Exercises: Process and Thread Distribution and Binding

Basic exercises

1. We return to the hybrid MPI/OpenMP example from the Slurm exercises.

   #!/bin/bash -l
   #SBATCH --partition=small           # Partition (queue) name
   #SBATCH --nodes=1                   # Total number of nodes
   #SBATCH --ntasks-per-node=8         # 8 MPI ranks per node
   #SBATCH --cpus-per-task=16          # 16 threads per task
   #SBATCH --time=5                    # Run time (minutes)
   #SBATCH --account=<project_id>      # Project for billing
   
   module load LUMI/24.03
   module load lumi-CPEtools/1.1-cpeGNU-24.03
   
   srun --cpus-per-task=$SLURM_CPUS_PER_TASK hybrid_check -n -r
   

   Improve the thread affinity with OpenMP runtime variables. Alter the above script and ensure that each thread is bound to a specific core.

   Click to see the solution.

   Add the following OpenMP environment variables definition to your script:

   export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
   export OMP_PROC_BIND=close
   export OMP_PLACES=cores
   

   You can also use an MPI runtime variable to have MPI itself report a cpu mask summary for each MPI rank:

   export MPICH_CPUMASK_DISPLAY=1
   

   Note hybrid_check and MPICH cpu mask may not be consistent. It is found to be confusing.

   To avoid having to use the --cpus-per-task flag, you can also set the environment variable SRUN_CPUS_PER_TASK instead:

   export SRUN_CPUS_PER_TASK=16 
   

   On LUMI this is not strictly necessary as the Slurm SBATCH processing has been modified to set this environment variable, but that was a clunky patch to reconstruct some old behaviour of Slurm and we have already seen cases where the patch did not work (but that were more complex cases that required different environment variables for a similar function).

   The list of environment variables that the srun command can use as input, is actually confusing, as some start with SLURM_ but a few start with SRUN_ while the SLURM_ equivalent is ignored.

   So we end up with the following script:

   #!/bin/bash -l
   #SBATCH --partition=small           # Partition (queue) name
   #SBATCH --nodes=1                   # Total number of nodes
   #SBATCH --ntasks-per-node=8         # 8 MPI ranks per node
   #SBATCH --cpus-per-task=16          # 16 threads per task
   #SBATCH --time=5                    # Run time (minutes)
   #SBATCH --account=<project_id>      # Project for billing
   
   module load LUMI/24.03
   module load lumi-CPEtools/1.1-cpeGNU-24.03
   
   export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK
   
   export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
   export OMP_PROC_BIND=close
   export OMP_PLACES=cores
   
   export MPICH_CPUMASK_DISPLAY=1
   
   srun hybrid_check -n -r
   

   Note that MPI returns the CPU mask per process in binary form (a long string of zeros and ones) where the last number is for core 0. Also, you'll see that with the OpenMP environment variables set, it will look like only one core can be used by each MPI task, but that is because it only shows the mask for the main process which becomes OpenMP thread 0. Remove the OpenMP environment variables and you'll see that each task now gets 16 possible cores to run on, and the same is true for each OpenMP thread (at least when using the GNU compilers, the Cray compilers have different default behaviour for OpenMP which actually makes more sense for most scientific computing codes).

2. Binding on GPU nodes: Allocate one GPU node with one task per GPU and bind tasks to each CCD (8-core group sharing L3 cache) leaving the first (#0) and last (#7) cores unused. Run a program with 6 threads per task and inspect the actual task/threads affinity using the gpu_check command from the lumi-CPEtools module.

   Click to see the solution.

   We can chose between different approaches. In the example below, we follow the "GPU binding: Linear GCD, match cores" slides and we only need to adapt the CPU mask:

   #!/bin/bash -l
   #SBATCH --partition=standard-g      # Partition (queue) name
   #SBATCH --nodes=1                   # Total number of nodes
   #SBATCH --ntasks-per-node=8         # 8 MPI ranks per node
   #SBATCH --gpus-per-node=8           # Allocate one gpu per MPI rank
   #SBATCH --time=5                    # Run time (minutes)
   #SBATCH --account=<project_id>      # Project for billing
   #SBATCH --hint=nomultithread
   
   module load LUMI/24.03 partition/G
   module load lumi-CPEtools/1.1-cpeGNU-24.03
   
   cat << EOF > select_gpu_$SLURM_JOB_ID
   #!/bin/bash
   export ROCR_VISIBLE_DEVICES=\$SLURM_LOCALID
   exec \$*
   EOF
   chmod +x ./select_gpu_$SLURM_JOB_ID
   
   CPU_BIND="mask_cpu:0x7e000000000000,0x7e00000000000000,"
   CPU_BIND="${CPU_BIND}0x7e0000,0x7e000000,"
   CPU_BIND="${CPU_BIND}0x7e,0x7e00,"
   CPU_BIND="${CPU_BIND}0x7e00000000,0x7e0000000000"
   
   export OMP_NUM_THREADS=6
   export OMP_PROC_BIND=close
   export OMP_PLACES=cores
   
   srun --cpu-bind=${CPU_BIND} ./select_gpu_$SLURM_JOB_ID gpu_check -l
   

   The base mask we need for this exercise, with each first and last core of a chiplet disabled, is 01111110 which is 0x7e in hexadecimal notation (though using 0xfe as the building block would also have worked as we already limit the number of threads to 6 through OMP_NUM_THREADS and use other binding variables that will bind all threads as close as possible to the core with relative number 1 of each chiplet).

   Save the job script as job_step.sh then simply submit it with sbatch. Inspect the job output.

   Note that in fact, if you had used the cpeCray version of the lumi-CPEtools module, you don't even need to use the OMP_* environment variables above as the threads are automatically pinned to a single core and as the correct number of threads is derived from the affinity mask for each task.