[Swift-commit] r8293 - SwiftApps/subjobs

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-10-24 14:16:30 -0500 (Fri, 24 Oct 2014)
New Revision: 8293

Modified:
   SwiftApps/subjobs/README.txt
   SwiftApps/subjobs/bg.sh
Log:
add note about VMD

Modified: SwiftApps/subjobs/README.txt
===================================================================
--- SwiftApps/subjobs/README.txt	2014-10-22 20:39:53 UTC (rev 8292)
+++ SwiftApps/subjobs/README.txt	2014-10-24 19:16:30 UTC (rev 8293)
@@ -153,6 +153,8 @@
 Similarly, in order to change the scale and size of runs, make changes to the
 parameters in the sites file as described in section 1 above.
 
+ToDo: Visualize NAMD results with VMD.
+
 Rosetta
 ~~~~~~~~
 

Modified: SwiftApps/subjobs/bg.sh
===================================================================
--- SwiftApps/subjobs/bg.sh	2014-10-22 20:39:53 UTC (rev 8292)
+++ SwiftApps/subjobs/bg.sh	2014-10-24 19:16:30 UTC (rev 8293)
@@ -13,6 +13,8 @@
 # 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"
@@ -54,7 +56,7 @@
     echo "$0": running runjob  --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" --ranks-per-node 1 : "$REMAINING_ARGS"
     
     #without timeout
-    runjob --strace 0 --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 1 --np "$SUBBLOCK_SIZE" : "$@"
+    runjob --strace 0 --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$SUBBLOCK_SIZE" : "$@"
     
     echo "Runjob finished."
 else