lammps mpich

Dear all,

I am a new user of lammps and I am trying to compile lammps with mpi (to run lammps in parallel) but I have some problems

I am using Mandriva 2010.2 and the next version of lammps: Lammps-1Dec10.

I have modified the make files to my system and I have already compiled mpich libraries (mpich2-1.3.1.tar.gz) …but I still have some problems. First I build lammps in a single processor and I run some examples and everything was ok, but I can not obtain the executable with the parallel options

Here I attached the makefile I use and the output I obtain

It says that I do not have

Thank you so much for all your help

best

david

$$$$$$$$$$$$$$$$$$$$$$$$$ MAKEFILE

linux = RedHat Linux box, Intel icc, Intel ifort, MPICH2, FFTW

SHELL = /bin/sh

---------------------------------------------------------------------

compiler/linker settings

specify flags and libraries needed for your compiler

CC = g++
CCFLAGS = -g -O -I/home/dcereceda/phD/LAMMPS/Lammps_mpi/My_mpich/include -DFFT_none
DEPFLAGS = -M
LINK = g++
LINKFLAGS = -g -O -L/home/dcereceda/phD/LAMMPS/Lammps_mpi/My_mpich/lib
LIB =
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 = -I/home/dcereceda/phD/LAMMPS/Lammps_mpi/My_mpich/include
MPI_PATH = -L/home/dcereceda/phD/LAMMPS/Lammps_mpi/My_mpich/lib
MPI_LIB = libmpich.a

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_NONE
FFT_PATH =
FFT_LIB =

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)

$$$$$$$$$$$$$$$$$$$$$$ ERROR OBTAINED

g++ -g -O -I/home/dcereceda/phD/LAMMPS/Lammps_mpi/My_mpich/include -DFFT_none -DLAMMPS_GZIP -I/home/dcereceda/phD/LAMMPS/Lammps_mpi/My_mpich/include -DFFT_NONE -c modify.cpp
g++ -g -O -L/home/dcereceda/phD/LAMMPS/Lammps_mpi/My_mpich/lib -L/home/dcereceda/phD/LAMMPS/Lammps_mpi/My_mpich/lib angle.o atom.o atom_vec_atomic.o atom_vec_charge.o atom_vec.o atom_vec_hybrid.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_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.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 compute_ti.o create_atoms.o create_box.o delete_atoms.o delete_bonds.o dihedral.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 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_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_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_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 improper.o input.o integrate.o irregular.o kspace.o lammps.o lattice.o library.o main.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 pack.o pair_born.o pair_buck_coul_cut.o pair_buck.o pair_coul_cut.o pair_coul_debye.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_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_morse.o pair_soft.o pair_table.o pair_yukawa.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 replicate.o respa.o run.o set.o shell.o special.o thermo.o timer.o universe.o update.o variable.o velocity.o verlet.o write_restart.o libmpich.a -o …/lmp_quevedo
g++: libmpich.a: No such file or directory
make[1]: *** […/lmp_quevedo] Error 1
make[1]: Leaving directory `/home/dcereceda/phD/LAMMPS/Lammps_mpi/lammps-1Dec10/src/Obj_quevedo’
make: *** [quevedo] Error 2
[[email protected]…436… src] locate libmpich.a /home/dcereceda/phD/LAMMPS/Lammps_mpi/My_mpich/lib/libmpich.a /usr/lib64/libmpich.a [[email protected] src]

Dear all,

I am a new user of lammps and I am trying to compile lammps with mpi (to run
lammps in parallel) but I have some problems

I am using Mandriva 2010.2 and the next version of lammps: Lammps-1Dec10.

I have modified the make files to my system and I have already compiled
mpich libraries (mpich2-1.3.1.tar.gz) ...but I still have some problems.
First I build lammps in a single processor and I run some examples and
everything was ok, but I can not obtain the executable with the parallel
options

Here I attached the makefile I use and the output I obtain

It says that I do not have

libraries are specified differently. you have to strip off the "lib"
and the ".a" or ".so"
so you link to libmpich.a with -lmpich
or you don't use the -L flag to set a path and then have to use the
full path to libmpich.a

but then again. i would advise overall against using MPICH at all,
since in my experience OpenMPI is a significantly better MPI
implementation. for example you don't even need to specify
the location of the MPI header or library since the mpicxx
wrappers do work well. :wink:

cheers,
    axel.

Dear all,

after some days trying to figure out how to solve the problem I had with lammps I have finally compiled LAMMPS in parallel with openmpi

thank you so much for your help and all your advices

best

david

2011/3/30 Axel Kohlmeyer <[email protected]>