Running FIDASIM

Running FIDASIM

Running FIDASIM is as easy as running

lstagner@computer:~/FIDASIM$ ./fidasim
   ____ ____ ___   ___    ____ ____ __  ___
  / __//  _// _ \ / _ |  / __//  _//  |/  /
 / _/ _/ / / // // __ | _\ \ _/ / / /|_/ /
/_/  /___//____//_/ |_|/___//___//_/  /_/

Version: 3.0.0-dev

FIDASIM is released as open source code under the MIT Licence.
For more information visit http://d3denergetic.github.io/FIDASIM/

Actually having FIDASIM produce something takes a bit of thought

Recommended Hardware for OpenMP Parallelized FIDASIM

The following settings will give a reasonable runtime.

32 threads on a shared memory node (All calculations are done on a single node)
At least 2 GB of memory (amount of memory varies depending on user settings and inputs)

Warning

By default FIDASIM will use all the threads available. If another process is hogging a core it will cause FIDASIM to stall. To prevent this use the num_threads optional argument

Recommended Hardware for MPI Parallelized FIDASIM

The following settings will give a reasonable runtime.

32 processes
At least 2 GB of memory per process (amount of memory varies depending on user settings and inputs)

Running Interactively

For OpenMP parallelized FIDASIM run with 16 threads run

[lstagner@dawson061]% ./fidasim /p/fida/lstagner/TEST/test_inputs.dat 16

For MPI parallelized FIDASIM run with 16 processes run

[lstagner@dawson061]% mpirun -np 16 ./fidasim /p/fida/lstagner/TEST/test_inputs.dat

Submitting to a cluster job schedular

The recommended way of running FIDASIM is through a job schedular such as Slurm or PBS.

FIDASIM provides submit_fidasim: a python script that schedules a FIDASIM job on a cluster. For example

lstagner@computer:~$ submit_fidasim /u/lstagner/TEST

will submit any incomplete FIDASIM runs in the /u/lstagner/TEST directory. Alternatively

lstagner@computer:~$ submit_fidasim /u/lstagner/TEST/test_inputs.dat

will submit just the test FIDASIM run. Slurm and PBS resource managers are supported. submit_fidasim works for both OpenMP and MPI. Run submit_fidasim -h for the full documentation.

User Guide