Hello all,
I am trying to compile the most recent version of LAMMPS (checked out today) on an XT5 using PGI. I can compile successfully and uneventfully with GNU, but need a PGI version. At link time, I get many “undefined reference to” errors, mostly involving functions of Memory with dressed headers. I’ve attached the full output of make (after compiling once); here’s the beginning:
grep: angle_.h: No such file or directory
grep: dihedral_.h: No such file or directory
grep: improper_*.h: No such file or directory
make[1]: Entering directory /nics/c/home/afrachi1/LAMMPS_9-12-12/LAMMPS_9-12-12/src/Obj_kraken_pgi' CC -fastsse -DLAMMPS_GZIP -DMPICH_SKIP_MPICXX -c force.cpp CC -fastsse -DLAMMPS_GZIP -DMPICH_SKIP_MPICXX -c lammps.cpp CC -O angle.o atom.o atom_map.o atom_vec_atomic.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 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_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_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_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.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_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 -o ../lmp_kraken_pgi angle.o: In function ev_setup__Q2_9LAMMPS_NS5AngleFiT1’:
/nics/c/home/afrachi1/LAMMPS_9-12-12/LAMMPS_9-12-12/src/Obj_kraken_pgi/./angle.cpp:88: undefined reference to LAMMPS_NS::Memory::smalloc( (long, char const *))' /nics/c/home/afrachi1/LAMMPS_9-12-12/LAMMPS_9-12-12/src/Obj_kraken_pgi/./angle.cpp:95: undefined reference to LAMMPS_NS::Memory::smalloc( (long, char const *))’
/nics/c/home/afrachi1/LAMMPS_9-12-12/LAMMPS_9-12-12/src/Obj_kraken_pgi/./angle.cpp:95: undefined reference to LAMMPS_NS::Memory::smalloc( (long, char const *))' angle.o: In function create__tm__2_d__Q2_9LAMMPS_NS6MemoryFRPZ1ZiPCc_PZ1Z’:
/nics/c/home/afrachi1/LAMMPS_9-12-12/LAMMPS_9-12-12/src/Obj_kraken_pgi/./memory.h:46: undefined reference to LAMMPS_NS::Memory::smalloc( (long, char const *))' angle.o: In function create__tm__2_d__Q2_9LAMMPS_NS6MemoryFRPPZ1ZiT2PCc_PPZ1Z’:
/nics/c/home/afrachi1/LAMMPS_9-12-12/LAMMPS_9-12-12/src/Obj_kraken_pgi/./memory.h:116: undefined reference to `LAMMPS_NS::Memory::smalloc( (long, char const *))
I understand this is likely an issue unique to my system, but can’t figure out what might be broken about my environment or what libraries might be misconfigured. Any feedback would be greatly appreciated.
Many thanks,
Anthony Frachioni
Binghamton University, NY
out.txt (59.7 KB)