Wien2k - Revision history

Thw at 10:44, 3 December 2019

2019-12-03T10:44:43Z

2012-05-09T07:05:16Z

‎Parallel runs with Slurm

2012-05-09T07:02:12Z

‎Parallel runs with Slurm

2012-01-03T13:22:45Z

‎Parallel runs with Slurm

2012-01-03T11:01:46Z

2012-01-03T11:00:08Z

2009-03-06T14:25:49Z

2009-03-06T14:25:22Z

2009-02-20T15:37:35Z

2009-02-20T14:45:01Z

@@ Line 87: / Line 87: @@
 # Run your caclulation
 x lapw1 -p
 </pre>

@@ Line 55: / Line 55: @@
 	factor=${BASH_REMATCH[2]}
 	for j in $(seq 1 $factor); do
 	    conv=( ${conv[*]} $value )
 	done
       else
-	 #echo ${conv[@]}
+	conv=( ${conv[*]} $cpu )
       fi
 done

@@ Line 21: / Line 21: @@
+#
 # Allocated resources are encode like this:
-#  SLURM_JOB_CPUS_PER_NODE="4,2"
+#  SLURM_JOB_CPUS_PER_NODE="4,2(2x)"
-#  SLURM_NODELIST="bree,carla"
+#  SLURM_NODELIST="bree,carla,mike"
+#
-# = Run 4 tasks on bree and 2 on carla.
+# = Run 4 tasks on bree and 2 on carla and mike.
+#
 # Slurm paramters (read 'man sbatch')
@@ Line 44: / Line 44: @@
 # Convert string to array
 hcpus=($SLURM_JOB_CPUS_PER_NODE)
 # Build .machines file
@@ Line 50: / Line 69: @@
 nhost=0
 for node in $SLURM_NODELIST
 do
-     declare -i cpuspernode=${hcpus[$nhost]};
+     declare -i cpuspernode=${conv[$nhost]};
      for ((i=0; i<${cpuspernode}; i++))
      do
 	echo 1:$node >> .machines
      done
      let nhost+=1
 done

@@ Line 10: / Line 10: @@
 == Parallel runs with Slurm ==
 <pre>
@@ Line 68: / Line 70: @@
 x lapw1 -p
 </pre>
 == Parallel runs in the Grid Engine  ==

@@ Line 35: / Line 35: @@
+#
 # Set internal parallelization code in mkl to only use
-# on thread per process.
+# one thread per process.
 export OMP_NUM_THREADS=1

← Older revision		Revision as of 11:00, 3 January 2012
Line 9:		Line 9:
	<br>		<br>

		+	== Parallel runs with Slurm ==
		+
		+	<pre>
		+	#! /bin/bash
		+	#
		+	# Running wien2k job with slurm using k-point parallelization.
		+	#
		+	# Create an apropriate .machine file for wien2k
		+	#
		+	# Allocated resources are encode like this:
		+	# SLURM_JOB_CPUS_PER_NODE="4,2"
		+	# SLURM_NODELIST="bree,carla"
		+	#
		+	# = Run 4 tasks on bree and 2 on carla.
		+	#
		+	# Slurm paramters (read 'man sbatch')
		+	#
		+	#SBATCH --partition=dfg
		+	#SBATCH --mem-per-cpu=4000
		+	#SBATCH --ntasks=8
		+	#SBATCH --output=job.out
		+	# (--output includes STDERR)
		+	#
		+	#
		+	#
		+	# Set internal parallelization code in mkl to only use
		+	# on thread per process.
		+	export OMP_NUM_THREADS=1
		+
		+	# Use , as list seperator
		+	IFS=','
		+	# Convert string to array
		+	hcpus=($SLURM_JOB_CPUS_PER_NODE)
		+
		+	# Build .machines file
		+	rm -f .machines
		+
		+	nhost=0
		+
		+	for node in $SLURM_NODELIST
		+	do
		+	declare -i cpuspernode=${hcpus[$nhost]};
		+
		+	for ((i=0; i<${cpuspernode}; i++))
		+	do
		+	echo 1:$node >> .machines
		+	done
		+
		+	let nhost+=1
		+	done
		+
		+	echo 'granularity:1' >>.machines
		+	echo 'extrafine:1' >>.machines
		+
		+	# .machines file complete
		+
		+	# Run your caclulation
		+	x lapw1 -p
		+	</pre>
	== Parallel runs in the Grid Engine ==		== Parallel runs in the Grid Engine ==

@@ Line 46: / Line 46: @@
 # Selected parallel environment and number of slots/processes
 # mpi is needed, although we do not start a mpi job
-#$ -pe mpi 6
+#$ -pe mpil 6
 # define the environment, eventually not needed

@@ Line 63: / Line 63: @@
 # read the mpi machines files (generated by the sge)
 proclist=(`cat $TMPDIR/machines`)
 nproc=$NSLOTS
 echo $nproc nodes for this job: $proclist

@@ Line 13: / Line 13: @@
 To access the compute nodes it is necessary that you use the batch system. Please make sure that the [[Sun Grid Engine|'''SUN grid engine''']] is configured correctly for your account. See the [[Sun Grid Engine|wiki page]] for further instruction. Furthermore you need the [[Intel Compiler Temp|'''Intel&nbsp;MKL libraries''']] in your LD_LIBRARY_PATH. <br>
 You need one slot for the the master process which start and controles the slaves. If you allocate 8 Slots you will get 7 worker.
 Up to now, only the k-point parallelization is working. Here is a annotated example script:
@@ Line 63: / Line 63: @@
 # read the mpi machines files (generated by the sge)
 proclist=(`cat $TMPDIR/machines`)
-# Remove first array element (this is the master)
+# Remove first array element (this will be the master)
-proclist=${proclist[*]:1}
+proclist=(${proclist[*]:1})
 nproc=$NSLOTS
 echo $nproc nodes for this job: $proclist
@@ Line 72: / Line 72: @@
 # Convert proclist to one line per slot/k-point.
 # In a single queue all nodes have equal performance.
-for a in $proclist; do
+for a in ${proclist[*]}; do
      echo 1:$a &gt;&gt; .machines
 done

← Older revision		Revision as of 14:45, 20 February 2009
Line 12:		Line 12:

	To access the compute nodes it is necessary that you use the batch system. Please make sure that the [[Sun Grid Engine\|'''SUN grid engine''']] is configured correctly for your account. See the [[Sun Grid Engine\|wiki page]] for further instruction. Furthermore you need the [[Intel Compiler Temp\|'''Intel MKL libraries''']] in your LD_LIBRARY_PATH. <br>		To access the compute nodes it is necessary that you use the batch system. Please make sure that the [[Sun Grid Engine\|'''SUN grid engine''']] is configured correctly for your account. See the [[Sun Grid Engine\|wiki page]] for further instruction. Furthermore you need the [[Intel Compiler Temp\|'''Intel MKL libraries''']] in your LD_LIBRARY_PATH. <br>
		+
		+	You need one slot for the the master process which start and controles the slaves. If you allocate 8 Slots you will get 7 worker.

	Up to now, only the k-point parallelization is working. Here is a annotated example script:		Up to now, only the k-point parallelization is working. Here is a annotated example script: