Pawsey's way for requesting resources on GPU nodes (different to standard Slurm)The request of resources for the GPU nodes has changed dramatically. The main reason for this change has to do with Pawsey's efforts to provide a method for optimal binding of the GPUs to the CPU cores in direct physical connection for each task. For this, we decided to completely separate the options used for resource request via salloc or (#SBATCH pragmas) and the options for the use of resources during execution of the code via srun. | Note |
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| title | Request for the amount of "allocation-packs" required for the job |
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| With a new CLI filter that Pawsey staff had put in place for the GPU nodes, the request of resources in GPU nodes should be thought as requesting a number of "allocation-packs". Each "allocation-pack" provides: - 1 whole CPU chiplet (8 CPU cores)
- a bit less of 32 GB memory (29.44 GB of memory, to be exact, allowing some memory for the system to operate the node) = 1/8 of the total available RAM
- 1 GCD directly connected to that chiplet
For that, the request of resources only needs the number of nodes (–-nodes, -N) and the number of allocation-packs per node (--gres=gpu:number). The total of allocation-packs requested results from the multiplication of these two parameters. Note that the standard Slurm meaning of the second parameter IS NOT used at Pawsey. Instead, Pawsey's CLI filter interprets this parameter as: - the number of requested "allocation-packs" per node
Note that the "equivalent" option --gpus-per-node=number (which is also interpreted as the number of "allocation-packs" per node) is not recommended as we have found some bugs with its use. |
Furthermore, in the request of resources, users should not indicate any other Slurm allocation option related to memory or CPU cores. Therefore, users should not use --ntasks, --cpus-per-task, --mem, etc. in the request headers of the script ( #SBATCH directives), or in the request options given to salloc for interactive sessions. If, for some reason, the requirements for a job are indeed determined by the number of CPU cores or the amount of memory, then users should estimate the number of "allocation-packs" that cover their needs. The "allocation-pack" is the minimal unit of resources that can be managed, so that all allocation requests should be indeed multiples of this basic unit. Pawsey also has some site specific recommendations for the use/management of resources with srun command. Users should explicitly provide a list of several parameters for the use of resources by srun. (The list of these parameters is made clear in the examples below.) Users should not assume that srun will inherit any of these parameters from the allocation request. Therefore, the real management of resources at execution time is performed by the command line options provided to srun. Note that, for the case of srun, options do have the standard Slurm meaning.
| Warning |
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| title | --gpu-bind=closest may NOT work for all applications |
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| Within the full explicit srun options for "managing resources", there are some that help to achieve optimal binding of GPUs to their directly connected chiplet on the CPU. There are two methods to achieve this optimal binding of GPUs. So, together with the full explicit srun options, the following two methods can be used: - Include these two Slurm parameters:
--gpus-per-task=<number> together with --gpu-bind=closest - "Manual" optimal binding with the use of "two auxiliary techniques" (explained later in the main document).
The first method is simpler, but may still launch execution errors for some codes. "Manual" binding may be the only useful method for codes relying OpenMP or OpenACC pragma's for moving data from/to host to/from GPU and attempting to use GPU-to-GPU enabled MPI communication. An example of such a code is Slate. |
The following table provides some examples that will serve as a guide for requesting resources in the GPU nodes (those interested in cases where multiple GPUs are accessible by 1 or more tasks, pay attention to cases 4,5 & 7): | Required Resources per Job | New "simplified" way of requesting resources | Total Allocated resources | Charge per hour | The use of full explicit srun options is now required
(only the 1st method for optimal binding is listed here) |
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| 1 CPU task (single CPU thread) controlling 1 GCD (Slurm GPU) | #SBATCH --nodes=1
#SBATCH --gres=gpu:1 | 1 allocation-pack =
1 GPU, 8 CPU cores (1 chiplet), 29.44 GB CPU RAM | 64 SU | *1
export OMP_NUM_THREADS=1
srun -N 1 -n 1 -c 8 --gres=gpu:1 --gpus-per-task=1 --gpu-bind=closest <executable>
| 1 CPU task (with 14 CPU threads each) all threads controlling the same 1 GCD | #SBATCH --nodes=1
#SBATCH --gres=gpu:2
| 2 allocation-packs=
2 GPUs, 16 CPU cores (2 chiplets), 58.88 GB CPU RAM | 128 SU | *2
export OMP_NUM_THREADS=14
srun -N 1 -n 1 -c 16 --gres=gpu:1 --gpus-per-task=1 --gpu-bind=closest <executable>
| | 3 CPU tasks (single thread each), each controlling 1 GCD with GPU-aware MPI communication | #SBATCH --nodes=1
#SBATCH --gres=gpu:3 | 3 allocation-packs=
3 GPUs, 24 CPU cores (3 chiplets), 88.32 GB CPU RAM | 192 SU | *3
export MPICH_GPU_SUPPORT_ENABLED=1
export OMP_NUM_THREADS=1
srun -N 1 -n 3 -c 8 --gres=gpu:3 --gpus-per-task=1 --gpu-bind=closest <executable>
| | 2 CPU tasks (single thread each), each task controlling 2 GCDs with GPU-aware MPI communication | #SBATCH --nodes=1
#SBATCH --gres=gpu:4
| 4 allocation-packs=
4 GPU, 32 CPU cores (4 chiplets), 117.76 GB CPU RAM | 256 SU | *4 export MPICH_GPU_SUPPORT_ENABLED=1
export OMP_NUM_THREADS=1
srun -N 1 -n 2 -c 16 --gres=gpu:4 --gpus-per-task=2 --gpu-bind=closest <executable>
| 5 CPU tasks (single thread each) all threads/tasks able to see all 5 GPUs | #SBATCH --nodes=1
#SBATCH --gres=gpu:5
| 5 allocation-packs=
5 GPUs, 40 CPU cores (5 chiplets), 147.2 GB CPU RAM | 320 SU | *5
export MPICH_GPU_SUPPORT_ENABLED=1
export OMP_NUM_THREADS=1
srun -N 1 -n 5 -c 8 --gres=gpu:5 <executable>
| | 8 CPU tasks (single thread each), each controlling 1 GCD with GPU-aware MPI communication | #SBATCH --nodes=1
#SBATCH --exclusive | 8 allocation-packs=
8 GPU, 64 CPU cores (8 chiplets), 235 GB CPU RAM | 512 SU | *6 export MPICH_GPU_SUPPORT_ENABLED=1
export OMP_NUM_THREADS=1
srun -N 1 -n 8 -c 8 --gres=gpu:8 --gpus-per-task=1 --gpu-bind=closest <executable>
| | 8 CPU tasks (single thread each), each controlling 4 GCD with GPU-aware MPI communication | #SBATCH --nodes=4
#SBATCH --exclusive | 32 allocation-packs=
4 nodes, each with: 8 GPU, 64 CPU cores (8 chiplets), 235 GB CPU RAM | 2048 SU | *7 export MPICH_GPU_SUPPORT_ENABLED=1
export OMP_NUM_THREADS=1
srun -N 4 -n 8 -c 32 --gres=gpu:8 --gpus-per-task=4 --gpu-bind=closest <executable>
| | 1 CPU task (single thread), controlling 1 GCD but avoiding other jobs to run in the same node for ideal performance test. | #SBATCH --nodes=1
#SBATCH --exclusive | 8 allocation-packs=
8 GPU, 64 CPU cores (8 chiplets), 235 GB CPU RAM | 512 SU | *8 export OMP_NUM_THREADS=1
srun -N 1 -n 1 -c 8 --gres=gpu:1 --gpus-per-task=1 --gpu-bind=closest <executable>
| Notes for the request of resources: - Note that this simplified way of resource request is based on requesting a number of "allocation-packs", so that standard use of Slurm parameters for allocation should not be used for GPU resources.
- The
--nodes (-N) option indicates the number of nodes requested to be allocated. - The
--gres=gpu:number option indicates the number of allocation-packs requested to be allocated per node. (The "equivalent" option --gpus-per-node=number is not recommended as we have found some bugs with its use.) - The
--exclusive option requests all the resources from the number of requested nodes. When this option is used, there is no need for the use of --gres=gpu:number during allocation and, indeed, its use is not recommended in this case. - Users should not include any other Slurm allocation option that may indicate some "calculation" of required memory or CPU cores. The management of resources should only be performed after allocation via
srun options. - The same simplified resource request should be used for the request of interactive sessions with
salloc. - IMPORTANT: In addition to the request parameters shown in the table, users should indeed use other Slurm request parameters related to partition, walltime, job naming, output, email, etc. (Check the examples of the full Slurm batch scripts.)
Notes for the use/management of resources with srun: - Note that, for the case of
srun, options do have the standard Slurm meaning. - The following options need to be explicitly provided to
srun and not assumed to be inherited with some default value from the allocation request:- The
--nodes (-N) option indicates the number of nodes to be used by the srun step. - The
--ntasks (-n) option indicates the total number of tasks to be spawned by the srun step. By default, tasks are spawned evenly across the number of allocated nodes. - The
--cpus-per-task (-c) option should be set to multiples of 8 (whole chiplets) to guarantee that srun will distribute the resources in "allocation-packs" and then "reserving" whole chiplets per srun task, even if the real number is 1 thread per task. The real number of threads is controlled with the OMP_NUM_THREADS environment variable. - The
--gres=gpu:number option indicates the number of GPUs per node to be used by the srun step. (The "equivalent" option --gpus-per-node=number is not recommended as we have found some bugs with its use.) - The
--gpus-per-task option indicates the number of GPUs to be binded to each task spawned by the srun step via the -n option. Note that this option neglects sharing of the assigned GPUs to a task with other tasks. (See cases *4, *5 and *7 and their notes for non-intuitive cases.)
- And for optimal binding, the following should be used:
- The
--gpu-bind=closest indicates that the chosen GPUs to be binded to each task should be the optimal (physically closest) to the chiplet assigned to each task. - IMPORTANT: The use of
--gpu-bind=closest will assign optimal binding but may still NOT work and launch execution errors for codes relying OpenMP or OpenACC pragma's for moving data from/to host to/from GPU and attempting to use GPU-to-GPU enabled MPI communication. For those cases, the use of the "manual" optimal binding (method 2) is required. Method 2 is explained later in the main document.
- (*1) This is the only case where
srun may work fine with default inherited option values. Nevertheless, it is a good practice to always use full explicit options of srun to indicate the resources needed for the executable. In this case, the settings explicitly "reserve" a whole chiplet (-c 8) for the srun task and control the real number of threads with the OMP_NUM_THREADS environment variable. Although the use of gres=gpu, gpus-per-task & gpu-bind is reduntant in this case, we keep them for encouraging their use, which is strictly needed in the most of cases (except case *5). - (*2) The required CPU threads per task is 14 and that is controlled with the
OMP_NUM_THREADS environment variable. But still the two full chiplets (-c 16) are indicated for each srun task. - (*3) The settings explicitly "reserve" a whole chiplet (
-c 8) for each srun task. This provides "one-chiplet-long" separation among each of the CPU cores to be allocated for the tasks spawned by srun (-n 3). The real number of threads is controlled with the OMP_NUM_THREADS variable. The requirement of optimal binding of GPU to corresponding chiplet is indicated with the option --gpu-bind=closest. And, in order to allow GPU-aware MPI communication, the environment variable MPICH_GPU_SUPPORT_ENABLED is set to 1. - (*4) Each task needs to be in direct communication with 2 GCDs. For that, each of the CPU task reserve "two-full-chiplets". IMPORTANT: The use of of
-c 16 "reserves" a "two-chiplets-long" separation among the two CPU cores that are to be used (one for each of the srun tasks, -n 2 ). In this way, each task will be in direct communication to the two logical GPUs in the MI250X card that has optimal connection to the chiplets reserved for each task. The real number of threads is controlled with the OMP_NUM_THREADS variable. The requirement of optimal binding of GPU to corresponding chiplet is indicated with the option --gpu-bind=closest. And, in order to allow GPU-aware MPI communication, the environment variable MPICH_GPU_SUPPORT_ENABLED is set to 1. - (*5) Sometimes, the executable (and not the scheduler) performs all the management of GPUs requested, like in the case of Tensorflow distributed training, and other Machine Learning Applications. If all the management logic for the GPUs is performed by the executable, then all the available resources should be exposed to it. IMPORTANT: In this case, the option for optimal binding is not
--gpu-bind option should not be provided. Neither the the --gpus-per-task option is should be provided, as all the available GPUs are to be shared among available to all tasks. The real number of threads is controlled with the OMP_NUM_THREADS variable. And, in order to allow GPU-aware MPI communication, the environment variable MPICH_GPU_SUPPORT_ENABLED is is set to 1. These last two settings may not be necessary for aplications like Tensorflow. - (*6) All GPUs in the node are requested, which mean all the resources available in the node via the
--exclusive allocation option (there is no need to indicate the number of GPUs per node when using exclusive allocation). The use of -c 8 provides "one-chiplet-long" separation among each of the CPU cores to be allocated for the tasks spawned by srun (-n 8). The real number of threads is controlled with the OMP_NUM_THREADS variable. The requirement of optimal binding of GPU to corresponding chiplet is indicated with the option --gpu-bind=closest. And, in order to allow GPU-aware MPI communication, the environment variable MPICH_GPU_SUPPORT_ENABLED is set to 1. - (*7) All resources in each node are requested via the
--exclusive allocation option (there is no need to indicate the number of GPUs per node when using exclusive allocation). Each task needs to be in direct communication with 4 GCDs. For that, each of the CPU task reserve "four-full-chiplets". IMPORTANT: The use of of -c 32 "reserves" a "four-chiplets-long" separation among the two CPU cores that are to be used per node (8 srun tasks in total, -n 8 ). The real number of threads is controlled with the OMP_NUM_THREADS variable. The requirement of optimal binding of GPU to corresponding chiplet is indicated with the option --gpu-bind=closest. In this way, each task will be in direct communication to the closest four logical GPUs in the node with respect to the chiplets reserved for each task. And, in order to allow GPU-aware MPI communication, the environment variable MPICH_GPU_SUPPORT_ENABLED is set to 1. The --gres=gpu:8 option assigns 8 GPUs per node to the srun step (32 GPUs in total as 4 nodes are being assigned). - (*8) All GPUs in the node are requested using the --
exclusive option, but only 1 CPU chiplet - 1 GPU "unit" (or allocation-pack) is used in the srun step.
General notes: - The allocation charge is for the total of allocated resources and not for the ones that are explicitly used in the execution, so all idle resources will also be charged
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