LAMMPS in Ubuntu

[B]####### NB: This thread is outdated. I haven't deleted it just for historical reference. Please follow the new post and do not post new comments to this thread. #######[/B]

Step 1, install MPICH and FFTW2 (FFTW3 does not work as evidenced in LAMMPS documentation)

sudo apt-get install build-essential mpich-bin libmpich1.0-dev mpi-doc fftw2 fftw-dev libxaw7-dev

Step 2, Add an include line to [FONT="Courier New"]src/change_box.cpp[/FONT]

#include <cstring>

Step 3, run the following command in the [FONT="Courier New"]src[/FONT] directory

make debian

And it compiles! I don't know if those steps were obvious to people, but it caused me to do a fair bit of detective work to figure out. The [FONT="Courier New"]libxaw7-dev[/FONT] package was installed to allow xmovie to be compiled. Just one [FONT="Courier New"]make[/FONT] and it was good.

PS: This should be helpful information for people taking CEE 2324 under Professor To at the University of Pittsburgh. Instead of dealing with cygwin, I would *highly* recommend installing Ubuntu inside of Windows (you can do that)! It's just as if it were a Windows program, and no partitioning or hassle involved! Then, you can work on a *real* Linux platform instead of a Linux emulation

There is a problem with lamboot/mpich and lamboot/openmpi: if you compile with mpich, then the code will not be executed via mpirun.

The trick is to select the "right" mpirun via

sudo update-alternatives --config mpirun

selecting

/usr/bin/mpirun.mpich

as preferred choice

cheers a

Many thanks you have very much helped!

спасибо, очень выручили с этим лэмпсом, а то застрял уже :)

Yoshis88 said: I was stumped on how to get LAMMPS (21 May 2008 version) molecular modeling and MD simulation software to work on this Ubuntu 8.10 computer (64-bit OS, shouldn't be relevant) and I tried searching the forums to no avail (though, the forums were down for the second half of that day). But I finally got it to compile, and I was like, if only that was on the forums. So, I'm going to come put it on here :)

Step 1, install MPICH and FFTW2 (FFTW3 does not work as evidenced in LAMMPS documentation)

sudo apt-get install build-essential mpich-bin libmpich1.0-dev mpi-doc fftw2 fftw-dev libxaw7-dev

Step 2, Add an include line to [FONT="Courier New"]src/change_box.cpp[/FONT]

#include <cstring>

Step 3, run the following command in the [FONT="Courier New"]src[/FONT] directory

make debian

And it compiles! I don't know if those steps were obvious to people, but it caused me to do a fair bit of detective work to figure out. The [FONT="Courier New"]libxaw7-dev[/FONT] package was installed to allow xmovie to be compiled. Just one [FONT="Courier New"]make[/FONT] and it was good.

PS: This should be helpful information for people taking CEE 2324 under Professor To at the University of Pittsburgh. Instead of dealing with cygwin, I would *highly* recommend installing Ubuntu inside of Windows (you can do that)! It's just as if it were a Windows program, and no partitioning or hassle involved! Then, you can work on a *real* Linux platform instead of a Linux emulation

Thanks for the info Yoshis88. I've just compiled LAMMPS on my Ubuntu laptop, but every time I run a job on both cores it asks me for my user password... Has anyone encountered the same problem or is it just me? LAMMPS requires no password for single processor jobs, but it asks for it if there's communication between processors. This makes me think my mpich might not be configured properly, but I'm no expert. Any advice on how to get rid of this annoying password prompt would be appreciated.

Cheers, D

Thanks for the info Yoshis88. I've just compiled LAMMPS on Ubuntu. But I don't be able to run any samples. Sample: Lammps manual has instructions following for one of the Lennard−Jones tests.

cd src make debian cp lmp_debian ../examples/lj cd ../examples/lj mpirun &#8722;np 4 lmp_debian <in.lj.nve

I tried above instructions but &#304;t isn't run.

please help me

Thanks in advance

Hey I think I might have the same issue.

Just want to throw it out there that I am very new to this but being asked a vp for some help,

Following the documentation when I try and do

mpirun -np 4 lmp_linux < in.lj.nve

I get the following

mpirun -np 4 lmp_debian < in.obstalce

ssh: connect to host localhost port 22: Connection refused p0_3932: p4_error: Child process exited while making connection to remote process on localhost: 0 p0_3932: (6.127177) net_send: could not write to fd=4, errno = 32 root@greg-desktop:~/Desktop/Lammps#

Does this mean anything to anyone? Any help at all would be helpful.

cd src make debian cp lmp_debian ../examples/lj cd ../examples/lj ./lmp_debian <in.lj.nve

problem solved by using above commands.

The "mpirun -np 4" means that you want to run on 4 processors. For 1 processor, you can just use:

./lmp_debian < in.lj.nve

Hi all,

I have the following ERROR. What can I do? ahmedo@ahmedo:~/Masaüstü$ cd lammps ahmedo@ahmedo:~/Masaüstü/lammps$ cd src ahmedo@ahmedo:~/Masaüstü/lammps/src$ cp lmp_debian ../examples/GB-test ahmedo@ahmedo:~/Masaüstü/lammps/src$ cd - /home/ahmedo/Masaüstü/lammps ahmedo@ahmedo:~/Masaüstü/lammps$ cd examples ahmedo@ahmedo:~/Masaüstü/lammps/examples$ cd GB-test ahmedo@ahmedo:~/Masaüstü/lammps/examples/GB-test$ ./lmp_debian < in.ellipse.gayb erne LAMMPS (9 Jan 2009) *ERROR: Invalid atom style* ahmedo@ahmedo:~/Masaüstü/lammps/examples/GB-test./lmp_debian < in.ellipse.gayb erne

*NOT&#304;CE:* in input file in.ellipse.gayberne

# GayBerne ellipsoids in LJ background fluid

units lj atom_style ellipsoid dimension 2 . . . *1. try* ahmedo@ahmedo:~/Masaüstü$ cd lammps ahmedo@ahmedo:~/Masaüstü/lammps$ cd src ahmedo@ahmedo:~/Masaüstü/lammps/src$ cp lmp_debian ../examples/GB-test ahmedo@ahmedo:~/Masaüstü/lammps/src$ cd - /home/ahmedo/Masaüstü/lammps ahmedo@ahmedo:~/Masaüstü/lammps$ cd examples ahmedo@ahmedo:~/Masaüstü/lammps/examples$ cd GB-test ahmedo@ahmedo:~/Masaüstü/lammps/examples/GB-test$ ./lmp_debian < in.ellipse.gayb erne LAMMPS (9 Jan 2009) *ERROR: Invalid atom style* ahmedo@ahmedo:~/Masaüstü/lammps/examples/GB-test./lmp_debian < in.ellipse.gayb erne

*NOT&#304;CE:* in input file in.ellipse.gayberne

# GayBerne ellipsoids in LJ background fluid

units lj atom_style ellipsoid dimension 2 . . . *2.try*

ahmedo@ahmedo:~$ cd Masaüstü ahmedo@ahmedo:~/Masaüstü$ cd lammps ahmedo@ahmedo:~/Masaüstü/lammpscd src ahmedo@ahmedo:~/Masaüstü/lammps/src$ make yes-ellipsoid *Package ellipsoid does not exist* ahmedo@ahmedo:~/Masaüstü/lammps/src$ [B] *3.try*[/B] ahmedo@ahmedo:~/Masaüstü/lammps/src$ make yes-asphere *Installing package asphere [B]/bin/sh: csh: not found make: *** [yes-asphere] Error 127*[/B]

please help me Thanks in advance

The problem solved after I installed to ubuntu the csh package. ahmedo@ahmedo:~/Masaüstü/lammps/src$ make yes-asphere Installing package asphere ahmedo@ahmedo:~/Masaüstü/lammps/src$ make debian

ahmedo@ahmedo:~/Masaüstü$ cd lammps ahmedo@ahmedo:~/Masaüstü/lammps$ cd src ahmedo@ahmedo:~/Masaüstü/lammps/src$ cp lmp_debian ../examples/GB-test ahmedo@ahmedo:~/Masaüstü/lammps/src$ cd - /home/ahmedo/Masaüstü/lammps ahmedo@ahmedo:~/Masaüstü/lammps$ cd examples ahmedo@ahmedo:~/Masaüstü/lammps/examples$ cd GB-test ahmedo@ahmedo:~/Masaüstü/lammps/examples/GB-test$ ./lmp_debian < in.ellipse.gayberne

Step rot E_pair TotEng Press Volume 0 2.2718861 0 2.394 0.04788 20000 100 1.7442957 0 1.8380516 0.035762064 20558.675 200 2.2770743 0 2.399467 0.046545738 20620.294 300 1.8572884 0 1.9571177 0.042405959 18460.78 400 2.1710835 -0.00050891124 2.2872701 0.06679187 13689.462 ....

Hi everyone !

Im from Peru and i was trying to run LAMMPS (9sep09 version) in ubuntu 9.04, i follow all the steps but i think my problem is with some libraries, this is the error i get when i execute make debian:[INDENT]......... -lfftw -lmpich -lblas -llapack -lifcore -lsvml -lompstub -limf -lifcore -lsvml -lompstub -limf -lcudart -o ../lmp_debian /usr/bin/ld: cannot find -latc collect2: ld devolvió el estado de salida 1 make[1]: * [../lmp_debian] Error 1 make[1]: se sale del directorio `/home/led/Escritorio/lammps-29Sep09/src/Obj_debian' make: * [debian] Error 2 [/INDENT]latc is refered to ATC library that needs to be compile before the LAMMPS and was in the {LAMMPS}/lib/atc directory. The problem is that i dont know how to compile it, i dont understand what i have to config in the makefile.g++. in the readme says:

"Note that the ATC library makes MPI calls, so you must build it with the same MPI library that is used to build LAMMPS, e.g. as specified by settings in the lammps/src/MAKE/Makefile.foo file"

well what i do is this:

------ SETTINGS ------

include any MPI settings needed for the ATC library to build with

the same MPI library that LAMMPS is built with

CC = g++ #CCFLAGS = -O -g -I../../src -DMPICH_IGNORE_CXX_SEEK [B]CCFLAGS = $(PKGINC) -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP [/B]ARCHIVE = ar ARCHFLAG = -rc DEPFLAGS = -M LINK = g++ LINKFLAGS = -O USRLIB = -lblas -llapack SYSLIB =

this was the any change i made, but i have erros with linking the headers (*.h), Anything will help !!

Thanks in advance

well i solve my firsts problems, but i cant compile the gpu library. I dont know if gpu only runs in NVIDIA devices =S, is there any posible way to run with no NVIDIA chip ? or maybe compile the LAMMPS without compiling GPU??.

Thanks i advance.

Hi Led Sama I'm battling the same issues installing Lammps under 9.04 -- how did you solve the first problem of 'errors with linking the headers (*.h),' for ATC many thanks

Hi, can someone tell me wich intel fortran compiler you use to compile the REAX and POEMS libraries, i have tried wich some of them but i got erros like:

/usr/bin/ld: warning: libintlc.so.5, needed by /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5, not found (try using -rpath or -rpath-link) /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __gtq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to tbk_string_stack_signal' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to _intel_fast_memcpy' /opt/intel/Compiler/11.1/056/lib/intel64/libsvml.so: undefined reference to __intel_cpu_indicator' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to a_csubq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __dtoq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __qtof' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to a_addq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __divq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to a_leq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __eqq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __qtod' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __jtoq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to a_subq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __addq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __ltq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to a_divq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to _intel_fast_memset' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __subq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to a_caddq' /opt/intel/Compiler/11.1/056/lib/intel64/libsvml.so: undefined reference to __intel_cpu_indicator_init' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __negq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __qtoj' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __compareq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to _intel_fast_memcmp' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __itoq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __mulq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __qtoi' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to a_geq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to __intel_sse2_strlen' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to a_cmulq' /opt/intel/Compiler/11.1/056/lib/intel64/libifcore.so.5: undefined reference to a_mulq' collect2: ld devolvió el estado de salida 1 make[1]: * [../lmp_debian] Error 1 make[1]: se sale del directorio `/home/led/LAMMPS/src/Obj_debian' make: * [debian] Error 2

the reax and meam library uses the -lifcore, is there some other way to compile please let me know !! ..

PD: i have a amd64 version of ubuntu.

Thanks in advance !

Yoshis88, Thanks a lot for the help. I was trying to install Lammps but in the latest release Lammps-3Nov09, there is no make file for the debian (i.e. no Makefile.debian) as it was in the previous versions. However for the time being I have installed the older version but what should I do now to install the latest version ?

Hello everyone I followed the above steps but when I run the 'make debian' command i get an error message '' make: *** [debian] Error 1''. Please help

Regards Puroorava Chakravarthy

I figured a way to do it, keep reading below

Download it from lammps.sandia.gov

In the terminal write the following:

gunzip lammps*.tar.gz tar xvf lammps*.tar

This will create a file named: ''lammps-21Nov09'' (The date may change depending of the updates in the website).

It will contain the following files: bench, doc, examples, lib, potentials, src, tools.

christian@christian-laptop:~/lammps/lammps-21Nov09$ cd src christian@christian-laptop:~/lammps/lammps-21Nov09$ cd MAKE

Before keep going it is necessary to solve some dependencies: build-essential (to compile in C), MPIch (to work in parallel) , FFTW ( to compute long-range interactions), libxaw7 (to compute the movies). In one line code you choose

sudo apt-get install build-essential mpich-bin libmpich1.0-dev fftw2 fftw-dev libxaw7-dev

If you are working in your personal computer you just need

sudo apt-get install build-essential sudo apt-get install libxaw7-dev

To avoid future problems it will be better installing with the first line code Now in the MAKE file you will see a lot of makefiles.xxx. Most users think Makefile.linux is the one they should use because they use ''linux.'' If you open the Makefile.linux you will see that it requires MPICH and FFTW. Things that we actually don't need (especially if we are starting the use of lammps). What a Beginner needs to install is Makefile.serial. If you open this file you will see in the first line that it says: no MPICH, no FFTW.

If you read carefully the Makefile.serial, in one line it says: # MPI library, can be src/STUBS dummy lib. If you go to STUBS you will find a Makefile, this will create a dummy lib for MPI in accordance to the Makefile.serial. So in the STUBS file you type:

christian@christian-laptop:~/lammps/lammps-21Nov09/src/STUBS$ make clean christian@christian-laptop:~/lammps/lammps-21Nov09/src/STUBS$ make

Then you go back to src and compile lammps

christian@christian-laptop:~/lammps/lammps-21Nov09/src$ make clean-all christian@christian-laptop:~/lammps/lammps-21Nov09/src$ make serial

Continuing from the previous post I sent....

It will work correctly, to verify your installation we will run some examples. First type

[EMAIL="christian@christian-laptop"]christian@christian-laptop[/EMAIL]:~/lammps/lammps-21Nov09/src$ ./lmp_serial You should get:

LAMMPS (7 Jul 2009)

This means you are ok in the installation process, ctrl-C to get out and let's go to the examples file (cd ../examples), Choose any, and get deep in learning the meaning of the codes. Each example has one or more lammps input files. For instance I will choose ''flow'' (cd flow). It has two in.flow.xxx files. (input files). I will run one of them by typing:

christian@christian-laptop:~/lammps/lammps-21Nov09/examples/flow$ ../../src/lmp_serial < in.flow.couette

Where is the data stored? Check the in.flow.couette file to see where it is. Almost at the end it says:

dump 1 all atom 50 dump.flow

So the data is stored in dump.flow To finish this test let's visualize the data in a movie. First let's install xmovie For this

christian@christian-laptop:~/lammps/lammps-21Nov09/examples/flow$ cd ../../tools/ christian@christian-laptop:~/lammps/lammps-21Nov09/tools$ cd xmovie christian@christian-laptop:~/lammps/lammps-21Nov09/tools/xmovie$ make christian@christian-laptop:~/lammps/lammps-21Nov09/tools/xmovie$ ./xmovie

Now you will be able to visualize your data using xmovie just by typing in the flow directory

[EMAIL="christian@christian-laptop"]christian@christian-laptop[/EMAIL]:~/lammps/lammps-21Nov09/examples/flow$ ../../tools/xmovie/xmovie -scale dump.flow

This will open the program, maybe your screen will appear black, change the color of your particles and click in Start to watch it.

Hi I have tried to install LAMMPS in ubuntu 9.10. but after I install what you have suggested I tried to insert the command _Make Linux_ using the terminal in the source file directory as the manual specified and I have got error message as bellow

semabay@aaus-07-1414:~/Desktop/lammps-11Nov09/src$ make linux make[1]: Entering directory /home/semabay/Desktop/lammps-11Nov09/src/Obj_linux' 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_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_centro_atom.d: No such file or directory Makefile:93: compute_cna_atom.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_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_heat_flux.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_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_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: create_atoms.d: No such file or directory Makefile:93: create_box.d: No such file or directory Makefile:93: delete_atoms.d: No such file or directory Makefile:93: delete_bonds.d: No such file or directory Makefile:93: dihedral_charmm.d: No such file or directory Makefile:93: dihedral.d: No such file or directory Makefile:93: dihedral_harmonic.d: No such file or directory Makefile:93: dihedral_helix.d: No such file or directory 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 Makefile:93: displace_box.d: No such file or directory Makefile:93: domain.d: No such file or directory Makefile:93: dump_atom.d: No such file or directory Makefile:93: dump_bond.d: No such file or directory Makefile:93: dump_cfg.d: No such file or directory Makefile:93: dump.d: No such file or directory Makefile:93: dump_custom.d: No such file or directory Makefile:93: dump_dcd.d: No such file or directory Makefile:93: dump_xyz.d: No such file or directory Makefile:93: error.d: No such file or directory Makefile:93: ewald.d: No such file or directory Makefile:93: fft3d.d: No such file or directory Makefile:93: fft3d_wrap.d: No such file or directory Makefile:93: finish.d: No such file or directory Makefile:93: fix_add_force.d: No such file or directory Makefile:93: fix_ave_atom.d: No such file or directory Makefile:93: fix_ave_force.d: No such file or directory Makefile:93: fix_ave_spatial.d: No such file or directory Makefile:93: fix_ave_time.d: No such file or directory Makefile:93: fix_bond_break.d: No such file or directory Makefile:93: fix_bond_create.d: No such file or directory Makefile:93: fix_bond_swap.d: No such file or directory Makefile:93: fix_box_relax.d: No such file or directory Makefile:93: fix_com.d: No such file or directory Makefile:93: fix_coord_original.d: No such file or directory Makefile:93: fix.d: No such file or directory Makefile:93: fix_deform.d: No such file or directory Makefile:93: fix_deposit.d: No such file or directory Makefile:93: fix_drag.d: No such file or directory Makefile:93: fix_dt_reset.d: No such file or directory Makefile:93: fix_efield.d: No such file or directory Makefile:93: fix_enforce2d.d: No such file or directory Makefile:93: fix_evaporate.d: No such file or directory Makefile:93: fix_gravity.d: No such file or directory Makefile:93: fix_gyration.d: No such file or directory Makefile:93: fix_heat.d: No such file or directory Makefile:93: fix_indent.d: No such file or directory Makefile:93: fix_langevin.d: No such file or directory Makefile:93: fix_line_force.d: No such file or directory Makefile:93: fix_minimize.d: No such file or directory Makefile:93: fix_momentum.d: No such file or directory Makefile:93: fix_msd.d: No such file or directory Makefile:93: fix_nph.d: No such file or directory Makefile:93: fix_npt.d: No such file or directory Makefile:93: fix_npt_sphere.d: No such file or directory 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 Makefile:93: fix_nvt_sllod.d: No such file or directory Makefile:93: fix_nvt_sphere.d: No such file or directory Makefile:93: fix_orient_fcc.d: No such file or directory Makefile:93: fix_plane_force.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_rdf.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 Makefile:93: fix_shear_history.d: No such file or directory Makefile:93: fix_spring.d: No such file or directory Makefile:93: fix_spring_rg.d: No such file or directory Makefile:93: fix_spring_self.d: No such file or directory Makefile:93: fix_temp_berendsen.d: No such file or directory Makefile:93: fix_temp_rescale.d: No such file or directory Makefile:93: fix_thermal_conductivity.d: No such file or directory Makefile:93: fix_tmd.d: No such file or directory Makefile:93: fix_ttm.d: No such file or directory Makefile:93: fix_viscosity.d: No such file or directory Makefile:93: fix_viscous.d: No such file or directory Makefile:93: fix_wall_lj126.d: No such file or directory Makefile:93: fix_wall_lj93.d: No such file or directory Makefile:93: fix_wall_reflect.d: No such file or directory Makefile:93: fix_wiggle.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 Makefile:93: library.d: No such file or directory Makefile:93: main.d: No such file or directory Makefile:93: memory.d: No such file or directory Makefile:93: min_cg.d: No such file or directory Makefile:93: min.d: No such file or directory 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 Makefile:93: min_sd.d: No such file or directory Makefile:93: modify.d: No such file or directory Makefile:93: neigh_bond.d: No such file or directory Makefile:93: neighbor.d: No such file or directory Makefile:93: neigh_derive.d: No such file or directory Makefile:93: neigh_full.d: No such file or directory Makefile:93: neigh_gran.d: No such file or directory Makefile:93: neigh_half_bin.d: No such file or directory Makefile:93: neigh_half_multi.d: No such file or directory Makefile:93: neigh_half_nsq.d: No such file or directory Makefile:93: neigh_list.d: No such file or directory Makefile:93: neigh_request.d: No such file or directory Makefile:93: neigh_respa.d: No such file or directory Makefile:93: neigh_stencil.d: No such file or directory Makefile:93: output.d: No such file or directory Makefile:93: pack.d: No such file or directory Makefile:93: pair_airebo.d: No such file or directory Makefile:93: pair_born_coul_long.d: No such file or directory Makefile:93: pair_buck_coul_cut.d: No such file or directory Makefile:93: pair_buck_coul_long.d: No such file or directory Makefile:93: pair_buck.d: No such file or directory Makefile:93: pair_coul_cut.d: No such file or directory Makefile:93: pair_coul_debye.d: No such file or directory Makefile:93: pair_coul_long.d: No such file or directory Makefile:93: pair.d: No such file or directory Makefile:93: pair_eam_alloy.d: No such file or directory Makefile:93: pair_eam.d: No such file or directory Makefile:93: pair_eam_fs.d: No such file or directory Makefile:93: pair_hybrid.d: No such file or directory Makefile:93: pair_hybrid_overlay.d: No such file or directory Makefile:93: pair_lj96_cut.d: No such file or directory Makefile:93: pair_lj_charmm_coul_charmm.d: No such file or directory Makefile:93: pair_lj_charmm_coul_charmm_implicit.d: No such file or directory Makefile:93: pair_lj_charmm_coul_long.d: No such file or directory Makefile:93: pair_lj_cut_coul_cut.d: No such file or directory Makefile:93: pair_lj_cut_coul_debye.d: No such file or directory Makefile:93: pair_lj_cut_coul_long.d: No such file or directory Makefile:93: pair_lj_cut_coul_long_tip4p.d: No such file or directory Makefile:93: pair_lj_cut.d: No such file or directory Makefile:93: pair_lj_expand.d: No such file or directory Makefile:93: pair_lj_gromacs_coul_gromacs.d: No such file or directory Makefile:93: pair_lj_gromacs.d: No such file or directory Makefile:93: pair_lj_smooth.d: No such file or directory Makefile:93: pair_morse.d: No such file or directory Makefile:93: pair_soft.d: No such file or directory Makefile:93: pair_sw.d: No such file or directory Makefile:93: pair_table.d: No such file or directory Makefile:93: pair_tersoff.d: No such file or directory Makefile:93: pair_tersoff_zbl.d: No such file or directory Makefile:93: pair_yukawa.d: No such file or directory Makefile:93: pppm.d: No such file or directory Makefile:93: pppm_tip4p.d: No such file or directory Makefile:93: random_mars.d: No such file or directory Makefile:93: random_park.d: No such file or directory Makefile:93: read_data.d: No such file or directory Makefile:93: read_restart.d: No such file or directory Makefile:93: region_block.d: No such file or directory Makefile:93: region_cone.d: No such file or directory Makefile:93: region.d: No such file or directory Makefile:93: region_cylinder.d: No such file or directory Makefile:93: region_intersect.d: No such file or directory Makefile:93: region_prism.d: No such file or directory Makefile:93: region_sphere.d: No such file or directory Makefile:93: region_union.d: No such file or directory Makefile:93: remap.d: No such file or directory Makefile:93: remap_wrap.d: No such file or directory Makefile:93: replicate.d: No such file or directory Makefile:93: respa.d: No such file or directory Makefile:93: run.d: No such file or directory Makefile:93: set.d: No such file or directory Makefile:93: shell.d: No such file or directory Makefile:93: special.d: No such file or directory Makefile:93: temper.d: No such file or directory Makefile:93: thermo.d: No such file or directory Makefile:93: timer.d: No such file or directory Makefile:93: universe.d: No such file or directory Makefile:93: update.d: No such file or directory Makefile:93: variable.d: No such file or directory Makefile:93: velocity.d: No such file or directory icc -O -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DFFT_FFTW -M velocity.cpp > velocity.d /bin/sh: icc: not found make[1]: * [velocity.d] Error 127 make[1]: Leaving directory /home/semabay/Desktop/lammps-11Nov09/src/Obj_linux' make: * [linux] Error 2

When I see the source file there is no *.d file rather it is *.h file. Do you have any solution for such error? Any idea may give me some hint to solve this problem. Have a great time!

I have attached the makefile for debian. Using this file I am able to make LAMMPS (13Nov09) on my ubuntu 9.10.

Rename the file and remove the .txt from its name and then copy it to src/MAKE directory. That's it!

Guys, this may be a bit out of topic here, but I dont know where else to ask this..I have compiled LAMMPS in Ubuntu 9.10 and it works great. We have a small cluster in our University, operating under Red Hat Linux Enterprise 5.3

The .d errors and the [Error 1] and [Error 2] appear here as well, could any of you guys help me out with this. I am trying to compile using MPICH and FFTW on RHEL 5.3 using Intel Math Kernel Libraries (make type:intel_mkl)

Wow! I didn't realize all the additional replies here. Unfortunately, I'm gonna have to deprecate this thread.

/close

Please redirect additional traffic and replies to the new LAMMPS 24Jan10 in Ubuntu 9.10 post (link).

Hi,there I am from Australia. I can build lammps very easyly,but the problems how to build the additional package,like the meam, poems,and reax package. BTW, my system is ubuntu 9.10, and the lammps is the latest 6 Mar 2010 Looking forward your help.

Thank y

puroorava said: Hello everyone

I followed the above steps but when I run the 'make debian' command i get an error message '' make: *** [debian] Error 1''. Please help

Regards Puroorava Chakravarthy

It is also my problem, Please guide our to solve this problem I use the last version (27 mar 2010)

[LEFT][RIGHT] [/LEFT][/RIGHT] [LEFT][RIGHT]Hello everyone[/LEFT][/RIGHT] [LEFT][RIGHT] I followed the above steps but when I run the 'make debian' command ( 27 mar 2010 version),I also get an error message '' make: * [debian] Error 1''.[/LEFT][/RIGHT] [LEFT][RIGHT][/LEFT][/RIGHT] [LEFT][RIGHT]I found it was some others problem but I didn’t find its solution[/LEFT][/RIGHT] [LEFT][RIGHT] [/LEFT][/RIGHT] [LEFT][RIGHT] Please help me Regards**[/LEFT][/RIGHT] [LEFT][RIGHT] Gholamhosain Haidari[/LEFT][/RIGHT]

moh1135 said: [LEFT][RIGHT]

[/RIGHT]

[RIGHT]Hello everyone[/RIGHT]

[RIGHT] I followed the above steps but when I run the 'make debian' command ( 27 mar 2010 version),I also get an error message '' make: * [debian] Error 1''.**[/RIGHT] [/LEFT] [LEFT][RIGHT]I found it was some others problem but I didn’t find its solution[/RIGHT]

[RIGHT] [/RIGHT]

[RIGHT] Please help me Regards[/RIGHT] [/LEFT] [LEFT][RIGHT] Gholamhosain Haidari[/RIGHT] [/LEFT]

Dear

I followed the above steps but when I run the 'make debian' command, and also get follow error masage:

sorena@sorena-desktop:~/Public/lammps-7Apr10/src$ make debian make[1]: Entering directory /home/sorena/Public/lammps-7Apr10/src/Obj_debian' Makefile:50: fix_atc.d: No such file or directory Makefile:50: force.d: No such file or directory g++ -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP -M improper_hybrid.cpp > improper_hybrid.d g++ -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP -M improper_harmonic.cpp > improper_harmonic.d g++ -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP -M improper_cvff.cpp > improper_cvff.d g++ -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP -M improper_class2.cpp > improper_class2.d g++ -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP -M force.cpp > force.d g++ -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP -M fix_wall_gran.cpp > fix_wall_gran.d g++ -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP -M fix_wall_colloid.cpp > fix_wall_colloid.d g++ -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP -M fix_reax_bonds.cpp > fix_reax_bonds.d In file included from fix_reax_bonds.cpp:21: pair_reax_fortran.h:53:23: error: reax_defs.h: No such file or directory make[1]: * [fix_reax_bonds.d] Error 1 make[1]: Leaving directory /home/sorena/Public/lammps-7Apr10/src/Obj_debian' make: * [debian] Error 2

Please help me

Since regards, Rahmati

As indicated in the first post, this is an old thread. Please refer to the information here, which will likely help solve the problems mentioned: http://ubuntuforums.org/showthread.php?t=1390490

Thread closed