LAMMPS kurulum sorunu

[zeusmaster]

Linkteki anlatımı takip ettim ama serial olanını kurmaya çalıştım. Öncelikle yaptıklarım

Kod Seç Genişlet

sudo apt-get install build-essential
sudo apt-get install libxaw7-dev
sudo apt-get install mpich2

fftw kurulumu;

Kod Seç Genişlet

./configure CC=gcc F77=gfortran --enable-shared=PKGS --prefix=$PWD
make
make check
make install

Lammps Kurulum;

Kod Seç Genişlet

cd lib/reax
make -f Makefile.gfortran

Kod Seç Genişlet

cd lib/meam
make -f Makefile.gfortran

Kod Seç Genişlet

cd lib/poems
make -f Makefile.g++

Kod Seç Genişlet

cd src
make yes-standard
make serial

Make.serial dosyası;

Kod Seç Genişlet

# serial = RedHat Linux box, g++, no MPI, no FFTs

SHELL = /bin/sh

# ---------------------------------------------------------------------
# compiler/linker settings
# generally no need to edit this section
# unless additional compiler/linker flags or libraries needed for your machine

CC = g++
CCFLAGS = -O
DEPFLAGS = -M
LINK = g++
LINKFLAGS = -O
LIB =           
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size

# ---------------------------------------------------------------------
# LAMMPS-specific settings
# edit as needed for your machine

# 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../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi

# 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 =-I/usr/local/lammps/fftw/iclude       -DFFT_NONE
FFT_PATH =/usr/local/lammps/fftw
FFT_LIB =-L/usr/local/lammps/fftw/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)

Aldığım hata ise ;

Kod Seç Genişlet

└──>>make serial
make[1]: Entering directory `/usr/local/lammps/lammps/src/Obj_serial'
g++ -O -L../../lib/reax -L../../lib/poems -L../../lib/meam -L../../lib/gpu  -L../STUBS /usr/local/lammps/fftw     angle_charmm.o angle_class2.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_colloid.o atom_vec.o atom_vec_dipole.o atom_vec_ellipsoid.o atom_vec_full.o atom_vec_granular.o atom_vec_hybrid.o atom_vec_molecular.o atom_vec_peri.o bond_class2.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_damage_atom.o compute_dihedral_local.o compute_displace_atom.o compute_erotate_asphere.o compute_erotate_sphere.o compute_event_displace.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_asphere.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_class2.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_xtc.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_event.o fix_freeze.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_asphere.o fix_nph.o fix_nph_sphere.o fix_npt_asphere.o fix_npt.o fix_npt_sphere.o fix_nve_asphere.o fix_nve.o fix_nve_limit.o fix_nve_noforce.o fix_nve_sphere.o fix_nvt_asphere.o fix_nvt.o fix_nvt_sllod.o fix_nvt_sphere.o fix_orient_fcc.o fix_peri_neigh.o fix_planeforce.o fix_poems.o fix_pour.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_colloid.o fix_wall.o fix_wall_gran.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_class2.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_colloid.o pair_coul_cut.o pair_coul_debye.o pair_coul_long.o pair.o pair_dipole_cut.o pair_dpd.o pair_dpd_tstat.o pair_dsmc.o pair_eam_alloy.o pair_eam_alloy_opt.o pair_eam.o pair_eam_fs.o pair_eam_fs_opt.o pair_eam_opt.o pair_gayberne.o pair_gayberne_gpu.o pair_gran_hertz_history.o pair_gran_hooke.o pair_gran_hooke_history.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_charmm_coul_long_opt.o pair_lj_class2_coul_cut.o pair_lj_class2_coul_long.o pair_lj_class2.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_cut_gpu.o pair_lj_cut_opt.o pair_lj_expand.o pair_lj_gromacs_coul_gromacs.o pair_lj_gromacs.o pair_lj_smooth.o pair_lubricate.o pair_meam.o pair_morse.o pair_morse_opt.o pair_peri_pmb.o pair_reax.o pair_resquared.o pair_soft.o pair_sw.o pair_table.o pair_tersoff.o pair_tersoff_zbl.o pair_yukawa_colloid.o pair_yukawa.o pppm.o pppm_tip4p.o prd.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 xdr_compat.o -lreax -lpoems -lmeam -lgpu  -lmpi -L/usr/local/lammps/fftw/lib      -o ../lmp_serial
/usr/bin/ld: cannot find /usr/local/lammps/fftw: File format not recognized
/usr/bin/ld: cannot find -lgpu
collect2: ld returned 1 exit status
make[1]: *** [../lmp_serial] Error 1
make[1]: Leaving directory `/usr/local/lammps/lammps/src/Obj_serial'
make: *** [serial] Error 2

Birşeyleri bulamıyor ama nasıl düzelteceğim tıkandım

[ct]

fftw2 fftw-dev paketlerine ihtiyaç duyuyor olabilir mi?

[zeusmaster]

@ct, hocam onları kurdum. Makefile dosyasının içine yollarını verdim ama hatalı bir şeyler var ortada

Kod Seç Genişlet

/usr/bin/ld: cannot find /usr/local/lammps/fftw: File format not recognized
/usr/bin/ld: cannot find -lgpu

[heartsmagic]

Kod Seç Genişlet

ls -l /usr/local/lammps/fftw ne diyor?

[zeusmaster]

@heartsmagic;

Kod Seç Genişlet

└──>>ls -l /usr/local/lammps/fftw
total 1492
-rw-r--r-- 1 bahdem bahdem   7387 Mar 17  2003 acinclude.m4
-rw-r--r-- 1 bahdem bahdem 158632 Mar 24  2003 aclocal.m4
-rw-r--r-- 1 bahdem bahdem   3178 Mar 17  2003 acx_mpi.m4
-rw-r--r-- 1 bahdem bahdem   8991 Mar 17  2003 acx_pthread.m4
-rw-r--r-- 1 bahdem bahdem    120 Mar 17  2003 AUTHORS
-rw-r--r-- 1 bahdem bahdem    344 Mar 17  2003 bootstrap.sh
-rw-r--r-- 1 bahdem bahdem 164890 Mar 24  2003 ChangeLog
drwxrwsrwx 2 bahdem bahdem   4096 Mar 24  2003 cilk
-rwxr-xr-x 1 bahdem bahdem  41362 Mar 16  2003 config.guess
-rw-rw-r-- 1 bahdem bahdem  48569 Dec 19 18:49 config.log
-rwxrwxr-x 1 bahdem bahdem  38998 Dec 19 18:49 config.status
-rwxr-xr-x 1 bahdem bahdem  29973 Mar 16  2003 config.sub
-rwxr-xr-x 1 bahdem bahdem 459925 Mar 24  2003 configure
-rw-r--r-- 1 bahdem bahdem  12407 Mar 24  2003 configure.in
-rw-r--r-- 1 bahdem bahdem  18104 Mar 17  2003 COPYING
-rw-r--r-- 1 bahdem bahdem    797 Mar 17  2003 COPYRIGHT
-rwxr-xr-x 1 bahdem bahdem  12123 Sep 17  2002 depcomp
drwxrwsrwx 2 bahdem bahdem   4096 Dec 19 18:49 doc
drwxrwsrwx 3 bahdem bahdem   4096 Mar 24  2003 FAQ
drwxrwsrwx 4 bahdem bahdem   4096 Dec 19 18:49 fftw
-rw-rw-r-- 1 bahdem bahdem   5750 Dec 19 18:49 fftw.spec
-rw-r--r-- 1 bahdem bahdem   5854 Mar 17  2003 fftw.spec.in
drwxrwsrwx 2 bahdem bahdem   4096 Mar 24  2003 fortran
drwxrwsrwx 2 bahdem bahdem   4096 Mar 24  2003 gensrc
drwxrwsr-x 2 bahdem bahdem   4096 Dec 19 18:50 include
drwxrwsr-x 2 bahdem bahdem   4096 Dec 19 18:50 info
-rw-r--r-- 1 bahdem bahdem   9224 Mar 17  2003 INSTALL
-rwxr-xr-x 1 bahdem bahdem   5569 Sep 17  2002 install-sh
drwxrwsr-x 2 bahdem bahdem   4096 Dec 19 18:50 lib
-rwxrwxr-x 1 bahdem bahdem 151407 Dec 19 18:49 libtool
-rw-r--r-- 1 bahdem bahdem 142449 Jan  7  2003 ltmain.sh
-rw-rw-r-- 1 bahdem bahdem  19060 Dec 19 18:49 Makefile
-rw-r--r-- 1 bahdem bahdem   2072 Mar 17  2003 Makefile.am
-rw-r--r-- 1 bahdem bahdem  18972 Mar 24  2003 Makefile.in
drwxrwsrwx 2 bahdem bahdem   4096 Mar 24  2003 matlab
-rwxr-xr-x 1 bahdem bahdem  10270 Sep 17  2002 missing
-rwxr-xr-x 1 bahdem bahdem   1801 Sep 17  2002 mkinstalldirs
drwxrwsrwx 3 bahdem bahdem   4096 Dec 19 18:49 mpi
-rw-r--r-- 1 bahdem bahdem  13548 Mar 24  2003 NEWS
-rw-r--r-- 1 bahdem bahdem   2443 Mar 17  2003 README
-rw-r--r-- 1 bahdem bahdem   5147 Mar 17  2003 README.hacks
drwxrwsrwx 4 bahdem bahdem   4096 Dec 19 18:50 rfftw
drwxrwsrwx 4 bahdem bahdem   4096 Dec 19 18:50 tests
drwxrwsrwx 3 bahdem bahdem   4096 Dec 19 18:49 threads
-rw-r--r-- 1 bahdem bahdem   3165 Mar 17  2003 TODO


[heartsmagic]

Dizinmiş yani orası. Kısacası dosyanın asıl yolu şöyle oluyor:
/usr/local/lammps/fftw/fftw

Bu bir yerlerde elle mi ayarlanıyor?

[zeusmaster]

Make dosyasının içine gösteriyorum yolu. Şimdi deniyorum hemen