Re: Trouble running the same simulation with gas particles

From: Volker Springel <volker_at_MPA-Garching.MPG.DE>
Date: Tue, 20 Jan 2015 14:17:07 +0100

Hi Phil,

You would get an error of this kind if you set the temperature of your particles to zero and don't impose a temperature floor. Then the sound-speed ends up being zero, causing a division by zero when the Courant timestep criterion is evaluated.

Volker

On 20 Jan 2015, at 13:26, Arman Khalatyan <arm2arm_at_gmail.com> wrote:

>
> 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 14:16:54

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