Changes between Version 2 and Version 3 of cypress/GNUparallel

Timestamp:

09/22/23 16:10:09 (14 months ago)

Author:

fuji

Comment:

—

cypress/GNUparallel

@@ -39 +39 @@
 [fuji@cypress1 JobArray2]$ parallel -j 4 sh ::: script??.sh
 }}}
+
+=== Run Gnu Parallel in Slurm script ===
+==== Single Node ====
+The job script below requests 1 node 20 cores (one whole node). Assuming that each task is multi-thread, and '''OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK''' determines the number of threads. '''"-j $SLURM_NTASKS"''' determines the number of concurrently running tasks.
+{{{
+#!/bin/bash
+#SBATCH --partition=defq        # Partition
+#SBATCH --qos=normal            # Quality of Service
+#SBATCH --job-name=GNU_Paralle  # Job Name
+#SBATCH --time=00:10:00         # WallTime
+#SBATCH --nodes=1               # Number of Nodes
+#SBATCH --ntasks-per-node=5     # Number of tasks 
+#SBATCH --cpus-per-task=4       # Number of processors per task OpenMP threads()
+#SBATCH --gres=mic:0            # Number of Co-Processors
+
+module load parallel
+
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+
+parallel --record-env
+
+parallel --joblog log \
+        -j $SLURM_NTASKS \
+        --workdir $SLURM_SUBMIT_DIR \
+        --env OMP_NUM_THREADS \
+        sh ./run_hostname.sh {} ::: `seq 1 100`
+}}}
+
+The example task script is:
+{{{
+#!/bin/bash
+hostname
+echo $1
+sleep 1
+}}}
+
+==== Multiple Nodes ====
+The job script below requests 4 nodes 20 cores for each. Assuming that each task is multi-thread, and '''OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK''' determines the number of threads. '''"-j $TASKS_PER_NODE"''' determines the number of concurrently running tasks per node, which is defined by '''TASKS_PER_NODE=`echo $SLURM_NTASKS / $SLURM_NNODES | bc`'''. '''scontrol show hostname $SLURM_NODELIST > machinefile''' makes a list of nodes and send it to GNU parallel by "--slf $MACHINEFILE".
+{{{
+#!/bin/bash
+#SBATCH --partition=defq        # Partition
+#SBATCH --qos=normal            # Quality of Service
+#SBATCH --job-name=GNU_Paralle  # Job Name
+#SBATCH --time=00:10:00         # WallTime
+#SBATCH --nodes=4               # Number of Nodes
+#SBATCH --ntasks-per-node=5     # Number of tasks 
+#SBATCH --cpus-per-task=4       # Number of processors per task OpenMP threads()
+#SBATCH --gres=mic:0            # Number of Co-Processors
+
+module load parallel
+
+MACHINEFILE="machinefile"
+scontrol show hostname $SLURM_NODELIST > machinefile
+cat $MACHINEFILE
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+TASKS_PER_NODE=`echo $SLURM_NTASKS / $SLURM_NNODES | bc`
+echo "TASKS_PER_NODE=" $TASKS_PER_NODE
+
+parallel --record-env
+
+parallel --joblog log \
+        -j $TASKS_PER_NODE \
+        --slf $MACHINEFILE \
+        --workdir $SLURM_SUBMIT_DIR \
+        --sshdelay 0.1 \
+        --env OMP_NUM_THREADS \
+        sh ./run_hostname.sh {} ::: `seq 1 100`
+
+echo "took $SECONDS sec"
+}}}