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Installing and Testing FabSim

Dependencies

FabSim requires the following Python modules:

  • PyYaml
  • Fabric (version 1.5.3 and 1.10.0 have worked OK for us)

You can install them any way you like. Most people prefer pip, although you could also choose to use easy_install.

Installation

  1. Clone the code from the GitHub repository.
  2. The 'fab' command, which comes with Fabric, needs to be usable directly from the command line. You can make it usable by ensuring that the command resides in your $PATH environment.
  3. Copy machines_user_example.yml in the deploy/ subdirectory to machines_user.yml. Modify its contents so that it matches with your local settings. For first (local) testing, one must change the settings under the sections default: and localhost: so as to update the paths of FabSim directory and lammps executable respectively.

Testing FabSim

LAMMPS testing on the local host

  1. Install LAMMPS (see http://lammps.sandia.gov for detailed download and installation instructions).
  2. Modify machines_user.yml to make the lammps_exec variable point to the location of the LAMMPS executable. e.g., lammps_exec: "/home/james/bin/lmp_serial".
  3. FabSim contains a trial LAMMPS configuration, so there's no need to download that.
  4. (first time use only) Create the required FabSim directory using the following command: fab localhost setup_fabric_dirs.
  5. Run the LAMMPS test data set using: fab localhost lammps:lammps_lj_liquid,cores=1,wall_time=1:00:0.
  6. You can find the output of your job in the results directory. By default this will be a subdirectory in ~/FabSim/results.

FabBioMD testing on the local or remote host

  1. Install NAMD (required just for local host).
  2. Modify machines_user.yml to make the namd_exec variable point to the location of the NAMD executable. e.g., namd_exec: "/home/james/bin/namd/2.9" (This needs to be done individually for all local or remote hosts).
  3. FabSim contains a trial NAMD configuration, so there's no need to download that.
  4. Run the NAMD test data set using: fab machine_name namd:namd_toy_model,cores=x,wall_time=y, where you can choose the values of x and y depending on your machine.
  5. You can find the output of your job in the results directory. By default this will be a subdirectory in ~/FabSim/results.

Creating the relevant FabSim directories on a local or remote host

  1. Ensure that you have modified machines_user.yml to contain correct information for your target machine.