SUBFIND: writing group catalogue block 14 (Group_R_Crit500)...
> > FOF/SUBFIND: writing group catalogue block 15 (Group_M_TopHat200)...
> > FOF/SUBFIND: writing group catalogue block 16 (Group_R_TopHat200)...
> > FOF/SUBFIND: writing group catalogue block 17 (GroupNsubs)...
> > FOF/SUBFIND: writing group catalogue block 18 (GroupFirstSub)...
> > FOF/SUBFIND: writing group catalogue block 19 (SubhaloGroupNr)...
> > FOF/SUBFIND: writing group catalogue block 20 (SubhaloRankInGr)...
> > FOF/SUBFIND: writing group catalogue block 21 (SubhaloLen)...
> > FOF/SUBFIND: writing group catalogue block 22 (SubhaloMass)...
> > FOF/SUBFIND: writing group catalogue block 23 (SubhaloPos)...
> > FOF/SUBFIND: writing group catalogue block 24 (SubhaloVel)...
> > FOF/SUBFIND: writing group catalogue block 25 (SubhaloLenType)...
> > FOF/SUBFIND: writing group catalogue block 26 (SubhaloOffsetType)...
> > FOF/SUBFIND: writing group catalogue block 27 (SubhaloMassType)...
> > FOF/SUBFIND: writing group catalogue block 28 (SubhaloCM)...
> > FOF/SUBFIND: writing group catalogue block 29 (SubhaloSpin)...
> > FOF/SUBFIND: writing group catalogue block 30 (SubhaloVelDisp)...
> > FOF/SUBFIND: writing group catalogue block 31 (SubhaloVmax)...
> > FOF/SUBFIND: writing group catalogue block 32 (SubhaloVmaxRad)...
> > FOF/SUBFIND: writing group catalogue block 33 (SubhaloHalfmassRad)...
> > FOF/SUBFIND: writing group catalogue block 34 (SubhaloHalfmassRadType)...
> > FOF/SUBFIND: writing group catalogue block 35 (SubhaloIDMostbound)...
> > FOF/SUBFIND: writing group catalogue block 36 (SubhaloParentRank)...
> > FOF/SUBFIND: Group catalogues saved. took = 8.89541 sec, total size
> 3525.03 MB, corresponds to effective I/O rate of 396.275 MB/sec
> > SUBFIND: Subgroup catalogues saved. took = 9.7367 sec
> > SUBFIND: Finished with SUBFIND. (total time=4092.76 sec)
> > SUBFIND: Total number of subhalos with at least 32 particles: 9849779
> > SUBFIND: Largest subhalo has 4419279 particles/cells.
> > SUBFIND: Total number of particles/cells in subhalos: 2897277494
> > ```
> >
> > Many thanks for any suggestions. Please let me know if you need any more
> information.
> >
> > Best,
> > Weiguang
> >
> > -------------------------------------------
> > https://weiguangcui.github.io/
> >
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Received on 2021-08-11 10:46:53

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