CFDEM compiling error

Submitted by hamedhoori on Sat, 03/07/2020 - 22:33

Hi everyone I have a problem compiling a cfdem case with my computer, I checked the files on another stronger computer and they're ok, but I think I'm missing something here. I'll appreciate any help of yours if you could tell me what is wrong.
mesh was built before - using old mesh
Decomposing case.
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 5.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 5.x-538044ac05c4
Exec : decomposePar -force
Date : Mar 08 2020
Time : 00:55:37
Host : "hamed-hoorijani"
PID : 27961
I/O : uncollated
Case : /home/hamed/Desktop/test/ads/CFD
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Decomposing mesh region0

Create mesh

Calculating distribution of cells
Selecting decompositionMethod simple

Finished decomposition in 0.04 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Distributing points to processors

Constructing processor meshes

Processor 0
Number of cells = 24000
Number of faces shared with processor 1 = 12306
Number of processor patches = 1
Number of processor faces = 12306
Number of boundary faces = 13858

Processor 1
Number of cells = 24000
Number of faces shared with processor 0 = 12306
Number of processor patches = 1
Number of processor faces = 12306
Number of boundary faces = 13582

Number of processor faces = 12306
Max number of cells = 24000 (0% above average 24000)
Max number of processor patches = 1 (0% above average 1)
Max number of faces between processors = 12306 (0% above average 12306)

Time = 0

Processor 0: field transfer
Processor 1: field transfer

End

do nothing.

// run_parallel_cfdemSolverPiso_voidfractionTest_CFDDEM //

/home/hamed/Desktop/test/ads/CFD

rm: cannot remove 'couplingFiles/*': No such file or directory
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 5.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 5.x-538044ac05c4
Exec : cfdemSolverPiso -parallel
Date : Mar 08 2020
Time : 00:55:39
Host : "hamed-hoorijani"
PID : 27990
I/O : uncollated
Case : /home/hamed/Desktop/test/ads/CFD
nProcs : 2
Slaves : 1("hamed-hoorijani.27991")
Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

PISO: Operating solver in PISO mode

Reading field p

Reading physical velocity field U
Note: only if voidfraction at boundary is 1, U is superficial velocity!!!

Reading momentum exchange field Ksl

Reading voidfraction field voidfraction = (Vgas/Vparticle)

Creating density field rho

Reading particle velocity field Us

Reading/calculating face flux field phi

Generating interstitial face flux field phiByVoidfraction

Selecting incompressible transport model Newtonian
Selecting turbulence model type laminar
Selecting laminar stress model Stokes
No finite volume options present

Reading g
Selecting locateModel engine
Selecting dataExchangeModel twoWayMPI
Starting up LIGGGHTS for first time execution
Executing input script '../DEM/in.liggghts_init'
LIGGGHTS (Version LIGGGHTS-PUBLIC 3.8.0, compiled 2020-02-17-21:05:11 by hamed, git commit ce1931e377a2945e3fa25dae0eebc1f697009a32)
log ../DEM/log.liggghts
thermo_log ../DEM/post/thermo.txt

# read packed bed and calc convective heat transfer

atom_style granular
atom_modify map array
communicate single vel yes
boundary f f f
newton off

units si
#processors 1 2 1

#read the restart file
read_restart ../DEM/post/restart/liggghts.restart
Reading restart file ...
version 3 7
WARNING: Restart file version does not match LIGGGHTS version (../read_restart.cpp:507)
--> restart file = Version LIGGGHTS-PUBLIC 3.7.0, compiled 2017-07-18-23:47:28 by root, git commit unknown
--> LIGGGHTS = Version LIGGGHTS-PUBLIC 3.8.0, compiled 2020-02-17-21:05:11 by hamed, git commit ce1931e377a2945e3fa25dae0eebc1f697009a32
version 3 7
WARNING: Restart file used different # of processors (../read_restart.cpp:574)
orthogonal box = (-0.1 -0.03 -0.05) to (0.1 0.03 2.1)
1 by 1 by 2 MPI processor grid
1000 atoms

neighbor 0.005 bin
neigh_modify delay 0

#Material properties required for new pair styles
fix m1 all property/global youngsModulus peratomtype 11.2e7 11.2e7
fix m2 all property/global poissonsRatio peratomtype 0.33 0.33
fix m3 all property/global coefficientRestitution peratomtypepair 2 0.97 0.97 0.97 0.97
fix m4 all property/global coefficientFriction peratomtypepair 2 0.1 0.1 0.1 0.1
fix m5 all property/global coefficientRollingFriction peratomtypepair 2 0.025 0.025 0.025 0.025

#pair style
pair_style gran model hertz tangential history rolling_friction cdt
pair_coeff * *

#timestep, gravity
timestep 0.0002
fix gravi all gravity 9.81 vector 0. 0.0 -1.0

fix cad1 all mesh/surface file ../DEM/sfb.stl type 2 curvature 1e-5
INFO: mesh file (../DEM/sfb.stl) is required, but data will be taken from restart file (../fix_mesh.cpp:417)
Resetting global state of Fix cad1 Style mesh/surface from restart file info
fix geometry all wall/gran model hertz tangential history rolling_friction cdt mesh n_meshes 1 meshes cad1
Resetting global state of Fix n_neighs_mesh_cad1 Style property/atom from restart file info
Resetting per-atom state of Fix n_neighs_mesh_cad1 Style property/atom from restart file info
Resetting global state of Fix tracker_cad1 Style contacthistory/mesh from restart file info
Resetting per-atom state of Fix tracker_cad1 Style contacthistory/mesh from restart file info

#heat transfer
fix ftco all property/global thermalConductivity peratomtype 5. 5. # lambda in [W/(K*m)]
fix ftca all property/global thermalCapacity peratomtype 0.1 0.1 # cp in [J/(kg*K)]
fix heattransfer all heat/gran initial_temperature 600.

#set particle temperature for the bed
run 0
Resetting global state of Fix contacthistory Style contacthistory from restart file info
Resetting per-atom state of Fix contacthistory Style contacthistory from restart file info
Setting up run at Sun Mar 8 00:55:39 2020

Import and parallelization of mesh cad1 containing 12 triangle(s) successful
Memory usage per processor = 12.2048 Mbytes
Step Atoms KinEng CPU
180001 1000 0.13378357 0
Loop time of 3.8205e-06 on 2 procs for 0 steps with 1000 atoms, finish time Sun Mar 8 00:55:39 2020

Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 3.8205e-06 (100)

Nlocal: 500 ave 1000 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 327 ave 654 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 654
Ave neighs/atom = 0.654
Neighbor list builds = 0
Dangerous builds = 0
region total block INF INF INF INF INF INF units box
set region total property/atom Temp 600. # former property/paratom
Setting atom values ...
1000 settings made for property/atom

#cfd coupling
fix cfd all couple/cfd couple_every 20 mpi
couple_every as specified in LIGGGHTS is overriden by calling external program (../fix_cfd_coupling.cpp:114)
fix cfd2 all couple/cfd/force

#this one invokes heat transfer calculation, transfers per-particle temperature and adds convective heat flux to particles
fix cfd3 all couple/cfd/convection T0 600

#apply nve integration to all particles that are inserted as single particles
fix integr all nve/sphere

#screen output
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
WARNING: Changing thermo_temp compute object. This object is deprecated and will be removed in the future. (../compute.cpp:161)

#insert the first particles so that dump is not empty
run 1
Setting up run at Sun Mar 8 00:55:39 2020

Memory usage per processor = 12.7682 Mbytes
Step Atoms KinEng 1 Volume
180001 1000 0.13378357 0.0015969925 0.0258
180002 1000 1.4336137 0.01773943 0.0258
Loop time of 0.000252571 on 2 procs for 1 steps with 1000 atoms, finish time Sun Mar 8 00:55:39 2020

Pair time (%) = 2.532e-05 (10.0249)
Neigh time (%) = 0 (0)
Comm time (%) = 2.467e-06 (0.976753)
Outpt time (%) = 9.808e-05 (38.8326)
Other time (%) = 0.000126704 (50.1658)

Nlocal: 500 ave 1000 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 327 ave 654 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 654
Ave neighs/atom = 0.654
Neighbor list builds = 0
Dangerous builds = 0
dump dmp all custom 10000 ../DEM/post/dump*.liggghts_init id type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius

run 1
Setting up run at Sun Mar 8 00:55:39 2020

Memory usage per processor = 12.7682 Mbytes
Step Atoms KinEng 1 Volume
180002 1000 1.4336137 0.01773943 0.0258
180003 999 8.8171891 0.086929544 0.0258
Loop time of 0.00254941 on 2 procs for 1 steps with 999 atoms, finish time Sun Mar 8 00:55:39 2020

Pair time (%) = 2.0988e-05 (0.823248)
Neigh time (%) = 0.000486621 (19.0876)
Comm time (%) = 5.7889e-05 (2.27068)
Outpt time (%) = 0.00105516 (41.3884)
Other time (%) = 0.000928754 (36.4301)

Nlocal: 499.5 ave 999 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 331 ave 662 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 662
Ave neighs/atom = 0.662663
Neighbor list builds = 1
Dangerous builds = 1
--> FOAM Warning : You are using sub-time-steps (i.e. CFD TS < coupling time)! Check your settings properly.
Selecting IOModel basicIO
Selecting probeModel off
Selecting voidFractionModel divided
Selecting averagingModel dense
Selecting clockModel off
start clock measurement at t >0.008
Selecting smoothingModel off
Selecting meshMotionModel noMeshMotion

CFDEMcoupling version: cfdem-3.8.1
, compatible to LIGGGHTS version: 3.8.0
, compatible to OF version and build: 5.x-commit-538044ac05c4672b37c7df607dca1116fa88df88

You are currently using:
OF version: 5.x
OF build: 5.x-538044ac05c4
CFDEM build: 3.8.0-3-gb237264

cg is set to: 1
LIGGGHTS hosts 2 atom types.
If BC are important, please provide volScalarFields -imp/expParticleForces-
ignoring ddt(voidfraction)
Selecting momCoupleModel implicitCouple

implicit momentum exchange field calculate if alphaP larger than : 1
Selecting forceModel KochHillDrag
Selecting forceSubModel ImEx
reading switches:
looking for treatForceExplicit ... not found in dict, using default. treatForceExplicit = false
looking for implForceDEM ... not found in dict, using default. implForceDEM = false
looking for verbose ... not found in dict, using default. verbose = false
looking for interpolation ... not found in dict, using default. interpolation = false
looking for implForceDEMaccumulated ... not found in dict, using default. implForceDEMaccumulated = false
looking for scalarViscosity ... not found in dict, using default. scalarViscosity = false

Selecting forceModel gradPForce
Selecting forceSubModel ImEx
reading switches:
looking for treatForceExplicit ... not found in dict, using default. treatForceExplicit = true
looking for verbose ... not found in dict, using default. verbose = false
looking for interpolation ... not found in dict, using default. interpolation = false

Selecting forceModel viscForce
Selecting forceSubModel ImEx
reading switches:
looking for treatForceExplicit ... not found in dict, using default. treatForceExplicit = true
looking for verbose ... not found in dict, using default. verbose = false
looking for interpolation ... found in dict. interpolation = false
looking for scalarViscosity ... not found in dict, using default. scalarViscosity = false

Selecting forceModel particleCellVolume
Selecting forceSubModel ImEx
reading switches:
looking for verbose ... found in dict. verbose = false

--> FOAM Warning : Please make sure you use the new nomenclature for verbose force model settings, please have a look at the forceSubModel doc.
Selecting liggghtsCommandModel runLiggghts ,provide dicts, numbered from 0 to n
solving volume averaged Navier Stokes equations of type A
check if Archimedes lift is necessary (depends on pressure formulation)

Starting time loop

[0] [1]
[1]
[1] --> FOAM FATAL IO ERROR:
[1] 'functions' entry is not a dictionary
[1]
[1] file: IOstream from line 0 to line 0.
[1]
[1] From function bool Foam::functionObjectList::read()
[1] in file db/functionObjects/functionObjectList/functionObjectList.C at line 586.
[1]
FOAM parallel run exiting
[1]

[0]
[0] --------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--> FOAM FATAL IO ERROR:
[0] 'functions' entry is not a dictionary
[0]
[0] file: /home/hamed/Desktop/test/ads/CFD/system/controlDict from line 18 to line 218.
[0]
[0] From function bool Foam::functionObjectList::read()
[0] in file db/functionObjects/functionObjectList/functionObjectList.C at line 586.
[0]
FOAM parallel run exiting
[0]
[hamed-hoorijani:27980] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[hamed-hoorijani:27980] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
simulation finished? ...press enter to proceed

starting LIGGGHTS memory optimized parallel post processing
chunksize: 8 --> 8 files are processed per chunk. If you run out of memory reduce chunksize.
Working with 4 processes...
calculating chunks 1 - 4 of 91
calculating chunks 5 - 8 of 91
calculating chunks 9 - 12 of 91
calculating chunks 13 - 16 of 91
calculating chunks 17 - 20 of 91
calculating chunks 21 - 24 of 91
calculating chunks 25 - 28 of 91
calculating chunks 29 - 32 of 91
calculating chunks 33 - 36 of 91
calculating chunks 37 - 40 of 91
calculating chunks 41 - 44 of 91
calculating chunks 45 - 48 of 91
calculating chunks 49 - 52 of 91
calculating chunks 53 - 56 of 91
calculating chunks 57 - 60 of 91
calculating chunks 61 - 64 of 91
calculating chunks 65 - 68 of 91
calculating chunks 69 - 72 of 91
calculating chunks 73 - 76 of 91
calculating chunks 77 - 80 of 91
calculating chunks 81 - 84 of 91
calculating chunks 85 - 88 of 91
calculating chunks 89 - 91 of 91
wrote 724 granular snapshots in VTK format
time needed: 14.1872138977 sec

Lowered | Mon, 03/23/2020 - 12:48

Hi,
it seems like you just want to run the case... nothing to compile at all.
There is one warning regarding different numbers of processors in current calculation compared to restart file - in CFDEM there are at least 3 locations where you have to change the number of processors you want to use.
Can you check this?

Kind regards
Henrik

hamedhoori | Tue, 03/24/2020 - 22:13

Hi,
Thank you henry
I have managed to solve the error I was getting, It was for the software update. The script I had, was written with an older version of cfdem, Liggghts, and OpenFoam, when I attempt to run the case some changes in function in the cfdem and OpenFoam caused the error. After finding them and updating them for the current version, I managed to run my case.
Thank you for your reply.

Sincerely
Hamed