Running Gromacs Training

Submitting a Gromacs Training Job

Example 1. Explicit resources
$ ssh bhn20 (1)
$ runai-bgu submit gromacs \ (2)
  -n conv-2-64 \ (3)
  -c 2 \ (4)
  -m 4Gi \ (5)
  -g 1 \ (6)
  -- "gmx-mpi sub-commands and flags" (7)
1 Configure SSH connection to bhn20
2 Specifies it is a Gromacs.
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 gmx-mpi.
The space ( ) between the two dashes (--) and the command is intentional. As are the quotes (") surrounding the command.
You can run Gromacs trainings using the scripts, make sure to specify the correct path to your training file, set it to bash with the shebang command (#!/bin/bash), and chain the gmx commands with `&&` to run them in sequence.

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 gromacs \ (1)
  -n conv-2-64 (2)
  --ut train-over-quota-user (3)
  -- "gmx-mpi sub-commands and flags" (4)
1 Submit a gromacs workload
2 Specify the job name
3 Use the --ut specify the user template
4 The command to run, here gmx-mpi.
The space ( ) between the two dashes (--) and the command is intentional. As are the quotes (") surrounding the command.
You can run Gromacs trainings using the scripts, make sure to specify the correct path to your training file, set it to bash with the shebang command (#!/bin/bash), and chain the gmx commands with `&&` to run them in sequence.
Example 3. Using Group Templates:
$ runai-bgu submit gromacs \ (1)
  -n conv-2-64 (2)
  --ug train-over-quota-group  (3)
  -- "gmx-mpi sub-commands and flags" (4)
1 Submit a gromacs workload
2 Specify the job name
3 Use the --ug specify the group template
4 The command to run, here gmx-mpi sub-commands and flags.
The space ( ) between the two dashes (--) and the command is intentional. As are the quotes (") surrounding the command.
You can run Gromacs trainings using the scripts, make sure to specify the correct path to your training file, set it to bash with the shebang command (#!/bin/bash), and chain the gmx commands with `&&` to run them in sequence.

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 gromacs -n conv-2-64 --ut train-over-quota -- "gmx-mpi sub-commands and flags" (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]