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xiaoh / sediFoam

CFD-DEM Solver with emphasis on sediment transport
GNU General Public License v2.0
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Package installation error #1

Open sdzahedi opened 8 years ago

sdzahedi commented 8 years ago

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

iurnus commented 8 years ago

This is because the link to the openmpi library is not correct.

  1. Ensure openmpi is installed.
  2. Find lammpsFoam/Make/options, and update the the addresses of openmpi file and libraries. (In my machine, the lines are 8, 9, and 32)

Best, Rui

On Mon, Apr 11, 2016 at 4:03 PM, sdzahedi notifications@github.com wrote:

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

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/xiaoh/sediFoam/issues/1

Rui Sun Ph.D. Candidate Department of Aerospace and Ocean Engineering Virginia Polytechnic Institute and State University Blacksburg, VA, USA

sdzahedi commented 8 years ago

Hello Rui, Thank you for your reply. I have installed the openmpi and I looked to the option file in lammpsFoam/Make/options. But I could not figure it out. This how the file script is in my machine:

LAMMPS_DIR =/home/szv/sediFoam-master /_LAMMPSDIR = ../lammps-1Feb14/src/

EXE_INC = \ -I$lammpsFoamTurbulenceModels/include \ -I$(PWD)/include \ -I$(LAMMPS_DIR)/ \ -I$(LAMMPS_DIR)/GRANULAR \ -I/usr/include/openmpi-x86_64/ \ -I/usr/lib64/openmpi/lib/ \ -I$(LAMMPS_DIR)/Obj_shanghailinux \ -I$(FOAM_SRC)/lagrangian/basic/lnInclude \ -I$(FOAM_SRC)/meshTools/lnInclude \ -I$(LIB_SRC)/cfdTools/incompressible \ -I$(LIB_SRC)/cfdTools/general/lnInclude \ -I$(LIB_SRC)/finiteVolume/lnInclude \ -I$(LIB_SRC)/triSurface/lnInclude \ -IchPressureGrad/lnInclude \ -I$(LIB_SRC)/transportModels \ -I$(LIB_SRC)/transportModels/incompressible/singlePhaseTransportModel \ -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \ -I$(LIB_SRC)/TurbulenceModels/incompressible/lnInclude \ -I$(LIB_SRC)/TurbulenceModels/phaseIncompressible/lnInclude \ -IdragModels/lnInclude

EXE_LIBS = \ -L$(FOAM_USER_LIBBIN) \ -L$(LAMMPS_DIR) \ -L$(LAMMPS_DIR)/STUBS \ -lLagrangianInterfacialModels \ -lfiniteVolume \ -lmeshTools \ -llagrangian \ -L/usr/lib64/openmpi/lib/ -lmpi -lmpi_cxx\ -llammps_shanghailinux \ -ltriSurface \ -lchPressureGrad-DEM \ -lincompressibleTransportModels \ -lturbulenceModels \ -lincompressibleTurbulenceModels \ -llammpsFoamTurbulenceModels \ -lstdc++

sdzahedi commented 8 years ago

Here there is another option file which is called: options-ubuntu-openmpi and this is the script for this file either: LAMMPS_DIR = ../lammps-1Feb14/src

EXE_INC = \ -I$lammpsFoamTurbulenceModels/include \ -I$(PWD)/include \ -I$(LAMMPS_DIR)/ \ -I$(LAMMPS_DIR)/GRANULAR \ -I/usr/lib/openmpi/include \ -I/usr/lib/openmpi/lib \ -I$(LAMMPS_DIR)/Obj_shanghailinux \ -I$(FOAM_SRC)/lagrangian/basic/lnInclude \ -I$(FOAM_SRC)/meshTools/lnInclude \ -I$(LIB_SRC)/cfdTools/incompressible \ -I$(LIB_SRC)/cfdTools/general/lnInclude \ -I$(LIB_SRC)/finiteVolume/lnInclude \ -I$(LIB_SRC)/triSurface/lnInclude \ -IchPressureGrad/lnInclude \ -I$(LIB_SRC)/transportModels \ -I$(LIB_SRC)/transportModels/incompressible/singlePhaseTransportModel \ -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \ -I$(LIB_SRC)/TurbulenceModels/incompressible/lnInclude \ -I$(LIB_SRC)/TurbulenceModels/phaseIncompressible/lnInclude \ -IdragModels/lnInclude

EXE_LIBS = \ -L$(FOAM_USER_LIBBIN) \ -L$(LAMMPS_DIR) \ -lLagrangianInterfacialModels \ -lfiniteVolume \ -lmeshTools \ -llagrangian \ -L/usr/lib/openmpi/lib -lmpi -lmpi_cxx \
-llammps_shanghailinux \ -ltriSurface \ -lchPressureGrad-DEM \ -lincompressibleTransportModels \ -lturbulenceModels \ -lincompressibleTurbulenceModels \ -llammpsFoamTurbulenceModels \ -lstdc++

sdzahedi commented 8 years ago

I am wondering which address should I modify, for your information I have installed the openmpi in this address: /home/szv Thanks, Saeid

sdzahedi commented 8 years ago

This us where the errors started when I tried to install sediFoam:

szv@szv-Inspiron-560:~/sediFoam-master$ ./Allwmake.sh Installing lammpsFoam (for mac/linux).. Enter the directory of your LAMMPS and press [ENTER](default directory ./lammps-1Feb14): ./lammps-1Feb14 Directory NOT found! Use default directory instead. ./Allwmake.sh: line 20: cd: /home/szv/sediFoam-master/lammps-1Feb14: No such file or directory Directory of LAMMPS is: /home/szv/sediFoam-master ./Allwmake.sh: line 26: cd: /home/szv/sediFoam-master/src: No such file or directory /home/szv/sediFoam-master ./Allwmake.sh: line 30: cd: /home/szv/sediFoam-master/src/MAKE: No such file or directory ./Allwmake.sh: line 34: cd: /home/szv/sediFoam-master/src/STUBS: No such file or directory make: *\ No targets specified and no makefile found. Stop. ./Allwmake.sh: line 36: cd: /home/szv/sediFoam-master/src: No such file or directory

iurnus commented 8 years ago

Do you compile OpenFOAM successfully in your machine?

The allwmake file may not be working because of your system is different with ours. But I think if you follow the instructions in the sediFoam documentation, you can make it step by step.

The address of openmpi will be shown using command "which mpicc" in your terminal. You still have to find the "include" and "lib" of openmpi yourself.

On Wed, Apr 13, 2016 at 6:27 PM, sdzahedi notifications@github.com wrote:

This us where the errors started when I tried to install sediFoam:

szv@szv-Inspiron-560:~/sediFoam-master$ ./Allwmake.sh Installing lammpsFoam (for mac/linux).. Enter the directory of your LAMMPS and press ENTER http://default%20directory%20./lammps-1Feb14: ./lammps-1Feb14 Directory NOT found! Use default directory instead. ./Allwmake.sh: line 20: cd: /home/szv/sediFoam-master/lammps-1Feb14: No such file or directory Directory of LAMMPS is: /home/szv/sediFoam-master ./Allwmake.sh: line 26: cd: /home/szv/sediFoam-master/src: No such file or directory /home/szv/sediFoam-master ./Allwmake.sh: line 30: cd: /home/szv/sediFoam-master/src/MAKE: No such file or directory ./Allwmake.sh: line 34: cd: /home/szv/sediFoam-master/src/STUBS: No such file or directory make: *\ No targets specified and no makefile found. Stop. ./Allwmake.sh: line 36: cd: /home/szv/sediFoam-master/src: No such file or directory

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/xiaoh/sediFoam/issues/1#issuecomment-209674082

Rui Sun Ph.D. Candidate Department of Aerospace and Ocean Engineering Virginia Polytechnic Institute and State University Blacksburg, VA, USA

sdzahedi commented 8 years ago

Hello there, Thank you for your reply. I have started to follow the instruction. I am wondering I should install the lammps-1Feb14 before I follow the instruction or when I do it step by step it will install lammps either?

Thanks Saeid

sdzahedi commented 8 years ago

Hello, I followed the the instructions in the sediFoam. in step 5 after I enter the command make shanghailinux, It started to install some packages but it s been terminated with this error.

In file included from ../compute_voronoi_atom.cpp:21:0: ../compute_voronoi_atom.h:24:21: fatal error: voro++.hh: No such file or directory

include "voro++.hh"

                 ^

compilation terminated. make[1]: * [compute_voronoi_atom.o] Error 1 make[1]: Leaving directory `/home/sz/lammps-1Feb14/src/Obj_shanghailinux' make: * [shanghailinux] Error 2

I appreciate your consideration and advices Thanks, Saeid

rqwang commented 8 years ago

Hi Saeid,

I met the exact problem. The reason is the new version of Lammps cannot automatically install this new software "voro++" for you.

Please follow the instruction at http://lammps.sandia.gov/doc/Section_packages.html?highlight=voro#voronoi to install it.

Good luck. Roger

On Fri, Apr 22, 2016 at 4:39 PM, sdzahedi notifications@github.com wrote:

Hello, I followed the the instructions in the sediFoam. in step 5 after I enter the command make shanghailinux, It started to install some packages but it s been terminated with this error.

In file included from ../compute_voronoi_atom.cpp:21:0: ../compute_voronoi_atom.h:24:21: fatal error: voro++.hh: No such file or directory

include "voro++.hh"

^ compilation terminated. make[1]: * [compute_voronoi_atom.o] Error 1 make[1]: Leaving directory `/home/sz/lammps-1Feb14/src/Obj_shanghailinux' make: * [shanghailinux] Error 2

I appreciate your consideration and advices Thanks, Saeid

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/xiaoh/sediFoam/issues/1#issuecomment-213627139

sdzahedi commented 8 years ago

Hello Roger, could you install it finally? I did follow what you told me and it works but after gave me this error:

../compute_gran_local.cpp: In member function ‘int LAMMPS_NS::ComputeGranLocal::compute_pairs(int)’: ../compute_gran_local.cpp:158:49: error: invalid conversion from ‘int’ to ‘LAMMPSNS::NeighList’ [-fpermissive] if (flag == 0) neighbor->build_one(list->index); ^ In file included from ../accelerator_kokkos.h:37:0, from ../pair.h:18, from ../compute_gran_local.cpp:21: ../neighbor.h:90:8: error: initializing argument 1 of ‘void LAMMPS_NS::Neighbor::build_one(LAMMPSNS::NeighList, int)’ [-fpermissive] void build_one(class NeighList list, ^ make[1]: ** [compute_gran_local.o] Error 1 make[1]: Leaving directory `/home/sz/lammps-22Apr16/src/Obj_shanghailinux' make: *\ [shanghailinux] Error 2

Thanks, Saeid

rqwang commented 8 years ago

Hi Saeid,

I could finally install with some minor modifications to the source code. Please switch to below trial branch and let me know if there is any problem.

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 notifications@github.com wrote:

Hello Roger, could you install it finally? I did follow what you told me and it works but after gave me this error:

../compute_gran_local.cpp: In member function ‘int LAMMPS_NS::ComputeGranLocal::compute_pairs(int)’: ../compute_gran_local.cpp:158:49: error: invalid conversion from ‘int’ to ‘LAMMPS_NS::NeighList

_’ [-fpermissive] if (flag == 0) neighbor->build_one(list->index); ^ In file included from ../accelerator_kokkos.h:37:0, from ../pair.h:18, from ../compute_gran_local.cpp:21: ../neighbor.h:90:8: error: initializing argument 1 of ‘void LAMMPS_NS::Neighbor::build_one(LAMMPSNS::NeighList, int)’ [-fpermissive] void build_one(class NeighList

list, ^ make[1]: ** [compute_gran_local.o] Error 1 make[1]: Leaving directory `/home/sz/lammps-22Apr16/src/Obj_shanghailinux' make: *\ [shanghailinux] Error 2

Thanks, Saeid

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/xiaoh/sediFoam/issues/1#issuecomment-214058283

sdzahedi commented 8 years ago

Hello Roger, Thank you for your reply. I can not see any git checkout building_update files in this post. This is my email: sdzahedi@yahoo.com

Thanks, Saeid

rqwang commented 8 years ago

Hi Saeid,

Please enter the line in your terminal. This should switch the branch of your git.

Thanks. Roger

On Mon, Apr 25, 2016 at 3:53 PM, sdzahedi notifications@github.com wrote:

Hello Roger, Thank you for your reply. I can not see any git checkout building_update files in this post. This is my email: sdzahedi@yahoo.com

Thanks, Saeid

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/xiaoh/sediFoam/issues/1#issuecomment-214555420

sdzahedi commented 8 years ago

Hello Roger, I could not install sedifoam anyway I have tried. when I enter that line you told me I got this line: fatal: Not a git repository (or any of the parent directories): .git

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 ‘LAMMPSNS::NeighList’ [-fpermissive] if (flag == 0) neighbor->build_one(list->index); ^ In file included from ../accelerator_kokkos.h:37:0, from ../pair.h:18, from ../compute_gran_local.cpp:21: ../neighbor.h:90:8: note: initializing argument 1 of ‘void LAMMPS_NS::Neighbor::build_one(LAMMPSNS::NeighList, int)’ void build_one(class NeighList _list, ^ Makefile:101: recipe for target 'compute_granlocal.o' failed make[1]: ** [compute_gran_local.o] Error 1 make[1]: Leaving directory '/home/szv/lammps-14May16/src/Obj_shanghailinux' Makefile:130: recipe for target 'shanghailinux' failed make: *\ [shanghailinux] Error 2

rqwang commented 8 years ago

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, Roger

On Thu, May 26, 2016 at 11:57 AM, sdzahedi notifications@github.com wrote:

Hello Roger, I could not install sedifoam anyway I have tried. when I enter that line you told me I got this line: fatal: Not a git repository (or any of the parent directories): .git

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] if (flag == 0) neighbor->build_one(list->index); ^ In file included from ../accelerator_kokkos.h:37:0, from ../pair.h:18, from ../compute_gran_local.cpp:21: ../neighbor.h:90:8: note: initializing argument 1 of ‘void LAMMPS_NS::Neighbor::build_one(LAMMPSNS::NeighList, int)’ void build_one(class NeighList

_list, ^ Makefile:101: recipe for target 'compute_granlocal.o' failed make[1]: ** [compute_gran_local.o] Error 1 make[1]: Leaving directory '/home/szv/lammps-14May16/src/Obj_shanghailinux' Makefile:130: recipe for target 'shanghailinux' failed make: *\ [shanghailinux] Error 2

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/xiaoh/sediFoam/issues/1#issuecomment-221962615

sdzahedi commented 8 years ago

Thanks Roger,I ll check it and inform you how it goes. Best Regards,Saeid 

On Thursday, June 16, 2016 11:42 PM, rqwang <notifications@github.com> wrote:

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, Roger

On Thu, May 26, 2016 at 11:57 AM, sdzahedi notifications@github.com wrote:

Hello Roger, I could not install sedifoam anyway I have tried. when I enter that line you told me I got this line: fatal: Not a git repository (or any of the parent directories): .git

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] if (flag == 0) neighbor->build_one(list->index); ^ In file included from ../accelerator_kokkos.h:37:0, from ../pair.h:18, from ../compute_gran_local.cpp:21: ../neighbor.h:90:8: note: initializing argument 1 of ‘void LAMMPS_NS::Neighbor::build_one(LAMMPSNS::NeighList, int)’ void build_one(class NeighList

_list, ^ Makefile:101: recipe for target 'compute_granlocal.o' failed make[1]: ** [compute_gran_local.o] Error 1 make[1]: Leaving directory '/home/szv/lammps-14May16/src/Obj_shanghailinux' Makefile:130: recipe for target 'shanghailinux' failed make: *\ [shanghailinux] Error 2

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/xiaoh/sediFoam/issues/1#issuecomment-221962615

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

sdzahedi commented 8 years ago

Hello Roger, Unfortunately I could not compile this code. I am getting error same as before. I am wondering if you can make a tutorial on how finally you could install the package with minor connections to the source code as you mentioned before. I appreciate your consideration and advice.

Thanks, Saeid

KhuramWalayat commented 7 years ago

Hello all can any body help me out with this. Thanks lammpsFoam: error while loading shared libraries: liblammps_shanghailinux.so: cannot open shared object file: No such file or directory

iurnus commented 7 years ago

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

KhuramWalayat commented 7 years ago

Thanks iurnus, it works.

KhuramWalayat commented 7 years ago

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

iurnus commented 7 years ago

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 notifications@github.com 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

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/xiaoh/sediFoam/issues/1#issuecomment-264070174, or mute the thread https://github.com/notifications/unsubscribe-auth/AGjsU328Lc0cvFK3d38VwWRDAFriFd7Xks5rDkCZgaJpZM4IEwty .

-- Rui Sun Ph.D. Candidate Department of Aerospace and Ocean Engineering Virginia Polytechnic Institute and State University Blacksburg, VA, USA

KhuramWalayat commented 7 years ago

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 <notifications@github.com> 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 notifications@github.com 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

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/xiaoh/sediFoam/issues/1#issuecomment-264070174, or mute the thread https://github.com/notifications/unsubscribe-auth/AGjsU328Lc0cvFK3d38VwWRDAFriFd7Xks5rDkCZgaJpZM4IEwty .

-- Rui Sun Ph.D. Candidate Department of Aerospace and Ocean Engineering Virginia Polytechnic Institute and State University Blacksburg, VA, USA — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

ssong-kmou commented 7 years ago

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

cojua8 commented 5 years ago

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

iurnus commented 5 years ago

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 notifications@github.com 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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zhazhazhaz commented 5 years ago

when i was compiling using command 'wmake' in directory:lammpsFoam i meet this error: opt/openfoam30/src/OpenFOAM/lnInclude/dimensionedType.C:197:25: note: candidate expects 3 arguments, 4 provided In file included from lammpsFoam.C:64:0: /opt/openfoam30/src/finiteVolume/lnInclude/initContinuityErrs.H:37:8: warning: unused variable ‘cumulativeContErr’ [-Wunused-variable] scalar cumulativeContErr =0; ^ make: *** [/opt/openfoam30/platforms/linux64GccDPInt32Opt/applications/solvers/lagrangian/DEMFoam/lammpsFoam/lammpsFoam.o] Error 1

zhazhazhaz commented 5 years ago

when i fix the error ,the another error appear: /opt/openfoam30/src/OpenFOAM/lnInclude/dimensionedType.C:197:25: note: static Foam::dimensioned Foam::dimensioned::lookupOrDefault(const Foam::word&, const Foam::dictionary&, const Type&) [with Type = double] Foam::dimensioned Foam::dimensioned::lookupOrDefault ^ /opt/openfoam30/src/OpenFOAM/lnInclude/dimensionedType.C:197:25: note: candidate expects 3 arguments, 4 provided make: *** [/opt/openfoam30/platforms/linux64GccDPInt32Opt/applications/solvers/lagrangian/DEMFoam/lammpsFoam/lammpsFoam.o] Error 1

i don;t know how to deal with it,i will appreciate if you meet the similar error and know how to handle it.

Niteshdubey1 commented 5 years ago

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 Max Ur Courant Number = 0.096 Dispersed phase volume fraction = 0.000353135 Min(alpha) = 2.48135e-25 Max(alpha) = 0.0404105 DICPCG: Solving for p, Initial residual = 0.0125163, Final residual = 8.40199e-11, No Iterations 158 DICPCG: Solving for p, Initial residual = 8.4126e-11, Final residual = 8.4126e-11, No Iterations 0 DICPCG: Solving for p, Initial residual = 8.4126e-11, Final residual = 8.4126e-11, No Iterations 0 DICPCG: Solving for p, Initial residual = 8.4126e-11, Final residual = 8.4126e-11, No Iterations 0 DICPCG: Solving for p, Initial residual = 0.00157104, Final residual = 9.3532e-11, No Iterations 150 DICPCG: Solving for p, Initial residual = 9.35416e-11, Final residual = 9.35416e-11, No Iterations 0 DICPCG: Solving for p, Initial residual = 9.35416e-11, Final residual = 9.35416e-11, No Iterations 0 DICPCG: Solving for p, Initial residual = 9.35416e-11, Final residual = 9.35416e-11, No Iterations 0 DILUPBiCG: Solving for k, Initial residual = 0.00106239, Final residual = 8.0097e-07, No Iterations 1 bounding k, min: -0.000315745 max: 0.290225 average: 0.00973746 Moving Particles Time to add particle: 0.0005 is: x0 0.100000, x1 0.300000, y0 0.000000; y1 0.300000 z0 0.000000, z1 0.150000. Incoming drag not consistent with local particle number. LAMMPS evolving.. Step Temp E_pair E_mol TotEng Press 506800 0.0013906323 0 0 9.6647755e-08 0.025900342 506900 0.0013935887 0 0 9.6853223e-08 0.025881173 Loop time of 0.107697 on 6 procs for 100 steps with 21583 atoms finished moving the particles in LAMMPS. the number of particles in LAMMPS now is: 21583 data transformed into each processor! Incoming drag is: 1584, local particle number is: 1585.-------------------------------------------------------------------------- mpirun noticed that process rank 5 with PID 3219 on node cmg10-HP-Z640-Workstation exited on signal 11 (Segmentation fault).