Running NAMD Training

Submitting a NAMD Training Job

Example 1. Explicit resources
$ ssh bhn20 (1)
$ runai-bgu submit namd \ (2)
  -n conv-2-64 \ (3)
  -c 2 \ (4)
  -m 4Gi \ (5)
  -g 1 \ (6)
  -- "namd3 file.namd +p <num-cores> +devices <gpu-array>" (7)
1 Configure SSH connection to bhn20
2 Specifies it is a NAMD.
3 Specifies the name of the job.
4 Allocates 2 CPU cores.
5 Allocates 4GiB of memory*.
6 Specifies the GPU allocation(Whole or fractions). If you do not need GPU, do not use this flag.
7 The command to run, here namd3.
The space ( ) between the two dashes (--) and the command is intentional. As are the quotes (") surrounding the command.
When running the command you can change directory to the location of your namd file (cd ~/path/to/file && file.namd +p1 +devices 0 +setcpuaffinity), or give the full path (namd3 ~/path/to/file/file.namd +p1 +devices 0 +setcpuaffinity ). +p should match requested CPU cores, and +devices should be a an array that starts with 0.

You can also use a predefined resource template. Check out the guide for the template CLI Introduction.

Example 2. Using User Templates:
$ runai-bgu submit namd \ (1)
  -n conv-2-64 (2)
  --ut train-over-quota-user (3)
  -- "namd3 file.namd +p <num-cores> +devices <gpu-array>" (4)
1 Submit a namd workload
2 Specify the job name
3 Use the --ut specify the user template
4 The command to run, here namd3.
The space ( ) between the two dashes (--) and the command is intentional. As are the quotes (") surrounding the command.
When running the command you can change directory to the location of your namd file (cd ~/path/to/file && file.namd +p1 +devices 0 +setcpuaffinity), or give the full path (namd3 ~/path/to/file/file.namd +p1 +devices 0 +setcpuaffinity ). +p should match requested CPU cores, and +devices should be a an array that starts with 0.
Example 3. Using Group Templates:
$ runai-bgu submit namd \ (1)
  -n conv-2-64 (2)
  --ug train-over-quota-group  (3)
  -- "namd3 file.namd +p <num-cores> +devices <gpu-array>" (4)
1 Submit a namd workload
2 Specify the job name
3 Use the --ug specify the group template
4 The command to run, here namd3 file.namd +p <num-cores> +devices <gpu-array>.
The space ( ) between the two dashes (--) and the command is intentional. As are the quotes (") surrounding the command.
When running the command you can change directory to the location of your namd file (cd ~/path/to/file && file.namd +p1 +devices 0 +setcpuaffinity), or give the full path (namd3 ~/path/to/file/file.namd +p1 +devices 0 +setcpuaffinity ). +p should match requested CPU cores, and +devices should be a an array that starts with 0.

Submitting Job

The CLI will display messages about the job creation and status.

Example 4. Synopsis
Start job for training
$ ssh bhn20 (1)
$ runai-bgu submit namd -n conv-2-64 --ut train-over-quota -- "namd3 file.namd +p <num-cores> +devices <gpu-array>" (2)
Waiting for the job to be created...

Job conv-2-64 submitted successfully.
You can check the status of the job by running:
        runai describe job conv-2-64 -p myproj
1 Configure SSH connection to bhn20 manual.adoc[runai-bgu]