Merge pull request #63 from JoseJVS/main

Updated pinning instructions for slurm 22.05

config/templates/hpc_benchmark_config_template.yaml

@@ -36,7 +36,7 @@ parameterset:
        - {name: tasks_per_node, type: int, _: "TASKS_PER_NODE"}  # number of (MPI) tasks per node, accepts a list in the format a,b,c,... for generating multiple runs
        - {name: threads_per_task, type: int, _: "THREADS_PER_TASK"}  # number of threads per task, accepts a list in the format a,b,c,... for generating multiple runs
        - {name: walltime, type: string, _: "WALLTIME"}  # wall time for the job in format hh:mm:ss
-       - {name: affinity, type: string, separator: ";", _: "--cpu-bind=verbose,threads --distribution=block:cyclic:fcyclic --hint=nomultithread"}  # processor affinity/pinning
+       - {name: affinity, type: string, separator: ";", _: "--cpu-bind=verbose,threads --distribution=block:cyclic:fcyclic --threads-per-core=1"}  # processor affinity/pinning
     - name: software_parameters
       parameter:
        - {name: simulator, _: "nest-simulator"}  # simulator to be installed (plan file must be provided)

config/templates/microcircuit_config_template.yaml

@@ -41,7 +41,7 @@ parameterset:
        - {name: tasks_per_node, type: int, _: "TASKS_PER_NODE"}  # number of (MPI) tasks per node, accepts a list in the format a,b,c,... for generating multiple runs
        - {name: threads_per_task, type: int, _: "THREADS_PER_TASK"}  # number of threads per task, accepts a list in the format a,b,c,... for generating multiple runs
        - {name: walltime, type: string, _: "WALLTIME"}  # wall time for the job in format hh:mm:ss
-       - {name: affinity, type: string, separator: ";", _: "--cpu-bind=verbose,threads --distribution=block:cyclic:fcyclic --hint=nomultithread"}  # processor affinity/pinning
+       - {name: affinity, type: string, separator: ";", _: "--cpu-bind=verbose,threads --distribution=block:cyclic:fcyclic --threads-per-core=1"}  # processor affinity/pinning
     - name: software_parameters
       parameter:            
        - {name: simulator, _: "nest-simulator"}  # simulator to be installed (plan file must be provided)

config/templates/multi-area-model_2_config_template.yaml

@@ -37,7 +37,7 @@ parameterset:
        - {name: tasks_per_node, type: int, _: "TASKS_PER_NODE"}  # number of (MPI) tasks per node, accepts a list in the format a,b,c,... for generating multiple runs
        - {name: threads_per_task, type: int, _: "THREADS_PER_TASK"}  # number of threads per task, accepts a list in the format a,b,c,... for generating multiple runs
        - {name: walltime, type: string, _: "WALLTIME"}  # wall time for the job in format hh:mm:ss
-       - {name: affinity, type: string, separator: ";", _: "--cpu-bind=verbose,threads --distribution=block:cyclic:fcyclic --hint=nomultithread"}  # processor affinity/pinning
+       - {name: affinity, type: string, separator: ";", _: "--cpu-bind=verbose,threads --distribution=block:cyclic:fcyclic --threads-per-core=1"}  # processor affinity/pinning
     - name: software_parameters
       parameter:            
        - {name: simulator, _: "nest-simulator"}  # simulator to be installed (plan file must be provided)

config/templates/multi-area-model_3_config_template.yaml

@@ -39,7 +39,7 @@ parameterset:
        - {name: tasks_per_node, type: int, _: "TASKS_PER_NODE"}  # number of (MPI) tasks per node, accepts a list in the format a,b,c,... for generating multiple runs
        - {name: threads_per_task, type: int, _: "THREADS_PER_TASK"}  # number of threads per task, accepts a list in the format a,b,c,... for generating multiple runs
        - {name: walltime, type: string, _: "WALLTIME"}  # wall time for the job in format hh:mm:ss
-       - {name: affinity, type: string, separator: ";", _: "--cpu-bind=verbose,threads --distribution=block:cyclic:fcyclic --hint=nomultithread"}  # processor affinity/pinning
+       - {name: affinity, type: string, separator: ";", _: "--cpu-bind=verbose,threads --distribution=block:cyclic:fcyclic --threads-per-core=1"}  # processor affinity/pinning
     - name: software_parameters
       parameter:            
        - {name: simulator, _: "nest-simulator"}  # simulator to be installed (plan file must be provided)

helpers/helpers.yaml

@@ -25,7 +25,6 @@ substituteset:
         - {source: "#NODES#", dest: $num_nodes}
         - {source: "#NTASKS#", dest: $num_tasks}
         - {source: "#NTASKS_PER_NODE#", dest: $tasks_per_node}
-        - {source: "#CPUS_PER_TASK#", dest: $threads_per_task}
         - {source: "#TIME#", dest: $walltime}
         - {source: "#ERRPATH#", dest: $err_file}
         - {source: "#OUTPATH#", dest: $out_file}
@@ -40,7 +39,6 @@ substituteset:
         - {source: "#NODES#", dest: 1}
         - {source: "#NTASKS#", dest: 1}
         - {source: "#NTASKS_PER_NODE#", dest: 1}
-        - {source: "#CPUS_PER_TASK#", dest: 16}
         - {source: "#TIME#", dest: "00:15:00"}
         - {source: "#ERRPATH#", dest: $err_file}
         - {source: "#OUTPATH#", dest: $out_file}
@@ -82,8 +80,11 @@ parameterset:
            module load $simulator/$version/$variant_$suffix
         fi
         export OMP_NUM_THREADS=$threads_per_task
+        export OMP_DISPLAY_ENV=VERBOSE
+        export OMP_DISPLAY_AFFINITY=TRUE
+        export OMP_PROC_BIND=TRUE
         ${optional_run_command}
-        srun ${affinity} python ${run_file} ${run_args}
+        srun --cpus-per-task=${threads_per_task} ${affinity} python ${run_file} ${run_args}
         srun -n 1 --nodes 1 python ${base_path}/helpers/collect_timer_data.py ${log_path}
         srun -n 1 --nodes 1 python ${base_path}/helpers/cpu_logging.py ${jube_wp_abspath}
         cd ${model_path}

helpers/job.slurm.in

@@ -22,7 +22,6 @@
 #SBATCH -e #ERRPATH#
 #SBATCH --nodes=#NODES#
 #SBATCH --ntasks-per-node=#NTASKS_PER_NODE#
-#SBATCH --cpus-per-task=#CPUS_PER_TASK#
 #SBATCH --time=#TIME#
 #SBATCH --exclusive
 #SBATCH --account=#ACCOUNT#