Lammps - Revision history

Kristiankuppart: /* seed tests */

2014-05-16T11:23:46Z

seed tests

← Older revision		Revision as of 14:23, 16 May 2014
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	== seed tests ==		== Random seed tests ==

	Tests for the random seed in LAMMPS command "velocity" (http://lammps.sandia.gov/doc/velocity.html) were performed.		Tests for the random seed in LAMMPS command "velocity" (http://lammps.sandia.gov/doc/velocity.html) were performed.

Kristiankuppart at 11:23, 16 May 2014

2014-05-16T11:23:29Z

← Older revision		Revision as of 14:23, 16 May 2014
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	File:nodes.jpg\|Nodes scaling		File:nodes.jpg\|Nodes scaling
	</gallery>		</gallery>



			== seed tests ==

			Tests for the random seed in LAMMPS command "velocity" (http://lammps.sandia.gov/doc/velocity.html) were performed.

			results:

			when using ''same'' number of different processors with the same random seed, the velocities created in simulatsions with identical inputs were the same.

			when using ''different'' number of processors with the same random seed, the velocities created in simulations with identical inputs were different.

			Naturally, when using different random seed in simulations with identical input, the velocities created were different.

			The results were also tested to hold for both uniform and gaussian velocity distributions.

Simvig: /* Scaling tests */

2013-12-06T11:25:40Z

Scaling tests

← Older revision		Revision as of 14:25, 6 December 2013
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	== Scaling tests ==		== Scaling tests ==

	Lammps calculation time scales linearly with the number of atoms and increasing the number of processors decreases calculation time proportionally. It distributes well among different processor nodes.		Lammps calculation time scales linearly with the number of atoms and increasing the number of processors decreases calculation time proportionally. It distributes well among different processor nodes. Simulations were run with a timestep of 1 ps for 10 000 timesteps.

	<gallery>		<gallery>

Simvig at 07:59, 17 October 2013

2013-10-17T07:59:08Z

← Older revision		Revision as of 10:59, 17 October 2013
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	</tt>'''		</tt>'''

			== Scaling tests ==

			Lammps calculation time scales linearly with the number of atoms and increasing the number of processors decreases calculation time proportionally. It distributes well among different processor nodes.

			<gallery>
			File:size.jpg\|Size scaling
			File:procs.jpg\|Processor scaling
			File:nodes.jpg\|Nodes scaling
			</gallery>

Simvig: Created page with " == Lammps minimal install on Linux == 1. [http://lammps.sandia.gov/download.html Download Lammps] current C++ tarball and extract it. 2. Install either OpenMPI or MPICH2. ..."

2013-06-04T09:47:46Z

Created page with " == Lammps minimal install on Linux == 1. [http://lammps.sandia.gov/download.html Download Lammps] current C++ tarball and extract it. 2. Install either OpenMPI or MPICH2. ..."

New page

== Lammps minimal install on Linux ==

1. [http://lammps.sandia.gov/download.html Download Lammps] current C++ tarball and extract it.

2. Install either OpenMPI or MPICH2. I found that MPICH2 works slightly better. You will need both the base and development packages for your system. For example:

'''<tt>

::: yum install mpich2.x86_64

::: yum install mpich2-devel.x86_64

</tt>''

Note where the framework has been installed.

3. Set your PATH to point to the MPI binaries. Edit the user's .bash_profile and add the MPI bin directory to the existing PATH modification there. This will take effect on your next session. To add to PATH on your current session, type (use the correct bin directory location)

'''<tt>

::: export PATH=$PATH:/lib64/mpich2/bin

</tt>'''

4. Make sure the system can find the MPI libraries. Open /etc/ld.so.conf. It should either contain a list of library directories or something like

::: <code> include ld.so.conf.d/*.conf </code>

In the first case, add you MPI library directory, for example:

::: <code> /lib64/mpich2/lib </code>

In the latter case, go to the folder mentioned in the include and create a new file. Make sure it conforms to the format specified in the include statement. Put your MPI library directory path into that file.

5. Download the [[media:Makefile.minmpi|minmpi makefile]] and put into your lammps directory in src/MAKE.

6. Go to the src directory and type (the -j switch uses parallel compilation; remove it if causes problems)

'''<tt>

::: make -j minmpi

</tt>'''

7. If no errors occur, you now have the executable file lmp_minmpi. If the compilation failed because of missing dependencies, you need to specify the location of MPI includes and libraries for lammps. Edit Makefile.minmpi, and make sure that MPI_INC points to the location of mpi.h, MPI_PATH points to the libraries and MPI_LIB links the MPI. For example:

::: <code>MPI_INC = -I/usr/include/mpich2-x86_64/
::: MPI_PATH = -L/lib64/mpich2/lib
::: MPI_LIB = lmpi </code>

Go back to src and type

'''<tt>

::: make clean-all
::: make -j minmpi

</tt>'''