Re: Trouble running the same simulation with gas particles

From: Arman Khalatyan <arm2arm_at_gmail.com>
Date: Tue, 20 Jan 2015 13:26:59 +0100

Hi,
If you have all particles with the same mass why the output is:
> Type 1 (halo): 32767 (tot= 0000032767) masstab=0
Are there MASS block per particle type? If not you should correct your header.


***********************************************************

 Dr. Arman Khalatyan eScience -SuperComputing
 Leibniz-Institut für Astrophysik Potsdam (AIP)
 An der Sternwarte 16, 14482 Potsdam, Germany

***********************************************************


On Tue, Jan 20, 2015 at 1:16 PM, Matthias Kühtreiber
<a0749244_at_unet.univie.ac.at> wrote:
>
> Hi Phil,
>
> I assume that all physical units set in the parameter file fit the units
> in your initial conditions. You could also try if you can get the gas
> sphere ICs to run which are delivered with Gadget-2. There is also a
> parameter file included which could be helpful for comparisons.
>
> Otherwise you could try to track down the error in timestep.c. The value
> for dt seems to get "nan". There could be for instance a division by 0
> somewhere in the calculation of dt. The endrun(818) is in function
> "get_timestep". I hope this helps a little.
>
> Best wishes,
> Matthias
>
> On Di, 20.01.2015, 12:26, Phil Sutton wrote:
>>
>> Hi Matthias,
>>
>> Unfortunately I have this set to a rather large non-zero value. Would
>> there be anything else in the parameter file that might throw up this
>> error? Although I have tried to not have any zero values. I can only
>> assume it something to do with hydrodynamical element of the time step
>> performed by Gadget?
>>
>> Thanks
>>
>> Phil
>>
>> -----Original Message-----
>> From: Matthias Kühtreiber [mailto:a0749244_at_unet.univie.ac.at]
>> Sent: 20 January 2015 10:52
>> To: Gadget General Discussion
>> Subject: Re: [gadget-list] Trouble running the same simulation with gas
>> particles
>>
>>
>> Hi Phil,
>>
>> Have you double-checked that the value of "SofteningGas" in your parameter
>> file is set to a non-zero value?
>> A gravitational softening of 0 can lead to similar errors you described
>> above.
>>
>> Best wishes,
>>
>> Matthias Kühtreiber
>> Department of Astrophysics
>> University of Vienna
>>
>>
>>
>> On Di, 20.01.2015, 10:58, Phil Sutton wrote:
>>> Hi all,
>>>
>>> For a while now I have been running a few simulations successfully
>>> using non-gas particles. However, I now wish to include some gas
>>> particles and have run into some problems getting Gadget2 to initial
>>> run. I now have two initial conditions that creates a ring of
>>> particles around a larger central mass. The velocities all assume
>>> circular Keplerian motions with the following:
>>> [cid:image003.jpg_at_01D03497.9310C440]
>>>
>>> All particle number densities, velocities and masses are the same (I
>>> added in a new array for internal energies of gas particles). The only
>>> difference is the particle type. The non-gas IC runs fine with no
>>> errors and continues to evolve in a Keplerian way. However, when gas
>>> particles are used for the ring a zero time step is assigned. I have
>>> tried altering the smoothing lengths, mass, number of particles and
>>> scale of the system from ridiculously small and large with no effect.
>>> The only thing that allows Gadget2 to run is if I reduce the central
>>> mass down by a factor of 10, which obviously results in the ring
>>> particles no longer having Keplerian motions about the centre. I have
>>> probably made a simple error in setting up of the initial conditions
>>> or an assumptions I’ve made when using gas particles but am running
>>> out of ideas to try. Any help would be great.
>>>
>>> Here is the errors for the gas particle IC followed by the successful
>>> non-gas IC if it helps:
>>>
>>>
>>> This is Gadget, version `2.0'.
>>>
>>>
>>>
>>> Running on 12 processors.
>>>
>>>
>>>
>>> Allocated 30 MByte communication buffer per processor.
>>>
>>>
>>>
>>> Communication buffer has room for 604946 particles in gravity
>>> computation
>>>
>>> Communication buffer has room for 245760 particles in density
>>> computation
>>>
>>> Communication buffer has room for 196608 particles in hydro
>>> computation
>>>
>>> Communication buffer has room for 196608 particles in domain
>>> decomposition
>>>
>>>
>>>
>>>
>>>
>>> Hubble (internal units) = 3.24078e-18
>>>
>>> G (internal units) = 6.672e-08
>>>
>>> UnitMass_in_g = 1
>>>
>>> UnitTime_in_s = 1
>>>
>>> UnitVelocity_in_cm_per_s = 1
>>>
>>> UnitDensity_in_cgs = 1
>>>
>>> UnitEnergy_in_cgs = 1
>>>
>>>
>>>
>>>
>>>
>>> Allocated 0.567307 MByte for particle storage. 68
>>>
>>>
>>>
>>> Allocated 0.70079 MByte for storage of SPH data. 84
>>>
>>>
>>>
>>>
>>>
>>> reading file `gas.dat' on task=0 (contains 35000 particles.)
>>>
>>> distributing this file to tasks 0-11
>>>
>>> Type 0 (gas): 34999 (tot= 0000034999) masstab=0
>>>
>>> Type 1 (halo): 0 (tot= 0000000000) masstab=0
>>>
>>> Type 2 (disk): 1 (tot= 0000000001) masstab=0
>>>
>>> Type 3 (bulge): 0 (tot= 0000000000) masstab=0
>>>
>>> Type 4 (stars): 0 (tot= 0000000000) masstab=0
>>>
>>> Type 5 (bndry): 0 (tot= 0000000000) masstab=0
>>>
>>>
>>>
>>> reading done.
>>>
>>> Total number of particles : 0000035000
>>>
>>>
>>>
>>> allocated 0.0762939 Mbyte for ngb search.
>>>
>>>
>>>
>>> Allocated 1.63065 MByte for BH-tree. 64
>>>
>>>
>>>
>>> domain decomposition...
>>>
>>> NTopleaves= 1436
>>>
>>> work-load balance=1.01143 memory-balance=1.01143
>>>
>>> exchange of 0000032087 particles
>>>
>>> domain decomposition done.
>>>
>>> begin Peano-Hilbert order...
>>>
>>> Peano-Hilbert done.
>>>
>>> Begin Ngb-tree construction.
>>>
>>> Ngb-Tree contruction finished
>>>
>>> ngb iteration 1: need to repeat for 0000034999 particles.
>>>
>>> ngb iteration 2: need to repeat for 0000034999 particles.
>>>
>>> ngb iteration 3: need to repeat for 0000034967 particles.
>>>
>>> ngb iteration 4: need to repeat for 0000034163 particles.
>>>
>>> ngb iteration 5: need to repeat for 0000027944 particles.
>>>
>>> ngb iteration 6: need to repeat for 0000014669 particles.
>>>
>>> ngb iteration 7: need to repeat for 0000004986 particles.
>>>
>>> ngb iteration 8: need to repeat for 0000001284 particles.
>>>
>>> ngb iteration 9: need to repeat for 0000000446 particles.
>>>
>>> ngb iteration 10: need to repeat for 0000000211 particles.
>>>
>>> ngb iteration 11: need to repeat for 0000000088 particles.
>>>
>>> ngb iteration 12: need to repeat for 0000000026 particles.
>>>
>>> ngb iteration 13: need to repeat for 0000000005 particles.
>>>
>>>
>>>
>>> Setting next time for snapshot file to Time_next= 0
>>>
>>>
>>>
>>>
>>>
>>> writing snapshot file...
>>>
>>> done with snapshot.
>>>
>>>
>>>
>>> Setting next time for snapshot file to Time_next= 500
>>>
>>>
>>>
>>>
>>>
>>> Begin Step 0, Time: 0, Systemstep: 0
>>>
>>> domain decomposition...
>>>
>>> NTopleaves= 1436
>>>
>>> work-load balance=1.01143 memory-balance=1.01143
>>>
>>> domain decomposition done.
>>>
>>> begin Peano-Hilbert order...
>>>
>>> Peano-Hilbert done.
>>>
>>> Start force computation...
>>>
>>> Tree construction.
>>>
>>> Tree construction done.
>>>
>>> Begin tree force.
>>>
>>> tree is done.
>>>
>>> Begin tree force.
>>>
>>> tree is done.
>>>
>>> Start density computation...
>>>
>>> Start hydro-force computation...
>>>
>>> force computation done.
>>>
>>>
>>>
>>> Error: A timestep of size zero was assigned on the integer timeline!
>>>
>>> We better stop.
>>>
>>> Task=0 Part-ID=0 dt=-nan tibase=3.72529e-05 ti_step=-2147483648
>>> ac=-nan
>>> xyz=(2.05361e+11|-1.32362e+09|0) tree=(-0.999847|0.006444340)
>>>
>>>
>>>
>>> hydro-frc=(-nan|-nan|-nan)
>>>
>>> task 0: endrun called with an error level of 818
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Error: A timestep of size zero was assigned on the integer timeline!
>>>
>>> We better stop.
>>>
>>> Task=1 Part-ID=0 dt=-nan tibase=3.72529e-05 ti_step=-2147483648
>>> ac=-nan
>>> xyz=(1.40842e+11|-1.21532e+11|0) tree=(-0.922557|0.796070)
>>>
>>>
>>>
>>> hydro-frc=(-nan|-nan|-nan)
>>> task 1: endrun called with an error level of 818
>>>
>>>
>>>
>>>
>>> This is Gadget, version `2.0'.
>>>
>>>
>>>
>>> Running on 12 processors.
>>>
>>>
>>>
>>> Allocated 30 MByte communication buffer per processor.
>>>
>>>
>>>
>>> Communication buffer has room for 604946 particles in gravity
>>> computation
>>>
>>> Communication buffer has room for 245760 particles in density
>>> computation
>>>
>>> Communication buffer has room for 196608 particles in hydro
>>> computation
>>>
>>> Communication buffer has room for 196608 particles in domain
>>> decomposition
>>>
>>>
>>>
>>>
>>>
>>> Hubble (internal units) = 3.24078e-18
>>>
>>> G (internal units) = 6.672e-08
>>>
>>> UnitMass_in_g = 1
>>>
>>> UnitTime_in_s = 1
>>>
>>> UnitVelocity_in_cm_per_s = 1
>>>
>>> UnitDensity_in_cgs = 1
>>>
>>> UnitEnergy_in_cgs = 1
>>>
>>>
>>>
>>>
>>>
>>> Allocated 0.53112 MByte for particle storage. 68
>>>
>>>
>>>
>>>
>>>
>>> reading file `non_gas.dat' on task=0 (contains 32768 particles.)
>>>
>>> distributing this file to tasks 0-11
>>>
>>> Type 0 (gas): 0 (tot= 0000000000) masstab=0
>>>
>>> Type 1 (halo): 32767 (tot= 0000032767) masstab=0
>>>
>>> Type 2 (disk): 1 (tot= 0000000001) masstab=0
>>>
>>> Type 3 (bulge): 0 (tot= 0000000000) masstab=0
>>>
>>> Type 4 (stars): 0 (tot= 0000000000) masstab=0
>>>
>>> Type 5 (bndry): 0 (tot= 0000000000) masstab=0
>>>
>>>
>>>
>>> reading done.
>>>
>>> Total number of particles : 0000032768
>>>
>>>
>>>
>>> allocated 0.0762939 Mbyte for ngb search.
>>>
>>>
>>>
>>> Allocated 1.5753 MByte for BH-tree. 64
>>>
>>>
>>>
>>> domain decomposition...
>>>
>>> NTopleaves= 1450
>>>
>>> work-load balance=1.01807 memory-balance=1.01807
>>>
>>> exchange of 0000030112 particles
>>>
>>> domain decomposition done.
>>>
>>> begin Peano-Hilbert order...
>>>
>>> Peano-Hilbert done.
>>>
>>> Begin Ngb-tree construction.
>>>
>>> Ngb-Tree contruction finished
>>>
>>>
>>>
>>> Setting next time for snapshot file to Time_next= 0
>>>
>>>
>>>
>>>
>>>
>>> writing snapshot file...
>>>
>>> done with snapshot.
>>>
>>>
>>>
>>> Setting next time for snapshot file to Time_next= 500
>>>
>>>
>>>
>>>
>>>
>>> Begin Step 0, Time: 0, Systemstep: 0
>>>
>>> domain decomposition...
>>>
>>> NTopleaves= 1450
>>>
>>> work-load balance=1.01807 memory-balance=1.01807
>>>
>>> domain decomposition done.
>>>
>>> begin Peano-Hilbert order...
>>>
>>> Peano-Hilbert done.
>>>
>>> Start force computation...
>>>
>>> Tree construction.
>>>
>>> Tree construction done.
>>>
>>> Begin tree force.
>>>
>>> tree is done.
>>>
>>> Begin tree force.
>>>
>>> tree is done.
>>>
>>> force computation done.
>>>
>>>
>>>
>>> Begin Step 1, Time: 4.88281, Systemstep: 4.88281
>>>
>>> domain decomposition...
>>>
>>> NTopleaves= 1450
>>>
>>> work-load balance=1.02153 memory-balance=1.38647
>>>
>>> exchange of 0000004772 particles
>>>
>>> domain decomposition done.
>>>
>>> begin Peano-Hilbert order...
>>>
>>> Peano-Hilbert done.
>>>
>>> Start force computation...
>>>
>>> Tree construction.
>>>
>>> Tree construction done.
>>>
>>> Begin tree force.
>>>
>>> tree is done.
>>>
>>> force computation done.
>>>
>>>
>>>
>>> Begin Step 2, Time: 9.76562, Systemstep: 4.88281
>>>
>>> domain decomposition...
>>>
>>> NTopleaves= 1457
>>>
>>> work-load balance=1.03279 memory-balance=1.36597
>>>
>>> exchange of 0000000226 particles
>>>
>>> domain decomposition done.
>>>
>>> begin Peano-Hilbert order...
>>>
>>> Peano-Hilbert done.
>>>
>>> Start force computation...
>>>
>>> Tree construction.
>>>
>>> Tree construction done.
>>>
>>> Begin tree force.
>>>
>>> tree is done.
>>>
>>> force computation done.
>>>
>>> Regards
>>>
>>> Phil Sutton
>>> Physics Department
>>> Loughborough University
>>>
>>>
>>
>>
>>
>>
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>
>
>
>
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Received on 2015-01-20 13:27:02

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