problem installing software package with MPI support


 
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Special Forums UNIX and Linux Applications High Performance Computing problem installing software package with MPI support
# 1  
Old 01-25-2009
problem installing software package with MPI support

So I have been struggling for the past few days to install a simulation package lammps (http://lammps.sandia.gov/) on my Mac OS X. I am well aware that this is a Ubuntu forum, but you guys seem to know a lot of UNIX stuff, so I was hoping someone might have a solution to my problem...

To run lammps on parallel processors, I have installed the Message Passaging Interface package, MPICH. The problem is that when compiling lammps, it doesn't recognize library elements from MPICH, giving me the following error output:

-------------------------------------------------------------
g++ -g -O -L/Users/andy/mpich/mpich2-install/lib angle.o angle_charmm.o angle_cosine.o angle_cosine_delta.o angle_cosine_squared.o angle_harmonic.o angle_hybrid.o atom.o atom_vec.o atom_vec_angle.o atom_vec_atomic.o atom_vec_bond.o atom_vec_charge.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 change_box.o comm.o compute.o compute_centro_atom.o compute_coord_atom.o compute_displace_atom.o compute_erotate_sphere.o compute_group_group.o compute_ke.o compute_ke_atom.o compute_pe.o compute_pe_atom.o compute_pressure.o compute_reduce.o compute_stress_atom.o compute_temp.o compute_temp_com.o compute_temp_deform.o compute_temp_partial.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.o dihedral_charmm.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.o dump_atom.o dump_bond.o dump_custom.o dump_dcd.o dump_xyz.o error.o ewald.o fft3d.o fft3d_wrap.o finish.o fix.o fix_add_force.o fix_ave_atom.o fix_ave_force.o fix_ave_spatial.o fix_ave_time.o fix_bond_break.o fix_bond_create.o fix_bond_swap.o fix_com.o fix_coord_original.o fix_deform.o fix_deposit.o fix_drag.o fix_dt_reset.o fix_efield.o fix_enforce2d.o fix_gravity.o fix_gyration.o fix_heat.o fix_indent.o fix_langevin.o fix_line_force.o fix_minimize.o fix_momentum.o fix_msd.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_plane_force.o fix_press_berendsen.o fix_print.o fix_rdf.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_temp_berendsen.o fix_temp_rescale.o fix_thermal_conductivity.o fix_tmd.o fix_viscosity.o fix_viscous.o fix_wall_lj126.o fix_wall_lj93.o fix_wall_reflect.o fix_wiggle.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.o min_cg.o min_sd.o minimize.o modify.o neigh_bond.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 neighbor.o output.o pack.o pair.o pair_airebo.o pair_buck.o pair_buck_coul_cut.o pair_buck_coul_long.o pair_coul_cut.o pair_coul_debye.o pair_coul_long.o pair_eam.o pair_eam_alloy.o pair_eam_fs.o pair_hybrid.o pair_hybrid_overlay.o pair_lj_charmm_coul_charmm.o pair_lj_charmm_coul_charmm_implicit.o pair_lj_charmm_coul_long.o pair_lj_cut.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_expand.o pair_lj_gromacs.o pair_lj_gromacs_coul_gromacs.o pair_lj_smooth.o pair_morse.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.o region_block.o region_cylinder.o region_intersect.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 -lfftw -lfmpich -lmpich -L/sw/lib/ -lg2c -g77libs -lpthread -o ../lmp_g++test3
/usr/libexec/gcc/i686-apple-darwin8/4.0.1/ld: Undefined symbols:
_MPI_Bcast
_MPI_Allreduce
_MPI_Scan
_MPI_Barrier
_MPI_Cart_create
_MPI_Cart_get
.
. + a whole bunch more...
.
_MPI_Allgather
_MPI_Comm_dup
_MPI_Waitany
collect2: ld returned 1 exit status
-------------------------------------------------------------

The lammps source files contain variables such as

MPI_Bcast
MPI_Allgather
...
with no initial underscore. In investigating this, I've found that the problem lies in the fact that MPICH was compiled using a fortran compiler (g77), but lammps uses g++. I was told it might be possible to create a separate library to translate between the two types, but do not have much experience in doing so. Does anyone see a resolution to this problem?

Thanks.
# 2  
Old 01-27-2009
The general rule when compiling mpi programs is to use mpicc, and not to directly invoke the compiler. I have experience with MPICH, and that is what you normally do. You can, of course invoke the compiler, but then you have to specify the right location of the MPI libraries: you only told to load them (-lmpich), but the compiler doesn't know where to look.

You gave it "-L/Users/andy/mpich/mpich2" but I suspect this is incorrect. Try:
Code:
-L$HOME/mpich/mpich2/lib

However, it might be in lib. You can use mpicc -v to see what paths mpicc is passing to gcc.
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