I’m trying to build LAMMPS with MKL. I changed the makefile because the MKL version on this system is different but still get some errors. These are the errors and the makefile. Any idea
Thanks
[mgalanve@…12…1948… src]$ make mkl
make[1]: Entering directory /home/mgalanve/LAMMPS_May10/lammps-29May10/src/Obj_mkl' mpicc -O -L/packages/intel/mkl/[10.0.2.018/lib/em64t](http://10.0.2.018/lib/em64t) -L../../lib/reax -L/opt/intel/fce/10.0.023/lib angle_charmm.o angle_cosine.o angle_cosine_delta.o angle_cosine_squared.o angle.o angle_harmonic.o angle_hybrid.o angle_table.o atom.o atom_vec_angle.o atom_vec_atomic.o atom_vec_bond.o atom_vec_charge.o atom_vec.o atom_vec_full.o atom_vec_hybrid.o atom_vec_molecular.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 comm.o compute_angle_local.o compute_bond_local.o compute_centro_atom.o compute_cna_atom.o compute_com.o compute_com_molecule.o compute_coord_atom.o compute.o compute_dihedral_local.o compute_displace_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_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_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 displace_box.o domain.o dump_atom.o dump_cfg.o dump.o dump_custom.o dump_dcd.o dump_local.o dump_xyz.o error.o ewald.o fft3d.o fft3d_wrap.o finish.o fix_addforce.o fix_ave_atom.o fix_aveforce.o fix_ave_histo.o fix_ave_spatial.o fix_ave_time.o fix_bond_break.o fix_bond_create.o fix_bond_swap.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_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_asphere.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_reax_bonds.o fix_recenter.o fix_respa.o fix_rigid.o fix_rigid_nve.o fix_rigid_nvt.o fix_setforce.o fix_shake.o fix_shear_history.o fix_spring.o fix_spring_rg.o fix_spring_self.o fix_store_coord.o fix_store_force.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 improper.o improper_cvff.o improper_harmonic.o improper_hybrid.o input.o integrate.o kspace.o lammps.o lattice.o library.o main.o memory.o min_cg.o min.o min_hftn.o minimize.o min_linesearch.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 pack.o pair_airebo.o pair_born_coul_long.o pair_buck_coul_cut.o pair_buck_coul_long.o pair_buck.o pair_coul_cut.o pair_coul_debye.o pair_coul_long.o pair.o pair_dpd.o pair_dpd_tstat.o pair_eam_alloy.o pair_eam.o pair_eam_fs.o pair_hybrid.o pair_hybrid_overlay.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_cut_coul_cut.o pair_lj_cut_coul_debye.o pair_lj_cut_coul_long.o pair_lj_cut_coul_long_tip4p.o pair_lj_cut.o pair_lj_expand.o pair_lj_gromacs_coul_gromacs.o pair_lj_gromacs.o pair_lj_smooth.o pair_morse.o pair_reax.o pair_soft.o pair_sw.o pair_table.o pair_tersoff.o pair_tersoff_zbl.o pair_yukawa.o pppm.o pppm_tip4p.o random_mars.o random_park.o read_data.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 respa.o run.o set.o shell.o special.o temper.o thermo.o timer.o universe.o update.o variable.o velocity.o verlet.o write_restart.o -lreax -mt_mpi /packages/intel/mkl/[10.0.2.018/lib/em64t/libfftw3xc_intel.a](http://10.0.2.018/lib/em64t/libfftw3xc_intel.a) -lifcore -lsvml -lompstub -limf -lstdc++ -libmkl_intel_thread -libmkl_em64t -libguide -o ../lmp_mkl icc: command line error: invalid argument for option '-m' make[1]: *** [../lmp_mkl] Error 1 make[1]: Leaving directory /home/mgalanve/LAMMPS_May10/lammps-29May10/src/Obj_mkl’
make: *** [mkl] Error 2
mkl = Intel Cluster Tools, mpiicc, MKL MPI, MKL FFT
Intel recommends Intel Cluster Tools Compiler Edition
to build libfftw2xc_intel.a:
> cd /opt/intel/mkl/10.0.011/interfaces/fftw2xc
> become root via su
> gmake libem64t
SHELL = /bin/sh
---------------------------------------------------------------------
compiler/linker settings
specify flags and libraries needed for your compiler
CC = mpicc
CCFLAGS = -O3 -fno-alias -ip -unroll0
DEPFLAGS = -M
LINK = mpicc
LINKFLAGS = -O -L/packages/intel/mkl/10.0.2.018/lib/em64t
LIB = -lstdc++ -libmkl_intel_thread -libmkl_em64t -libguide
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
---------------------------------------------------------------------
LAMMPS-specific settings
specify settings for LAMMPS features you will use
LAMMPS ifdef options, see doc/Section_start.html
LMP_INC = -DLAMMPS_GZIP
MPI library, can be src/STUBS dummy lib
INC = path for mpi.h, MPI compiler settings
PATH = path for MPI library
LIB = name of MPI library
MPI_INC = -DMPICH_IGNORE_CXX_SEEK
MPI_PATH =
MPI_LIB = -mt_mpi
FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
PATH = path for FFT library
LIB = name of FFT library
FFT_INC = -DFFT_FFTW -I/packages/intel/mkl/10.0.2.018/include/fftw
FFT_PATH =
FFT_LIB = /packages/intel/mkl/10.0.2.018/lib/em64t/libfftw3xc_intel.a
additional system libraries needed by LAMMPS package libraries
these settings are IGNORED if the corresponding LAMMPS package
(e.g. gpu, meam) is NOT included in the LAMMPS build
SYSLIB = names of libraries
SYSPATH = paths of libraries
gpu_SYSLIB = -lcudart
meam_SYSLIB = -lifcore -lsvml -lompstub -limf
reax_SYSLIB = -lifcore -lsvml -lompstub -limf
user-atc_SYSLIB = -lblas -llapack
gpu_SYSPATH = -L/usr/local/cuda/lib64
meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
user-atc_SYSPATH =
---------------------------------------------------------------------
build rules and dependencies
no need to edit this section
include Makefile.package
EXTRA_INC = (LMP_INC) (PKG_INC) (MPI_INC) (FFT_INC)
EXTRA_PATH = (PKG_PATH) (MPI_PATH) (FFT_PATH) (PKG_SYSPATH)
EXTRA_LIB = (PKG_LIB) (MPI_LIB) (FFT_LIB) (PKG_SYSLIB)
Link target
(EXE): (OBJ)
(LINK) (LINKFLAGS) (EXTRA_PATH) (OBJ) (EXTRA_LIB) (LIB) -o (EXE)
(SIZE) $(EXE)
Library target
lib: (OBJ) (ARCHIVE) (ARFLAGS) (EXE) $(OBJ)
Compilation rules
.o:.cpp
(CC) (CCFLAGS) (EXTRA_INC) -c <
.d:.cpp
(CC) (CCFLAGS) (EXTRA_INC) (DEPFLAGS) < > @
Individual dependencies
DEPENDS = (OBJ:.o=.d) include (DEPENDS)