longbow-examples contains a set of Molecular Dynamics input files that you can use to learn how to use Longbow.
In the section below there is a list of the commands that will show you how to submit the Longbow examples as jobs on an external resource (HPC) using these files.
Prior to attempting the examples you should firstly ensure that you have an active account on a HPC machine and that the MD package of interest is installed, then follow the documentation for adding your first HPC machine account to Longbow at the following link
https://www.hecbiosim.ac.uk/longbow-docs?showall=&start=2#2.1
Note - We ensure that these examples work on the UK national supercomputer ARCHER, whilst there is no reason to suspect that they will not work elsewhere, there is a chance that software has been installed with different executable names or in other non-default ways. In these cases you might need to slightly modify the procedures described below. We are happy to provide support if required.
The following instructions will assume you have downloaded and extracted the examples and changed into the 'longbow-examples' directory path.
In the 'quick_start' directory, you can choose examples for your favourite Molecular Dynamics package and learn how to submit a simple longbow job from your local machine.
Change into 'longbow-examples/quick_start/amber' and run:
longbow --verbose pmemd.MPI -O -i example.in -c example.min -p example.top -o example.out
Change into 'longbow-examples/quick_start/charmm' and run:
longbow --verbose charmm -i example.inp ">" example.out
Change into 'longbow-examples/quick_start/gromacs' and run:
longbow --verbose gmx mdrun -s example.tpr -deffnm output
Change into 'longbow-examples/quick_start/lammps' and run:
longbow --verbose lmp_xc30 -i example.in -l output
Change into 'longbow-examples/quick_start/namd' and run:
longbow --verbose namd2 example.in ">" example.out
or for SMP builds (NAMD v2.12+)*:
longbow --verbose namd2 +ppn 23 +pemap 1-23 +commap 0 example.in ">" example.out
*The parameters "cores" and "corespernode" must be set to "1" in your hosts.conf
In this directory, you will learn how to submit a replicate job. These are useful for submitting ensembles of jobs where the command-line is identical but a number of different runs or slightly different input files are used.
Change into 'longbow-examples/replicate_job' and run:
longbow --verbose --replicates 5 namd2 example.in
or for SMP builds (NAMD v2.12+)*:
longbow --verbose --replicates 5 namd2 +ppn 23 +pemap 1-23 +commap 0 example.in ">" example.out
*The parameters "cores" and "corespernode" must be set to "1" in your hosts.conf
Multi-jobs are the most flexible type of job Longbow offers, they are basically a fully customisable ensemble of jobs. The following examples show the flexibility and power of using this type of job. These jobs use a job configuration file to gain control over each jobs parameters separately.
In the 'multiple-jobs/different_applications' directory, you can learn how to submit multiple jobs that each use a different molecular dynamics package.
Change into 'longbow-examples/multiple-jobs/different_applications' and run:
longbow --job job.conf --verbose
Have a bunch of simulations where some are replicates and some are simple single use jobs? Then you can mix these too.
In the 'multiple-jobs/different_job_types' directory, you can learn how to submit multiple jobs that are different types.
Change into 'longbow-examples/multiple-jobs/different_job_types' and run:
longbow --job job.conf --verbose
That's it for our quick start guide, check out the documentation for more in-depth information on what is configurable. You can build on the basic concepts in these examples to create large-scale, multi-machine, large-volume jobs where you no longer have to worry about job scripts and moving around files.