Changes between Version 1 and Version 2 of Workshops/cypress/ManyTaskComputing

Timestamp:

12/12/22 14:03:53 (3 years ago)

Author:

fuji

Comment:

—

Workshops/cypress/ManyTaskComputing

@@ -28 +28 @@
 date
 hostname
+# $i = 1,2,3,..$SLURM_NTASKS_PER_NODE
 for i in $(seq $SLURM_NTASKS_PER_NODE)
 do
+        # $TASK_ID=1,2,...100
         TASK_ID=$((SLURM_ARRAY_TASK_ID + i))
         cust_func $TASK_ID > log${TASK_ID}.out & # Put a function in the background
@@ -36 +38 @@
 ## Put all cust_func in the background and bash
 ## would wait until those are completed
-## before displaying done message
+## before displaying 'done' message
 wait
 echo "done"
@@ -43 +45 @@
 
 == Many MPI jobs in a single job ==
-If you have some MPI jobs that must run concurrently, Many-task computing may be the way to go.
+If you have some MPI jobs that must run concurrently, Many-task computing may be the way to go. 
+
+The example below requests 6 nodes and puts 3 MPI jobs into the single job.
+
+{{{
+#!/bin/bash
+#SBATCH --partition=defq        # Partition
+#SBATCH --qos=normal            # Quality of Service
+#SBATCH --job-name=PilotJob   # Job Name
+#SBATCH --time=00:10:00         # WallTime
+#SBATCH --nodes=6               # Number of Nodes
+#SBATCH --ntasks-per-node=20    # Number of tasks (MPI presseces)
+#SBATCH --cpus-per-task=1       # Number of processors per task OpenMP threads()
+#SBATCH --gres=mic:0            # Number of Co-Processors
+
+module load intel-psxe
+
+# NUMBER OF SUB-JOBS
+NUM_OF_SUBJOBS=3
+
+# Make hostlist
+HOSTLIST=${SLURM_JOB_ID}_HOSTS
+mpirun hostname -s | sort > ${SLURM_JOB_ID}_HOSTS
+#
+python jobLauncher.py $NUM_OF_SUBJOBS $HOSTLIST
+}}}
+
+'jobLauncher.py' manages sub-jobs.
+
+{{{
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Jan 22 16:33:57 2016
+
+@author: fuji
+"""
+
+import sys
+import os
+import time
+import subprocess
+
+dirname = os.path.dirname(os.path.abspath(sys.argv[0]))
+numOfSubJobs = int(sys.argv[1])
+nodeFile = sys.argv[2]
+#
+# Get nodes
+with open(nodeFile, 'r') as f:
+    nodes = f.readlines()
+#
+numOfNodes = len(nodes)
+#print "N", numOfNodes, nodes
+if (numOfNodes < numOfSubJobs) or (numOfSubJobs < 1):
+    os.abort()
+#
+# Dvide processors into numOfJobs
+numOfNodesSubJob = [0] *  numOfSubJobs
+for id in range(numOfSubJobs):
+    numOfNodesSubJob[id] = numOfNodes / numOfSubJobs
+    if (numOfNodes % numOfSubJobs != 0):
+        if (id < numOfNodes % numOfSubJobs):
+            numOfNodesSubJob[id] += 1
+    #print "n", numOfNodesSubJob[id]
+#
+# Allocate Nodes
+idx = 0
+nodesSubJob = [None] * numOfSubJobs
+for id in range(numOfSubJobs):
+    nodesSubJob[id] = [None] * numOfNodesSubJob[id]
+    for n in range(numOfNodesSubJob[id]):
+        nodesSubJob[id][n] = nodes[idx]
+        idx += 1
+    #print nodesSubJob[id]
+#
+# Create Nodes Files
+nodeFileName = []
+for id in range(numOfSubJobs):
+    nodeFileName.append("%s_%04d.nod" % (nodeFile,id))
+    with open(nodeFileName[id],'wt') as outp:
+        for node in nodesSubJob[id]:
+            outp.write(node)
+#
+# Launch SubJobs
+proc = []
+for id in range(numOfSubJobs):
+    commandToLaunchSubJobs = []
+    commandToLaunchSubJobs.append(dirname + "/launch_subjob.sh")
+    commandToLaunchSubJobs.append(nodeFileName[id])
+    #
+    #print commandToLaunchSubJobs
+    p = subprocess.Popen(commandToLaunchSubJobs,
+                         shell=False,
+                         stdout=subprocess.PIPE,
+                         stderr=subprocess.PIPE)
+    proc.append(p)
+
+# Wait Until All subjobs done
+while(True):
+    runningtasks = 0
+    for id in range(numOfSubJobs):
+        if (proc[id].poll() == None):
+            runningtasks += 1
+    if runningtasks == 0:
+        break
+    time.sleep(5) # Checks every 5 seconds
+#
+# Show outputs
+for id in range(numOfSubJobs):
+    comm = proc[id].communicate()
+    sout = comm[0]
+    serr = comm[1]
+    #
+    print "SubJob", id
+    print sout
+    print serr
+}}}
 
 
+
+and 'launch_subjob.sh' script launch a sub-job.
+
+
+{{{
+#!/bin/bash
+export HOST_LIST=$1
+
+# Run Sub-job
+mpirun -hostfile $HOST_LIST hostname -s
+}}}
+
+
+