Run a fixed MESA grid
Default evolutionary parameters
POSYDON makes it easy to run a fixed grid of binaries with MESA within a high performance computing environment. Note that these instructions assume you are using slurm as your job scheduler. We just need to start by setting a few environmental variables. We recommend you add these to your .bashrc or .bash_profile so they are included at login. The filepaths of these need to be edited for your own installation.
export MESA_DIR="/projects/b1119/mesa_sdk/mesa-r11701" export MESASDK_ROOT="/projects/b1119/mesa_sdk/mesasdk" source $MESASDK_ROOT/bin/mesasdk_init.sh
Next, you will want to create a working directory for your grid of binaries. For this example, we will create a working directory called example_grid:
mkdir example_grid cd example_grid
This directory will contain all the binary runs and associated data generated by the individual MESA runs as well as the functionality for slurm to run the grid.
Now that we have our grid, we need to create two separate files: a file containing the list of binaries we want to evolve and an .ini file that contains all the parameters associated with running the grid. Let’s start with the list of binaries we want to evolve. For the case of this example, let’s evolve a series of high-mass X-ray binaries with neutron star accretors at a series of initial binary periods. We’ll use our favorite text editor to add the following lines into a file we’ll call grid.csv. As we’ll see below, it can be given any name, but the entries must be separated by commas.
m1,m2,initial_period_in_days 10,1.4,1 10,1.4,10 10,1.4,100 10,1.4,1000
POSYDON internally allows any variable to be included here, so long as it has the same name as a variable in MESA. However, these three parameters ought to always be specified, otherwise you will be evolving a binary with a default orbital period and masses.
As for the .ini file, you can copy over the example from the .ini file documentation for POSYDON GRIDS page, which provides a more detailed description of all the entries. Make sure to carefully go through each of the separate entries and adjust them for your particular needs. Place that .ini file (which we have named example_grid.ini) in our example_grid directory.
Now, with our grid.csv and example_grid.ini files ready to go, we use a POSYDON script posydon-setup-grid to generate all the necessary files to run the grid using slurm. Note the different arguments here. We are designating that: 1) we are using a fixed grid, 2) the name of the .ini file, and 3) that our job scheduler is slurm. We may expand compatibility for other job schedulers in the future, but for now slurm is the only implemented option.
posydon-setup-grid --grid-type fixed --inifile example_grid.ini --submission-type slurm
This will take a minute to run. You will note that it includes a pull from the POSYDON GitHub repository to ensure the correct, designated version of the MESA inlists are being used. It is possible that you will need to enter your GitHub username and password during this step. Additionally, note that this step takes some time to run, as several MESA files are being compiled.
Once finished, you will note that in our example_grid directory, we now have several new files and new directories. One advantage of this implementation is that all the binaries we run use a single version of the MESA executables, rather than each binary having its own copy of the same files.
Finally, we are ready to submit our jobs with:
Once the grid of runs is completed, we recommend you use our provided PSyGrid functionality to interpret and collate the individual binary runs (link for documentation: The PSyGrid Object.)
Non-default evolutionary parameters
If you want to change the binary evolution parameters so you are using non-default options, we have constructed a hierarchy of MESA inlists. You can provide a non-default option in your own user-provided MESA inlist, which is explicitly linked in the inifile (make sure you uncomment the appropriate lines). We additionally provide the capability to use your own run_star_extras.f and run_binary_extras.f as well as provide your own list of history and profile columns. See .ini file documentation for POSYDON GRIDS for details.