- Mail actions: [ respond to this message ] [ mail a new topic ]
- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

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
*

*>>>>
*

*>>>>
*

*>>>
*

*>>>
*

*>>>
*

*>>>
*

*>>> -----------------------------------------------------------
*

*>>>
*

*>>> If you wish to unsubscribe from this mailing, send mail to
*

*>>> minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe gadget-list
*

*>>> A web-archive of this mailing list is available here:
*

*>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
*

*>>>
*

*>>>
*

*>>>
*

*>>>
*

*>>> -----------------------------------------------------------
*

*>>>
*

*>>> If you wish to unsubscribe from this mailing, send mail to
*

*>>> minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe gadget-list
*

*>>> A web-archive of this mailing list is available here:
*

*>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
*

*>>>
*

*>>
*

*>>
*

*>>
*

*>>
*

*>> -----------------------------------------------------------
*

*>>
*

*>> If you wish to unsubscribe from this mailing, send mail to
*

*>> minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe gadget-list
*

*>> A web-archive of this mailing list is available here:
*

*>> http://www.mpa-garching.mpg.de/gadget/gadget-list
*

*>
*

*>
*

*>
*

*>
*

*> -----------------------------------------------------------
*

*>
*

*> If you wish to unsubscribe from this mailing, send mail to
*

*> minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe gadget-list
*

*> A web-archive of this mailing list is available here:
*

*> http://www.mpa-garching.mpg.de/gadget/gadget-list
*

Received on 2015-01-20 14:16:54

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:

Received on 2015-01-20 14:16:54

*
This archive was generated by hypermail 2.3.0
: 2023-01-10 10:01:32 CET
*