PLUMED compilation withe LAMMPS error

Anna Lappala

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Dec 2, 2013, 9:35:41 AM12/2/13

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Dear PLUMED users/developers!

I have done the following to patch my lammps with plumed, and after I attempt to

make package-USER-PLUMED

followed by

make openmpi

I get this error upon compilation:

lfftw -lstdc++ -o ../lmp_openmpi

fix_plumed.o: In function `LAMMPS_NS::FixPlumed::post_force(int)':

fix_plumed.cpp:(.text+0x1b7): undefined reference to `plumed_cmd'

fix_plumed.cpp:(.text+0x1d3): undefined reference to `plumed_cmd'

fix_plumed.cpp:(.text+0x2d5): undefined reference to `plumed_cmd'

fix_plumed.cpp:(.text+0x2fb): undefined reference to `plumed_cmd'

fix_plumed.cpp:(.text+0x315): undefined reference to `plumed_cmd'

fix_plumed.o:fix_plumed.cpp:(.text+0x33b): more undefined references to `plumed_cmd' follow

fix_plumed.o: In function `LAMMPS_NS::FixPlumed::FixPlumed(LAMMPS_NS::LAMMPS*, int, char**)':

fix_plumed.cpp:(.text+0x82b): undefined reference to `plumed_create'

fix_plumed.cpp:(.text+0x84e): undefined reference to `plumed_cmd'

fix_plumed.cpp:(.text+0x92a): undefined reference to `plumed_cmd'

fix_plumed.cpp:(.text+0x944): undefined reference to `plumed_cmd'

fix_plumed.cpp:(.text+0x95e): undefined reference to `plumed_cmd'

fix_plumed.cpp:(.text+0xb80): undefined reference to `plumed_cmd'

fix_plumed.o:fix_plumed.cpp:(.text+0xbad): more undefined references to `plumed_cmd' follow

fix_plumed.o: In function `PLMD::Plumed::~Plumed()':

fix_plumed.cpp:(.text._ZN4PLMD6PlumedD2Ev[_ZN4PLMD6PlumedD5Ev]+0x15): undefined reference to `plumed_finalize'

fix_plumed.o: In function `PLMD::Plumed::~Plumed()':

fix_plumed.cpp:(.text._ZN4PLMD6PlumedD0Ev[_ZN4PLMD6PlumedD0Ev]+0x16): undefined reference to `plumed_finalize'

collect2: error: ld returned 1 exit status

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

make[1]: Leaving directory `/home/anna/Downloads/lammps-14Mar13/src/Obj_openmpi'

make: *** [openmpi] Error 2

Thank you in advanced for any input!

With best wishes,

Anna

davide branduardi

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Dec 2, 2013, 9:47:33 AM12/2/13

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Hi Anna!
It looks like the linking is not aware of plumed. Can you send also
what is before lfftw -lstdc++ ?
I guess that for some reason the compiler is not aware of plumed.
D
******************************************************
Davide Branduardi
davide.b...@gmail.com
Web:
https://sites.google.com/site/davidebranduardi
******************************************************

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Anna Lappala

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Dec 2, 2013, 9:58:22 AM12/2/13

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Dear Davide! Thank you for your reply!

Here it is:

mpic++ -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -DLAMMPS_GZIP -DFFT_FFTW -I/home/s0793217/localfft/include -c velocity.cpp

velocity.cpp:343:6: warning: unused parameter ‘narg’ [-Wunused-parameter]

velocity.cpp:512:6: warning: unused parameter ‘narg’ [-Wunused-parameter]

velocity.cpp:551:6: warning: unused parameter ‘narg’ [-Wunused-parameter]

velocity.cpp:631:6: warning: unused parameter ‘narg’ [-Wunused-parameter]

mpic++ -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -DLAMMPS_GZIP -DFFT_FFTW -I/home/s0793217/localfft/include -c verlet.cpp

mpic++ -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -DLAMMPS_GZIP -DFFT_FFTW -I/home/s0793217/localfft/include -c write_restart.cpp

write_restart.cpp: In member function ‘void LAMMPS_NS::WriteRestart::command(int, char**)’:

write_restart.cpp:85:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses]

mpic++ -O -L/home/s0793217/localfft/lib angle.o atom.o atom_map.o atom_vec_atomic.o atom_vec_body.o atom_vec_charge.o atom_vec.o atom_vec_ellipsoid.o atom_vec_hybrid.o atom_vec_line.o atom_vec_sphere.o atom_vec_tri.o balance.o body.o bond.o bond_hybrid.o change_box.o comm.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 compute_ti.o create_atoms.o create_box.o delete_atoms.o delete_bonds.o dihedral.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 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_efield.o fix_enforce2d.o fix_evaporate.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_orient_fcc.o fix_planeforce.o fix_plumed.o fix_press_berendsen.o fix_print.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_force.o fix_store_state.o fix_temp_berendsen.o fix_temp_rescale.o fix_thermal_conductivity.o fix_tmd.o fix_ttm.o fix_viscosity.o fix_viscous.o fix_wall.o fix_wall_harmonic.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 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 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_beck.o pair_born_coul_wolf.o pair_born.o pair_buck_coul_cut.o pair_buck.o pair_coul_cut.o pair_coul_debye.o pair_coul_dsf.o pair_coul_wolf.o pair.o pair_dpd.o pair_dpd_tstat.o pair_gauss.o pair_hybrid.o pair_hybrid_overlay.o pair_lj96_cut.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.o pair_lj_expand.o pair_lj_gromacs_coul_gromacs.o pair_lj_gromacs.o pair_lj_smooth.o pair_lj_smooth_linear.o pair_mie_cut.o pair_morse.o pair_soft.o pair_table.o pair_yukawa.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 replicate.o rerun.o respa.o run.o set.o special.o thermo.o timer.o universe.o update.o variable.o velocity.o verlet.o write_restart.o -lfftw -lstdc++ -o ../lmp_openmpi