Package installation error #1
Comments
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This is because the link to the openmpi library is not correct.
Best, On Mon, Apr 11, 2016 at 4:03 PM, sdzahedi [email protected] wrote:
Rui Sun |
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Hello Rui, LAMMPS_DIR =/home/szv/sediFoam-master EXE_INC = EXE_LIBS = |
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Here there is another option file which is called: options-ubuntu-openmpi EXE_INC = EXE_LIBS = |
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I am wondering which address should I modify, for your information I have installed the openmpi in this address: /home/szv |
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This us where the errors started when I tried to install sediFoam: szv@szv-Inspiron-560:~/sediFoam-master$ ./Allwmake.sh |
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Do you compile OpenFOAM successfully in your machine? The allwmake file may not be working because of your system is different The address of openmpi will be shown using command "which mpicc" in your On Wed, Apr 13, 2016 at 6:27 PM, sdzahedi [email protected] wrote:
Rui Sun |
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Hello there, Thanks |
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Hello, In file included from ../compute_voronoi_atom.cpp:21:0: I appreciate your consideration and advices |
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Hi Saeid, I met the exact problem. The reason is the new version of Lammps cannot Please follow the instruction at Good luck. On Fri, Apr 22, 2016 at 4:39 PM, sdzahedi [email protected] wrote:
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Hello Roger, ../compute_gran_local.cpp: In member function ‘int LAMMPS_NS::ComputeGranLocal::compute_pairs(int)’: Thanks, |
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Hi Saeid, I could finally install with some minor modifications to the source code. git checkout building_update We are currently working on the branch merging. Should be done soon. Thanks. On Sun, Apr 24, 2016 at 3:53 PM, sdzahedi [email protected] wrote:
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Hello Roger, Thanks, |
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Hi Saeid, Please enter the line in your terminal. This should switch the branch of Thanks. On Mon, Apr 25, 2016 at 3:53 PM, sdzahedi [email protected] wrote:
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Hello Roger, Many thanks and Please let me know how did you manage finally to compile it. When I tried to compile it with the guideline that the author provided us I see this error: ../compute_gran_local.cpp:158:44: error: invalid conversion from ‘int’ to ‘LAMMPS_NS::NeighList_’ [-fpermissive] |
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Hi Saeid, Sorry for a reply. Maybe this tutorial can help you. Check this out https://try.github.io/levels/1/challenges/1 Please let me know whether you could checkout my branch. Best, On Thu, May 26, 2016 at 11:57 AM, sdzahedi [email protected] wrote:
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Thanks Roger,I ll check it and inform you how it goes. Hi Saeid, Sorry for a reply. Maybe this tutorial can help you. Check this out https://try.github.io/levels/1/challenges/1 Please let me know whether you could checkout my branch. Best, On Thu, May 26, 2016 at 11:57 AM, sdzahedi [email protected] wrote:
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Hello Roger, Thanks, |
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Hello all can any body help me out with this. Thanks |
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Khuram,
When you compile lammpsFoam, you have to add the compiled LAMMPS library to
the path that OpenFOAM knows. Please check the Step 8 in the installation
process.
Change to “$FOAM USER LIBBIN” and make a soft link of “liblammps
shanghailinux.so” in this folder. “liblammps shanghailinux.so” is the file
generated in the previous step.
Best,
Rui
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Thanks iurnus, it works. |
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Is there any user guide for data analysis and visualization, and which application is used? I am using Paraview but facing problem to build visualizations. Kind regards |
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Congratulations!
Please see Thread #2:
http://www.cfd-online.com/Forums/openfoam-paraview/82036-do-particle-tracking-paraview.html
And note that there is no Lagrangian particle data in 0 folder. So use
"foamToVTK -time 0.1:" to convert openFoam data after 0.1s (or any other
time).
Best,
Rui
…On Wed, Nov 30, 2016 at 10:35 PM, KhuramWalayat ***@***.***> wrote:
Is there any user guide for data analysis and visualization, and which
application is used? I am using Paraview but facing problem to build
visualizations.
Kind regards
Khuram
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Virginia Polytechnic Institute and State University
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Dear Rui Sun,
Thank you very much for your time and help. It is really very helpful for me. Again thanks for the kindness.
Kind regardsKhuram Walayat.
On Thursday, December 1, 2016 11:08 PM, iurnus <[email protected]> wrote:
Congratulations!
Please see Thread #2:
http://www.cfd-online.com/Forums/openfoam-paraview/82036-do-particle-tracking-paraview.html
And note that there is no Lagrangian particle data in 0 folder. So use
"foamToVTK -time 0.1:" to convert openFoam data after 0.1s (or any other
time).
Best,
Rui
…On Wed, Nov 30, 2016 at 10:35 PM, KhuramWalayat ***@***.***> wrote:
Is there any user guide for data analysis and visualization, and which
application is used? I am using Paraview but facing problem to build
visualizations.
Kind regards
Khuram
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--
Rui Sun
Ph.D. Candidate
Department of Aerospace and Ocean Engineering
Virginia Polytechnic Institute and State University
Blacksburg, VA, USA
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Dear Roger, I downloaded building_update with OpenFOAM 3.0.x in Ubuntu 16.04 and tried to install this code but I faced the problem after I typed the command "make mode=shlib shanghailinx" in Allwmake.sh. step 1 : downloaded the building_update.zip under $WM_PROJECT_USER_DIR step 2 : move lammps-31Mar17 to sediFoam-building_update step 3 : change the line 43 in Allwmake.sh (make yes-FLD to make yes-COLLOID) and download voro++0.4.6 and make install (not sudo) and create two soft links step 4 : run Allwmake script and the last part of the log file is as follows mpic++ -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -fPIC -DLAMMPS_GZIP -I../../lib/voronoi/includelink -c ../compute_improper.cpp Thank you in advance for your help, Song |
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I have the exact same error when doing step 7: voro++ was installed without sudo on a custom directory |
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Hi Song,
You should compile the voro++ library as a dynamic library (using -fPIC
option).
Or, you can turn off the voro++ option in LAMMPS.
Rui
…On Mon, Oct 1, 2018 at 10:36 AM cojua8 ***@***.***> wrote:
Dear Roger,
I downloaded building_update with OpenFOAM 3.0.x in Ubuntu 16.04 and tried
to install this code but I faced the problem after I typed the command
"make mode=shlib shanghailinx" in Allwmake.sh.
step 1 : downloaded the building_update.zip under $WM_PROJECT_USER_DIR
step 2 : move lammps-31Mar17 to sediFoam-building_update
step 3 : change the line 43 in Allwmake.sh (make yes-FLD to make
yes-COLLOID) and download voro++0.4.6 and make install (not sudo) and
create two soft links
step 4 : run Allwmake script and the last part of the log file is as
follows
mpic++ -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized
-fPIC -DLAMMPS_GZIP -I../../lib/voronoi/includelink -c
../compute_improper.cpp
mpic++ -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized
-fPIC -DLAMMPS_GZIP -I../../lib/voronoi/includelink -c
../nstencil_half_bin_2d_newtoff.cpp
mpic++ -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized
-fPIC -shared -fPIC -L../../lib/voronoi/liblink -L.. -o
../liblammps_shanghailinux.so
npair_skip.o fix_external.o math_special.o finish.o run.o image.o
npair_skip_respa.o fix_ave_histo.o fix_rigid_nvt.o displace_atoms.o
reader_xyz.o fix_rigid_npt_small.o pair_lj_long_tip4p_long.o pair_airebo.o
fix_deform.o rerun.o pair_lj_charmm_coul_charmm.o atom.o
pair_gran_hertz_history.o nstencil_half_multi_2d_newton.o
fix_wall_harmonic.o compute_chunk_atom.o npair_half_size_bin_newtoff.o
math_extra.o nstencil_half_bin_3d_newtoff.o npair_half_size_nsq_newtoff.o
pair_buck.o fix_controller.o atom_vec_charge.o atom_vec_body.o
compute_rdf.o pair_rebo.o npair_full_multi.o lattice.o fix_rigid_nve.o
write_dump.o npair_full_nsq.o pair_buck_coul_long.o input.o
npair_full_bin_atomonly.o compute_angle_local.o nbin.o region_plane.o
fix_lineforce.o fix_wall_region.o fix_enforce2d.o min_fire.o create_box.o
pair_lj_expand.o angle_harmonic.o compute_temp_sphere.o fix_wall.o
nstencil_half_ghost_bin_2d_newtoff.o compute_gyration_chunk.o
pair_lj_gromacs_coul_gromacs.o dump_movie.o atom_vec_line.o fix_nph.o
pair_buck_coul_cut.o compute_pair_local.o fix_rigid_nph_small.o pppm_cg.o
random_mars.o imbalance_var.o fix_oneway.o fix_wall_colloid.o change_box.o
compute_ke_rigid.o region_prism.o pair_coul_streitz.o compute_omega_chunk.o
pair_nb3b_harmonic.o pppm_disp_tip4p.o npair_full_bin_ghost.o
fix_orient_bcc.o nstencil_full_multi_2d.o fix_momentum.o
npair_half_respa_nsq_newton.o read_dump.o group.o dump_xyz.o
pair_eam_alloy.o fix_balance.o improper_cvff.o fix_ehex.o fix_deposit.o
pair_coul_wolf.o fix_heat.o fix_nve_limit.o fix_temp_berendsen.o
compute_temp_profile.o pair_born.o compute_temp_partial.o
pair_lj_cut_tip4p_long.o fix_ave_chunk.o memory.o angle_cosine_squared.o
fix_aveforce.o fix_viscosity.o fix_spring_rg.o compute_angmom_chunk.o
fix_ave_atom.o compute_com_chunk.o pppm_disp.o
nstencil_half_multi_3d_newton.o pair_born_coul_long.o
npair_half_multi_newton_tri.o compute_global_atom.o fix_move.o
fix_nve_sphere.o bond_harmonic.o remap.o region_cone.o fix_wall_gran.o
pair_lj_cut_tip4p_cut.o dihedral_harmonic.o fix_rigid_small.o
pair_lj_cut_coul_long.o create_atoms.o pppm.o
pair_lj_charmmfsw_coul_charmmfsh.o ntopo.o gridcomm.o atom_map.o
replicate.o ntopo_angle_partial.o fix_nve.o ewald_disp.o
nstencil_full_bin_2d.o npair_copy.o fix_read_restart.o compute_com.o
timer.o improper_hybrid.o npair_full_nsq_ghost.o
nstencil_half_bin_2d_newton.o npair_half_nsq_newtoff_ghost.o fix_store.o
pair_lj_long_coul_long.o atom_vec_molecular.o min_quickmin.o
compute_rigid_local.o improper_zero.o compute_contact_atom.o
region_sphere.o pair_lubricateU_poly.o region_intersect.o fix_restrain.o
fix_langevin.o fix_shake.o fix_nvt.o dihedral.o npair_full_bin.o fix.o
fix_ave_correlate.o bond.o compute_cna_atom.o compute_msd.o
ntopo_angle_template.o compute_reduce.o velocity.o fix_store_state.o
pair_lj_smooth.o region.o ntopo_dihedral_partial.o imbalance_time.o
fix_temp_csld.o fix_spring_chunk.o fix_deprecated.o region_union.o
fix_temp_rescale.o pair_lubricateU.o neighbor.o
nstencil_half_ghost_bin_3d_newtoff.o fix_nvt_sphere.o pair_table.o
fix_vector.o pair_polymorphic.o write_restart.o dihedral_multi_harmonic.o
compute_temp_deform.o fix_temp_csvr.o write_coeff.o neigh_list.o min_cg.o
procmap.o pair_bop.o pppm_tip4p.o npair_half_respa_bin_newtoff.o
pair_born_coul_dsf.o imbalance_neigh.o compute_erotate_sphere.o
pair_airebo_morse.o pair_coul_long.o compute_property_atom.o pair_comb3.o
pair_lj_cut_coul_msm.o pair_lj_charmm_coul_charmm_implicit.o
atom_vec_full.o atom_vec_sphere.o dump_dcd.o min_sd.o pair_tersoff.o
verlet.o pair_eam_fs.o pair_lubricate.o compute_ti.o kspace.o
compute_temp_com.o atom_vec_ellipsoid.o pair_colloid.o pair_coul_cut.o
pair_born_coul_msm.o fix_rigid_nph.o fix_adapt.o atom_vec_angle.o
fix_rigid_nh.o pair_brownian.o npair_half_multi_newton.o reader_native.o
atom_vec_atomic.o comm.o npair_half_nsq_newton.o nstencil_full_bin_3d.o
dihedral_hybrid.o compute_reduce_region.o dump_atom.o
compute_orientorder_atom.o pair_adp.o fix_fluid_drag.o pair_buck_coul_msm.o
dump_cfg.o angle.o dihedral_zero.o compute_slice.o pair_vashishta_table.o
fix_halt.o fix_rigid.o force.o fix_wall_lj126.o variable.o info.o
atom_vec_tri.o pair_yukawa_colloid.o atom_vec_template.o fix_gravity.o
irregular.o xdr_compat.o fix_thermal_conductivity.o
npair_skip_size_off2on_oneside.o nstencil_half_multi_3d_newton_tri.o
fft3d_wrap.o fix_setforce.o fix_tune_kspace.o minimize.o fix_recenter.o
fix_wall_lj93.o reader.o pair_nm_cut.o fix_box_relax.o
pair_lj_cut_coul_debye.o compute_group_group.o pair_beck.o bond_zero.o
pair_born_coul_wolf.o fix_wall_lj1043.o compute_dipole_chunk.o fix_efield.o
pair_nm_cut_coul_long.o fix_nh.o fix_drag.o compute_hexorder_atom.o
fix_rigid_npt.o output.o npair_halffull_newtoff.o compute.o
nstencil_half_bin_2d_newton_tri.o pair_gran_hooke.o neigh_request.o
fix_indent.o fix_wall_gran_region.o domain.o improper_harmonic.o
read_data.o npair.o dump_custom.o pair_nm_cut_coul_cut.o fix_evaporate.o
compute_pe.o msm.o fix_nph_sphere.o compute_gyration.o dihedral_opls.o
imbalance_group.o nstencil.o bond_morse.o npair_skip_size.o molecule.o
compute_voronoi_atom.o npair_half_bin_newtoff.o compute_gran_local.o
pair_lj_smooth_linear.o pair_lj_cut.o pair_zbl.o pair_eim.o error.o
ntopo_bond_partial.o pair_lubricate_poly.o angle_table.o
npair_halffull_newton.o nstencil_full_ghost_bin_2d.o comm_brick.o
bond_table.o pair_tersoff_mod.o msm_cg.o fix_rigid_nvt_small.o
pair_lj_cut_coul_cut.o bond_fene_expand.o ntopo_improper_partial.o
fix_rattle.o ewald.o comm_tiled.o nstencil_half_multi_2d_newtoff.o
min_linesearch.o remap_wrap.o pair_gran_hooke_history.o
fix_press_berendsen.o fix_rigid_nh_small.o compute_msd_nongauss.o min.o
fix_print.o ntopo_bond_template.o pair_lcbop.o pair_dpd.o
pair_lj_cut_coul_dsf.o compute_pressure.o compute_msd_chunk.o
nstencil_half_multi_2d_newton_tri.o fix_nvt_sllod.o
ntopo_improper_template.o pair_lj96_cut.o fix_tmd.o
compute_property_local.o npair_half_bin_atomonly_newton.o improper.o
angle_cosine_periodic.o pair_brownian_poly.o fix_rigid_nve_small.o
compute_ke.o pair_soft.o nstencil_full_multi_3d.o dihedral_charmm.o
library.o pair_dpd_tstat.o dump_xtc.o fix_spring_self.o fix_nve_noforce.o
pair_hybrid.o angle_hybrid.o compute_angle.o fix_shear_history.o
fix_planeforce.o compute_pe_atom.o npair_skip_size_off2on.o min_hftn.o
pair_zero.o compute_heat_flux.o compute_temp_region.o fix_qeq_comb.o
pair_mie_cut.o fix_nh_sphere.o atom_vec.o pair_tersoff_zbl.o bond_hybrid.o
compute_vcm_chunk.o compute_stress_atom.o fix_respa.o integrate.o
fix_cmap.o pair_comb.o npair_half_size_nsq_newton.o pair_eam.o dump_local.o
angle_cosine.o fix_viscous.o dump_image.o npair_half_size_bin_newton.o
npair_half_respa_bin_newton.o compute_temp_ramp.o compute_pair.o
ntopo_dihedral_template.o pair_coul_dsf.o compute_temp.o
compute_cluster_atom.o nbin_standard.o fft3d.o npair_half_multi_newtoff.o
pair_tip4p_long.o pair_lj_charmm_coul_msm.o fix_ttm.o
npair_half_nsq_newtoff.o delete_atoms.o pair_sw.o compute_dihedral.o
pair_yukawa.o delete_bonds.o pair_vashishta.o atom_vec_bond.o fix_gld.o
compute_bond_local.o dihedral_charmmfsh.o fix_dt_reset.o angle_zero.o
pair_coul_msm.o nstencil_full_ghost_bin_3d.o npair_half_bin_newtoff_ghost.o
read_restart.o pair_tip4p_cut.o nstencil_half_bin_3d_newton.o
compute_vacf.o citeme.o npair_half_bin_newton_tri.o compute_centro_atom.o
create_bonds.o write_data.o body.o fix_ave_histo_weight.o region_block.o
fix_npt.o universe.o pppm_stagger.o compute_property_chunk.o
compute_coord_atom.o special.o pair_hybrid_overlay.o compute_ke_atom.o
respa.o ntopo_bond_all.o improper_umbrella.o bond_fene.o fix_ave_time.o
bond_nonlinear.o compute_temp_chunk.o bond_quartic.o fix_minimize.o
ntopo_improper_all.o pair_gauss.o pair_morse.o ntopo_angle_all.o
imbalance_store.o fix_wall_reflect.o pair_tersoff_mod_c.o
npair_half_respa_nsq_newtoff.o modify.o compute_dihedral_local.o
imbalance.o fix_spring.o angle_cosine_delta.o compute_erotate_sphere_atom.o
rcb.o balance.o dihedral_helix.o fix_pour.o fix_property_atom.o
pair_hbond_dreiding_morse.o pair_lj_cubic.o compute_displace_atom.o
npair_half_bin_newton.o dump.o npair_half_size_bin_newton_tri.o
nstencil_half_multi_3d_newtoff.o thermo.o update.o angle_charmm.o
fix_store_force.o compute_improper_local.o lammps.o fix_orient_fcc.o
ntopo_dihedral_all.o pair_buck_long_coul_long.o fix_addforce.o
atom_vec_hybrid.o random_park.o set.o pair_hbond_dreiding_lj.o
fix_npt_sphere.o region_cylinder.o npair_half_respa_bin_newton_tri.o
pair_lj_charmm_coul_long.o compute_erotate_rigid.o pair_lj_gromacs.o
compute_bond.o pair_lj_charmmfsw_coul_long.o compute_torque_chunk.o pair.o
pair_coul_debye.o compute_inertia_chunk.o fix_freeze.o
nstencil_half_bin_3d_newton_tri.o fix_group.o compute_improper.o
nstencil_half_bin_2d_newtoff.o -lvoro++ -lstdc++
/usr/bin/ld: ../../lib/voronoi/liblink/libvoro++.a(cell.o): relocation
R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared
object; recompile with -fPIC
../../lib/voronoi/liblink/libvoro++.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
Makefile:95: recipe for target 'shlib' failed
make[1]: *** [shlib] Error 1
make[1]: Leaving directory
'/home/ocean/OpenFOAM/ocean-3.0.x/sediFoam-building_update/lammps-31Mar17/src/Obj_shared_shanghailinux'
Makefile:132: recipe for target 'shanghailinux' failed
make: *** [shanghailinux] Error 2
Thank you in advance for your help,
Song
I have the exact same error when doing step 7:
/usr/bin/ld: /home/joaquin/voroinstall/lib/libvoro++.a(cell.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/home/joaquin/voroinstall/lib/libvoro++.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
make[1]: *** [shlib] Error 1
make[1]: Leaving directory `/home/joaquin/sediFoam/lammps-1Feb14/src/Obj_shlib_shanghailinux'
make: *** [shanghailinux] Error 2
voro++ was installed without sudo on a custom directory
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San Diego, CA, USA
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when i was compiling using command 'wmake' in directory:lammpsFoam i meet this error: |
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when i fix the error ,the another error appear: i don;t know how to deal with it,i will appreciate if you meet the similar error and know how to handle it. |
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Greetings, I just started using SediFoam. It would be great if I will get rids of this problem. I am using sediFoam Solver for fluid-particle interaction. I am giving a run time of 50 sec... but, my simulation stops at 0.5 sec. giving below result: Need the help of experts. My workstation has a RAM of 32 GB and during the simulation, RAM utilization is around 20- 30% of the total. I think the size of RAM is not the issue, somewhere LAMMPS has the issue which I am not able to figure out. Time = 0.5069 Courant Number mean: 0.0434342 max: 0.0771597 |
Dear Xiaoh,
I tried to install this code as you explained in readme with Allwmake.sh but I faced two issue to install the package.
Error:
lammpsFoam.C:41:17: fatal error: mpi.h: No such file or directory
#include "mpi.h"
^
compilation terminated.
make: *** [Make/linux64GccDPInt32Opt/lammpsFoam.o] Error 1
Thanks,
Saeid
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