LAMMPS

Description
	LAMMPS is a classical molecular dynamics code, which stands for Large-scale Atomic/Molecular Massively Parallel Simulator.
Site	Version (Latest: 17-Apr-2009)	Notes
ngs.rl.ac.uk	17-APR-2009, 21-May-2008, 10-Aug-2007, 22-Jun-2007	64 bit

License

This licensing description is taken from the LAMMPS web site here http://lammps.sandia.gov/open_source.html

"LAMMPS is a copyrighted code that is distributed free-of- charge, under the terms of the GNU Public License (GPL). This is often referred to as open-source distribution - see www.gnu.org or www.opensource.org. The legal text of the GPL is in the LICENSE file that is included in the LAMMPS distribution.

Here is a summary of what the GPL means for LAMMPS users:

• Anyone is free to use, modify, or extend LAMMPS in any way they choose, including for commercial purposes.
• If you distribute a modified version of LAMMPS, it must remain open-source, meaning you distribute it under the terms of the GPL. You should clearly annotate such a code as a derivative version of LAMMPS.
• If you release any code that includes LAMMPS source code, then it must also be open-sourced, meaning you distribute it under the terms of the GPL.
• If you give LAMMPS files to someone else, the GPL LICENSE file and source file headers (including the copyright and GPL notices) should remain part of the code."

Running the LAMMPS on the NGS (General)

There a multiple ways in which jobs can be launched on the NGS. The input files used in the examples used below can be found at:

gsiftp://ngs.rl.ac.uk:2811/apps/lammps/10Aug07/bench
or
gsiftp://ngs.rl.ac.uk:2811/apps/lammps/10Aug07/examples

• Submission Using the UI/WMS

  To submit the rho parallel fixed size LAMMPS benchmark as a job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

  glite-wms-job-submit -o jobIDs -a lammps.jdl

  Type = "Job";
  JobType = "mpich";
  Executable = "/usr/ngs/LAMMPS";
  Arguments = "-in in.lj -log log.lj.fixed";
  CpuNumber = 16;
  StdOutput = "std.out";
  StdError = "std.err";
  Myproxyserver= "myproxy.ngs.ac.uk";
  InputSandbox = {"in.lj"};
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxx/lammps/inputs";
  OutputSandbox = {"log.lj.fixed","std.out","std.err"};
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxx/lammps/outputs";
  Requirements = (
          Member("NGS-UEE-LAMMPS", other.GlueHostApplicationSoftwareRunTimeEnvironment)
  );
  Rank = other.GlueCEStateFreeCPUs;
  ShallowRetryCount = -1;
  
      

• NGS Web Portal Submission

After logging in to the NGS Portal, select the "LAMMPS" template under the " Chemistry" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

• Submission Using Globus

  The string 'xxx' in the subsequent commands is to be replaced with your id on NGS. You can also create a directory within your home directory (named lammps in the following examples) which will be the working directory.

  Any input files required should be copied on NGS (using gsiscp) in the appropriate directory (/home/xxx/lammps in our example). 

  • Example run of the rho parallel fixed size LAMMPS benchmark.

  To submit the rho fixed size benchmark, using 8 processors, and the 22-Jun-07 version on the NGS (ngs.rl.ac.uk), use the following command (one line). :

   

  globus-job-submit ngs.rl.ac.uk/jobmanager-lsf -x \
  '& (jobType=mpi)(count = 8) \
  (directory=/home/xxx/lammps)(stderr=/home/xxx/lammps/StdErr.txt) \
  (stdout=/home/xxx/lammps/StdOut.txt)(arguments= -in in.lj -log log.lj.fixed)' /usr/ngs/LAMMPS_090417
  

  • Example run of the rho variable size LAMMPS benchmark.

  To submit the rho fixed size benchmark, using 16 processors, and the 10-Aug-07 version on the NGS (ngs.rl.ac.uk), use the following command (one line). :

   

  globus-job-submit ngs.rl.ac.uk/jobmanager-lsf -x \
  '& (jobType=mpi)(count = 16) \
  (directory=/home/xxx/lammps)(stderr=/home/xxx/lammps/StdErr.txt) \
  (stdout=/home/xxx/lammps/StdOut.txt) \
  (arguments= -var x 2 -var y 2 -var z 4 -in in.rhodo.scaled -log log.rhodo.scaled)' /usr/ngs/LAMMPS_090417
  

  Compilation Information for ngs.rl.ac.uk 

   The latest version of LAMMPS was compiled on ngs.rl.ac.uk using G++ compiler and linked to the ScaliMPI and fftw (gcc compiled).

  Pre Apr 2009 versions of LAMMPS were compiled on ngs.rl.ac.uk using PGI 6.2 C++ compiler and linked to the Scali-MPI and fftw 2.1.5 (pgi, goto blas compiled) libraries.

  Further Information 

  The online LAMMPS manual can be found on the LAMMPS web site here :

  • LAMMPS Manual: http://lammps.sandia.gov/doc/Manual.html

  There are available the example and benchmark test input files, above, and others for LAMMPS at

  • Examples: ngs.rl.ac.uk:/apps/lammps/10Aug07/examples
  • Benchmarks: ngs.rl.ac.uk:/apps/lammps/10Aug07/bench