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HPC Coursework

Base coursework for the Advanced High Performance Computing class.

  • Source code is in the d2q9-bgk.c file
  • Results checking scripts are in the check/ directory

Compiling and running

To compile type make. Editing the values for CC and CFLAGS in the Makefile can be used to enable different compiler options or use a different compiler. These can also be passed on the command line:

$ make CFLAGS="-O3 -fopenmp -DDEBUG"

Input parameter and obstacle files are all specified on the command line of the d2q9-bgk executable.

Usage:

$ ./d2q9-bgk <paramfile> <obstaclefile>

eg:

$ ./d2q9-bgk input_256x256.params obstacles_256x256.dat

Checking results

An automated result checking function is provided that requires you to load a particular Python module (module load languages/anaconda2/5.0.1). Running make check will check the output file (average velocities and final state) against some reference results. By default, it should look something like this:

$ make check
python check/check.py --ref-av-vels-file=check/128x128.av_vels.dat --ref-final-state-file=check/128x128.final_state.dat --av-vels-file=./av_vels.dat --final-state-file=./final_state.dat
Total difference in av_vels : 5.270812566515E-11
Biggest difference (at step 1219) : 1.000241556248E-14
  1.595203170657E-02 vs. 1.595203170658E-02 = 6.3e-11%

Total difference in final_state : 5.962977334129E-11
Biggest difference (at coord (6,2)) : 1.000588500943E-14
  3.329122639178E-02 vs. 3.329122639179E-02 = 3e-11%

Both tests passed!

This script takes both the reference results and the results to check (both average velocities and final state). This is also specified in the makefile and can be changed like the other options:

$ make check REF_AV_VELS_FILE=check/128x256.av_vels.dat REF_FINAL_STATE_FILE=check/128x256.final_state.dat
python check/check.py --ref-av-vels-file=check/128x256.av_vels.dat --ref-final-state-file=check/128x256.final_state.dat --av-vels-file=./av_vels.dat --final-state-file=./final_state.dat
...

All the options for this script can be examined by passing the --help flag to it.

$ python check/check.py --help
usage: check.py [-h] [--tolerance TOLERANCE] --ref-av-vels-file
                REF_AV_VELS_FILE --ref-final-state-file REF_FINAL_STATE_FILE
...

Running on BlueCrystal Phase 4

When you wish to submit a job to the queuing system on BlueCrystal, you should use the job submission script provided.

$ sbatch job_submit_d2q9-bgk

This will dispatch a job to the queue, which you can monitor using the squeue command:

$ squeue -u $USER

When finished, the output from your job will be in a file called d2q9-bgk.out:

$ less d2q9-bgk.out

If you wish to run a different set of input parameters, you should modify job_submit_d2q9-bgk to update the value assigned to options.

Checking submission content

Before handing in the coursework, you can use the check_submission.sh script to make sure that your code builds in a clean environment. This will reduce the chances of the automarker failing to build or run your code.

To use the script, simply run it from the directory containing the files you intend to submit:

$ /path/to/check_submission.sh

The script will:

  1. Unload all the modules currently loaded.
  2. Load your modules and environment variables specified in env.sh.
  3. Use make to build your code and verify that an executable with the expected name is produced.

If the submission checking script prints any errors, you should try to address those before you hand in.

Note that check_submission.sh does not run your code, and so you cannot verify that the results produced by your application validate just by running this script. You should check the correctness of your results separately, e.g. using make check.

Serial output for sample inputs

Run times were taken on a Phase 4 node using the base (gcc) compiler and base compiler flags as found in the Makefile:

  • 128x128
./d2q9-bgk  input_128x128.params obstacles_128x128.dat
==done==
Reynolds number:                9.751927375793E+00
Elapsed Init time:                      0.008549 (s)
Elapsed Compute time:                   32.706913 (s)
Elapsed Collate time:                   0.000000 (s)
Elapsed Total time:                     32.715462 (s)
  • 128x256
==done==
Reynolds number:                3.715003967285E+01
Elapsed Init time:                      0.026452 (s)
Elapsed Compute time:                   65.973017 (s)
Elapsed Collate time:                   0.000000 (s)
Elapsed Total time:                     65.999469 (s)
  • 256x256
./d2q9-bgk  input_256x256.params obstacles_256x256.dat
==done==
Reynolds number:                1.005141162872E+01
Elapsed Init time:                      0.018062 (s)
Elapsed Compute time:                   263.480558 (s)
Elapsed Collate time:                   0.000000 (s)
Elapsed Total time:                     263.498620 (s)
  • 1024x1024
./d2q9-bgk  input_1024x1024.params obstacles_1024x1024.dat
==done==
Reynolds number:                3.375851392746E+00
Elapsed Init time:                      0.013054 (s)
Elapsed Compute time:                   1097.257147 (s)
Elapsed Collate time:                   0.000000 (s)
Elapsed Total time:                     1097.270201 (s)

Visualisation

You can view the final state of the simulation by creating a .png image file using a provided Gnuplot script:

$ gnuplot final_state.plt