Compilation problem with Fedora 13 and OpenMPI

Submitted by WGJ Theron on Tue, 07/06/2010 - 10:55

I have downloaded the tar ball for version 1.1.1, I am struggling with the make fedora command in the /src directory

Operating system: Fedora 13 – 32 Bit

+ Install paraview by typing "sudo yum install paraview" in a console – only works if i run the command as root
+ Install Open MPI by typing "sudo yum install openmpi openmpi-devel" in a console – only works if i run the command as root

Updated the sudoers file to allow the my username...

I think paraview & Open MPI is installed correctly will it make a difference if i install as root?

Open a new console and check if the symbolic links for Open MPI are set up correctly by typing "which mpirun". – i get a line that states it cannot find the file.

When I manually set up the following symbolic links:
+ Type "sudo ln -s /usr/lib[64]/openmpi/bin/mpirun /usr/bin" – i run the following command: sudo ln -s /usr/lib[32]/openmpi/bin/mpirun /usr/bin – finds file
+ Type "sudo ln -s /usr/lib[64]/openmpi/bin/mpic++ /usr/bin"– i run the following command: sudo ln -s /usr/lib[32]/openmpi/bin/mpic++ /usr/bin – finds file

After unpacking Liggits in the /src directory i run make clean-all 1 File is cleared
Obj_fedora'
When i make fedora i get the following error:
make: *** [Fedora] Error 2

Any Ideas? - I went through the Lammps manual and the suggested it is errors with the operating system...

Forums:

ckloss's picture

ckloss | Tue, 07/06/2010 - 12:05

>> Install Open MPI by typing "sudo yum install openmpi openmpi-devel" in a console – only works if i run the command as root

sudo does this... sure, you have to be in the sudoers list

>>sudo ln -s /usr/lib[32]/openmpi/bin/mpirun /usr/bin – finds file
Please read carefully!!! where lib is used in case of a 32 bit system and lib64 in case of a 64 bit system

>>When i make fedora i get the following error:
>>make: *** [Fedora] Error 2

This is too unspecific to tell what the reason is. probably the reason is that you "sudo ln -s /usr/lib[32]/openmpi/bin/mpirun /usr/bin" command was not correct

Christoph

WGJ Theron | Tue, 07/06/2010 - 13:27

Thanks for the quick response

ckloss's picture

ckloss | Tue, 07/06/2010 - 15:29

The problems you are having are not LIGGGHTS specific, but related to the MPI installation. Let me know if it worked out for you.

Christoph

WGJ Theron | Tue, 07/06/2010 - 18:07

Ok i have managed to correct the links and double checked them in the usr/bin directory.

however i still get the following error when i make fedora in the Liggghts - src directory

[William@localhost src]$ make clean-all
rm -rf Obj_*
[William@localhost src]$ make fedora
make[1]: Entering directory `/home/William/Documents/LIGGGHTS/liggghts_1p1p1/src/Obj_fedora'
Makefile:93: angle_charmm.d: No such file or directory
Makefile:93: angle_cosine.d: No such file or directory
Makefile:93: angle_cosine_delta.d: No such file or directory
Makefile:93: angle_cosine_squared.d: No such file or directory
Makefile:93: angle.d: No such file or directory
Makefile:93: angle_harmonic.d: No such file or directory
Makefile:93: angle_hybrid.d: No such file or directory
Makefile:93: angle_table.d: No such file or directory
Makefile:93: atom.d: No such file or directory
Makefile:93: atom_vec_angle.d: No such file or directory
Makefile:93: atom_vec_atomic.d: No such file or directory
Makefile:93: atom_vec_bond.d: No such file or directory
Makefile:93: atom_vec_charge.d: No such file or directory
Makefile:93: atom_vec.d: No such file or directory
Makefile:93: atom_vec_full.d: No such file or directory
Makefile:93: atom_vec_granular.d: No such file or directory
Makefile:93: atom_vec_hybrid.d: No such file or directory
Makefile:93: atom_vec_molecular.d: No such file or directory
Makefile:93: bond.d: No such file or directory
Makefile:93: bond_fene.d: No such file or directory
Makefile:93: bond_fene_expand.d: No such file or directory
Makefile:93: bond_harmonic.d: No such file or directory
Makefile:93: bond_hybrid.d: No such file or directory
Makefile:93: bond_morse.d: No such file or directory
Makefile:93: bond_nonlinear.d: No such file or directory
Makefile:93: bond_quartic.d: No such file or directory
Makefile:93: bond_table.d: No such file or directory
Makefile:93: change_box.d: No such file or directory
Makefile:93: comm.d: No such file or directory
Makefile:93: compute_angle_local.d: No such file or directory
Makefile:93: compute_bond_local.d: No such file or directory
Makefile:93: compute_centro_atom.d: No such file or directory
Makefile:93: compute_cna_atom.d: No such file or directory
Makefile:93: compute_com.d: No such file or directory
Makefile:93: compute_com_molecule.d: No such file or directory
Makefile:93: compute_coord_atom.d: No such file or directory
Makefile:93: compute.d: No such file or directory
Makefile:93: compute_dihedral_local.d: No such file or directory
Makefile:93: compute_displace_atom.d: No such file or directory
Makefile:93: compute_erotate_sphere.d: No such file or directory
Makefile:93: compute_group_group.d: No such file or directory
Makefile:93: compute_gyration.d: No such file or directory
Makefile:93: compute_gyration_molecule.d: No such file or directory
Makefile:93: compute_heat_flux.d: No such file or directory
Makefile:93: compute_improper_local.d: No such file or directory
Makefile:93: compute_ke_atom.d: No such file or directory
Makefile:93: compute_ke.d: No such file or directory
Makefile:93: compute_msd.d: No such file or directory
Makefile:93: compute_msd_molecule.d: No such file or directory
Makefile:93: compute_pair_local.d: No such file or directory
Makefile:93: compute_pe_atom.d: No such file or directory
Makefile:93: compute_pe.d: No such file or directory
Makefile:93: compute_pressure.d: No such file or directory
Makefile:93: compute_property_atom.d: No such file or directory
Makefile:93: compute_property_local.d: No such file or directory
Makefile:93: compute_property_molecule.d: No such file or directory
Makefile:93: compute_rdf.d: No such file or directory
Makefile:93: compute_reduce.d: No such file or directory
Makefile:93: compute_reduce_region.d: No such file or directory
Makefile:93: compute_stress_atom.d: No such file or directory
Makefile:93: compute_temp_com.d: No such file or directory
Makefile:93: compute_temp.d: No such file or directory
Makefile:93: compute_temp_deform.d: No such file or directory
Makefile:93: compute_temp_partial.d: No such file or directory
Makefile:93: compute_temp_profile.d: No such file or directory
Makefile:93: compute_temp_ramp.d: No such file or directory
Makefile:93: compute_temp_region.d: No such file or directory
Makefile:93: compute_temp_sphere.d: No such file or directory
Makefile:93: compute_totalmass.d: No such file or directory
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Makefile:93: dihedral_hybrid.d: No such file or directory
Makefile:93: dihedral_multi_harmonic.d: No such file or directory
Makefile:93: dihedral_opls.d: No such file or directory
Makefile:93: displace_atoms.d: No such file or directory
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Makefile:93: dump_dcd.d: No such file or directory
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Makefile:93: dump_stl.d: No such file or directory
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Makefile:93: fft3d.d: No such file or directory
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Makefile:93: finish.d: No such file or directory
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Makefile:93: fix_check_timestep_gran.d: No such file or directory
Makefile:93: fix.d: No such file or directory
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Makefile:93: fix_efield.d: No such file or directory
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Makefile:93: fix_gravity.d: No such file or directory
Makefile:93: fix_heat.d: No such file or directory
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Makefile:93: fix_langevin.d: No such file or directory
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Makefile:93: fix_minimize.d: No such file or directory
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Makefile:93: fix_nph.d: No such file or directory
Makefile:93: fix_npt.d: No such file or directory
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Makefile:93: fix_nve.d: No such file or directory
Makefile:93: fix_nve_limit.d: No such file or directory
Makefile:93: fix_nve_noforce.d: No such file or directory
Makefile:93: fix_nve_sphere.d: No such file or directory
Makefile:93: fix_nvt.d: No such file or directory
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Makefile:93: fix_orient_fcc.d: No such file or directory
Makefile:93: fix_particledistribution_discrete.d: No such file or directory
Makefile:93: fix_planeforce.d: No such file or directory
Makefile:93: fix_pour.d: No such file or directory
Makefile:93: fix_pour_dev.d: No such file or directory
Makefile:93: fix_pour_dev_packing.d: No such file or directory
Makefile:93: fix_pour_legacy.d: No such file or directory
Makefile:93: fix_press_berendsen.d: No such file or directory
Makefile:93: fix_print.d: No such file or directory
Makefile:93: fix_propertyGlobal.d: No such file or directory
Makefile:93: fix_propertyPerAtom.d: No such file or directory
Makefile:93: fix_recenter.d: No such file or directory
Makefile:93: fix_respa.d: No such file or directory
Makefile:93: fix_rigid.d: No such file or directory
Makefile:93: fix_set_force.d: No such file or directory
Makefile:93: fix_shake.d: No such file or directory
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Makefile:93: fix_store_coord.d: No such file or directory
Makefile:93: fix_store_force.d: No such file or directory
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Makefile:93: fix_viscosity.d: No such file or directory
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Makefile:93: fix_wall.d: No such file or directory
Makefile:93: fix_wall_gran.d: No such file or directory
Makefile:93: fix_wall_gran_hertz_history.d: No such file or directory
Makefile:93: fix_wall_gran_hooke.d: No such file or directory
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Makefile:93: fix_wall_harmonic.d: No such file or directory
Makefile:93: fix_wall_lj126.d: No such file or directory
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Makefile:93: fix_wall_reflect.d: No such file or directory
Makefile:93: fix_wall_region.d: No such file or directory
Makefile:93: force.d: No such file or directory
Makefile:93: group.d: No such file or directory
Makefile:93: improper.d: No such file or directory
Makefile:93: improper_cvff.d: No such file or directory
Makefile:93: improper_harmonic.d: No such file or directory
Makefile:93: improper_hybrid.d: No such file or directory
Makefile:93: input.d: No such file or directory
Makefile:93: integrate.d: No such file or directory
Makefile:93: kspace.d: No such file or directory
Makefile:93: lammps.d: No such file or directory
Makefile:93: lattice.d: No such file or directory
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Makefile:93: main.d: No such file or directory
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Makefile:93: min_cg.d: No such file or directory
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Makefile:93: min_hftn.d: No such file or directory
Makefile:93: minimize.d: No such file or directory
Makefile:93: min_linesearch.d: No such file or directory
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Makefile:93: modify.d: No such file or directory
Makefile:93: neigh_bond.d: No such file or directory
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Makefile:93: neigh_gran.d: No such file or directory
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Makefile:93: pair_gran_hertzcustom_history.d: No such file or directory
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Makefile:93: pair_gran_hooke.d: No such file or directory
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Makefile:93: pair_hybrid.d: No such file or directory
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Makefile:93: write_restart.d: No such file or directory
mpic++ -g -O -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DFFT_NONE -M write_restart.cpp > write_restart.d
--------------------------------------------------------------------------
The Open MPI wrapper compiler was unable to find the specified compiler
g++ in your PATH.

Note that this compiler was either specified at configure time or in
one of several possible environment variables.
--------------------------------------------------------------------------
make[1]: *** [write_restart.d] Error 1
make[1]: Leaving directory `/home/William/Documents/LIGGGHTS/liggghts_1p1p1/src/Obj_fedora'
make: *** [fedora] Error 2
[William@localhost src]$

raguelmoon's picture

raguelmoon | Tue, 07/06/2010 - 20:29

hi,
please type this command in the terminal:
sudo ln -s /usr/lib/openmpi/bin/mpirun /usr/bin
and then install liggghts..

best,
Ram

Ram

raguelmoon's picture

raguelmoon | Sat, 07/10/2010 - 20:32

Hi William,
Please install openMPI, it might work. I have given installation method in LAMMPS mailing list. Please search on LAMMPS site with keywords LAMMPS installation, raguelmoon, Ram Chand etc. You will find step-bye-step method of installation with openPMI and FFTW.
Cheers,
Ram Chand

Ram

WGJ Theron | Tue, 07/13/2010 - 13:48

Thanks Ram,

I have however intalled Open MPI using the steps described in the LAMMPS Manual, but they also recommend asking a local expert....

We have a expert here but he is away for the next two weeks, if i get any tips ill post them.

Also if anyone has any ideas please lelt me know...

raguelmoon's picture

raguelmoon | Tue, 07/13/2010 - 15:43

Hi William,
You must install MPICH as suggested by Christoph or get my method from LAMMPS site which is different method and i hope it will work..
cheers,

Ram

Ram

ckloss's picture

ckloss | Tue, 07/06/2010 - 21:01

Hi William,

is seems that something went wrong with the OpenMPI installation. A co-worker of mine had a similar problem with Fedora 13 and OpenMPI.

You need to set forther symbolic links for g++ and maybe also for some MPI libraries - this is system specific so I would recommend you to ask a local Linux expert how to correct these things

You can also use other makefiles - you can e.g. install mpich instead of OpenMPI and try it with that...

Best regards,
Christoph

ckloss's picture

ckloss | Fri, 07/09/2010 - 18:52

Hi BrianW,

as I said, there are problems with the OpenMPI installation on Fedora sometimes. Get yourself a local Linux expert and I am sure he/her can resolve this without problems.

Alternatively, install another MPI (like MPICH)

Wishing you success,

Christoph