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howto:liggghts [2015/01/27 14:16]
agill 		howto:liggghts [2021/12/09 16:42] (current)
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 LIGGGHTS and lammps at the CHPC LIGGGHTS and lammps at the CHPC
  
-The molecular dynamics code lammps and the related LIGGGHTS descreet element method code are now installed at the CHPC, although only limited support is available for them at this point. Lammps is installed at /opt/gridware/non-supported/lammps, and LIGGGHTS is at /opt/gridware/non-supported/LIGGGHTS .+The LIGGGHTS descreet element method code is installed at the CHPC, although only limited support is available for them at this point. LIGGGHTS version 3.8 is at /apps/chpc/compmech/DEM/LIGGGHTS-3.8, but you can access it by loading the module: 
 +<code>module add chpc/compmech/LIGGGHTS/3.8_gcc830</code> 
 +At present this does not support VTK output, though this will be corrected in the near future. 
 +A module for the older version 3.6 is also available.
  
-In either case, the directory contains a file named lammps_env or liggghts_env. This should be sourced from your submit script before running the executable, for which a symbolic link is provided in the same directory. An example script for lights, parallelized across three nodes (select = 3) with 12 processors per node (ncpus =12:mpiprocs=12) is shown below:+An example script for lights, parallelized across three nodes (select = 3) with 24 processors per node (ncpus =24:mpiprocs=24) is shown below:
  
-  #!/bin/bash  +<file bash liggghts.qsub> 
-  #PBS -l select=3:ncpus=12:mpiprocs=12:mem=4GB:jobtype=dell,place=free:group=nodetype +  #!/bin/bash 
-  #PBS -q workq+  #PBS -P projectid 
 +  #PBS -l select=3:ncpus=24:mpiprocs=24:mem=12GB:nodetype=haswell_reg 
 +  #PBS -q normal
   #PBS -l walltime=01:00:00   #PBS -l walltime=01:00:00
-  #PBS -o /export/home/username/scratch5/liggghtsJobs/job01/stdout +  #PBS -o /mnt/lustre3p/users/username/liggghtsJobs/job01/stdout 
-  #PBS -e /export/home/username/scratch5/liggghts>Jobs/job01/stderr+  #PBS -e /mnt/lustre3p/users/username/liggghtsJobs/job01/stderr
   #PBS -m abe   #PBS -m abe
   #PBS -M username@email.co.za   #PBS -M username@email.co.za
-  ### Source the LIGGGHTS environment: +  ### load the LIGGGHTS module 
-  . /opt/gridware/non-supported/LIGGGHTS/liggghts_env+  module add chpc/compmech/LIGGGHTS/3.8_gcc830
   ##### Running commands   ##### Running commands
   # The -d option used with moab no longer works.  Set this environment variable explicitly.   # The -d option used with moab no longer works.  Set this environment variable explicitly.
-  export PBS_JOBDIR=/export/home/username/scratch5/liggghtsJobs/job01+  export PBS_JOBDIR=/mnt/lustre3p/users/username/liggghtsJobs/job01
   # Explicitly change to the job directory   # Explicitly change to the job directory
   cd $PBS_JOBDIR   cd $PBS_JOBDIR
   nproc=`cat $PBS_NODEFILE | wc -l`   nproc=`cat $PBS_NODEFILE | wc -l`
-  mpirun -np $nproc liggghts < in.lj +  mpirun -np $nproc liggghts < in.lj > ligghtsrun.out 
 +  </file>
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