The official repo for all files on the first semester project.

HPC Access

Connect to vpn.ruc.dk, then ssh into one of the following targets:

• dirac - main entry point:
  ssh <username>@dirac.ruc.dk
• i42 & i43 - internet access for file sync (repo cloning, rsync):
  ssh -J <username>@dirac.ruc.dk <username>@<i42/i43>
• bead50 - RTX 2080 Ti:
  ssh -J <username>@dirac.ruc.dk <username>@bead50
• bead67 - RTX 4090:
  ssh -J <username>@dirac.ruc.dk <username>@bead67

Alternatively, add this snippet to your ssh config:

Host dirac
    HostName dirac.ruc.dk
    User <username>

Host i42 i43 bead50 bead67
    User <username>
    ProxyJump dirac

and run ssh <target-hostname>.

Collecting Data

Set up preferred system sizes in main.py.

While on bead67, run main.py to start the benchmark and save the measurements to csv:

# Example: run gamdpy with autotuned compute plans and save data with the prefix "default"
python3 main.py -p default gamdpy -a

You can use the following arguments:

usage: main.py [-h] [-p [PREFIX]] [-d] {gamdpy,lammps} ...

positional arguments:
  {gamdpy,lammps}       backend

options:
  -h, --help            show this help message and exit
  -p, --prefix [PREFIX]
                        identifying prefix for this run (can overwrite data if not unique)
  -d, --debug           run benchmark with small system sizes (~30-60 seconds per run)

# for gamdpy
usage: main.py gamdpy [-h] [-a]

options:
  -h, --help      show this help message and exit
  -a, --autotune  use autotuned compute plans

# for lammps
usage: main.py lammps [-h] [-g]

options:
  -h, --help  show this help message and exit
  -g, --gpu   enable GPU-acceleration

Alternatively, edit and run ./batch_run.sh for multiple runs back-to-back.

Data is written to disk after each measurement, so you can check the progress with tail -f data/<filename>.csv.

Send/Retrieve Data

Use rsync from your local machine to copy files to/from the server:

rsync <source-path> <destination-path>

where a remote path follows the syntax: <username>@dirac.ruc.dk:/absolute/path, or if you've set up your ssh config: dirac:/absolute/path.