What should I know when requesting GPU resources on the Lilac Cluster

This page documents the various GPU settings and modes for the Lilac cluster in more detail than the Lilac Cluster Intro page provides. This page looks specifically at the new GTX 1080 GPUs, although many of the options apply to other Nvidia GPUs as well. Where applicable, this primer will talk about how these properties interact with the Lilac Cluster

Topics Covered in this Primer

  1. Looking at the status of the GPUs on a node though nvidia-smi

    1. The difference between process exclusive and shared mode on nVidia GPUs (Compute Modes)

    2. Important terminology notes

  2. Identifying and running on specific GPUs by the CUDA_VISIBLE_DEVICES environment variable
    1. How processes are distributed when CUDA_VISIBLE_DEVICES is set
  3. Running multiple processes on the same GPU through the CUDA Multi-Process Service (MPS) 
    1. Changes MPS makes to GPU identification and control

    2. Limitations of the MPS feature

Looking at the status of the GPUs on a node through nvidia-smi

nVidia provides a tool to view the status of GPUs, such as their current memory load, temperature, and operating mode. The command to see this info is nvidia-smi, but this can only be run on nodes which have GPUs, so this command fails on the head nodes. Here is a sample output from a Lilac node with 4 GPUs on it.

| NVIDIA-SMI 367.48                 Driver Version: 367.48                    |
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|   0  GeForce GTX 1080    Off  | 0000:02:00.0     Off |                  N/A |
|  0%   39C    P8     6W / 180W |      2MiB /  8113MiB |      0%   E. Process |
|   1  GeForce GTX 1080    Off  | 0000:03:00.0     Off |                  N/A |
|  0%   41C    P8    11W / 180W |      2MiB /  8113MiB |      0%   E. Process |
|   2  GeForce GTX 1080    Off  | 0000:83:00.0     Off |                  N/A |
|  0%   36C    P8     9W / 180W |      2MiB /  8113MiB |      0%   E. Process |
|   3  GeForce GTX 1080    Off  | 0000:84:00.0     Off |                  N/A |
|  0%   35C    P8    11W / 180W |      2MiB /  8113MiB |      0%   E. Process |
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|  No running processes found                                                 |

The entries at the top match with the entries per GPU by position, e.g. the Bus-Id entry in the top center cell matches to the 0000:02:00.0 in the second row, center cell. There are many things to digest here, but let's only cover the items that will most likely be important to your jobs.

| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|   0  GeForce GTX 1080    Off  | 0000:02:00.0     Off |                  N/A |
|  0%   39C    P8     6W / 180W |      2MiB /  8113MiB |      0%   E. Process |

These individual items of note will use the above, shortened example.

  • GPU: The index of the GPU available to your processes. Indexing always starts from 0, but your job may not have GPU 0 assigned to it, so your indices may be different.
    • This example: GPU = 0
    • Important: The GPU is not always mapped to the physical hardware slots
      • There are ways to re-order the GPUs, or even mask some GPUs from showing up to a given job. 
      • Lilac jobs are given GPUs and typically indexed starting at 0, even if your job is running on GPUs in different physical slots on the hardware.
      • This number cannot change during a job, so you don't have to worry about your GPUs being re-assigned or shuffled while a job is running.
  • Name: The human-readable name of the GPU, quite often this is simply the model name, truncated to fit.
    • This example: Name = GeForce GTX 1080
  • Memory-Usage: How much memory is being consumed, and how much memory is available on this GPU. As you run jobs on the GPU, this memory is consumed. This is NOT the same as the RAM you request as part of your job, this is on GPU memory and is constant per GPU.
    • This example: Memory-Usage = 2MiB / 8113MiB
    • Fun Trivia: MiB is "mebibyte", which is a base 2 unit of memory instead of the base 10 that megabyte are in. These are often used interchangeably, even though in reality they are not equal, just close. 1 MB = 1000 kB, 1MiB = 1024 kB.
  • Compute M.: "Compute Mode" of the GPU, how the GPU handles process and thread execution on it. Valid options for the GTX 1080s: E. Process and Default which correspond to exclusive process and shared mode as referenced in the Intro to Lilac documentation.
    • This example: Compute M. = E. Process
    • The Lilac cluster's mode is natively E. Process or "exclusive process"
    • Some nVidia GPUs support a thread exclusive mode, but the GTX 1080s do not, so no further discussion of it will be held here. 

The bottom table labeled "Processes" is the list of processes running on the GPUs listed in the top table. The entries in the box are self explanitory and there will be an entry for every process running. Here is a simple example where a python process is running on 1 GPU

| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|    0      3505    C   python                                         115MiB |

Here you can see the process is "python", the process ID you would see in top is 3505, it is running on the GPU with index 0, and it is using 115 MiB of that GPUs on board memory. The type field will either be "C" for compute (what most of your processes will be), "G" for graphics (if the GPU is doing rendering like being connected to a monitor), or "C+G" if its doing both.

Important Terminology Notes

  • Because of the possible confusion involving the word "Default" as it relates to the Compute Mode of the GPUs, the Compute M. = Default case will be referred to as shared mode through this document. 
  • Shared in this document refers only to the computation mode of the GPU in that multiple Contexts can share this GPU. Shared does not mean that a GPU is shared between different jobs submitted to the LSF queue.
  • Exclusive process will be shortened to exclusive since there are not multiple modes of exclusivity on the GTX 1080s.
  • Exclusive in this document will only refer to the compute mode of the GPU.

Identifying and running on specific GPUs by the CUDA_VISIBLE_DEVICES environment variable

Each physical machine has some number of physical GPUs associated with it. When you start a process on a GPU, which physical GPU it start on depends on a few factors:

  1. If the GPUs are in shared or exclusive mode
  2. The value of the CUDA_VISIBLE_DEVICES environment variable.

CUDA_VISIBLE_DEVICES serves as the identifier as to which GPU slots are available for processes to start on. Lilac LSF jobs automatically assign you the CUDA_VISIBLE_DEVICES environment variable per node matching to the GPUs that are available to you job. For instance, you request 2 GPUs per node on 2 nodes, you are given the GPUs in slots 0 and 1 on NodeA, and the GPUs in slots 1 and 2 on NodeB. Your CUDA_VISIBLE_DEVICES variables will look like this:


These indexes match up with the GPU entry from the nvidia-smi output above. When your job starts, these are assigned to you, however, you can change them to control exactly what device your process starts on. If you tell your job to sign into NodeA and then export CUDA_VISIBLE_DEVICES=0, any process which uses the GPU can then only execute on the GPU in slot 0. You can only set this to devices assigned to your job, if you attempt to set this to GPUs not assigned to you, then your processes will not start.

Lilac is configured to only give you access to the devices you request, and renumbers the GPUs starting at 0. So if you request 2 GPUs and you get the GPUs in physical slots 1 and 3, you will only see 2 GPUs though nvidia-smi and they will be given the indices 0 and 1. 

Unsetting CUDA_VISIBLE_DEVICES is the same as setting it to the list of indices for all available GPUs. E.g. if you have 3 GPUs assigned to you in slots 0, 1 and 2; then unsetting CUDA_VISIBLE_DEVICES is the same as setting CUDA_VISIBLE_DEVICES=0,1,2

How processes are distributed when CUDA_VISIBLE_DEVICES is set

This section covers the behavior of how processes are distributed to GPUs with the CUDA_VISIBLE_DEVICES flag. Remember that the behavior for an unset CUDA_VISIBLE_DEVICES is also defined. Although Lilac jobs are started in exclusive mode, its important to cover the shared mode behavior because of the Multi-Process Service (MPS) covered in the next section.

  • exclusive mode:
    • CUDA_VISIBLE_DEVICES is checked
    • for each device in CUDA_VISIBLE_DEVICES
      • If no process on device, start process
      • Loop until process has started
    • If process has not started and all devices have been looped through
      • Fail state, "No Available Devices"
  • shared mode
    • CUDA_VISIBLE_DEVICES is checked
    • Pick the first device in CUDA_VISIBLE_DEVICES
      • Start process on device
    • If out of memory
      • Fail

As you can see, the behavior of shared mode requires some management of CUDA_VISIBLE_DEVICES otherwise only one GPU will be used.

Running multiple processes on the same GPU through the CUDA Multi-Process Service (MPS) 

It is possible to run multiple GPU Contexts (rough equivalent to a CPU process on the GPU) on a single device, even if the device is in exclusive mode through the CUDA Multi-Process Service (MPS). In short, this feature allows you to emulate shared mode on the GPU by running a single MPS daemon on the GPU which processes your job's processes to run them on the GPU together.

You can enable this feature with your Lilac jobs by adding the following flag to your bsub submission, or as a #BSUB directive in your job script:

-gpu "num=1:mode=exclusive_process:mps=yes:j_exclusive=yes"

This sets the environment variable that tells LSF to start the CUDA MPS daemon on the nodes and GPUs assigned to your job.

When you start processes with MPS, you will no longer see your own processes in the process list from nvidia-smi, instead, you will see that each GPU will have a single process called nvidia-cuda-mps-server, independent of how many processes that are running on that GPU.

Important: MPS does alter the behavior of CUDA_VISIBLE_DEVICES, your GPU indices, and has a few limitations as to what can be run on it.

Changes MPS makes to GPU identification and control

MPS does causes two major changes to your GPUs you should be aware of

  1. Devices are re-indexed starting from 0, no mater what index they were before

Since GPUs are re-indexed, your CUDA_VISIBLE_DEVICES variables should start at 0, however, your job will need to figure out how many GPUs per node you have either from the job environment variables, or hard coded in your script since you cannot determine how many GPUs you have from the CUDA_VISIBLE_DEVICES variable. One option is to look at the LSB_HOSTS variable once your job has started which is a space separated list of the hosts your job is running on, where each host is repeated for each task on that host. E.g. If you have 3 processes on host "ls02" and 2 processes on "ls05" with equal GPUs on each one, your LSB_HOSTS would look like 

LSB_HOSTS="ls02 ls02 ls02 ls05 ls05"

where you can then infer the what CUDA_VISIBLE_DEVICES per host should be by counting up from 0 on each host, so

  • ls02: CUDA_VISIBLE_DEVICES=0,1,2

Limitations of the MPS feature

Although MPS allows multiple processes to run on an exclusive GPU, there are a few limitations to this service.

  1. A maximum of 16 Contexts per GPU are supported
  2. You cannot run OpenCL Contexts on the GPU, only CUDA Contexts
  3. There is a small GPU memory overhead to running the MPS server on each GPU
    • This appears to be about 50-100 MiB per GPU total
    • This memory cost is per GPU, not per process
  4. Running MPS on shared GPUs is pointless

These will probably not affect most jobs and users, but please contact the HPC team if you feel these limitations will affect your work. Remember that MPS is optional and is off by default.

Lastly, if you find yourself running jobs on shared mode GPUs, do not run MPS. You can technically run MPS on shared mode GPUs, but there is no gain from this since you can already run multiple processes per GPU, but you do lose some memory on the GPU, there is a small computational overhead to running the MPS service, and you limit the number and type of Contexts you can start, so there really is no point in doing so.