[Swift-commit] r8456 - SwiftApps/subjobs

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2015-05-08 10:07:34 -0500 (Fri, 08 May 2015)
New Revision: 8456

Added:
   SwiftApps/subjobs/vaspbg.sh
Modified:
   SwiftApps/subjobs/bg.sh
Log:
adding vasp related script

Modified: SwiftApps/subjobs/bg.sh
===================================================================
--- SwiftApps/subjobs/bg.sh	2015-05-07 22:39:23 UTC (rev 8455)
+++ SwiftApps/subjobs/bg.sh	2015-05-08 15:07:34 UTC (rev 8456)
@@ -89,11 +89,11 @@
         #processedargs=$(echo "$@" | cut -d" " -f 1)
         echo "$0": running BLOCK="$COBALT_PARTNAME" SLOT="$SWIFT_JOB_SLOT"
         echo "$0": running cmd: "$0" args: "$@"
-        echo "$0": runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 1 : "$@" 
+        echo "$0": runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@" 
         
         #without timeout
         #runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
-        runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 1 : "$@"
+        runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
         
         echo "Runjob finished."
     fi

Added: SwiftApps/subjobs/vaspbg.sh
===================================================================
--- SwiftApps/subjobs/vaspbg.sh	                        (rev 0)
+++ SwiftApps/subjobs/vaspbg.sh	2015-05-08 15:07:34 UTC (rev 8456)
@@ -0,0 +1,124 @@
+#!/bin/bash
+
+#set -x
+
+mname=$(hostname)
+
+incarfile=$2
+poscarfile=$3
+potcarfile=$4
+kpointsfile=$5
+
+outcarfile=$6
+contcarfile=$7
+
+cp $incarfile .
+cp $poscarfile .
+cp $potcarfile .
+cp $kpointsfile .
+
+# vesta and mira has different path than cetus
+if [[ $mname == *vesta* || $mname == *mira* ]]
+then
+    export PATH=/soft/cobalt/bgq_hardware_mapper:$PATH
+else
+    export PATH=/soft/cobalt/cetus/bgq_hardware_mapper:$PATH    
+fi
+
+#Run the preprocessing script
+#/bin/bash $preproc "$@"
+
+#export SUBBLOCK_SIZE=16
+
+# Prepare shape based on subblock size
+# provided by user in sites environment
+case "$SUBBLOCK_SIZE" in
+1) SHAPE="1x1x1x1x1"
+;;
+8) SHAPE="1x2x2x2x1"
+;;
+16) SHAPE="2x2x2x2x1"
+;;
+32) SHAPE="2x2x2x2x2"
+;;
+64) SHAPE="2x2x4x2x2"
+;;
+128) SHAPE="2x4x4x2x2"
+;;
+256) SHAPE="2x4x4x4x2"
+;;
+512) SHAPE="4x4x4x4x2"
+;;
+*) echo "SUBBLOCK_SIZE not set or incorrectly set: will not use subblock jobs"
+;;
+esac
+
+# If subblock size is provided, do subblock business
+if [ "$SUBBLOCK_SIZE"_ != "_" ]
+then
+    # sub-block size larger than 512 nodes, currently untested
+    if [ "$SUBBLOCK_SIZE" -gt 512 ]
+    then
+        export SWIFT_SUBBLOCKS=$(get-bootable-blocks --size $SUBBLOCK_SIZE $COBALT_PARTNAME)
+        export SWIFT_SUBBLOCK_ARRAY=($SWIFT_SUBBLOCKS)
+
+        if [ "_$SWIFT_SUBBLOCKS" = _ ]; then
+          echo ERROR: "$0": SWIFT_SUBBLOCKS is null.
+          exit 1
+        fi
+        BLOCK=${SWIFT_SUBBLOCK_ARRAY[$SWIFT_JOB_SLOT]}
+        
+        #Some logging
+        echo "$0": running BLOCK="$BLOCK" SLOT="$SWIFT_JOB_SLOT"
+        echo "$0": running cmd: "$0" args: "$@"
+        echo "$0": running runjob --block "$BLOCK" : "$@"
+        
+        boot-block --block $BLOCK
+        runjob --block $BLOCK : "$@"
+        boot-block --block $BLOCK --free 
+
+        echo "Runjob finished"
+
+    else
+        export SWIFT_SUBBLOCKS=$(get-corners.py "$COBALT_PARTNAME" $SHAPE)
+        export SWIFT_SUBBLOCK_ARRAY=($SWIFT_SUBBLOCKS)
+        
+        if [ "_$SWIFT_SUBBLOCKS" = _ ]; then
+          echo ERROR: "$0": SWIFT_SUBBLOCKS is null.
+          exit 1
+        fi
+        
+        nsb=${#SWIFT_SUBBLOCK_ARRAY[@]}
+        
+        CORNER=${SWIFT_SUBBLOCK_ARRAY[$SWIFT_JOB_SLOT]}
+        
+        #Some logging
+        #processedargs=$(echo "$@" | cut -d" " -f 1)
+        echo "$0": running BLOCK="$COBALT_PARTNAME" SLOT="$SWIFT_JOB_SLOT"
+        echo "$0": running cmd: "$0" args: "$@"
+        echo "$0": runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 8 --np "$((8*$SUBBLOCK_SIZE))" : "$@" 
+        
+        #without timeout
+        #runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
+        runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 8 --np "$((8*$SUBBLOCK_SIZE))" : $1
+        
+        echo "Runjob finished."
+    fi
+else
+    # run w/o subblocks if no subblock size provided
+    echo "Running in nonsubblock mode."
+    echo "$0": running runjob -p 16 --block $COBALT_PARTNAME : "$@"
+
+    #strace -o "$HOME/strace.runjob.out" runjob --strace none -p 16 --block $COBALT_PARTNAME : "$@"
+    runjob -p 16 --block $COBALT_PARTNAME : "$@"
+
+    echo "Finished Running in nonsubblock mode."
+fi
+
+#Run the postprocessing script
+#/bin/bash $postproc "$@"
+mv OUTCAR $outcarfile
+mv CONTCAR $contcarfile
+
+exit 0
+


Property changes on: SwiftApps/subjobs/vaspbg.sh
___________________________________________________________________
Added: svn:executable
   + *