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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
*

*>>> >
*

*>>> >
*

*>>> >
*

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

*>>> >
*

*>>> > 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 15:31:24

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:

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

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