lammps install 02/23/2015

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Dear Lammps Users,

We are trying to install Lammps (Dec 9 2014), with the Meam library, in parallel, onto an Ubuntu 14.04 LTS system. The hardware is HP Z820 with 16 cores and 128GB of memory. We require parallel so the users can run simulations much more efficiently than in serial mode.

We are having problems getting it install, and hoping for help. Here’s what we’ve done so far:. Using the documentation as a guide, we have done the following:

  • Is MPI installed already? Yes. We have mpich, mpich2, and open mpi. (openmpi-bin 1.6.5-8, from Ubuntu repository)

  • We downloaded and untarred newest lammps (Dec 9th 2014)

  • meam library is required, so we did:

  • /usr/local/lammp…/lib/meam/ sudo make -f Makefile.gfortran

  • however, we are wondering if we need to do a make for Makefile.min64-cross-mpi, because we MUST have parallel lammps (using more than 1 core for a simulation)? We didn’t do this because documentation doesn’t say anything about it

  • upon reading documentation, section “Step 0”, we think we have to run src/MAKE/OPTIONS/make Makefile.ompi_g++, but when we run that we get nothing, no error just nothing to be done:
    “

user1@…5446…:/usr/local/lammps-9Dec14/src/MAKE/OPTIONS$ sudo make Makefile.ompi_g++
make: Nothing to be done for `Makefile.ompi_g++’.
“

  • so, maybe we don’t need the above step?

Looked online and found this person who suggests using the MACHINE makefile for Ubuntu:

… (many more lines like this)

Makefile:40: velocity.d: No such file or directory
Makefile:40: verlet.d: No such file or directory
Makefile:40: write_data.d: No such file or directory
Makefile:40: write_dump.d: No such file or directory
Makefile:40: write_restart.d: No such file or directory
make[1]: *** No rule to make target write_restart.d'. Stop. make[1]: Leaving directory /usr/local/lammps-9Dec14/src/Obj_ubuntu’
make: *** [ubuntu] Error 2

At this point we are stuck. We’ve tried reading the documentation. I do have experience compiling on Linux and such, but yet I do need help.

Please let me know if you have an idea on how to help.

Appreciate your time and effort,

Mohamed

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You “get nothing” because you have to run make from src/ not from src/MAKE/OPTIONS/. Read section 2.2 of the manual where this has been explained in details.

Kasra.

3

You "get nothing" because you have to run make from src/ not from
src/MAKE/OPTIONS/. Read section 2.2 of the manual where this has been
explained in details.

... in addition to that useful-sounding comment, I have a few suggestions.

1) Don't worry about MEAM for now. First, see if you can get
plain-vanilla LAMMPS compiled. ...Worry about meam, later.

- upon reading documentation, section "Step 0", we think we have to run
src/MAKE/OPTIONS/make Makefile.ompi_g++, but when we run that we get
nothing, no error just nothing to be done:

Why src/MAKE/OPTIONS/make Makefile.ompi_g++ ??

2) Unless there's a specific reason you can not do so, I suggest using
the Makefile.ubuntu that is shipped with (recent versions of) LAMMPS.
(Dec 9th 2014 should be fine.) The Makefile.ubuntu supports MPI.
(It's located in the src/MAKE/MACHINES/ directory.) If you read the
comment section of that file, it says thatyou must install the
packages before compiling LAMMPS: g++ mpi-default-bin mpi-default-dev
libfftw3-dev libjpeg-dev libpng12-dev.

Here is how I currently build LAMMPS in ubuntu 14.04:

sudo apt-get install g++
sudo apt-get install mpi-default-bin mpi-default-dev # openmpi
sudo apt-get install libfftw3-dev # fftw3 (instead of fftw)
sudo apt-get install libjpeg-dev libpng12-dev
   #I don't remember, but it can't hurt to also install "build-essential"
sudo apt-get install build-essential gfortran #<--optional?

   # then
cd ~/lammps-09Dec14/src/ #
make clean-all
make ubuntu

   # Then copy the binary (lmp_ubuntu) to somewhere in your path,
(such as /usr/local/bin or ~/bin/)

This is how I currently install and run plain vanilla LAMMPS. Once
you have this working, go ahead and attempt MEAM.

3) I vaguely remember having a bad experience attempting to compile
LAMMPS on an ubuntu machine with both openmpi (mpidefault) AND mpich2
installed. If you don't specifically need mpich2, my inclination is
to uninstall it:
  sudo apt-get remove mpich2
(and, again, make sure you have the canonical version of openmpi:
  sudo apt-get install mpi-default-bin mpi-default-dev)

If you DO require mpich2 (instead of openmpi), then feel free to delete openmpi:
  sudo apt-get remove mpi-default-bin mpi-default-dev
and make sure you have the canonical version of mpich2:
  sudo apt-get install mpich2

LAMMPS does not care if you have mpich2 or openmpi, but it does effect
the Makefile you use. Incidentally, there is an old ubuntu makefile
compatible with mpich2 and fftw (not fftw3) here:
http://lammps.sandia.gov/threads/msg36437.html

4) More opinions:

   Since you are using ubuntu, I suggest installing all libraries you
need (and drivers) using the standard debian/ubuntu "apt-get"
package-management system. That's what makes debian great. This will
install libraries in the default paths. Alternately, if you want to
install from source into /usr/local or /opt/, that's okay too, but be
prepared to edit the Makefile.ubuntu file accordingly.
   In my opinion, either of those options is preferable to running
some random install script you found somewhere on the internet. (I
just ran into somebody who felt the need to reinstall the OS after
using the nvidia linux driver installer script.)

Cheers and good luck.

Andrew
The other link (http://katter-world.blogspot.com/2010/05/install-lammps-on-ubuntu.html)
is pretty old by LAMMPS standards.

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One more comment:

24.02.2015, 04:46, "Andrew Jewett" <[email protected]...>: