[lammps-users] Hi, I've a problem when building the ATC library

Dear All:

(Sorry sending this again. I just forgot to mention that I’m using the platform of Redhat, Openmpi)

I’ve a big problem when I was trying to make Lammps. It showed:

fix_atc.h(29): catastrophic error: could not open source file “ATC_Transfer.h”
#include “ATC_Transfer.h”
^

make[1]: *** [fix_atc.d] Error 4
make[1]: Leaving directory `/ifs/ibfs1/home/lyang/lammps-20Feb10/src/Obj_lewis’
make: *** [lewis] Error 2

Then I tried to build ATC library from the path: lib/atc

But I had problem again:

[[email protected]…1752… atc]$ make -f Makefile.g++
g++ -O -g -I…/…/src -DMPICH_IGNORE_CXX_SEEK -c ATC_HardyKernel.cpp
In file included from ATC_HardyKernel.h:5,
from ATC_HardyKernel.cpp:1:
LammpsInterface.h:6:17: mpi.h: No such file or directory
In file included from LammpsInterface.h:7,
from ATC_HardyKernel.h:5,
from ATC_HardyKernel.cpp:1:
…/…/src/lammps.h:17:17: mpi.h: No such file or directory
In file included from LammpsInterface.h:7,
from ATC_HardyKernel.h:5,
from ATC_HardyKernel.cpp:1:
…/…/src/lammps.h:41: error: MPI_Comm' does not name a type ../../src/lammps.h:46: error: MPI_Comm’ has not been declared
…/…/src/lammps.h:46: error: ISO C++ forbids declaration of parameter' with no type In file included from ATC_HardyKernel.h:5, from ATC_HardyKernel.cpp:1: LammpsInterface.h:63: error: MPI_Comm’ does not name a type
LammpsInterface.h: In member function void ATC::LammpsInterface::set_lammps(LAMMPS_NS::LAMMPS*)': LammpsInterface.h:58: error: 'class LAMMPS_NS::LAMMPS' has no member named 'world' LammpsInterface.h:58: error: MPI_Comm_rank’ was not declared in this scope
LammpsInterface.h: In member function void ATC::LammpsInterface::allsum(double*, double*, int)': LammpsInterface.h:67: error: MPI_DOUBLE’ was not declared in this scope
LammpsInterface.h:67: error: MPI_SUM' was not declared in this scope LammpsInterface.h:68: error: 'class LAMMPS_NS::LAMMPS' has no member named 'world' LammpsInterface.h:68: error: MPI_Allreduce’ was not declared in this scope
LammpsInterface.h:69: error: ‘class LAMMPS_NS::LAMMPS’ has no member named ‘world’
LammpsInterface.h:69: error: MPI_Barrier' was not declared in this scope LammpsInterface.h: In member function void ATC::LammpsInterface::int_allsum(int*, int*, int)’:
LammpsInterface.h:74: error: MPI_INT' was not declared in this scope LammpsInterface.h:74: error: MPI_SUM’ was not declared in this scope
LammpsInterface.h:75: error: ‘class LAMMPS_NS::LAMMPS’ has no member named ‘world’
LammpsInterface.h:75: error: MPI_Allreduce' was not declared in this scope LammpsInterface.h:76: error: 'class LAMMPS_NS::LAMMPS' has no member named 'world' LammpsInterface.h:76: error: MPI_Barrier’ was not declared in this scope
LammpsInterface.h: In member function void ATC::LammpsInterface::allmax(double*, double*, int)': LammpsInterface.h:81: error: MPI_DOUBLE’ was not declared in this scope
LammpsInterface.h:81: error: MPI_MAX' was not declared in this scope LammpsInterface.h:82: error: 'class LAMMPS_NS::LAMMPS' has no member named 'world' LammpsInterface.h:82: error: MPI_Allreduce’ was not declared in this scope
LammpsInterface.h:83: error: ‘class LAMMPS_NS::LAMMPS’ has no member named ‘world’
LammpsInterface.h:83: error: MPI_Barrier' was not declared in this scope LammpsInterface.h: In member function void ATC::LammpsInterface::int_allmax(int*, int*, int)’:
LammpsInterface.h:88: error: MPI_INT' was not declared in this scope LammpsInterface.h:88: error: MPI_MAX’ was not declared in this scope
LammpsInterface.h:89: error: ‘class LAMMPS_NS::LAMMPS’ has no member named ‘world’
LammpsInterface.h:89: error: MPI_Allreduce' was not declared in this scope LammpsInterface.h:90: error: 'class LAMMPS_NS::LAMMPS' has no member named 'world' LammpsInterface.h:90: error: MPI_Barrier’ was not declared in this scope
LammpsInterface.h: In member function void ATC::LammpsInterface::logical_or(int*, int*, int)': LammpsInterface.h:95: error: MPI_INT’ was not declared in this scope
LammpsInterface.h:95: error: MPI_LOR' was not declared in this scope LammpsInterface.h:96: error: 'class LAMMPS_NS::LAMMPS' has no member named 'world' LammpsInterface.h:96: error: MPI_Allreduce’ was not declared in this scope
LammpsInterface.h:97: error: ‘class LAMMPS_NS::LAMMPS’ has no member named ‘world’
LammpsInterface.h:97: error: `MPI_Barrier’ was not declared in this scope
make: *** [ATC_HardyKernel.o] Error 1

Anyway, please help me. I took me several days to make Lammps. It drives me crazy.

Thanks so much!

Nick Yang

2010/3/2 Lingqi Yang <[email protected]>:

Dear All:

(Sorry sending this again. I just forgot to mention that I'm using the
platform of Redhat, Openmpi)

try changing lib/atc/Makefile.g++ to have mpicxx instead of g++.

Hi:

Thanks so much. I finally build the ATC library. However, I still have problems via making lammsp. Please help me if you know how to do it. I really appreciate it.

The error is:

fix_atc.h(29): catastrophic error: could not open source file "ATC_Transfer.h"
  #include "ATC_Transfer.h"
                           ^
compilation aborted for fix_atc.cpp (code 4)
make[1]: *** [fix_atc.o] Error 4
make[1]: Leaving directory `/ifs/ibfs1/home/lyang/lammps-20Feb10/src/Obj_lewis'
make: *** [lewis] Error 2

The following is my Make file. Since the platform of my university is called lewis, I make a file named Makefile.lewis, besides, I've already built all libraries of atc, meam, poems, reax before making lammps:

# ttm = RedHat Linux box, Intel icc, MPICH2, FFTW

SHELL = /bin/sh

# System-specific settings

CC = mpiCC
CCFLAGS = -O -I/home/lyang/fftw2.1.5/include \
    -I../../lib/poems -I../../lib/reax \
    -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK
DEPFLAGS = -M
LINK = mpiCC
LINKFLAGS = -O -L/home/lyang/fftw2.1.5/lib \
    -L../../lib/poems -L../../lib/meam \
                -L../../lib/reax -L/opt/intel/fce/9.1.036/lib
USRLIB = -lfftw -lpoems -lmeam -lreax
SYSLIB = -lpthread -lstdc++ -lifcore -lsvml -lompstub -limf
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 = -lmpich -lpthread

# 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
FFT_PATH =
FFT_LIB = -lfftw

# 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) \(OBJ\) (USRLIB) \(SYSLIB\) \-o (EXE)
  \(SIZE\) (EXE)

# Library target

lib: \(OBJ\) &nbsp;&nbsp;(ARCHIVE) \(ARFLAGS\) (EXE) $(OBJ)

# Compilation rules

\.o:.cpp
  \(CC\) (CCFLAGS) -c $<

\.d:.cpp
  \(CC\) (CCFLAGS) \(DEPFLAGS\) < > [email protected]

# Individual dependencies

DEPENDS = \(OBJ:\.o=\.d\) include (DEPENDS)

CCFLAGS = -O -I/home/lyang/fftw2.1.5/include \
               -I../../lib/poems -I../../lib/reax \
               -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK

Why do you have these kinds of lines in your Makefile.foo? These settings
(for poems, reax, and atc) should be in Makefile.package which is
auto-generated,
when you type make yes-user-atc. You're subverting the auto system and trying
to do this yourself, and apparently screwing it up. Makefile.package
is included
by all lo-level Makefiles - is it included by yours?

Steve

Hi:

Should I type: make yes-all to build all packages to lammps? I've built lammps all over again. I build all packages and I just copy the lines in the Makefile.package into the Makefile.lewis (The machine's name of our unviersity is lewis). After I typing make lewis, the error comes again showing" cannot find lgpu". Is it because that I did not build gpu? I only build reax, meam, poems and atc.

Is there anyway to avoid this problem via ignoreing gpu?

Nick Yang

Hi:

hi nick,

why don't you just follow the instructions in the
LAMMPS documentation instead of making up your own?
if you are not familiar with the build system of LAMMPS,
this is a recipe for disaster.

Should I type: make yes-all to build all packages to lammps? I've built
lammps all over again. I build all packages and I just copy the lines in the
Makefile.package into the Makefile.lewis (The machine's name of our

that is not how it works. what you should do instead is to
adjust Makefile.linux (or a copy of it) and then take it from there.

unviersity is lewis). After I typing make lewis, the error comes again
showing" cannot find lgpu". Is it because that I did not build gpu? I only
build reax, meam, poems and atc.

Is there anyway to avoid this problem via ignoreing gpu?

how about 'make no-gpu'? it is all explained in detail
in the documentation... you have to read it, though.
it currently has no support for a Nuremberg funnel.

cheers,
   axel.

The problem is it doesn't work when I following the normal procedure.

I've built Lammps again and again. It seemed the error occurs when the building process reaches the final command: write_restart

Let me attach the error again.

mpiCC -O -I//home/lyang/fftw2.1.5/include -I../../lib/atc -I../../lib/meam -I../../lib/reax -I../../lib/poems -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -c variable.cpp
mpiCC -O -I//home/lyang/fftw2.1.5/include -I../../lib/atc -I../../lib/meam -I../../lib/reax -I../../lib/poems -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -c velocity.cpp
mpiCC -O -I//home/lyang/fftw2.1.5/include -I../../lib/atc -I../../lib/meam -I../../lib/reax -I../../lib/poems -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -c verlet.cpp
mpiCC -O -I//home/lyang/fftw2.1.5/include -I../../lib/atc -I../../lib/meam -I../../lib/reax -I../../lib/poems -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -c write_restart.cpp
mpiCC -O -L/home/lyang/fftw2.1.5/lib -L../../lib/atc -L../../lib/meam -L../../lib/reax -L../../lib/poems -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK 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_atc.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_nph.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_poems.o fix_press_berendsen.o fix_print.o fix_reax_bonds.o fix_recenter.o fix_respa.o fix_rigid.o fix_set_force.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_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_meam.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 -o ../lmp_lewis
/share/apps/intel/Compiler/11.1/046/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
fft3d.o(.text+0x6b): In function `fft_3d(fftw_complex*, fftw_complex*, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0xc8): In function `fft_3d(fftw_complex*, fftw_complex*, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0x125): In function `fft_3d(fftw_complex*, fftw_complex*, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0x1c9): In function `fft_3d(fftw_complex*, fftw_complex*, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0x1eb): In function `fft_3d(fftw_complex*, fftw_complex*, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0x20d): more undefined references to `fftw' follow
fft3d.o(.text+0xab2): In function `fft_3d_create_plan(ompi_communicator_t*, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int*)':
: undefined reference to `fftw_create_plan'
fft3d.o(.text+0xac8): In function `fft_3d_create_plan(ompi_communicator_t*, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int*)':
: undefined reference to `fftw_create_plan'
fft3d.o(.text+0xaf4): In function `fft_3d_create_plan(ompi_communicator_t*, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int*)':
: undefined reference to `fftw_create_plan'
fft3d.o(.text+0xb0a): In function `fft_3d_create_plan(ompi_communicator_t*, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int*)':
: undefined reference to `fftw_create_plan'
fft3d.o(.text+0xb67): In function `fft_3d_create_plan(ompi_communicator_t*, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int*)':
: undefined reference to `fftw_create_plan'
fft3d.o(.text+0xb84): more undefined references to `fftw_create_plan' follow
fft3d.o(.text+0xd3f): In function `fft_3d_destroy_plan(fft_plan_3d*)':
: undefined reference to `fftw_destroy_plan'
fft3d.o(.text+0xd4c): In function `fft_3d_destroy_plan(fft_plan_3d*)':
: undefined reference to `fftw_destroy_plan'
fft3d.o(.text+0xd63): In function `fft_3d_destroy_plan(fft_plan_3d*)':
: undefined reference to `fftw_destroy_plan'
fft3d.o(.text+0xd70): In function `fft_3d_destroy_plan(fft_plan_3d*)':
: undefined reference to `fftw_destroy_plan'
fft3d.o(.text+0xd7d): In function `fft_3d_destroy_plan(fft_plan_3d*)':
: undefined reference to `fftw_destroy_plan'
fft3d.o(.text+0xd87): more undefined references to `fftw_destroy_plan' follow
fft3d.o(.text+0x1005): In function `fft_1d_only(fftw_complex*, int, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0x1039): In function `fft_1d_only(fftw_complex*, int, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0x1063): In function `fft_1d_only(fftw_complex*, int, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0x1101): In function `fft_1d_only(fftw_complex*, int, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0x112f): In function `fft_1d_only(fftw_complex*, int, int, fft_plan_3d*)':
: undefined reference to `fftw'
fft3d.o(.text+0x1156): more undefined references to `fftw' follow
fix_atc.o(.text+0x6e): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::LammpsInterface::instance()'
fix_atc.o(.text+0x86): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::LammpsInterface::instance()'
fix_atc.o(.text+0x19c): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::ATC_TransferHardy::ATC_TransferHardy(std::string, std::string)'
fix_atc.o(.text+0x2bc): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::ATC_TransferHardy::ATC_TransferHardy(std::string, std::string)'
fix_atc.o(.text+0x43c): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::ATC_TransferThermal::ATC_TransferThermal(std::string, std::string, ATC::ExtrinsicModelType)'
fix_atc.o(.text+0x542): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::ATC_TransferThermal::ATC_TransferThermal(std::string, std::string, ATC::ExtrinsicModelType)'
fix_atc.o(.text+0x9ac): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::LammpsInterface::instance()'
fix_atc.o(.text+0x9c4): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::LammpsInterface::instance()'
fix_atc.o(.text+0xada): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::ATC_TransferHardy::ATC_TransferHardy(std::string, std::string)'
fix_atc.o(.text+0xbf5): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::ATC_TransferHardy::ATC_TransferHardy(std::string, std::string)'
fix_atc.o(.text+0xd70): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::ATC_TransferThermal::ATC_TransferThermal(std::string, std::string, ATC::ExtrinsicModelType)'
fix_atc.o(.text+0xe71): In function `LAMMPS_NS::FixATC::FixATC(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `ATC::ATC_TransferThermal::ATC_TransferThermal(std::string, std::string, ATC::ExtrinsicModelType)'
fix_atc.o(.text+0x18c9): In function `LAMMPS_NS::FixATC::memory_usage()':
: undefined reference to `ATC::ATC_Transfer::memory_usage()'
fix_atc.o(.text+0x18e9): In function `LAMMPS_NS::FixATC::grow_arrays(int)':
: undefined reference to `ATC::ATC_Transfer::grow_arrays(int)'
fix_atc.o(.text+0x18f9): In function `LAMMPS_NS::FixATC::copy_arrays(int, int)':
: undefined reference to `ATC::ATC_Transfer::copy_arrays(int, int)'
fix_atc.o(.text+0x1909): In function `LAMMPS_NS::FixATC::pack_exchange(int, double*)':
: undefined reference to `ATC::ATC_Transfer::pack_exchange(int, double*)'
fix_atc.o(.text+0x1919): In function `LAMMPS_NS::FixATC::unpack_exchange(int, double*)':
: undefined reference to `ATC::ATC_Transfer::unpack_exchange(int, double*)'
fix_atc.o(.text+0x1929): In function `LAMMPS_NS::FixATC::pack_comm(int, int*, double*, int, int*)':
: undefined reference to `ATC::ATC_Transfer::pack_comm(int, int*, double*, int, int*)'
fix_atc.o(.text+0x1939): In function `LAMMPS_NS::FixATC::unpack_comm(int, int, double*)':
: undefined reference to `ATC::ATC_Transfer::unpack_comm(int, int, double*)'
fix_atc.o(.gnu.linkonce.t._ZN9LAMMPS_NS6FixATC9init_listEiPNS_9NeighListE[.gnu.linkonce.t._ZN9LAMMPS_NS6FixATC9init_listEiPNS_9NeighListE]+0x9): In function `LAMMPS_NS::FixATC::init_list(int, LAMMPS_NS::NeighList*)':
: undefined reference to `ATC::LammpsInterface::instance()'
fix_atc.o(.gnu.linkonce.t._ZN9LAMMPS_NS6FixATC9init_listEiPNS_9NeighListE[.gnu.linkonce.t._ZN9LAMMPS_NS6FixATC9init_listEiPNS_9NeighListE]+0x16): In function `LAMMPS_NS::FixATC::init_list(int, LAMMPS_NS::NeighList*)':
: undefined reference to `ATC::LammpsInterface::init_list(int, LAMMPS_NS::NeighList*)'
fix_poems.o(.text+0xb75): In function `LAMMPS_NS::FixPOEMS::FixPOEMS(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `Workspace::Workspace()'
fix_poems.o(.text+0x2c35): In function `LAMMPS_NS::FixPOEMS::FixPOEMS(LAMMPS_NS::LAMMPS*, int, char**)':
: undefined reference to `Workspace::Workspace()'
fix_poems.o(.text+0x34ba): In function `LAMMPS_NS::FixPOEMS::~FixPOEMS()':
: undefined reference to `Workspace::~Workspace()'
fix_poems.o(.text+0x36e1): In function `LAMMPS_NS::FixPOEMS::~FixPOEMS()':
: undefined reference to `Workspace::~Workspace()'
fix_poems.o(.text+0x3911): In function `LAMMPS_NS::FixPOEMS::~FixPOEMS()':
: undefined reference to `Workspace::~Workspace()'
fix_poems.o(.text+0x4626): In function `LAMMPS_NS::FixPOEMS::setup(int)':
: undefined reference to `Workspace::MakeSystem(int&, double*&, double**&, double**&, double**&, double**&, double**&, double**&, double**&, int&, int**&, double**&, int&, int*, double, double, double, double)'
fix_poems.o(.text+0x4a2f): In function `LAMMPS_NS::FixPOEMS::final_integrate()':
: undefined reference to `Workspace::LobattoTwo(double**&, double**&, double**&, double**&)'
fix_poems.o(.text+0x7476): In function `LAMMPS_NS::FixPOEMS::initial_integrate(int)':
: undefined reference to `Workspace::LobattoOne(double**&, double**&, double**&, double**&, double**&, double**&, double**&, double**&)'
fix_reax_bonds.o(.text+0x4c7): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `getnsbmax_'
fix_reax_bonds.o(.text+0x4d4): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `getcutof3_'
fix_reax_bonds.o(.text+0x64c): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `cbkia_'
fix_reax_bonds.o(.text+0x659): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `cbkia_'
fix_reax_bonds.o(.text+0x6a2): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `cbkia_'
fix_reax_bonds.o(.text+0x6b7): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `cbkc_'
fix_reax_bonds.o(.text+0x6ce): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `cbkia_'
fix_reax_bonds.o(.text+0x6f1): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `cbknubon2_'
fix_reax_bonds.o(.text+0x6f9): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `cbkbo_'
fix_reax_bonds.o(.text+0x714): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `cbkabo_'
fix_reax_bonds.o(.text+0x720): In function `LAMMPS_NS::FixReaxBonds::end_of_step()':
: undefined reference to `cbklonpar_'
fix_reax_bonds.o(.text+0xc56): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `getnsbmax_'
fix_reax_bonds.o(.text+0xc63): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `getcutof3_'
fix_reax_bonds.o(.text+0xdda): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `cbkia_'
fix_reax_bonds.o(.text+0xde7): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `cbkia_'
fix_reax_bonds.o(.text+0xe30): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `cbkia_'
fix_reax_bonds.o(.text+0xe45): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `cbkc_'
fix_reax_bonds.o(.text+0xe5c): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `cbkia_'
fix_reax_bonds.o(.text+0xe80): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `cbknubon2_'
fix_reax_bonds.o(.text+0xe88): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `cbkbo_'
fix_reax_bonds.o(.text+0xea3): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `cbkabo_'
fix_reax_bonds.o(.text+0xeaf): In function `LAMMPS_NS::FixReaxBonds::OutputReaxBonds(int, _IO_FILE*)':
: undefined reference to `cbklonpar_'
pair_meam.o(.text+0x28f): In function `LAMMPS_NS::PairMEAM::~PairMEAM()':
: undefined reference to `meam_cleanup_'
pair_meam.o(.text+0x5bf): In function `LAMMPS_NS::PairMEAM::~PairMEAM()':
: undefined reference to `meam_cleanup_'
pair_meam.o(.text+0x8ff): In function `LAMMPS_NS::PairMEAM::~PairMEAM()':
: undefined reference to `meam_cleanup_'
pair_meam.o(.text+0x165c): In function `LAMMPS_NS::PairMEAM::compute(int, int)':
: undefined reference to `meam_dens_init_'
pair_meam.o(.text+0x1831): In function `LAMMPS_NS::PairMEAM::compute(int, int)':
: undefined reference to `meam_dens_final_'
pair_meam.o(.text+0x1ae0): In function `LAMMPS_NS::PairMEAM::compute(int, int)':
: undefined reference to `meam_force_'
pair_meam.o(.text+0x1fb3): In function `LAMMPS_NS::PairMEAM::coeff(int, char**)':
: undefined reference to `meam_setup_done_'
pair_meam.o(.text+0x2d38): In function `LAMMPS_NS::PairMEAM::read_files(char*, char*)':
: undefined reference to `meam_setup_global_'
pair_meam.o(.text+0x3245): In function `LAMMPS_NS::PairMEAM::read_files(char*, char*)':
: undefined reference to `meam_setup_param_'
pair_reax.o(.text+0x922): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkvirial_'
pair_reax.o(.text+0x92e): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkvirial_'
pair_reax.o(.text+0x942): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkvirial_'
pair_reax.o(.text+0x94e): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkvirial_'
pair_reax.o(.text+0x2305): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `rsmall_'
pair_reax.o(.text+0x2312): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `rsmall_'
pair_reax.o(.text+0x2330): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkc_'
pair_reax.o(.text+0x2340): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkc_'
pair_reax.o(.text+0x2351): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkc_'
pair_reax.o(.text+0x235d): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkch_'
pair_reax.o(.text+0x2374): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkia_'
pair_reax.o(.text+0x238b): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkia_'
pair_reax.o(.text+0x239a): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkc_'
pair_reax.o(.text+0x24ed): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x24f4): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlbo_'
pair_reax.o(.text+0x24fe): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x251b): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlbo_'
pair_reax.o(.text+0x252b): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x253d): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x2553): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x2576): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x2599): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x25a6): more undefined references to `cbknvlown_' follow
pair_reax.o(.text+0x2676): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x267d): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlbo_'
pair_reax.o(.text+0x2687): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x26a5): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlbo_'
pair_reax.o(.text+0x26b0): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x26dd): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x26e7): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x2701): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `srtbon1_'
pair_reax.o(.text+0x2720): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `molec_'
pair_reax.o(.text+0x2725): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `encalc_'
pair_reax.o(.text+0x2738): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `mdsav_'
pair_reax.o(.text+0x2771): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkd_'
pair_reax.o(.text+0x277e): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkd_'
pair_reax.o(.text+0x278b): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkd_'
pair_reax.o(.text+0x27c3): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x27cb): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x27d3): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x27db): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x27ec): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x27fd): more undefined references to `cbkenergies_' follow
pair_reax.o(.text+0x288c): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkd_'
pair_reax.o(.text+0x28b3): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkvirial_'
pair_reax.o(.text+0x28c8): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkvirial_'
pair_reax.o(.text+0x28dd): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkvirial_'
pair_reax.o(.text+0x28f2): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkvirial_'
pair_reax.o(.text+0x2907): In function `LAMMPS_NS::PairREAX::compute(int, int)':
: undefined reference to `cbkvirial_'
pair_reax.o(.text+0x291c): more undefined references to `cbkvirial_' follow
pair_reax.o(.text+0x358e): In function `LAMMPS_NS::PairREAX::pack_comm(int, int*, double*, int, int*)':
: undefined reference to `cbkabo_'
pair_reax.o(.text+0x3619): In function `LAMMPS_NS::PairREAX::unpack_comm(int, int, double*)':
: undefined reference to `cbkabo_'
pair_reax.o(.text+0x3651): In function `LAMMPS_NS::PairREAX::unpack_comm(int, int, double*)':
: undefined reference to `cbkabo_'
pair_reax.o(.text+0x36e2): In function `LAMMPS_NS::PairREAX::unpack_comm(int, int, double*)':
: undefined reference to `cbkabo_'
pair_reax.o(.text+0x3aa7): In function `LAMMPS_NS::PairREAX::write_reax_positions()':
: undefined reference to `rsmall_'
pair_reax.o(.text+0x3ab5): In function `LAMMPS_NS::PairREAX::write_reax_positions()':
: undefined reference to `rsmall_'
pair_reax.o(.text+0x3ad3): In function `LAMMPS_NS::PairREAX::write_reax_positions()':
: undefined reference to `cbkc_'
pair_reax.o(.text+0x3ae3): In function `LAMMPS_NS::PairREAX::write_reax_positions()':
: undefined reference to `cbkc_'
pair_reax.o(.text+0x3af3): In function `LAMMPS_NS::PairREAX::write_reax_positions()':
: undefined reference to `cbkc_'
pair_reax.o(.text+0x3aff): In function `LAMMPS_NS::PairREAX::write_reax_positions()':
: undefined reference to `cbkch_'
pair_reax.o(.text+0x3b16): In function `LAMMPS_NS::PairREAX::write_reax_positions()':
: undefined reference to `cbkia_'
pair_reax.o(.text+0x3b2d): In function `LAMMPS_NS::PairREAX::write_reax_positions()':
: undefined reference to `cbkia_'
pair_reax.o(.text+0x3b3c): In function `LAMMPS_NS::PairREAX::write_reax_positions()':
: undefined reference to `cbkc_'
pair_reax.o(.text+0x3ca0): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x3ca7): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlbo_'
pair_reax.o(.text+0x3cb1): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x3cce): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlbo_'
pair_reax.o(.text+0x3cde): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x3cf0): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x3d06): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x3d29): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x3d4c): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x3d59): more undefined references to `cbknvlown_' follow
pair_reax.o(.text+0x3e3c): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x3e43): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlbo_'
pair_reax.o(.text+0x3e4d): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x3e6a): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlbo_'
pair_reax.o(.text+0x3e75): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbknvlown_'
pair_reax.o(.text+0x3ea2): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x3eac): In function `LAMMPS_NS::PairREAX::write_reax_vlist()':
: undefined reference to `cbkpairs_'
pair_reax.o(.text+0x3ef5): In function `LAMMPS_NS::PairREAX::read_reax_forces()':
: undefined reference to `cbkd_'
pair_reax.o(.text+0x3f02): In function `LAMMPS_NS::PairREAX::read_reax_forces()':
: undefined reference to `cbkd_'
pair_reax.o(.text+0x3f0f): In function `LAMMPS_NS::PairREAX::read_reax_forces()':
: undefined reference to `cbkd_'
pair_reax.o(.text+0x855e): In function `LAMMPS_NS::PairREAX::output_itemized_energy(double)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x8565): In function `LAMMPS_NS::PairREAX::output_itemized_energy(double)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x856c): In function `LAMMPS_NS::PairREAX::output_itemized_energy(double)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x8573): In function `LAMMPS_NS::PairREAX::output_itemized_energy(double)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x857a): In function `LAMMPS_NS::PairREAX::output_itemized_energy(double)':
: undefined reference to `cbkenergies_'
pair_reax.o(.text+0x8581): more undefined references to `cbkenergies_' follow
pair_reax.o(.text+0x8ae1): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `readc_'
pair_reax.o(.text+0x8ae6): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `reaxinit_'
pair_reax.o(.text+0x8aeb): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `ffinpt_'
pair_reax.o(.text+0x8af0): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `tap7th_'
pair_reax.o(.text+0x8b02): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `setngeofor_'
pair_reax.o(.text+0x8b17): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `readgeo_'
pair_reax.o(.text+0x8b23): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `getswb_'
pair_reax.o(.text+0x8b51): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `getvlbora_'
pair_reax.o(.text+0x8b6d): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `getnso_'
pair_reax.o(.text+0x8b79): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `getswa_'
pair_reax.o(.text+0x8bdc): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `cbkchb_'
pair_reax.o(.text+0x8be4): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `cbkchb_'
pair_reax.o(.text+0x8bec): In function `LAMMPS_NS::PairREAX::init_style()':
: undefined reference to `cbkchb_'
make[1]: *** [../lmp_lewis] Error 1
make[1]: Leaving directory `/ifs/ibfs1/home/lyang/lammps-20Feb10/src/Obj_lewis'
make: *** [lewis] Error 2

And the Makefile: ( I appreciate it very much if someone can help me figure out what's wrong with my Makefile. I use mpicc to compile. The operating system on lewis is Platform OCS Linux 4.1.1 (based on Redhat Linux).In the "#System-specific settings", I just copy the path from the Makefile.package. "

# lewis = RedHat Linux box, Intel icc, MPICH2, FFTW

SHELL = /bin/sh

# System-specific settings

CC = mpiCC
CCFLAGS = -O -I//home/lyang/fftw2.1.5/include -I../../lib/atc -I../../lib/meam -I../../lib/reax -I../../lib/poems \
             -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK
DEPFLAGS = -M
LINK = mpiCC
LINKFLAGS = -O -L/home/lyang/fftw2.1.5/lib -L../../lib/atc -L../../lib/meam -L../../lib/reax -L../../lib/poems \
             -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK
LIB = -latc -lmeam -lreax -lpoems
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 =

# 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
FFT_PATH =
FFT_LIB = -lfftw

# 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) \(OBJ\) (USRLIB) \(SYSLIB\) \-o (EXE)
  \(SIZE\) (EXE)

# Library target

lib: \(OBJ\) &nbsp;&nbsp;(ARCHIVE) \(ARFLAGS\) (EXE) $(OBJ)

# Compilation rules

\.o:.cpp
  \(CC\) (CCFLAGS) -c $<

\.d:.cpp
  \(CC\) (CCFLAGS) \(DEPFLAGS\) < > [email protected]

# Individual dependencies

DEPENDS = \(OBJ:\.o=\.d\) include (DEPENDS)

Hi Lingqi,

The errors you're getting suggest to me that the you're not including (or
perhaps not finding) the directories where the header files (*.h) are
located. This seems to be the case for all the libraries you're linking to
(fftw, atc, meam and reax). Did you start out typing "make yes-user-atc",
"make yes-mean", etc, and create an appropriate Makefile.package file that
contains the correct information?

Jon Z.

Hi:

Thanks for your advice. I think the major mistake that I made before is because I add the path of those packages within the ccflags and linkflags by following what other people has done before. However, that's for the old version. For the new version, at least for me, I only need to include the path of fftw2 on those options.

Now, I've new problem just as I posted few minutes before. I cannot build lammps successfully when I add atc to the packages. I can build lammps by adding all packages except gpu and atc, but it goes wrong when I add atc. And I don't know how to set the user-atc_SYSPATH correct. Coz whether I set the real path or the default path, it always goes wrong.

So, do you know anything about that? I really appreciate it.

You can find my questions in detail in my recent email. Just few minutes ago.

Thanks

Nick Yang

0

Hi:

Thanks for your advice. I think the major mistake that I made before is
because I add the path of those packages within the ccflags and linkflags by
following what other people has done before. However, that's for the old
version. For the new version, at least for me, I only need to include the
path of fftw2 on those options.

Now, I've new problem just as I posted few minutes before. I cannot build
lammps successfully when I add atc to the packages. I can build lammps by
adding all packages except gpu and atc, but it goes wrong when I add atc.
And I don't know how to set the user-atc_SYSPATH correct. Coz whether I set
the real path or the default path, it always goes wrong.

user-atc_SYSPATH and user-atc_SYSLIB are to provide flags
to link to BLAS and LAPACK. so you have to provide the linker
flags for that. on my machine the former is empty (my BLAS/LAPACK
are in the default search path for the linker) and user-atc_SYSLIB is
-llapack -lblas
if you are using MKL, you can look up what to link to in the MKL docs.
similar for other optimized BLAS/LAPACK packages.

cheers,
   axel.

Every Makefile.lewis you have posted has bad settings
in wrong places in the Makefile. You appear to be modifying
settings randomly, hoping for success. Those Makefiles are
structured in very specific ways, all of it documented in
doc/Section_start.html.

For the ATC issues, you need to compile the lib/atc library with a
Fortran compiler. Then you need to include the package in
your LAMMPS build (make yes-user-atc). Then Makefile.lewis, which
does a C++ link,
needs to link in the appropriate Fortran libraries from your Fortran
compiler. If you don't do one of these steps correctly, it will fail.

The specific error message you get will be a hint as to why it failed,
e.g. it could not find a library file you have specified, or it cannot
link b/c you did not specify a needed library file.

Steve