Dear all,
I am a new user of GADGET.
I have created an initial condition file using MUSIC. But when I execute
the GADGET
code (mpirun -np 6 ./Gadget4 param.txt), I got the following error:
------------------------
Code termination on task=5, function mymalloc_movable_fullinfo(), file
src/data/mymalloc.cc, line 326:
Not enough memory in mymalloc_fullinfo() to allocate 685.336 MB for
variable 'rhogrid' at pmforce_zoom_optimized_prepare_density()/src/pm/
pm_periodic.cc/line 378 (FreeBytes=97.1207 MB).
-------------------------
But I have enough memory on my Laptop. I have also pasted below the full
message
printed out in the Terminal:
I would be very grateful if some one could help me in this issue.
With best regards,
Hassan
===================== Full Terminal Message =========================
pc_at_ubuntu:~/Desktop/SPH/gadget4-master/IC_from_MUSIC$ mpirun -np 6
./Gadget4 param.txt
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./IC_from_MUSIC//build -Isrc
Code was compiled with the following settings:
EVALPOTENTIAL
FOF
FOF_GROUP_MIN_LEN=32
FOF_PRIMARY_LINK_TYPES=2
GADGET2_HEADER
INDIVIDUAL_GRAVITY_SOFTENING=4+8+16+32
NSOFTCLASSES=4
PERIODIC
PMGRID=1024
PM_ZOOM_OPTIMIZED
POWERSPEC_ON_OUTPUT
SELFGRAVITY
SUBFIND
Running on 6 MPI tasks.
BEGRUN: Size of particle structure 84 [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 80 [bytes]
-------------------------------------------------------------------------------------------------------------------------
AvailMem: Largest = 2795.93 Mb (on task= 0), Smallest = 2795.93 Mb
(on task= 0), Average = 2795.93 Mb
Total Mem: Largest = 6267.95 Mb (on task= 0), Smallest = 6267.95 Mb
(on task= 0), Average = 6267.95 Mb
Committed_AS: Largest = 3472.02 Mb (on task= 0), Smallest = 3472.02
Mb (on task= 0), Average = 3472.02 Mb
SwapTotal: Largest = 2048.00 Mb (on task= 0), Smallest = 2048.00 Mb
(on task= 0), Average = 2048.00 Mb
SwapFree: Largest = 2048.00 Mb (on task= 0), Smallest = 2048.00 Mb
(on task= 0), Average = 2048.00 Mb
AllocMem: Largest = 3472.02 Mb (on task= 0), Smallest = 3472.02 Mb
(on task= 0), Average = 3472.02 Mb
avail /dev/shm: Largest = 3132.36 Mb (on task= 0), Smallest =
3132.36 Mb (on task= 0), Average = 3132.36 Mb
-------------------------------------------------------------------------------------------------------------------------
Task=0 has the maximum commited memory and is host: ubuntu
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Obtaining parameters from file 'param.txt':
InitCondFile ./ics_gadget.dat
OutputDir ./output
SnapshotFileBase snapshot
OutputListFilename ./ExpansionList_16
ICFormat 1
SnapFormat 3
TimeLimitCPU 86400
CpuTimeBetRestartFile 7200
MaxMemSize 100
TimeBegin 0.0078125
TimeMax 1
ComovingIntegrationOn 1
Omega0 2.20836e-06
OmegaLambda 0.75
OmegaBaryon 0.04
HubbleParam 0.73
BoxSize 100
Hubble 100
OutputListOn 1
TimeBetSnapshot 0
TimeOfFirstSnapshot 0
TimeBetStatistics 0.01
NumFilesPerSnapshot 1
MaxFilesWithConcurrentIO 1
ErrTolIntAccuracy 0.012
CourantFac 0.3
MaxSizeTimestep 0.005
MinSizeTimestep 0
TypeOfOpeningCriterion 1
ErrTolTheta 0.7
ErrTolThetaMax 1
ErrTolForceAcc 0.0025
TopNodeFactor 5
ActivePartFracForNewDomainDecomp 0.01
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 0.001
SofteningComovingClass1 0.007
SofteningComovingClass2 0.025
SofteningComovingClass3 0.081
SofteningMaxPhysClass0 0.0005
SofteningMaxPhysClass1 0.007
SofteningMaxPhysClass2 0.025
SofteningMaxPhysClass3 0.081
SofteningClassOfPartType0 0
SofteningClassOfPartType1 0
SofteningClassOfPartType2 1
SofteningClassOfPartType3 2
SofteningClassOfPartType4 3
SofteningClassOfPartType5 3
DesLinkNgb 20
ArtBulkViscConst 1
MinEgySpec 0
InitGasTemp 0
MALLOC: Allocation of shared memory took 0.000141637 sec
found 16 times in output-list.
BEGRUN: Hubble (internal units) = 100
BEGRUN: h = 0.73
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
READIC: filenr=0, './ics_gadget.dat' contains:
READIC: Type 0 (gas): 0 (tot= 0) masstab= 0
READIC: Type 1: 17576 (tot= 17576) masstab= 3.65236e-09
READIC: Type 2: 0 (tot= 0) masstab= 0
READIC: Type 3: 0 (tot= 0) masstab= 0
READIC: Type 4: 0 (tot= 0) masstab= 0
READIC: Type 5: 54196 (tot= 54196) masstab= 0
READIC: Reading file `./ics_gadget.dat' on task=0 and distribute it to 0 to
5.
READIC: reading block 0 (Coordinates)...
READIC: reading block 1 (Velocities)...
READIC: reading block 2 (ParticleIDs)...
READIC: reading block 3 (Masses)...
READIC: reading done. Took 0.00612891 sec, total size 2.12379 MB,
corresponds to effective I/O rate of 346.521 MB/sec
READIC: Total number of particles : 71772
INIT: Testing ID uniqueness...
INIT: success. took=0.00309694 sec
DOMAIN: Begin domain decomposition (sync-point 0).
DOMAIN: Sum=2 TotalCost=2 NumTimeBinsToBeBalanced=1 MultipleDomains=2
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: Increasing TopNodeAllocFactor=0.84836 new value=1.10287
DOMAIN: Increasing TopNodeAllocFactor=1.10287 new value=1.43373
DOMAIN: Increasing TopNodeAllocFactor=1.43373 new value=1.86385
DOMAIN: Increasing TopNodeAllocFactor=1.86385 new value=2.423
DOMAIN: Increasing TopNodeAllocFactor=2.423 new value=3.1499
DOMAIN: NTopleaves=246, determination of top-level tree involved 14
iterations and took 0.00647044 sec
DOMAIN: we are going to try at most 149 different settings for combining
the domains on tasks=6, nnodes=1
DOMAIN: total_cost=2 total_load=1
DOMAIN: best solution found after 1 iterations by task=5 for nextra=0,
reaching maximum imbalance of 1.02449|1.03052
DOMAIN: combining multiple-domains took 0.000829803 sec
DOMAIN: exchange of 71772 particles
DOMAIN: particle exchange done. (took 0.00680363 sec)
DOMAIN: domain decomposition done. (took in total 0.0150899 sec)
PEANO: Begin Peano-Hilbert order...
PEANO: done, took 0.00189733 sec.
INIT: AvgType1Mass = 3.65236e-09 (min=3.65236e-09 max=3.65236e-09)
Ndm1tot=17576
INIT: For this AvgType1Mass, the mean particle spacing is -nan and the
assigned softening is 0.001
SNAPSHOT: Setting next time for snapshot file to Time_next= 0.0288901
(DumpFlag=1)
Sync-Point 0, Time: 0.0078125, Redshift: 127, Systemstep: 0, Dloga: 0,
Nsync-grv: 71772, Nsync-hyd: 0
DOMAIN: Begin domain decomposition (sync-point 0).
DOMAIN: Sum=2 TotalCost=2 NumTimeBinsToBeBalanced=1 MultipleDomains=2
DOMAIN: NTopleaves=246, determination of top-level tree involved 14
iterations and took 0.00247401 sec
DOMAIN: we are going to try at most 149 different settings for combining
the domains on tasks=6, nnodes=1
DOMAIN: total_cost=2 total_load=1
DOMAIN: best solution found after 1 iterations by task=5 for nextra=0,
reaching maximum imbalance of 1.02449|1.03052
DOMAIN: combining multiple-domains took 0.00157532 sec
DOMAIN: exchange of 71772 particles
DOMAIN: particle exchange done. (took 0.00363552 sec)
DOMAIN: domain decomposition done. (took in total 0.00819422 sec)
PEANO: Begin Peano-Hilbert order...
PEANO: done, took 0.000835626 sec.
ACCEL: Start tree gravity force computation... (71772 particles)
PM-PERIODIC: Starting periodic PM calculation. (Rcut=0.854492) presently
allocated=1.83447 MB
-------------------------- Allocated Memory Blocks---- ( Step 0
)------------------
Task Nr F Variable MBytes Cumulative
Function|File|Linenumber
------------------------------------------------------------------------------------------
4 0 0 GetGhostRankForSimulCommRank 0.0001
0.0001 mymalloc_init()|src/data/mymalloc.cc|137
4 1 0 GetShmRankForSimulCommRank 0.0001
0.0001 mymalloc_init()|src/data/mymalloc.cc|138
4 2 0 GetNodeIDForSimulCommRank 0.0001
0.0002 mymalloc_init()|src/data/mymalloc.cc|139
4 3 0 SharedMemBaseAddr 0.0001
0.0002 mymalloc_init()|src/data/mymalloc.cc|153
4 4 1 slab_to_task 0.0039
0.0042 my_slab_based_fft_init()|src/pm/pm_mpi_fft.cc|45
4 5 1 slabs_x_per_task 0.0001
0.0042 my_slab_based_fft_init()|src/pm/pm_mpi_fft.cc|60
4 6 1 first_slab_x_of_task 0.0001
0.0043 my_slab_based_fft_init()|src/pm/pm_mpi_fft.cc|63
4 7 1 slabs_y_per_task 0.0001
0.0043 my_slab_based_fft_init()|src/pm/pm_mpi_fft.cc|66
4 8 1 first_slab_y_of_task 0.0001
0.0044 my_slab_based_fft_init()|src/pm/pm_mpi_fft.cc|69
4 9 1 P 1.5972
1.6016 allocate_memory()|src/io/../fof/../data/simparticles.h|273
4 10 1 SphP 0.0001
1.6017 allocate_memory()|src/io/../fof/../data/simparticles.h|274
4 11 1 NextActiveParticleHydro 0.0001
1.6017 timebins_allocate()|src/time_integration/timestep.cc|463
4 12 1 NextInTimeBinHydro 0.0001
1.6018 timebins_allocate()|src/time_integration/timestep.cc|466
4 13 1 PrevInTimeBinHydro 0.0001
1.6019 timebins_allocate()|src/time_integration/timestep.cc|469
4 14 1 NextActiveParticleGravity 0.0761
1.6780 timebins_allocate()|src/time_integration/timestep.cc|463
4 15 1 NextInTimeBinGravity 0.0761
1.7541 timebins_allocate()|src/time_integration/timestep.cc|466
4 16 1 PrevInTimeBinGravity 0.0761
1.8302 timebins_allocate()|src/time_integration/timestep.cc|469
4 17 1 FirstTopleafOfTask 0.0001
1.8303 domain_allocate()|src/domain/domain.cc|163
4 18 1 NumTopleafOfTask 0.0001
1.8303 domain_allocate()|src/domain/domain.cc|164
4 19 1 TopNodes 0.0022
1.8325 domain_allocate()|src/domain/domain.cc|165
4 20 1 TaskOfLeaf 0.0010
1.8335 domain_allocate()|src/domain/domain.cc|166
4 21 1 ListOfTopleaves 0.0010
1.8345 domain_decomposition()|src/domain/domain.cc|118
4 22 0 part 1.0726
2.9070 pmforce_zoom_optimized_prepare_density()|src/pm/pm_periodic.cc|184
4 23 1 localfield_globalindex 0.0001
2.9071 pmforce_zoom_optimized_prepare_density()|src/pm/pm_periodic.cc|272
4 24 1 localfield_data 0.0001
2.9072 pmforce_zoom_optimized_prepare_density()|src/pm/pm_periodic.cc|274
4 25 1 localfield_first 0.0001
2.9072 pmforce_zoom_optimized_prepare_density()|src/pm/pm_periodic.cc|275
4 26 1 localfield_sendcount 0.0001
2.9073 pmforce_zoom_optimized_prepare_density()|src/pm/pm_periodic.cc|276
4 27 1 localfield_offset 0.0001
2.9073 pmforce_zoom_optimized_prepare_density()|src/pm/pm_periodic.cc|277
4 28 1 localfield_recvcount 0.0001
2.9074 pmforce_zoom_optimized_prepare_density()|src/pm/pm_periodic.cc|278
------------------------------------------------------------------------------------------
Code termination on task=4, function mymalloc_movable_fullinfo(), file
src/data/mymalloc.cc, line 326:
Not enough memory in mymalloc_fullinfo() to allocate 685.336 MB for
variable 'rhogrid' at pmforce_zoom_optimized_prepare_density()/src/pm/
pm_periodic.cc/line 378 (FreeBytes=97.0926 MB).
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
pc_at_ubuntu:~/Desktop/SPH/gadget4-master/IC_from_MUSIC$
Received on 2021-02-11 19:58:51
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: 2023-01-10 10:01:32 CET