problem installing software package with MPI support

Thread Tools Search this Thread
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 ( 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:
. + a whole bunch more...
collect2: ld returned 1 exit status

The lammps source files contain variables such as

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?

# 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:

However, it might be in lib. You can use mpicc -v to see what paths mpicc is passing to gcc.
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Red Hat

Set Proxy In The Terminal & problem Package Installing

Centos Behind The Proxy Server In My System , How Can I Set In Terminal Proxy ( Username & Password ) When Using The Command yum & rpm online I Will Respond Error Thank You For Your Guidance (28 Replies)
Discussion started by: mnnn
28 Replies

2. Emergency UNIX and Linux Support

Problem when trying to remove a package using rpm command - error: package is not installed

Hello, i have installed a package by using the command sudo rpm -i filepackage.rpm package filepackage is already installed when i try to remove it, i get an error saying "is not installed": sudo rpm -e filepackage.rpm error: package filepackage is not installed How can... (4 Replies)
Discussion started by: g_p
4 Replies

3. Solaris

Facing problem with installing CF engine software in solaris 10

Dear experts, I am using solaris 10 OS.I am installing CF engine software in the server while doing so ,i am getting following error checking for BerkeleyDB location in default... configure: error: >> Cannot find BerkeleyDB I am installing the Berkely DB 5.3.I am strugging... (1 Reply)
Discussion started by: muraliinfy04
1 Replies

4. Red Hat

hp support package issue

hi all, and pludi: as command hpasmcli for linux server to check health, any such a same command to check hp server using windows server 2003 OS health ? (0 Replies)
Discussion started by: maxlee24
0 Replies

5. Solaris

Zoning permission problem when installing software

hi all i am working on zone and when i try to install software i face read and write permisssion on directory which zonning inherit from them so how can i add read and write permission to zone already running (3 Replies)
Discussion started by: jamisux
3 Replies

6. Solaris

Problem installing the software HDLM

I'm trying to install the software HDLM (Hitachi Dynamic Link Manager) and is presenting the following message: -Bash-3.00 #./Installhdlm In KAPL09187-W parameter is specified. I do not know which parameter is that? (3 Replies)
Discussion started by: to.brunoaugusto
3 Replies

7. Solaris

Problem installing the software HDLM

Estou tentando instalar o software de HDLM ( Hitachi Dynamic Link Manager ) e está apresentando a seguinte mensagem: -bash-3.00# ./installhdlm KAPL09187-W No parameter is specified. Não sei que parameter é esse ? (1 Reply)
Discussion started by: to.brunoaugusto
1 Replies

8. UNIX for Dummies Questions & Answers

Problem while installing WAS ND package

Hi everyone, Hope u doing good. I am trying to installl WebSphere Application Server(WAS) ND package, i got problem at initial level I hope, the problem is with Mozilla browzer. Can anyone trobleshoot the problem An error occurred while starting the launchpad for a WebSphere Application ... (0 Replies)
Discussion started by: sarfraz
0 Replies

9. UNIX for Dummies Questions & Answers

What is the difference between device driver and board support package?

What is the difference between device driver and board support package? (0 Replies)
Discussion started by: anupa
0 Replies

10. HP-UX

license of software package

Hi when i do a swlist on my HP-UX machine it displays the software packages ..How do i know whether those packages are licensed or freeware can any 1 help me best Regards vasanth (0 Replies)
Discussion started by: vasanthan
0 Replies
Login or Register to Ask a Question

Featured Tech Videos