Dear all,
I have to compile lammps on my university account, and it does not seem to work even thought it did for my own computer (I am using the 18Dec10 version) . I copied everything to my account, and tried to compile, and this is what I get:
make ubuntu_serial
make[1]: Entering directory `.../lammps-18Dec10/src/Obj_ubuntu_serial'
make[1]: *** No rule to make target `/usr/include/bits/predefs.h', needed by `angle_charmm.o'. Stop.
make[1]: Leaving directory `.../lammps-18Dec10/src/Obj_ubuntu_serial'
make: *** [ubuntu_serial] Error 2
I'd appreciate any suggestions!
Thank you very much.
Anna
Dear all,
I have to compile lammps on my university account, and it does not seem
to work even thought it did for my own computer (I am using the 18Dec10
version) . I copied everything to my account, and tried to compile, and
this is what I get:
the "copy everything" is the problem. it was copying too much.
type "make clean-ubuntu_serial"
and then again "make ubuntu_serial"
and let us know, if that works.
cheers,
axel.
Dear Dr Axel,
Thank you very much! Unfortunately, I still get an error:
make[1]: Entering directory `.../lammps-18Dec10/src/Obj_linux'
Makefile:93: angle_charmm.d: No such file or directory
Makefile:93: angle_cosine.d: No such file or directory
Makefile:93: angle_cosine_delta.d: No such file or directory
Makefile:93: angle_cosine_periodic.d: No such file or directory
Makefile:93: angle_cosine_squared.d: No such file or directory
Makefile:93: angle.d: No such file or directory
Makefile:93: angle_harmonic.d: No such file or directory
Makefile:93: angle_hybrid.d: No such file or directory
Makefile:93: angle_table.d: No such file or directory
Makefile:93: atom.d: No such file or directory
Makefile:93: atom_vec_angle.d: No such file or directory
Makefile:93: atom_vec_atomic.d: No such file or directory
Makefile:93: atom_vec_bond.d: No such file or directory
Makefile:93: atom_vec_charge.d: No such file or directory
Makefile:93: atom_vec.d: No such file or directory
Makefile:93: atom_vec_full.d: No such file or directory
Makefile:93: atom_vec_hybrid.d: No such file or directory
Makefile:93: atom_vec_molecular.d: No such file or directory
Makefile:93: bond.d: No such file or directory
Makefile:93: bond_fene.d: No such file or directory
Makefile:93: bond_fene_expand.d: No such file or directory
Makefile:93: bond_harmonic.d: No such file or directory
Makefile:93: bond_hybrid.d: No such file or directory
Makefile:93: bond_morse.d: No such file or directory
Makefile:93: bond_nonlinear.d: No such file or directory
Makefile:93: bond_quartic.d: No such file or directory
Makefile:93: bond_table.d: No such file or directory
Makefile:93: change_box.d: No such file or directory
Makefile:93: comm.d: No such file or directory
Makefile:93: compute_angle_local.d: No such file or directory
Makefile:93: compute_atom_molecule.d: No such file or directory
Makefile:93: compute_bond_local.d: No such file or directory
Makefile:93: compute_centro_atom.d: No such file or directory
Makefile:93: compute_cna_atom.d: No such file or directory
Makefile:93: compute_com.d: No such file or directory
Makefile:93: compute_com_molecule.d: No such file or directory
Makefile:93: compute_coord_atom.d: No such file or directory
Makefile:93: compute.d: No such file or directory
Makefile:93: compute_dihedral_local.d: No such file or directory
Makefile:93: compute_displace_atom.d: No such file or directory
Makefile:93: compute_erotate_sphere.d: No such file or directory
Makefile:93: compute_group_group.d: No such file or directory
Makefile:93: compute_gyration.d: No such file or directory
Makefile:93: compute_gyration_molecule.d: No such file or directory
Makefile:93: compute_heat_flux.d: No such file or directory
Makefile:93: compute_improper_local.d: No such file or directory
Makefile:93: compute_ke_atom.d: No such file or directory
Makefile:93: compute_ke.d: No such file or directory
Makefile:93: compute_msd.d: No such file or directory
Makefile:93: compute_msd_molecule.d: No such file or directory
Makefile:93: compute_pair.d: No such file or directory
Makefile:93: compute_pair_local.d: No such file or directory
Makefile:93: compute_pe_atom.d: No such file or directory
Makefile:93: compute_pe.d: No such file or directory
Makefile:93: compute_pressure.d: No such file or directory
Makefile:93: compute_property_atom.d: No such file or directory
Makefile:93: compute_property_local.d: No such file or directory
Makefile:93: compute_property_molecule.d: No such file or directory
Makefile:93: compute_rdf.d: No such file or directory
Makefile:93: compute_reduce.d: No such file or directory
Makefile:93: compute_reduce_region.d: No such file or directory
Makefile:93: compute_stress_atom.d: No such file or directory
Makefile:93: compute_temp_com.d: No such file or directory
Makefile:93: compute_temp.d: No such file or directory
Makefile:93: compute_temp_deform.d: No such file or directory
Makefile:93: compute_temp_partial.d: No such file or directory
Makefile:93: compute_temp_profile.d: No such file or directory
Makefile:93: compute_temp_ramp.d: No such file or directory
Makefile:93: compute_temp_region.d: No such file or directory
Makefile:93: compute_temp_sphere.d: No such file or directory
Makefile:93: compute_ti.d: No such file or directory
Makefile:93: create_atoms.d: No such file or directory
Makefile:93: create_box.d: No such file or directory
Makefile:93: delete_atoms.d: No such file or directory
Makefile:93: delete_bonds.d: No such file or directory
Makefile:93: dihedral_charmm.d: No such file or directory
Makefile:93: dihedral.d: No such file or directory
Makefile:93: dihedral_harmonic.d: No such file or directory
Makefile:93: dihedral_helix.d: No such file or directory
Makefile:93: dihedral_hybrid.d: No such file or directory
Makefile:93: dihedral_multi_harmonic.d: No such file or directory
Makefile:93: dihedral_opls.d: No such file or directory
Makefile:93: displace_atoms.d: No such file or directory
Makefile:93: displace_box.d: No such file or directory
Makefile:93: domain.d: No such file or directory
Makefile:93: dump_atom.d: No such file or directory
Makefile:93: dump_cfg.d: No such file or directory
Makefile:93: dump.d: No such file or directory
Makefile:93: dump_custom.d: No such file or directory
Makefile:93: dump_dcd.d: No such file or directory
Makefile:93: dump_local.d: No such file or directory
Makefile:93: dump_xyz.d: No such file or directory
Makefile:93: error.d: No such file or directory
Makefile:93: ewald.d: No such file or directory
Makefile:93: fft3d.d: No such file or directory
Makefile:93: fft3d_wrap.d: No such file or directory
Makefile:93: finish.d: No such file or directory
Makefile:93: fix_adapt.d: No such file or directory
Makefile:93: fix_addforce.d: No such file or directory
Makefile:93: fix_ave_atom.d: No such file or directory
Makefile:93: fix_ave_correlate.d: No such file or directory
Makefile:93: fix_aveforce.d: No such file or directory
Makefile:93: fix_ave_histo.d: No such file or directory
Makefile:93: fix_ave_spatial.d: No such file or directory
Makefile:93: fix_ave_time.d: No such file or directory
Makefile:93: fix_bond_break.d: No such file or directory
Makefile:93: fix_bond_create.d: No such file or directory
Makefile:93: fix_bond_swap.d: No such file or directory
Makefile:93: fix_box_relax.d: No such file or directory
Makefile:93: fix.d: No such file or directory
Makefile:93: fix_deform.d: No such file or directory
Makefile:93: fix_deposit.d: No such file or directory
Makefile:93: fix_drag.d: No such file or directory
Makefile:93: fix_dt_reset.d: No such file or directory
Makefile:93: fix_efield.d: No such file or directory
Makefile:93: fix_enforce2d.d: No such file or directory
Makefile:93: fix_evaporate.d: No such file or directory
Makefile:93: fix_external.d: No such file or directory
Makefile:93: fix_gravity.d: No such file or directory
Makefile:93: fix_heat.d: No such file or directory
Makefile:93: fix_indent.d: No such file or directory
Makefile:93: fix_langevin.d: No such file or directory
Makefile:93: fix_lineforce.d: No such file or directory
Makefile:93: fix_minimize.d: No such file or directory
Makefile:93: fix_momentum.d: No such file or directory
Makefile:93: fix_move.d: No such file or directory
Makefile:93: fix_nh.d: No such file or directory
Makefile:93: fix_nh_sphere.d: No such file or directory
Makefile:93: fix_nph.d: No such file or directory
Makefile:93: fix_nph_sphere.d: No such file or directory
Makefile:93: fix_npt.d: No such file or directory
Makefile:93: fix_npt_sphere.d: No such file or directory
Makefile:93: fix_nve.d: No such file or directory
Makefile:93: fix_nve_limit.d: No such file or directory
Makefile:93: fix_nve_noforce.d: No such file or directory
Makefile:93: fix_nve_sphere.d: No such file or directory
Makefile:93: fix_nvt.d: No such file or directory
Makefile:93: fix_nvt_sllod.d: No such file or directory
Makefile:93: fix_nvt_sphere.d: No such file or directory
Makefile:93: fix_orient_fcc.d: No such file or directory
Makefile:93: fix_planeforce.d: No such file or directory
Makefile:93: fix_press_berendsen.d: No such file or directory
Makefile:93: fix_print.d: No such file or directory
Makefile:93: fix_qeq_comb.d: No such file or directory
Makefile:93: fix_read_restart.d: No such file or directory
Makefile:93: fix_recenter.d: No such file or directory
Makefile:93: fix_respa.d: No such file or directory
Makefile:93: fix_rigid.d: No such file or directory
Makefile:93: fix_rigid_nve.d: No such file or directory
Makefile:93: fix_rigid_nvt.d: No such file or directory
Makefile:93: fix_setforce.d: No such file or directory
Makefile:93: fix_shake.d: No such file or directory
Makefile:93: fix_shear_history.d: No such file or directory
Makefile:93: fix_spring.d: No such file or directory
Makefile:93: fix_spring_rg.d: No such file or directory
Makefile:93: fix_spring_self.d: No such file or directory
Makefile:93: fix_store_force.d: No such file or directory
Makefile:93: fix_store_state.d: No such file or directory
Makefile:93: fix_temp_berendsen.d: No such file or directory
Makefile:93: fix_temp_rescale.d: No such file or directory
Makefile:93: fix_thermal_conductivity.d: No such file or directory
Makefile:93: fix_tmd.d: No such file or directory
Makefile:93: fix_ttm.d: No such file or directory
Makefile:93: fix_viscosity.d: No such file or directory
Makefile:93: fix_viscous.d: No such file or directory
Makefile:93: fix_wall.d: No such file or directory
Makefile:93: fix_wall_harmonic.d: No such file or directory
Makefile:93: fix_wall_lj126.d: No such file or directory
Makefile:93: fix_wall_lj93.d: No such file or directory
Makefile:93: fix_wall_reflect.d: No such file or directory
Makefile:93: fix_wall_region.d: No such file or directory
Makefile:93: force.d: No such file or directory
Makefile:93: group.d: No such file or directory
Makefile:93: improper.d: No such file or directory
Makefile:93: improper_cvff.d: No such file or directory
Makefile:93: improper_harmonic.d: No such file or directory
Makefile:93: improper_hybrid.d: No such file or directory
Makefile:93: improper_umbrella.d: No such file or directory
Makefile:93: input.d: No such file or directory
Makefile:93: integrate.d: No such file or directory
Makefile:93: irregular.d: No such file or directory
Makefile:93: kspace.d: No such file or directory
Makefile:93: lammps.d: No such file or directory
Makefile:93: lattice.d: No such file or directory
Makefile:93: library.d: No such file or directory
Makefile:93: main.d: No such file or directory
Makefile:93: memory.d: No such file or directory
Makefile:93: min_cg.d: No such file or directory
Makefile:93: min.d: No such file or directory
Makefile:93: min_fire.d: No such file or directory
Makefile:93: min_hftn.d: No such file or directory
Makefile:93: minimize.d: No such file or directory
Makefile:93: min_linesearch.d: No such file or directory
Makefile:93: min_quickmin.d: No such file or directory
Makefile:93: min_sd.d: No such file or directory
Makefile:93: modify.d: No such file or directory
Makefile:93: neigh_bond.d: No such file or directory
Makefile:93: neighbor.d: No such file or directory
Makefile:93: neigh_derive.d: No such file or directory
Makefile:93: neigh_full.d: No such file or directory
Makefile:93: neigh_gran.d: No such file or directory
Makefile:93: neigh_half_bin.d: No such file or directory
Makefile:93: neigh_half_multi.d: No such file or directory
Makefile:93: neigh_half_nsq.d: No such file or directory
Makefile:93: neigh_list.d: No such file or directory
Makefile:93: neigh_request.d: No such file or directory
Makefile:93: neigh_respa.d: No such file or directory
Makefile:93: neigh_stencil.d: No such file or directory
Makefile:93: output.d: No such file or directory
Makefile:93: pack.d: No such file or directory
Makefile:93: pair_airebo.d: No such file or directory
Makefile:93: pair_born_coul_long.d: No such file or directory
Makefile:93: pair_born.d: No such file or directory
Makefile:93: pair_buck_coul_cut.d: No such file or directory
Makefile:93: pair_buck_coul_long.d: No such file or directory
Makefile:93: pair_buck.d: No such file or directory
Makefile:93: pair_comb.d: No such file or directory
Makefile:93: pair_coul_cut.d: No such file or directory
Makefile:93: pair_coul_debye.d: No such file or directory
Makefile:93: pair_coul_long.d: No such file or directory
Makefile:93: pair.d: No such file or directory
Makefile:93: pair_dpd.d: No such file or directory
Makefile:93: pair_dpd_tstat.d: No such file or directory
Makefile:93: pair_eam_alloy.d: No such file or directory
Makefile:93: pair_eam.d: No such file or directory
Makefile:93: pair_eam_fs.d: No such file or directory
Makefile:93: pair_eim.d: No such file or directory
Makefile:93: pair_gauss.d: No such file or directory
Makefile:93: pair_hbond_dreiding_lj.d: No such file or directory
Makefile:93: pair_hbond_dreiding_morse.d: No such file or directory
Makefile:93: pair_hybrid.d: No such file or directory
Makefile:93: pair_hybrid_overlay.d: No such file or directory
Makefile:93: pair_lj96_cut.d: No such file or directory
Makefile:93: pair_lj_charmm_coul_charmm.d: No such file or directory
Makefile:93: pair_lj_charmm_coul_charmm_implicit.d: No such file or directory
Makefile:93: pair_lj_charmm_coul_long.d: No such file or directory
Makefile:93: pair_lj_cut_coul_cut.d: No such file or directory
Makefile:93: pair_lj_cut_coul_debye.d: No such file or directory
Makefile:93: pair_lj_cut_coul_long.d: No such file or directory
Makefile:93: pair_lj_cut_coul_long_tip4p.d: No such file or directory
Makefile:93: pair_lj_cut.d: No such file or directory
Makefile:93: pair_lj_expand.d: No such file or directory
Makefile:93: pair_lj_gromacs_coul_gromacs.d: No such file or directory
Makefile:93: pair_lj_gromacs.d: No such file or directory
Makefile:93: pair_lj_smooth.d: No such file or directory
Makefile:93: pair_morse.d: No such file or directory
Makefile:93: pair_soft.d: No such file or directory
Makefile:93: pair_sw.d: No such file or directory
Makefile:93: pair_table.d: No such file or directory
Makefile:93: pair_tersoff.d: No such file or directory
Makefile:93: pair_tersoff_zbl.d: No such file or directory
Makefile:93: pair_yukawa.d: No such file or directory
Makefile:93: pppm.d: No such file or directory
Makefile:93: pppm_tip4p.d: No such file or directory
Makefile:93: random_mars.d: No such file or directory
Makefile:93: random_park.d: No such file or directory
Makefile:93: read_data.d: No such file or directory
Makefile:93: read_restart.d: No such file or directory
Makefile:93: region_block.d: No such file or directory
Makefile:93: region_cone.d: No such file or directory
Makefile:93: region.d: No such file or directory
Makefile:93: region_cylinder.d: No such file or directory
Makefile:93: region_intersect.d: No such file or directory
Makefile:93: region_plane.d: No such file or directory
Makefile:93: region_prism.d: No such file or directory
Makefile:93: region_sphere.d: No such file or directory
Makefile:93: region_union.d: No such file or directory
Makefile:93: remap.d: No such file or directory
Makefile:93: remap_wrap.d: No such file or directory
Makefile:93: replicate.d: No such file or directory
Makefile:93: respa.d: No such file or directory
Makefile:93: run.d: No such file or directory
Makefile:93: set.d: No such file or directory
Makefile:93: shell.d: No such file or directory
Makefile:93: special.d: No such file or directory
Makefile:93: thermo.d: No such file or directory
Makefile:93: timer.d: No such file or directory
Makefile:93: universe.d: No such file or directory
Makefile:93: update.d: No such file or directory
Makefile:93: variable.d: No such file or directory
Makefile:93: velocity.d: No such file or directory
Makefile:93: verlet.d: No such file or directory
Makefile:93: write_restart.d: No such file or directory
icc -O -DLAMMPS_GZIP -DMPICH_SKIP_MPICXX -DFFT_FFTW -M write_restart.cpp > write_restart.d
/bin/sh: icc: command not found
make[1]: *** [write_restart.d] Error 127
make[1]: Leaving directory `.../lammps-18Dec10/src/Obj_linux'
make: *** [linux] Error 2
Thank you very much for your time!
Anna
Dear Dr Axel,
Thank you very much! Unfortunately, I still get an error:
[...]
Makefile:93: write_restart.d: No such file or directory
all those "No such file or directory" messages are harmless
and part of how the compilation works with lammps.
icc -O -DLAMMPS_GZIP -DMPICH_SKIP_MPICXX -DFFT_FFTW -M write_restart.cpp >
write_restart.d
/bin/sh: icc: command not found
this is where _you_ have to adjust the makefile to what the machine
that you are using has to offer. i.e. it looks like you were using intel's
c/c++ compiler, but the new machine doesn't have it installed, or you
haven't activated it (btw: the correct c++ compiler command for intel
is "icpc" and not "icc")
you can try using g++ instead. you also have to check, whether MPI
is installed in the same location and has to be linked in the same way
(most likely not. almost every sysadmin sets things up a little different).
make[1]: *** [write_restart.d] Error 127
make[1]: Leaving directory `.../lammps-18Dec10/src/Obj_linux'
make: *** [linux] Error 2
cheers,
axel.
Dear Dr Axel,
Thank you very much for your advice! Something is compiling now, but I wanted to ask you whether it is possible to correct this error ?
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_ave_histo.cpp > fix_ave_histo.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_aveforce.cpp > fix_aveforce.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_ave_correlate.cpp > fix_ave_correlate.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_ave_atom.cpp > fix_ave_atom.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_addforce.cpp > fix_addforce.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_adapt.cpp > fix_adapt.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M finish.cpp > finish.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fft3d_wrap.cpp > fft3d_wrap.d
In file included from fft3d_wrap.h:18,
from fft3d_wrap.cpp:15:
fft3d.h:164:18: error: fftw.h: No such file or directory
make[1]: *** [fft3d_wrap.d] Error 1
make[1]: Leaving directory `.../lammps-18Dec10/src/Obj_ubuntu_serial'
make: *** [ubuntu_serial] Error 2
Thank you very much in advance!
Anna
Dear Dr Axel,
Thank you very much for your advice! Something is compiling now, but I
wanted to ask you whether it is possible to correct this error ?
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_ave_histo.cpp >
fix_ave_histo.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_aveforce.cpp >
fix_aveforce.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_ave_correlate.cpp >
fix_ave_correlate.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_ave_atom.cpp >
fix_ave_atom.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_addforce.cpp >
fix_addforce.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fix_adapt.cpp > fix_adapt.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M finish.cpp > finish.d
g++ -O -DFFT_FFTW -DLAMMPS_GZIP -I../STUBS -M fft3d_wrap.cpp > fft3d_wrap.d
In file included from fft3d_wrap.h:18,
from fft3d_wrap.cpp:15:
fft3d.h:164:18: error: fftw.h: No such file or directory
you didn't configure the makefile to find the fftw-2.1.5 installation.
perhaps you should read the LAMMPS installation instructions
more thoroughly instead of playing "20 questions" with us/me?
this is all well documented and has been answered many,
many times on this list.
axel.