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Cycler to submit jobs iteratively on BlueHive (with OpenMM templates).
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README.md
cycle
cycler.sh
npt.py

README.md

bhcycler

Cycler to submit jobs iteratively on BlueHive (with OpenMM templates).

The cycler consists of 2 bash scripts (cycle and cycler.sh) + a python template file (PREFIX.py) that work together to run an iteration or cycle of a simulation. Below is a quick description of each of these files:

  1. cycle: the "laucher", this is where all the SLURM-related options are defined (partition, number of nodes, time allocation,...). This script also calls the driver (see below) to submit the job for the current iteration. For this reason, it is important to make sure that the variable 'DRIVER' is pointing to where the driver file (cycler.sh) actually is.

  2. cycler.sh: the "driver", this script 1) checks that the previous iteration was completed correctly, 2) starts the current work (runs the template script, see below) and 3) submits a dependent job for the next iteration that will start once the current job is completed.

  3. PREFIX.py: the "template", this is where all the OpenMM-related options are defined. I've included a sample template, so in this case PREFIX = npt, but it can be anything, really, and the template file can be modified as needed, depending on the system that needs to be run. The important thing to note is that the PREFIX of the job and the current iteration number are taken from the command line.

a) How to submit jobs

Using the cycler is rather simple. If the three files described above are in the same directory (along with the input files that are required for the simulation, e.g. PSF, parameters,...), then just type:

 ./cycle PREFIX-#iteration

where PREFIX needs to be replaced by the name of the template script and #iteration by the current iteration number. For example,

 ./cycle npt-10

will run the 10th iteration of the simulation indicated by npt.py.

Whenever you start the cycler, two jobs will appear in the queue. The one that says '(Dependency)' in the NODELIST column will start the next iteration once the current job is done. The other job corresponds to the current iteration.

Note that the cycler does not really handle a "0th" iteration, since the energy minimization/equilibration phases of a simulation can be carried out in many different ways and it would be hard to accomodate all. Instead, the cycler is intended for systems that already have at least a little bit of production and it requires you to already have a restart or a checkpoint file from where to continue the simulation (see below). These files should be named PREFIX_previous.xml or PREFIX_previous.chk, where previous corresponds to the iteration number previous to the one you want to run. For example, if you want to start the cycler in the 2nd iteration using the npt.py template, then npt_1.xml or npt_1.chk should already exist. Then, you can run the cycler as,

 ./cycle npt-2

If multiple simulations need be run using the same cyler, it might be useful to alias it in your ~/.bash profile. To do so, just open ~/.bash_profile in a text editor and add the following line,

 alias cycle='/path-to-cycle/cycle'

Then, the shell will be able to find the cycler even if it's not present in the working directory of the simulation. In that case, the cycler can be run like this,

 cycle PREFIX-#iteration

Do not forget to change the path to the driver accordingly in the script of the laucher.

b) How to stop jobs

If you need to stop a job the first thing you need to do is to cd into the directory of the corresponding simulation (where you first lauched the job).

Then, type in the terminal,

 echo "halt" > halt

this command will create a text file called 'halt'. In the next iteration, the cycler will identify this file when checking for errors in the previous iteration and the presence of this file will prevent a new iteration from being launched.

After doing this, go ahead and cancel the jobs that need to be cancelled like you normally would,

 scancel jobid

c) XML files vs. checkpoint files

Right now, the cycler can use checkpoint files or XML files to restart the simulations. To use one or the other just comment or comment out lines 72 and 73 of npt.py as needed.

Note that, even if it might seem easier, using checkpoint files might not always be the best choice because they are not platform independent. This means that if you first run a simulation in the CUDA platform (with GPUs) and then try to restart it in a different platform (e.g. CPU, OpenCL, Reference), you will get an error and your simulation will probably not run. This might also happen if you try using a different computer architecture or even a different version of OpenMM.

So, I think that the wiser choice is to use XML files whenever possible, since they are way more portable. The only problem I see with using XML files is that there is not a built-in reporter for them in OpenMM. This means that there is not a direct way (that I know) to generate an XML file every n simulation steps. Alan came up with a way to go around this issue and I have implemented it and tested it in the cycler, so it should be functional now. Just make sure to set the variable nsteps as a multiple of report_interval in PREFIX.py.

Based on these limitations, I am choosing to leave both as an option for now: As long as the simulation is run with the same version of OpenMM and in the same architecture, the checkpoint files should work just fine. However, it is still preferable to have platform independent restart files, just in case they are needed in the future. So, the lines for checkpoint files are commented out.

d) Final thoughts

Please note that this cycler is quite simple and that, even if I tested it, there might be some behavior(s) that I didn't accont for. So, I would recommend to keep checking on the simulations, especially at the beginning, to make sure that the cycler is stable.

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