Error Compiling LAAMPS update.cpp:(.text+0x1006): undefined reference to `LAMMPS_NS::Verlet::Verlet(LAMMPS_NS::LAMMPS*, int, char**)'

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1

UNRESTRICTED | ILLIMITÉ

I’ve been trying to lammps-30Aug13 using the Makefile.linux

I’ve edited the compiler/linker settings to suit my environment and used mpicc to compile.

I seem to be getting an error when it tries to link:

-lmpich -lpthread -lrt -lstdc++ -o …/lmp_linux

update.o: In function `LAMMPS_NS::Update::new_integrate(char*, int, char**, char*, int&)’:

update.cpp:(.text+0x1006): undefined reference to `LAMMPS_NS::Verlet::Verlet(LAMMPS_NS::LAMMPS*, int, char**)’

update.cpp:(.text+0x10bf): undefined reference to `LAMMPS_NS::Verlet::Verlet(LAMMPS_NS::LAMMPS*, int, char**)’

collect2: ld returned 1 exit status

make[1]: *** […/lmp_linux] Error 1

make[1]: Leaving directory `/var/tmp/pfeiffes/For_Jer/lammps/src/Obj_linux’

make: *** [linux] Error 2

2

UNRESTRICTED | ILLIMITÉ

I’ve been trying to lammps-30Aug13 using the Makefile.linux

I’ve edited the compiler/linker settings to suit my environment and used
mpicc to compile.

I seem to be getting an error when it tries to link:

-lmpich -lpthread -lrt -lstdc++ -o ../lmp_linux

update.o: In function `LAMMPS_NS::Update::new_integrate(char*, int, char**,
char*, int&)':

update.cpp:(.text+0x1006): undefined reference to
`LAMMPS_NS::Verlet::Verlet(LAMMPS_NS::LAMMPS*, int, char**)'

update.cpp:(.text+0x10bf): undefined reference to
`LAMMPS_NS::Verlet::Verlet(LAMMPS_NS::LAMMPS*, int, char**)'

collect2: ld returned 1 exit status

make[1]: *** [../lmp_linux] Error 1

make[1]: Leaving directory `/var/tmp/pfeiffes/For_Jer/lammps/src/Obj_linux'

make: *** [linux] Error 2

this looks like you have changed your makefile settings and didn't do
"make clean-linux" afterwards.

axel.

3

UNRESTRICTED | ILLIMITÉ

Yes, I did do a "make clean-all" and even tried "make clean-linux" after modifying the make file.
But i am still getting the same error message after compiling. Here are the last few lines during compile before it hits the error message:

*My apologies for the multiple lines*

mpicc -O -I/usr/local/mpich2/include -c ../special.cpp
mpicc -O -I/usr/local/mpich2/include -c ../thermo.cpp
mpicc -O -I/usr/local/mpich2/include -c ../timer.cpp
mpicc -O -I/usr/local/mpich2/include -c ../universe.cpp
mpicc -O -I/usr/local/mpich2/include -c ../update.cpp
mpicc -O -I/usr/local/mpich2/include -c ../variable.cpp
mpicc -O -I/usr/local/mpich2/include -c ../velocity.cpp
mpicc -O -I/usr/local/mpich2/include -c ../write_data.cpp
mpicc -O -I/usr/local/mpich2/include -c ../write_restart.cpp
mpicc -O -L/usr/local/mpich2/lib angle_charmm.o angle_cosine.o angle_cosine_delta.o angle_cosine_periodic.o angle_cosine_squared.o angle.o angle_harmonic.o angle_hybrid.o angle_table.o atom.o atom_map.o atom_vec_angle.o atom_vec_atomic.o atom_vec_body.o atom_vec_bond.o atom_vec_charge.o atom_vec.o atom_vec_ellipsoid.o atom_vec_full.o atom_vec_hybrid.o atom_vec_line.o atom_vec_molecular.o atom_vec_sphere.o atom_vec_tri.o balance.o body.o bond.o bond_fene.o bond_fene_expand.o bond_harmonic.o bond_hybrid.o bond_morse.o bond_nonlinear.o bond_quartic.o bond_table.o change_box.o citeme.o comm.o commgrid.o compute_angle_local.o compute_atom_molecule.o compute_bond_local.o compute_centro_atom.o compute_cluster_atom.o compute_cna_atom.o compute_com.o compute_com_molecule.o compute_contact_atom.o compute_coord_atom.o compute.o compute_dihedral_local.o compute_displace_atom.o compute_erotate_sphere_atom.o compute_erotate_sphere.o compute_group_group.o compute_gyration.o compute_gyration_molecule.o compute_heat_flux.o compute_improper_local.o compute_inertia_molecule.o compute_ke_atom.o compute_ke.o compute_msd.o compute_msd_molecule.o compute_pair.o compute_pair_local.o compute_pe_atom.o compute_pe.o compute_pressure.o compute_property_atom.o compute_property_local.o compute_property_molecule.o compute_rdf.o compute_reduce.o compute_reduce_region.o compute_slice.o compute_stress_atom.o compute_temp_com.o compute_temp.o compute_temp_deform.o compute_temp_partial.o compute_temp_profile.o compute_temp_ramp.o compute_temp_region.o compute_temp_sphere.o create_atoms.o create_box.o delete_atoms.o delete_bonds.o dihedral_charmm.o dihedral.o dihedral_harmonic.o dihedral_helix.o dihedral_hybrid.o dihedral_multi_harmonic.o dihedral_opls.o displace_atoms.o domain.o dump_atom.o dump_cfg.o dump.o dump_custom.o dump_dcd.o dump_image.o dump_local.o dump_xyz.o error.o ewald.o ewald_disp.o fft3d.o fft3d_wrap.o finish.o fix_adapt.o fix_addforce.o fix_ave_atom.o fix_ave_correlate.o fix_aveforce.o fix_ave_histo.o fix_ave_spatial.o fix_ave_time.o fix_balance.o fix_box_relax.o fix.o fix_deform.o fix_deposit.o fix_drag.o fix_dt_reset.o fix_enforce2d.o fix_external.o fix_gravity.o fix_heat.o fix_indent.o fix_langevin.o fix_lineforce.o fix_minimize.o fix_momentum.o fix_move.o fix_nh.o fix_nh_sphere.o fix_nph.o fix_nph_sphere.o fix_npt.o fix_npt_sphere.o fix_nve.o fix_nve_limit.o fix_nve_noforce.o fix_nve_sphere.o fix_nvt.o fix_nvt_sllod.o fix_nvt_sphere.o fix_planeforce.o fix_press_berendsen.o fix_print.o fix_property_atom.o fix_qeq_comb.o fix_read_restart.o fix_recenter.o fix_respa.o fix_restrain.o fix_setforce.o fix_shake.o fix_shear_history.o fix_spring.o fix_spring_rg.o fix_spring_self.o fix_store.o fix_store_force.o fix_store_state.o fix_temp_berendsen.o fix_temp_rescale.o fix_tmd.o fix_tune_kspace.o fix_viscous.o fix_wall.o fix_wall_harmonic.o fix_wall_lj1043.o fix_wall_lj126.o fix_wall_lj93.o fix_wall_reflect.o fix_wall_region.o force.o group.o image.o improper.o improper_cvff.o improper_harmonic.o improper_hybrid.o improper_umbrella.o input.o integrate.o irregular.o kspace.o lammps.o lattice.o library.o main.o math_extra.o memory.o min_cg.o min.o min_fire.o min_hftn.o minimize.o min_linesearch.o min_quickmin.o min_sd.o modify.o msm_cg.o msm.o neigh_bond.o neighbor.o neigh_derive.o neigh_full.o neigh_gran.o neigh_half_bin.o neigh_half_multi.o neigh_half_nsq.o neigh_list.o neigh_request.o neigh_respa.o neigh_stencil.o output.o pair_adp.o pair_airebo.o pair_beck.o pair_bop.o pair_born_coul_long.o pair_born_coul_msm.o pair_born_coul_wolf.o pair_born.o pair_buck_coul_cut.o pair_buck_coul_long.o pair_buck_coul_msm.o pair_buck.o pair_buck_long_coul_long.o pair_comb.o pair_coul_cut.o pair_coul_debye.o pair_coul_dsf.o pair_coul_long.o pair_coul_msm.o pair_coul_wolf.o pair.o pair_dpd.o pair_dpd_tstat.o pair_eam_alloy.o pair_eam.o pair_eam_fs.o pair_eim.o pair_gauss.o pair_hbond_dreiding_lj.o pair_hbond_dreiding_morse.o pair_hybrid.o pair_hybrid_overlay.o pair_lcbop.o pair_lj96_cut.o pair_lj_charmm_coul_charmm.o pair_lj_charmm_coul_charmm_implicit.o pair_lj_charmm_coul_long.o pair_lj_charmm_coul_msm.o pair_lj_cubic.o pair_lj_cut_coul_cut.o pair_lj_cut_coul_debye.o pair_lj_cut_coul_dsf.o pair_lj_cut_coul_long.o pair_lj_cut_coul_msm.o pair_lj_cut.o pair_lj_cut_tip4p_cut.o pair_lj_cut_tip4p_long.o pair_lj_expand.o pair_lj_gromacs_coul_gromacs.o pair_lj_gromacs.o pair_lj_long_coul_long.o pair_lj_long_tip4p_long.o pair_lj_smooth.o pair_lj_smooth_linear.o pair_mie_cut.o pair_morse.o pair_rebo.o pair_soft.o pair_sw.o pair_table.o pair_tersoff.o pair_tersoff_mod.o pair_tersoff_zbl.o pair_tip4p_cut.o pair_tip4p_long.o pair_yukawa.o pppm_cg.o pppm.o pppm_disp.o pppm_disp_tip4p.o pppm_old.o pppm_stagger.o pppm_tip4p.o procmap.o random_mars.o random_park.o read_data.o read_dump.o reader.o reader_native.o reader_xyz.o read_restart.o region_block.o region_cone.o region.o region_cylinder.o region_intersect.o region_plane.o region_prism.o region_sphere.o region_union.o remap.o remap_wrap.o replicate.o rerun.o respa.o run.o set.o special.o thermo.o timer.o universe.o update.o variable.o velocity.o write_data.o write_restart.o -lmpich -lpthread -lrt -lstdc++ -o ../lmp_linux
update.o: In function `LAMMPS_NS::Update::new_integrate(char*, int, char**, char*, int&)':
update.cpp:(.text+0x1006): undefined reference to `LAMMPS_NS::Verlet::Verlet(LAMMPS_NS::LAMMPS*, int, char**)'
update.cpp:(.text+0x10bf): undefined reference to `LAMMPS_NS::Verlet::Verlet(LAMMPS_NS::LAMMPS*, int, char**)'
collect2: ld returned 1 exit status
make[1]: *** [../lmp_linux] Error 1
make[1]: Leaving directory `/var/tmp/pfeiffes/For_Jer/lammps/src/Obj_linux'
make: *** [linux] Error 2

4

How come there is no
mpicc -O -I/usr/local/mpich2/include -c …/verlet.cpp

Is there a verlet.cpp in your src dir?

Steve

5

UNRESTRICTED | ILLIMITÉ

I was wondering that too.

No, there is no verlet.cpp in my src dir. I only have verlet.h

Sharon Pfeiffer

ext. 46654

6

UNRESTRICTED | ILLIMITÉ

Great! Thanks Steve.

I found verlet.cpp from the src directory – which somehow went missing during a copy from another directory.

Have managed to compile successfuly. I am now running it to see if it works.

Thanks for your help!!

Sharon Pfeiffer