Re: Setting PRODUCEGAS in N-GenIC Makefile returns error

From: Tiago Castro <tiagobscastro_at_gmail.com>
Date: Mon, 5 Jul 2021 14:43:04 +0200

Dear Hassan,

   I believe the problem is due to your compilation of G4 using the LEAN
configuration. In this configuration, particles are assumed to have all the
same mass.

Kind regards,
T.

Em seg., 5 de jul. de 2021 às 14:39, Hassan Fathivavsari <h.fathie_at_gmail.com>
escreveu:

> Dear Volker,
>
> Thank you very much for your reply.
>
> I have followed your instructions and included GENERATE_GAS_IN_ICS in the
> Config.sh file present in the /examples/DM-L50-N128/ folder. I also
> modified
> NTYPES=2 to NTYPES=5. I then recompiled the code and generated a new
> Gadget4 executable.
>
> I then included the following lines in the param.txt file in order to be
> compatible
> with NTYPES=5:
>
> SofteningClassOfPartType2 0
> SofteningClassOfPartType3 0
> SofteningClassOfPartType4 0
>
> But when I issue the following command:
>
> mpirun -np 6 ./Gadget4 param.txt
>
> the code stops running with following error report:
>
> I've found something odd!
> The mass content accounts only for Omega=0.616,
> but you specified Omega=0.308 in the parameterfile.
>
> I have also included below the whole terminal output when I run Gadget4:
>
> ============== The whole Terminal output =======
> Shared memory islands host a minimum of 6 and a maximum of 6 MPI ranks.
>
> ___ __ ____ ___ ____ ____ __
> / __) /__\ ( _ \ / __)( ___)(_ _)___ /. |
> ( (_-. /(__)\ )(_) )( (_-. )__) )( (___)(_ _)
> \___/(__)(__)(____/ \___/(____) (__) (_)
>
> This is Gadget, version 4.0.
> Git commit unknown, unknown
>
> Code was compiled with the following compiler and flags:
> mpicxx -std=c++11 -O3 -Wall -I/hdf5/build/include -I/usr/local/include
> -I/usr/local/include -I./examples/DM-L50-N128/Including_Gas//build -Isrc
>
>
> Code was compiled with the following settings:
> ASMTH=2.0
> CREATE_GRID
> DOUBLEPRECISION=2
> FOF
> GENERATE_GAS_IN_ICS
> IDS_32BIT
> LEAN
> NGENIC=256
> NGENIC_2LPT
> NSOFTCLASSES=1
> NTYPES=5
> PERIODIC
> PMGRID=384
> POSITIONS_IN_32BIT
> POWERSPEC_ON_OUTPUT
> RANDOMIZE_DOMAINCENTER
> SELFGRAVITY
> TREEPM_NOTIMESPLIT
>
>
> Running on 6 MPI tasks.
>
>
> BEGRUN: Size of particle structure 56 [bytes]
> BEGRUN: Size of sph particle structure 96 [bytes]
> BEGRUN: Size of gravity tree node 72 [bytes]
> BEGRUN: Size of neighbour tree node 112 [bytes]
> BEGRUN: Size of subfind auxiliary data 36 [bytes]
>
>
>
> -------------------------------------------------------------------------------------------------------------------------
> AvailMem: Largest = 65.37 Mb (on task= 0), Smallest = 65.37 Mb
> (on task= 0), Average = 65.37 Mb
> Total Mem: Largest = 4987.92 Mb (on task= 0), Smallest = 4987.92
> Mb (on task= 0), Average = 4987.92 Mb
> Committed_AS: Largest = 4922.55 Mb (on task= 0), Smallest =
> 4922.55 Mb (on task= 0), Average = 4922.55 Mb
> SwapTotal: Largest = 2048.00 Mb (on task= 0), Smallest = 2048.00
> Mb (on task= 0), Average = 2048.00 Mb
> SwapFree: Largest = 2046.48 Mb (on task= 0), Smallest = 2046.48 Mb
> (on task= 0), Average = 2046.48 Mb
> AllocMem: Largest = 4922.55 Mb (on task= 0), Smallest = 4922.55 Mb
> (on task= 0), Average = 4922.55 Mb
> avail /dev/shm: Largest = 4736.90 Mb (on task= 0), Smallest =
> 4736.90 Mb (on task= 0), Average = 4736.90 Mb
>
> -------------------------------------------------------------------------------------------------------------------------
> Task=0 has the maximum commited memory and is host: ubuntu
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Obtaining parameters from file 'param.txt':
>
> InitCondFile ./dummy.dat
> OutputDir ./output
> SnapshotFileBase snapshot
> OutputListFilename output_times.txt
> ICFormat 1
> SnapFormat 3
> TimeLimitCPU 86400
> CpuTimeBetRestartFile 72000
> MaxMemSize 300
> TimeBegin 0.04
> TimeMax 1
> ComovingIntegrationOn 1
> Omega0 0.308
> OmegaLambda 0.692
> OmegaBaryon 0.0482
> HubbleParam 0.678
> Hubble 100
> BoxSize 50
> OutputListOn 1
> TimeBetSnapshot 0.02
> TimeOfFirstSnapshot 0.02
> TimeBetStatistics 0.02
> NumFilesPerSnapshot 1
> MaxFilesWithConcurrentIO 1
> ErrTolIntAccuracy 0.01
> CourantFac 0.3
> MaxSizeTimestep 0.005
> MinSizeTimestep 0
> TypeOfOpeningCriterion 1
> ErrTolTheta 0.75
> ErrTolThetaMax 1
> ErrTolForceAcc 0.002
> TopNodeFactor 3
> ActivePartFracForNewDomainDecomp 0.01
> ActivePartFracForPMinsteadOfEwald 0.05
> DesNumNgb 64
> MaxNumNgbDeviation 1
> UnitLength_in_cm 3.08568e+24
> UnitMass_in_g 1.989e+43
> UnitVelocity_in_cm_per_s 100000
> GravityConstantInternal 0
> SofteningComovingClass0 0.01
> SofteningMaxPhysClass0 0.01
> SofteningClassOfPartType0 0
> SofteningClassOfPartType1 0
> SofteningClassOfPartType2 0
> SofteningClassOfPartType3 0
> SofteningClassOfPartType4 0
> ArtBulkViscConst 1
> MinEgySpec 0
> InitGasTemp 0
> NSample 128
> GridSize 128
> Seed 181170
> SphereMode 1
> PowerSpectrumType 0
> ReNormalizeInputSpectrum 1
> PrimordialIndex 1
> ShapeGamma 0.21
> Sigma8 0.9
> PowerSpectrumFile powerspec
> InputSpectrum_UnitLength_in_cm 3.08568e+21
>
> MALLOC: Allocation of shared memory took 0.000273652 sec
>
> found 13 times in output-list.
> BEGRUN: Hubble (internal units) = 100
> BEGRUN: h = 0.678
> BEGRUN: G (internal units) = 43.0187
> BEGRUN: UnitMass_in_g = 1.989e+43
> BEGRUN: UnitLenth_in_cm = 3.08568e+24
> BEGRUN: UnitTime_in_s = 3.08568e+19
> BEGRUN: UnitVelocity_in_cm_per_s = 100000
> BEGRUN: UnitDensity_in_cgs = 6.76991e-31
> BEGRUN: UnitEnergy_in_cgs = 1.989e+53
>
> EWALD: initialize Ewald correction...
>
> EWALD: reading Ewald tables from file
> `ewald_table_1-1-1_64-64-64_precision8-order3.dat'
> EWALD: Initialization of periodic boundaries finished.
> NGENIC: generated grid of size 128
> NGENIC: computing displacement fields...
> NGENIC: vel_prefac1= 1387.42 hubble_a=6937.72 fom1=0.999914
> NGENIC: vel_prefac2= 2774.86 hubble_a=6937.72 fom2=1.99984
> NGENIC: Dplus=19.594
> NGENIC_2LPT: Computing secondary source term, derivatices 0 0
> NGENIC: setting up modes in kspace...
> NGENIC_2LPT: Computing secondary source term, derivatices 1 1
> NGENIC: setting up modes in kspace...
> NGENIC_2LPT: Computing secondary source term, derivatices 2 2
> NGENIC: setting up modes in kspace...
> NGENIC_2LPT: Computing secondary source term, derivatices 0 1
> NGENIC: setting up modes in kspace...
> NGENIC_2LPT: Computing secondary source term, derivatices 0 2
> NGENIC: setting up modes in kspace...
> NGENIC_2LPT: Computing secondary source term, derivatices 1 2
> NGENIC: setting up modes in kspace...
> NGENIC_2LPT: Secondary source term computed in real space
> NGENIC_2LPT: Done transforming it to k-space
> NGENIC_2LPT: Obtaining second order displacements for axes=0
> NGENIC_2LPT: Obtaining second order displacements for axes=1
> NGENIC_2LPT: Obtaining second order displacements for axes=2
> NGENIC_2LPT: Obtaining Zeldovich displacements for axes=0
> NGENIC: setting up modes in kspace...
> NGENIC_2LPT: Obtaining Zeldovich displacements for axes=1
> NGENIC: setting up modes in kspace...
> NGENIC_2LPT: Obtaining Zeldovich displacements for axes=2
> NGENIC: setting up modes in kspace...
>
> NGENIC: Maximum displacement: 0.771307, in units of the part-spacing=
> 3.94909
>
>
> NGENIC: Maximum velocity component: 1090.86
>
>
> GENERATE_GAS_IN_ICS: Generated gas particles from DM particle
> distribution. TotNumGas=2097152
>
> INIT: Testing ID uniqueness...
> INIT: success. took=0.372065 sec
>
> DOMAIN: Begin domain decomposition (sync-point 0).
> DOMAIN: New shift vector determined (-16.519 13.407 4.74042)
> DOMAIN: Sum=2 TotalCost=3 NumTimeBinsToBeBalanced=1 MultipleDomains=3
> DOMAIN: Increasing TopNodeAllocFactor=0.08 new value=0.104
> DOMAIN: Increasing TopNodeAllocFactor=0.104 new value=0.1352
> DOMAIN: Increasing TopNodeAllocFactor=0.1352 new value=0.17576
> DOMAIN: Increasing TopNodeAllocFactor=0.17576 new value=0.228488
> DOMAIN: Increasing TopNodeAllocFactor=0.228488 new value=0.297034
> DOMAIN: Increasing TopNodeAllocFactor=0.297034 new value=0.386145
> DOMAIN: Increasing TopNodeAllocFactor=0.386145 new value=0.501988
> DOMAIN: Increasing TopNodeAllocFactor=0.501988 new value=0.652585
> DOMAIN: Increasing TopNodeAllocFactor=0.652585 new value=0.84836
> DOMAIN: NTopleaves=64, determination of top-level tree involved 2
> iterations and took 0.909439 sec
> DOMAIN: we are going to try at most 156 different settings for combining
> the domains on tasks=6, nnodes=1
> DOMAIN: total_cost=2 total_load=1
> DOMAIN: total_cost=2 total_load=1
> DOMAIN: total_cost=2 total_load=1
> DOMAIN: total_cost=2 total_load=1
> DOMAIN: best solution found after 4 iterations by task=1 for nextra=0,
> reaching maximum imbalance of 1.11106|1.11642
> DOMAIN: combining multiple-domains took 0.0813736 sec
> DOMAIN: exchange of 4194304 particles
> ALLOCATE: Changing to MaxPartSph = 0
> DOMAIN: particle exchange done. (took 3.19289 sec)
> DOMAIN: domain decomposition done. (took in total 4.38405 sec)
> PEANO: Begin Peano-Hilbert order...
> PEANO: done, took 0.514037 sec.
>
>
> I've found something odd!
> The mass content accounts only for Omega=0.616,
> but you specified Omega=0.308 in the parameterfile.
>
> I better stop.
> endrun called, calling MPI_Finalize()
> bye!
> ============================================
>
> I would be very grateful for your help on this issue.
> Best regards,
> Hassan
>
>
> On Sun, Jul 4, 2021 at 12:17 PM Volker Springel <
> vspringel_at_mpa-garching.mpg.de> wrote:
>
>>
>> Hi Hassan,
>>
>> You'd have to delete the statement
>>
>> if(WDM_On == 1 && WDM_Vtherm_On == 1)
>> add_WDM_thermal_speeds(&block[3 * pc]);
>>
>> from save.c in this old version of N-GenIC. This was left in there when
>> not fully cleaning up a modification for warm dark matter.
>>
>> Note that a simpler option is to simply feed Gadget/Arepo a DM initial
>> conditions, and create the gas component on the fly for it with the
>> GENERATE_GAS_IN_ICS option. Then you do not need to bother with PRODUCEGAS
>> in N-GenIC at all.
>>
>> Regards,
>> Volker
>>
>>
>>
>> > On 2. Jul 2021, at 19:34, Hassan Fathivavsari <h.fathie_at_gmail.com>
>> wrote:
>> >
>> > Dear all,
>> >
>> > I am creating an Initial Condition file using N-GenIC. I could
>> successfully create the
>> > initial condition with PRODUCEGAS being disabled.
>> >
>> > But when I set PRODUCEGAS in the Makefile, I get the following error:
>> >
>> > pc_at_ubuntu:~/N-GenIC$ make
>> > mpicc -DPRODUCEGAS -DNO64BITID -O3 -Wall
>> -I/usr/local/include -I/usr/local/include -c -o main.o main.c
>> > mpicc -DPRODUCEGAS -DNO64BITID -O3 -Wall
>> -I/usr/local/include -I/usr/local/include -c -o power.o power.c
>> > power.c: In function ‘read_power_table’:
>> > power.c:59:16: warning: format not a string literal and no format
>> arguments [-Wformat-security]
>> > 59 | sprintf(buf, FileWithInputSpectrum);
>> > | ^~~~~~~~~~~~~~~~~~~~~
>> > power.c:90:16: warning: format not a string literal and no format
>> arguments [-Wformat-security]
>> > 90 | sprintf(buf, FileWithInputSpectrum);
>> > | ^~~~~~~~~~~~~~~~~~~~~
>> > mpicc -DPRODUCEGAS -DNO64BITID -O3 -Wall
>> -I/usr/local/include -I/usr/local/include -c -o allvars.o allvars.c
>> > mpicc -DPRODUCEGAS -DNO64BITID -O3 -Wall
>> -I/usr/local/include -I/usr/local/include -c -o save.o save.c
>> > save.c: In function ‘save_local_data’:
>> > save.c:218:10: error: ‘WDM_On’ undeclared (first use in this function)
>> > 218 | if(WDM_On == 1 && WDM_Vtherm_On == 1)
>> > | ^~~~~~
>> > save.c:218:10: note: each undeclared identifier is reported only once
>> for each function it appears in
>> > save.c:218:25: error: ‘WDM_Vtherm_On’ undeclared (first use in this
>> function)
>> > 218 | if(WDM_On == 1 && WDM_Vtherm_On == 1)
>> > | ^~~~~~~~~~~~~
>> > save.c:57:20: warning: variable ‘maxidlen’ set but not used
>> [-Wunused-but-set-variable]
>> > 57 | int blockmaxlen, maxidlen, maxlongidlen;
>> > | ^~~~~~~~
>> > save.c:56:14: warning: variable ‘blocklongid’ set but not used
>> [-Wunused-but-set-variable]
>> > 56 | long long *blocklongid;
>> > | ^~~~~~~~~~~
>> > make: *** [<builtin>: save.o] Error 1
>> >
>> > I would be grateful if someone could help me with this issue.
>> >
>> > With best regards,
>> > Hassan
>> >
>> >
>> >
>> > -----------------------------------------------------------
>> >
>> > 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 2021-07-05 14:43:50

This archive was generated by hypermail 2.3.0 : 2022-09-01 14:03:43 CEST