MPI ERROR

Submitted by Pankhi Singh on Mon, 08/17/2020 - 22:19

I am trying in install liggghts on ubuntu and i have done half of the processes but i am stuck at the "make auto" command when i type make auto i am getting this error

Creating list of contact models completed.
make[1]: Entering directory '/home/pakhi/LIGGGHTS-PUBLIC/src/Obj_auto'
Makefile:456: *** 'Could not compile a simple MPI example. Test was done with MPI_INC="" and MPICXX="mpicxx"'. Stop.
make[1]: Leaving directory '/home/pakhi/LIGGGHTS-PUBLIC/src/Obj_auto'
make: *** [Makefile:114: auto] Error 2

Can some one plzz help me i have tried changing the AUTOINSTALL VTK to "ON"..

Forums:

mschramm | Tue, 08/18/2020 - 00:11

the autoinstall vtk flag will only install the vtk package... you still need mpi installed on your computer.
Have you installed a mpi package (openmpi or mpich)?
If you have not, please install mpi by
sudo apt install libopenmpi-dev

also if you have not installed vtk, do
sudo apt install vtk7-dev

mschramm | Tue, 08/18/2020 - 21:10

For Ubuntu 18.04, to install vtk-7 for liggghts (What I am using on my laptop's wsl enviroment)
sudo apt install libvtk7-dev

were you able to install mpi?

When dealing with apt, you can list available packages using "wildcards". To list all packages that start with
lib
and end with
dev
and have vtk somewhere between them, you would do
sudo apt list lib*vtk*dev

Pankhi Singh | Wed, 08/19/2020 - 15:27

Thank you for the help i was able to install LIGGGHTS.But when i tried to run the example simulation chute_wear.
It is giving that there are not enough slots available in the system to satisfy the 8 slots that were requested by the application:
lmp380

(Is this a due to lack of hardware in my laptop?)

mschramm | Wed, 08/19/2020 - 16:47

Hello
How did you call the program? (mpirun -n 4 liggghts -in in.chute_ware ?)
How many cores and how many threads does your laptop have?

I usually see that error when working on our cluster but I was able to replicate it on my wsl environment.
Try using less cores (-n 2) and see if that works.

Pankhi Singh | Wed, 08/19/2020 - 23:56

Thank you for the help it worked as a defined 1 instead of 8 slots.
But now i am trying to do my own simulation and i have nearly completed it, i am stuck at last as when i am trying to simulate the script files
i am getting a error

"ERROR:Could not find fix group ID"

What should i do? Can you help me out with this also.

Pankhi Singh | Thu, 08/20/2020 - 05:27

Here is the script.According to me the problem is there in the "dump" command..

# Preliminaries
units si
atom_style sphere
atom_modify map array
boundary f f f
newton off
communicate single vel yes
#processors 2 2 3

# Declare domain
region domain block -0.138 0.138 -0.138 0.138 -0.0045 0.43 units box
create_box 2 domain

# Neighbor listing
neighbor 0.003 bin
neigh_modify every 1 check no

#setup
# Material and interaction properties required
fix m1 all property/global youngsModulus peratomtype 2.5e7 2.5e7
fix m2 all property/global poissonsRatio peratomtype 0.25 0.25
fix m3 all property/global coefficientRestitution peratomtypepair 2 0.5 0.5 0.5 0.5
fix m4 all property/global coefficientFriction peratomtypepair 2 0.2 0.175 0.175 0.5

# Particle insertion
fix pts all particletemplate/sphere 15485863 atom_type 1 density constant 1000 radius constant 0.0015
fix pdd all particledistribution/discrete 67867967 1 pts 1.0
region factory cylinder z 0 0 0.10 0.4 0.41 units box
fix ins all insert/rate/region seed 86028157 distributiontemplate pdd &
nparticles 150000 particlerate 150000 insert_every 1000 &
overlapcheck yes vel constant 0. 0. -1.0 region factory ntry_mc 10000

# Import mesh from cad:
fix cad1 all mesh/surface file Body2.stl type 2 scale 0.001
fix cad2 all mesh/surface file Body1.stl type 2 scale 0.001

# Use the imported mesh as granular wall
fix all wall/gran model hertz history rolling_friction epsd2 mesh n_meshes 2 meshes cad1 cad2

# Define the physics
pair_style gran/hertz/history
pair_coeff * *

# Integrator
fix integrate all nve/sphere

# Gravity
fix grav all gravity 9.81 vector 0.0 0.0 -1.0

#timestep
timestep 0.00001

# Thermodynamic output settings
thermo_style custom step atoms ke cpu
thermo 10000
thermo_modify norm no lost ignore

# Check time step and initialize dump file
fix ctg all check/timestep/gran 1 0.01 0.01
run 1
unfix ctg

# Create imaging information
dump dmp all custom/vtk 200 post/input*.vtk id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius
dump dumpstress all mesh/gran/VTK 200 post/mesh_*.vtk stress wear cad

### Execution and further settings

# Fill the Body
run 150000 upto

run 300000

deepakpawar.2310 | Fri, 08/21/2020 - 09:24

Hi
Replace line

# Use the imported mesh as granular wall
fix all wall/gran model hertz history rolling_friction epsd2 mesh n_meshes 2 meshes cad1 cad2, with

fix granwalls all wall/gran model hertz history rolling_friction epsd2 mesh n_meshes 2 meshes cad1 cad2