Support for dynamic system topology discovery

[pentschev]

This PR introduces a new topology discovery feature that enables automatic detection of system topology, including GPU-to-NUMA-to-NIC mappings, using NVML to query GPU information and directly queries /sys to build a comprehensive view of the system's PCIe topology.

The core changes include:

• New TopologyDiscovery class with supporting data structures to compose system/GPU/network topology information
• CLI tool to inspect and dump system topology to a JSON file

This tool will later be integrated in the rrun launcher #616 for automatic topology discovery and configuration, it will also allow to read JSON files to override dynamic discovery and instead use the declarative file to set CPU/memory/network affinity.

Sample JSON output for a DGX-1

{
  "system": {
    "hostname": "dgx13",
    "num_gpus": 8,
    "num_numa_nodes": 2,
    "num_network_devices": 4
  },
  "gpus": [
    {
      "id": 0,
      "name": "Tesla V100-SXM2-32GB",
      "pci_bus_id": "00000000:06:00.0",
      "uuid": "GPU-b41abe4a-8553-43be-9d49-f1c4591959fa",
      "numa_node": 0,
      "cpu_affinity": {
        "cpulist": "0-19,40-59",
        "cores": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]
      },
      "memory_binding": [0],
      "network_devices": ["mlx5_0"]
    },
    {
      "id": 1,
      "name": "Tesla V100-SXM2-32GB",
      "pci_bus_id": "00000000:07:00.0",
      "uuid": "GPU-d30af75d-3d17-4155-9659-416789520ca5",
      "numa_node": 0,
      "cpu_affinity": {
        "cpulist": "0-19,40-59",
        "cores": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]
      },
      "memory_binding": [0],
      "network_devices": ["mlx5_0"]
    },
    {
      "id": 2,
      "name": "Tesla V100-SXM2-32GB",
      "pci_bus_id": "00000000:0A:00.0",
      "uuid": "GPU-d417ef25-b26f-4381-84fb-a6725b5b05ad",
      "numa_node": 0,
      "cpu_affinity": {
        "cpulist": "0-19,40-59",
        "cores": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]
      },
      "memory_binding": [0],
      "network_devices": ["mlx5_1"]
    },
    {
      "id": 3,
      "name": "Tesla V100-SXM2-32GB",
      "pci_bus_id": "00000000:0B:00.0",
      "uuid": "GPU-900a54bc-9e88-432e-b70f-42772a5c7f3e",
      "numa_node": 0,
      "cpu_affinity": {
        "cpulist": "0-19,40-59",
        "cores": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]
      },
      "memory_binding": [0],
      "network_devices": ["mlx5_1"]
    },
    {
      "id": 4,
      "name": "Tesla V100-SXM2-32GB",
      "pci_bus_id": "00000000:85:00.0",
      "uuid": "GPU-8cbe65cb-8b1f-4d32-af73-0d6267702fea",
      "numa_node": 1,
      "cpu_affinity": {
        "cpulist": "20-39,60-79",
        "cores": [20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79]
      },
      "memory_binding": [1],
      "network_devices": ["mlx5_2"]
    },
    {
      "id": 5,
      "name": "Tesla V100-SXM2-32GB",
      "pci_bus_id": "00000000:86:00.0",
      "uuid": "GPU-8c39dca7-bd84-46c7-80f5-86ef16e3e163",
      "numa_node": 1,
      "cpu_affinity": {
        "cpulist": "20-39,60-79",
        "cores": [20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79]
      },
      "memory_binding": [1],
      "network_devices": ["mlx5_2"]
    },
    {
      "id": 6,
      "name": "Tesla V100-SXM2-32GB",
      "pci_bus_id": "00000000:89:00.0",
      "uuid": "GPU-ef048cce-30c3-4844-8aec-9863bedbf67c",
      "numa_node": 1,
      "cpu_affinity": {
        "cpulist": "20-39,60-79",
        "cores": [20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79]
      },
      "memory_binding": [1],
      "network_devices": ["mlx5_3"]
    },
    {
      "id": 7,
      "name": "Tesla V100-SXM2-32GB",
      "pci_bus_id": "00000000:8A:00.0",
      "uuid": "GPU-ff15fdcb-3bba-4a21-8e2f-f3ab897e21a0",
      "numa_node": 1,
      "cpu_affinity": {
        "cpulist": "20-39,60-79",
        "cores": [20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79]
      },
      "memory_binding": [1],
      "network_devices": ["mlx5_3"]
    }
  ],
  "network_devices": [
    {
      "name": "mlx5_3",
      "numa_node": 1,
      "pci_bus_id": "0000:8b:00.0"
    },
    {
      "name": "mlx5_1",
      "numa_node": 0,
      "pci_bus_id": "0000:0c:00.0"
    },
    {
      "name": "mlx5_2",
      "numa_node": 1,
      "pci_bus_id": "0000:84:00.0"
    },
    {
      "name": "mlx5_0",
      "numa_node": 0,
      "pci_bus_id": "0000:05:00.0"
    }
  ]
}