Dear Leonard,
Thank you very much for your reply,
I have downloaded the latest Gadget 4 version and now
the simulation does not crash when it reaches the time 0.4.
Thank you again for your helpful reply.
Best regards,
Hassan
On Fri, Jul 9, 2021 at 10:48 AM Leonard Romano <leonard.romano_at_tum.de>
wrote:
>
> Dear Hassan,
>
> This looks very similar to this issue:
> https://wwwmpa.mpa-garching.mpg.de/gadget/gadget-list/0846.html
> Have you pulled from the main repository since April 15th?
> The issue here is that there is still a star in the gas block.
> In the fix included on April 15th a domain decomposition is enforced
> before FOF is run, making sure that this does not happen.
> Probably pulling from the main repository will fix your problem.
>
> Best,
> Leonard
>
> On 09.07.21 07:21, Hassan Fathivavsari wrote:
> > Dear all,
> >
> > I have run a DM + Gas simulation. Everything seemed to be working fine
> > but when it reached at redshift 1.49612 it crashed with following report:
> > (This redshift corresponds to time = 0.4 at which an output was requested
> > to be generated):
> >
> > Sync-Point 6985, Time: 0.400621, Redshift: 1.49612, Systemstep:
> > 7.87001e-05, Dloga: 0.000196465, Nsync-grv: 524288, Nsync-hyd: 261475
> > DOMAIN: Begin domain decomposition (sync-point 6985).
> > DOMAIN: New shift vector determined (-0.57978 -1.13576 -1.36276)
> > DOMAIN: Sum=4 TotalCost=4 NumTimeBinsToBeBalanced=1 MultipleDomains=4
> > DOMAIN: NTopleaves=316, determination of top-level tree involved 8
> > iterations and took 0.0430765 sec
> > DOMAIN: we are going to try at most 135 different settings for
> > combining the domains on tasks=5, nnodes=1
> > DOMAIN: total_cost=4 total_load=2
> > DOMAIN: total_cost=4 total_load=2
> > DOMAIN: total_cost=4 total_load=2
> > DOMAIN: total_cost=4 total_load=2
> > DOMAIN: total_cost=4 total_load=2
> > DOMAIN: total_cost=4 total_load=2
> > DOMAIN: best solution found after 6 iterations by task=3 for nextra=0,
> > reaching maximum imbalance of 1.14521|1.14552
> > DOMAIN: combining multiple-domains took 0.00363554 sec
> > DOMAIN: exchange of 262813 particles
> > DOMAIN: particle exchange done. (took 0.031764 sec)
> > DOMAIN: domain decomposition done. (took in total 0.0888818 sec)
> > PEANO: Begin Peano-Hilbert order...
> > PEANO: done, took 0.0318906 sec.
> > NGBTREE: Ngb-tree construction done. took 0.0324755 sec
> > <numnodes>=8117.4 NTopnodes=361 NTopleaves=316
> > SPH-DENSITY: Begin density calculation. (presently allocated=69.4507 MB)
> > SPH-DENSITY: Ndensities=261475 (task zero has: NumGas=59889,
> > Ndensities=59889)
> > SPH-DENSITY: ngb iteration 1: took 0.914 , need to repeat for
> > 000000000902 local particles.
> > SPH-DENSITY: ngb iteration 2: took 0.021
> > SPH-DENSITY: density computation done. took 1.186
> > SPH-HYDRO: Begin hydro-force calculation. (presently
> > allocated=70.3647 MB)
> > SPH-HYDRO: global Nhydro=261475 (task zero: NumGas=59889, Nhydro=59889)
> > SPH-HYDRO: hydro-force computation done. took 3.293
> > ACCEL: Start tree gravity force computation... (524288 particles)
> > TREEPM: Starting PM part of force calculation. (timebin=19)
> > PM-PERIODIC: Starting periodic PM calculation. (Rcut=0.109375)
> > presently allocated=69.4507 MB
> > PM-PERIODIC: done. (took 2.1174 seconds)
> > TREEPM: Finished PM part of force calculation.
> > TREE: Full tree construction for all particles. (presently
> > allocated=71.0386 MB)
> > GRAVTREE: Tree construction done. took 0.067678 sec
> > <numnodes>=17780.8 NTopnodes=361 NTopleaves=316
> > tree-build-scalability=0.983758
> > GRAVTREE: Begin tree force. timebin=19 (presently allocated=71.9547 MB)
> > GRAVTREE: tree-forces are calculated, with 2 cycles took 6.47065 sec
> > GRAVTREE: tree-force is done.
> > ACCEL: tree force computation done.
> > KICKS: 2nd gravity for highest active timebin=19: particles 524288
> > GRAVTREE/FMM: Setting OldAcc!
> > SFR: spawned 0 stars, converted 1 gas particles into stars
> >
> > FOF: We shall first compute a group catalog for this snapshot file
> > FOF: Begin to compute FoF group catalogue... (presently
> > allocated=71.4042 MB)
> > FOF: Comoving linking length: 0.009375
> > FOFTREE: Ngb-tree construction done. took 0.0579319 sec
> > <numnodes>=9876.4 NTopnodes=361 NTopleaves=316
> > FOF: Start linking particles (presently allocated=76.3867 MB)
> > FOF: linking of small cells took 0.000385365 sec
> > FOF: local links done (took 0.10742 sec, avg-work=0.088653,
> > imbalance=1.20979).
> > FOF: Marked=42436 out of the 262144 primaries which are linked
> > FOF: begin linking across processors (presently allocated=77.0021 MB)
> > FOF: have done 804 cross links (processed 42436, took
> > 0.0437611 sec)
> > FOF: have done 269 cross links (processed 25989, took
> > 0.0270564 sec)
> > FOF: have done 104 cross links (processed 4470, took
> > 0.00817215 sec)
> > FOF: have done 26 cross links (processed 537, took
> > 0.00249025 sec)
> > FOF: have done 5 cross links (processed 104, took
> > 0.00189013 sec)
> > FOF: have done 0 cross links (processed 20, took
> > 0.00173687 sec)
> > FOF: Local groups found.
> > FOF: primary group finding took = 0.200323 sec
> > FOF: Start finding nearest dm-particle (presently allocated=76.3867 MB)
> > FOF: done finding nearest dm-particle
> > FOF: attaching gas and star particles to nearest dm particles took =
> > 0.000317938 sec
> > FOF: compiling local group data and catalogue took = 0.037896 sec
> > FOF: Total number of FOF groups with at least 32 particles: 241
> > FOF: Largest FOF group has 29876 particles.
> > FOF: Total number of particles in FOF groups: 103518
> > FOF: group properties are now allocated.. (presently allocated=72.797 MB)
> > FOF: computation of group properties took = 0.000784035 sec
> > FOF: start assigning group numbers
> > FOF: Assigning of group numbers took = 0.00289581 sec
> > FOF: Finished computing FoF groups. Complete work took 0.308229 sec
> > (presently allocated=71.4239 MB)
> > FOF/SUBFIND: writing group catalogue file: './output/fof_tab_004'
> > (file 1 of 1)
> > 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 8 (GroupSFR)..
> > FOF/SUBFIND: Group catalogues saved. took = 0.00427187 sec, total size
> > 0.0312576 MB, corresponds to effective I/O rate of 7.31709 MB/sec
> > Code termination on task=4, function particle_exchange_based_on_PS(),
> > file src/domain/domain_exchange.cc, line 546: Bummer2
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
> > pc_at_ubuntu
> :~/Desktop/SPH/gadget4-master/examples/DM-L50-N128/Including_Gas$
> >
> > I would be grateful for any help with this issue,
> >
> > Best regards,
> > Hassan
> >
> >
> --
> ===================================================
> Leonard Romano, B.Sc.（レオナルド・ロマノ）
> Physics Department
> Technical University of Munich (TUM), Germany
> Theoretical Astrophysics Group
> Department of Earth and Space Science
> Graduate School of Science, Osaka University, Japan
> he / him / his
> ===================================================
>
>
>
>
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Received on 2021-07-09 18:26:31