LIGGGHTS3.1.0 Installation issue

Submitted by rahulsoni on Fri, 03/13/2015 - 14:53

I am trying to install LIGGGHTS 3.1.0 but it throws the error:
multisphere_parallel.h: No such file or directory

Checked with the LIGGGHTS GitHub repo as well, but I found that no such file is there in the repo.
Kindly help

rahulsoni | Sat, 03/14/2015 - 09:42

Surprsing... I went to LIGGGHTS git online repo and searched for the multisphere_parallel.h (https://github.com/CFDEMproject/LIGGGHTS-PUBLIC/search?utf8=%E2%9C%93&q=...) but couldn't find any such file. Anyway now it is with me.

However, Richter my compilation is getting terminated with the following message:

$ make fedora
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
Make.sh: line 18: git: command not found
make[1]: Entering directory '/cygdrive/c/LIGGGHTS-PUBLIC-310/src/Obj_fedora'
mpic++ -O2 -funroll-loops -fstrict-aliasing -Wall -Wno-unused-result -DLAMMPS_GZIP -c ../universe.cpp
mpic++ -O2 memory.o atom_vec_sph_var.o compute_temp_region.o compute_heat_flux.o neigh_stencil.o compute_temp_sphere.o compute_msd_molecule.o compute_pair_local.o min_hftn.o universe.o pair_zbl.o compute_pe_atom.o granular_styles.o mech_param_gran.o pair.o atom_vec_line.o fix_shear_history.o angle_hybrid.o input_multisphere.o fix_spring_self.o fix_insert.o fix_rigid_small.o pair_lj_gromacs_coul_gromacs.o pair_hybrid.o fix_rigid_nh.o compute_atom_molecule.o fix_sph_density_corr.o fix_wall.o tri_mesh.o cfd_datacoupling_mpi.o pair_lj_expand.o compute_ke.o compute_com.o fix_mesh_surface_stress.o region_mesh_tet.o pair_sph_artvisc_tenscorr.o fix_lineforce.o fix_nph_sphere.o pair_lj_cut.o fix_property_atom_tracer_stream.o region_plane.o neigh_list.o compute_angle_local.o thermo.o compute_property_local.o input.o fix_tmd.o fix_template_sphere.o cfd_regionmodel_none.o fix_nvt_sllod.o verlet.o fix_insert_pack.o fix_rigid_nve.o dump_movie.o compute_pressure.o pair_lj_cut_coul_dsf.o compute_rdf.o fix_heat_gran.o property_registry.o compute_com_molecule.o atom_vec_charge.o pair_buck.o fix_check_timestep_gran.o reader_native.o pair_beck.o pair_buck_coul_cut.o fix_cfd_coupling_convection.o input_mesh_tri.o fix_sph_pressure.o fix_print.o min.o compute_ke_atom.o minimize.o fix_heat_gran_conduction.o fix_press_berendsen.o atom.o neigh_respa.o fix_deform.o dump_decomposition_vtk.o fix_viscous.o pair_born.o min_linesearch.o fix_nve_sph_stationary.o reader_xyz.o delete_atoms.o improper.o displace_atoms.o fix_ave_histo.o compute_dihedral_local.o image.o run.o variable.o finish.o fix_momentum.o force.o delete_bonds.o pair_coul_cut.o update.o fix_external.o region_union.o compute_erotate_sphere.o pair_gauss.o verlet_implicit.o pair_lj96_cut.o fix_rigid_nvt.o cfd_datacoupling_file.o pair_sph.o compute_cluster_atom.o neigh_half_multi.o pair_soft.o procmap.o min_cg.o pair_lj_smooth_linear.o fix_nph.o fix_neighlist_mesh.o write_data.o pair_gran.o group.o read_dump.o modified_andrew.o compute_pe.o fix_gravity.o min_fire.o fix_temp_rescale.o library.o region_wedge.o custom_value_tracker.o fix_nve_sph.o pair_lj_cut_coul_cut.o fix_property_atom_tracer.o region_cone.o fix_rigid.o respa.o lammps.o compute_temp_deform.o fix_enforce2d.o fix_store_state.o region.o math_extra.o pair_table.o compute_reduce.o compute_msd.o domain.o dump_atom_vtk.o dump_mesh_stl.o neigh_derive.o compute_cna_atom.o bond.o fix_ave_correlate.o fix_planeforce.o output.o neigh_half_bin.o body.o fix_langevin.o fix_rigid_npt.o fix_restrain.o region_intersect.o region_sphere.o fix_nh.o set.o fix_sph_density_continuity.o granular_wall.o granular_pair_style.o pair_coul_dsf.o pair_coul_wolf.o fix_box_relax.o fix_wall_lj1043.o fix_cfd_coupling_force_implicit.o fix_spring.o dump_custom.o compute_group_group.o fix_store.o pair_dpd.o neigh_full.o reader.o particleToInsert.o fix_read_restart.o fix_recenter.o pair_mie_cut.o fix_nh_sphere.o fix_nve.o fix_region_variable.o fix_move_mesh.o atom_vec_sph.o atom_map.o fix_setforce.o fix_check_timestep_sph.o create_atoms.o compute_pair_gran_local.o region_cylinder.o read_data.o special.o compute_temp.o irregular.o fix_nvt.o pair_lj_smooth.o pair_lj_cut_coul_debye.o atom_vec_sphere_w.o atom_vec_tri.o fix_wall_lj93.o fix_nve_sphere.o fix_move.o fix_wall_lj126.o tri_mesh_planar.o fix_ave_atom.o region_prism.o compute_slice.o compute_centro_atom.o fix_wall_region.o change_box.o neigh_dummy.o dump_euler_vtk.o pair_gran_proxy.o pair_coul_debye.o dump_cfg.o fix_spring_rg.o fix_aveforce.o region_block.o dump_atom.o dihedral_hybrid.o compute_temp_profile.o fix_mesh.o fix_temp_berendsen.o atom_vec_atomic.o compute_temp_partial.o fix_nve_limit.o dump_mesh_vtk.o modify_liggghts.o fix_heat.o bond_hybrid.o fix_deposit.o compute_temp_ramp.o fix_ave_spatial.o dump_xyz.o fix_contact_history_mesh.o fix_adapt.o library_cfd_coupling.o fix_rigid_nph.o compute_nparticles_tracer_region.o comm.o fix_sph_density_summation.o global_properties.o compute_inertia_molecule.o atom_vec_ellipsoid.o compute_temp_com.o integrate.o kspace.o neigh_bond.o fix_nvt_sphere.o atom_vec_body.o min_quickmin.o min_sd.o compute_ke_rigid.o fix_contact_history.o dump_dcd.o pair_morse.o atom_vec_sphere.o dihedral.o bounding_box.o compute.o improper_hybrid.o fix_minimize.o fix_property_global.o read_restart.o input_mesh_tet.o write_dump.o compute_property_atom.o fix_ave_time.o fix_ave_euler.o fix_wall_gran.o neigh_request.o cfd_datacoupling.o fix_sph.o pair_hybrid_overlay.o fix_npt.o fix_drag.o compute_coord_atom.o fix_freeze.o lattice.o angle.o fix_massflow_mesh.o fix_template_multiplespheres.o mesh_mover.o fix_insert_stream.o write_restart.o fix_store_force.o fix_scalar_transport_equation.o pair_dpd_tstat.o pair_lj_gromacs.o contact_models.o neighbor.o compute_erotate_rigid.o pair_born_coul_wolf.o fix_mesh_surface.o fix_nve_noforce.o fix_npt_sphere.o fix_insert_rate_region.o compute_vacf.o random_park.o atom_vec_hybrid.o container_base.o citeme.o fix_addforce.o fix_dt_reset.o compute_improper_local.o fix_cfd_coupling_force.o compute_bond_local.o fix_wall_sph.o fix_particledistribution_discrete.o create_box.o replicate.o main.o compute_property_molecule.o pair_yukawa.o dump.o neigh_gran.o timer.o compute_displace_atom.o pair_lj_cubic.o compute_contact_atom.o random_mars.o fix.o fix_cfd_coupling.o fix_property_atom.o fix_pour.o fix_wall_region_sph.o error.o compute_reduce_region.o compute_gyration_molecule.o velocity.o compute_pair.o fix_mesh_surface_stress_servo.o rerun.o compute_erotate_sphere_atom.o dump_image.o fix_shake.o dump_local.o modify.o compute_gyration.o fix_respa.o compute_stress_atom.o fix_indent.o fix_wall_reflect.o atom_vec.o fix_wall_harmonic.o neigh_half_nsq.o -lstdc++ -o ../lmp_fedora
property_registry.o:property_registry.cpp:(.text+0xea): undefined reference to `LAMMPS_NS::Properties::Properties(LAMMPS_NS::LAMMPS*)'
property_registry.o:property_registry.cpp:(.text+0xea): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::Properties(LAMMPS_NS::LAMMPS*)'
property_registry.o:property_registry.cpp:(.text+0x3dd5): undefined reference to `LAMMPS_NS::Properties::~Properties()'
property_registry.o:property_registry.cpp:(.text+0x3dd5): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::~Properties()'
property_registry.o:property_registry.cpp:(.text+0x3e71): undefined reference to `LAMMPS_NS::Properties::~Properties()'
property_registry.o:property_registry.cpp:(.text+0x3e71): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::~Properties()'
property_registry.o:property_registry.cpp:(.text+0x288): undefined reference to `LAMMPS_NS::Properties::max_type()'
property_registry.o:property_registry.cpp:(.text+0x288): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::max_type()'
fix_check_timestep_gran.o:fix_check_timestep_gran.cpp:(.text+0x32b): undefined reference to `LAMMPS_NS::Properties::max_type()'
fix_check_timestep_gran.o:fix_check_timestep_gran.cpp:(.text+0x32b): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::max_type()'
fix_check_timestep_gran.o:fix_check_timestep_gran.cpp:(.text+0x843): undefined reference to `LAMMPS_NS::Properties::max_type()'
fix_check_timestep_gran.o:fix_check_timestep_gran.cpp:(.text+0x843): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::max_type()'
fix_heat_gran_conduction.o:fix_heat_gran_conduction.cpp:(.text+0x18a): undefined reference to `LAMMPS_NS::Properties::max_type()'
fix_heat_gran_conduction.o:fix_heat_gran_conduction.cpp:(.text+0x18a): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::max_type()'
pair_gran.o:pair_gran.cpp:(.text+0x30f8): undefined reference to `LAMMPS_NS::Properties::Properties(LAMMPS_NS::LAMMPS*)'
pair_gran.o:pair_gran.cpp:(.text+0x30f8): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::Properties(LAMMPS_NS::LAMMPS*)'
cfd_datacoupling.o:cfd_datacoupling.cpp:(.text+0x1845): undefined reference to `LAMMPS_NS::Properties::find_property(char const*, char const*, int&, int&)'
cfd_datacoupling.o:cfd_datacoupling.cpp:(.text+0x1845): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::find_property(char const*, char const*, int&, int&)'
cfd_datacoupling.o:cfd_datacoupling.cpp:(.text+0x1a45): undefined reference to `LAMMPS_NS::Properties::find_property(char const*, char const*, int&, int&)'
cfd_datacoupling.o:cfd_datacoupling.cpp:(.text+0x1a45): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `LAMMPS_NS::Properties::find_property(char const*, char const*, int&, int&)'
cfd_datacoupling.o:cfd_datacoupling.cpp:(.text+0x1f8): undefined reference to `LAMMPS_NS::Properties::find_property(char const*, char const*, int&, int&)'
cfd_datacoupling.o:cfd_datacoupling.cpp:(.text+0x1f8): additional relocation overflows omitted from the output
cfd_datacoupling.o:cfd_datacoupling.cpp:(.text+0x208): undefined reference to `LAMMPS_NS::Properties::find_property(char const*, char const*, int&, int&)'
fix_scalar_transport_equation.o:fix_scalar_transport_equation.cpp:(.text+0x15cd): undefined reference to `LAMMPS_NS::Properties::max_type()'
fix_property_atom.o:fix_property_atom.cpp:(.text+0x1217): undefined reference to `LAMMPS_NS::Properties::find_property(char const*, char const*, int&, int&)'
fix_property_atom.o:fix_property_atom.cpp:(.text+0x2997): undefined reference to `LAMMPS_NS::Properties::find_property(char const*, char const*, int&, int&)'
collect2: error: ld returned 1 exit status
Makefile:86: recipe for target '../lmp_fedora' failed
make[1]: *** [../lmp_fedora] Error 1
make[1]: Leaving directory '/cygdrive/c/LIGGGHTS-PUBLIC-310/src/Obj_fedora'
Makefile:77: recipe for target 'fedora' failed
make: *** [fedora] Error 2

--
Regards

Rahul Kumar Soni
Scientist, CSIR - IMMT, India

richti83's picture

richti83 | Sat, 03/14/2015 - 19:31

Try make clean-all and the start a fresh build... Is your cygwin and mpi 64 bit? Linker complains about wrong architecture of object files.

I'm not an associate of DCS GmbH and not a core developer of LIGGGHTS®
ResearchGate | Contact

rahulsoni | Sun, 03/15/2015 - 15:32

Yes, I tried it, but no luck. I think the new version comes up with in-built feature of dumping vtk files. And I think it requires some libraries to be linked. Don't know for sure.
Do I need to do so. If yes then how, Plz help

--
Regards

Rahul Kumar Soni
Scientist, CSIR - IMMT, India

richti83's picture

richti83 | Sun, 03/15/2015 - 16:42

I have no experience with cygwin, but maybe the make-clean command does not work correctly because on windows rm is called del ? try removing all object files (*.o) and the objFedora folder manualy.
Otherwise try in fresh folder whith a fresh download.
I'm sure you googled the error "relocation truncated to fit: R_X86_64_PC32 against undefined symbol" and read the first answer on stackoverflow:
http://stackoverflow.com/questions/10486116/what-does-this-gcc-error-rel...

On Windows I use mingw64 and MSVC 2010 & 2012 and a CMAKE as build system and have no problems with both compilers/linkers.

I'm not an associate of DCS GmbH and not a core developer of LIGGGHTS®
ResearchGate | Contact

ckloss's picture

ckloss | Mon, 03/16/2015 - 12:15

>>Yes, I tried it, but no luck. I think the new version comes up with in-built feature of dumping vtk files.
>>And I think it requires some libraries to be linked. Don't know for sure.
No if you stick to the same makefile, there are no additional libs required
Try a fresh "git clone", and if the error persists, please post here again with info on your system and compiler

Christoph

rahulsoni | Tue, 03/17/2015 - 06:00

Thanks a lot Richter. I downloaded fresh source directory of LIGGGHTS and compiled and it worked.
However, while running the chute_wear simulation, I am getting message of "Invalid dump style".
I am using new custom/vtk style in the following format:
"dump dmpvtk all custom/vtk 200 post/dump*.chute id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius"

The part of the messages from terminal are as follows:
$ liggghts -in in.chute_wear
LIGGGHTS (Version LIGGGHTS-PUBLIC 3.1.0, compiled 2015-03-17-10:02:04 by workstation, git commit based on LAMMPS 23 Nov 2013)
....
....
Total # of neighbors = 2
Ave neighs/atom = 0.166667
Neighbor list builds = 1
Dangerous builds = 0
ERROR: Invalid dump style (../output.cpp:574)

--
Regards

Rahul Kumar Soni
Scientist, CSIR - IMMT, India

Daniel Queteschiner | Tue, 03/17/2015 - 11:17

To recognize dump custom/vtk, LIGGGHTS needs to be compiled with the option -DLAMMPS_VTK and linked to the vtk 5.8 or 6 library (dev packages must be installed). For required vtk headers/libraries have a look at Make.ubuntuVTK and Make.ubuntuVTK6.

rahulsoni | Wed, 03/18/2015 - 05:35

Thanks Daniel
But I am on Cygwin in Windows. And I think dev packages won't work here. One way is to compiling and linking VTK library with the cmake. But I am finding it difficult. It there any guide or web link over the thank can help me getting the VTK library in Windows.

Thanks in advance.

--
Regards

Rahul Kumar Soni
Scientist, CSIR - IMMT, India