Re: Setting PRODUCEGAS in N-GenIC Makefile returns error

From: Hassan Fathivavsari <h.fathie_at_gmail.com>
Date: Mon, 5 Jul 2021 15:31:10 +0200

Dear Tiago,

Thank you very much for your reply.
Removing LEAN from Config.sh solved the problem.

Best regards,
Hassan

On Mon, Jul 5, 2021 at 2:44 PM Tiago Castro <tiagobscastro_at_gmail.com> wrote:

> 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
>>> >
>>> >
>>> >
>>> > -----------------------------------------------------------
>>> >
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>>>
>>>
>>>
>>>
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>>
Received on 2021-07-05 15:31:24

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