[Swift-commit] r8406 - in SwiftApps/subjobs: . dock largersubjobs namd

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2015-03-24 13:33:30 -0500 (Tue, 24 Mar 2015)
New Revision: 8406

Added:
   SwiftApps/subjobs/largersubjobs/
   SwiftApps/subjobs/largersubjobs/data.txt
   SwiftApps/subjobs/largersubjobs/myscript
   SwiftApps/subjobs/largersubjobs/outer
Modified:
   SwiftApps/subjobs/dock/dock.swift
   SwiftApps/subjobs/namd/namd.swift
Log:
namd and largersubjobs

Modified: SwiftApps/subjobs/dock/dock.swift
===================================================================
--- SwiftApps/subjobs/dock/dock.swift	2015-03-19 22:27:38 UTC (rev 8405)
+++ SwiftApps/subjobs/dock/dock.swift	2015-03-24 18:33:30 UTC (rev 8406)
@@ -7,7 +7,7 @@
 }
 
 // Files
-file infiles[] <filesys_mapper; location=".", suffix=".in">;
+file infiles[] <filesys_mapper; location="/home/ketan/SwiftApps/subjobs/dock", suffix=".in">;
 file logs[];
 
 file mol2<"zinc_nci_0010.mol2">;
@@ -22,7 +22,7 @@
 foreach infile,i in infiles {
    file dock_output <single_file_mapper; file=strcat("logs/dock.", i, ".stdout")>;
    file dock_error <single_file_mapper; file=strcat("logs/dock.", i, ".stderr")>;
-   file dockoutfile <single_file_mapper; file=strcat("dock.",i, ".out")>;
+   file dockoutfile <single_file_mapper; file=strcat("dock_", i, ".out")>;
 
    (dockoutfile, dock_output, dock_error) = dock(infile, mol2, defn, flexdefn, tbl, nrg, sph, bmp);
    logs[i] = dock_output;

Added: SwiftApps/subjobs/largersubjobs/data.txt
===================================================================
--- SwiftApps/subjobs/largersubjobs/data.txt	                        (rev 0)
+++ SwiftApps/subjobs/largersubjobs/data.txt	2015-03-24 18:33:30 UTC (rev 8406)
@@ -0,0 +1 @@
+this is my input

Added: SwiftApps/subjobs/largersubjobs/myscript
===================================================================
--- SwiftApps/subjobs/largersubjobs/myscript	                        (rev 0)
+++ SwiftApps/subjobs/largersubjobs/myscript	2015-03-24 18:33:30 UTC (rev 8406)
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+BLOCKS=$(get-bootable-blocks --size 128 $COBALT_PARTNAME)
+
+for BLOCK in $BLOCKS
+do
+  boot-block --block $BLOCK &
+done
+wait
+
+for BLOCK in $BLOCKS
+do
+  runjob --block $BLOCK : $(pwd)/mpicatnap data.txt ${BLOCK}.txt 1 &
+done
+wait
+
+for BLOCK in $BLOCKS
+do
+   boot-block --block $BLOCK --free &
+done
+wait


Property changes on: SwiftApps/subjobs/largersubjobs/myscript
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftApps/subjobs/largersubjobs/outer
===================================================================
--- SwiftApps/subjobs/largersubjobs/outer	                        (rev 0)
+++ SwiftApps/subjobs/largersubjobs/outer	2015-03-24 18:33:30 UTC (rev 8406)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+qsub -n 1024 -t 00:10:00 -A ExM --mode script --disable_preboot ./myscript


Property changes on: SwiftApps/subjobs/largersubjobs/outer
___________________________________________________________________
Added: svn:executable
   + *

Modified: SwiftApps/subjobs/namd/namd.swift
===================================================================
--- SwiftApps/subjobs/namd/namd.swift	2015-03-19 22:27:38 UTC (rev 8405)
+++ SwiftApps/subjobs/namd/namd.swift	2015-03-24 18:33:30 UTC (rev 8406)
@@ -32,8 +32,8 @@
 
 // Run scaling tests
 foreach i in [min:max:delta] {
-   file namd_output <single_file_mapper; file=@strcat("logs/h0scale.", i, ".out")>;
-   file namd_error <single_file_mapper; file=@strcat("logs/h0scale.", i, ".err")>;
+   file namd_output <single_file_mapper; file=strcat("logs/h0scale.", i, ".out")>;
+   file namd_error <single_file_mapper; file=strcat("logs/h0scale.", i, ".err")>;
    (namd_output, namd_error) = namd_wrapper(psf, pdb, coord_restart, velocity_restart, 
                                             system_restart, namd_config, charmm_parameters);
    logs[i] = namd_output;