[Swift-commit] r8271 - SwiftApps/subjobs/dock
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Fri Oct 10 13:41:32 CDT 2014
Author: ketan
Date: 2014-10-10 13:41:31 -0500 (Fri, 10 Oct 2014)
New Revision: 8271
Added:
SwiftApps/subjobs/dock/1VRT.rec.bmp
SwiftApps/subjobs/dock/1VRT.rec.nrg
SwiftApps/subjobs/dock/dock_infiles/
SwiftApps/subjobs/dock/rec.10A.sph
SwiftApps/subjobs/dock/runswift.sh
Modified:
SwiftApps/subjobs/dock/dock.swift
Log:
add dock input files and swift wrapper
Added: SwiftApps/subjobs/dock/1VRT.rec.bmp
===================================================================
(Binary files differ)
Property changes on: SwiftApps/subjobs/dock/1VRT.rec.bmp
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: SwiftApps/subjobs/dock/1VRT.rec.nrg
===================================================================
(Binary files differ)
Property changes on: SwiftApps/subjobs/dock/1VRT.rec.nrg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: SwiftApps/subjobs/dock/dock.swift
===================================================================
--- SwiftApps/subjobs/dock/dock.swift 2014-10-09 22:30:29 UTC (rev 8270)
+++ SwiftApps/subjobs/dock/dock.swift 2014-10-10 18:41:31 UTC (rev 8271)
@@ -1,21 +1,30 @@
type file;
// Dock
-app (file _dockoutfile, file out, file err) dock (file _dockinfile)
+app (file _dockoutfile, file out, file err) dock (file _dockinfile, file _mol2, file _defn, file _flexdefn, file _tbl, file _nrg, file _sph, file _bmp)
{
- bgsh "/home/ketan/dock6/bin/dock" "-i" @_dockinfile "-o" @_dockoutfile stdout=@out stderr=@err;
+ bgsh "/home/ketan/dock6/bin/dock6" "-i" @_dockinfile "-o" @_dockoutfile stdout=@out stderr=@err;
}
// Files
-file infiles[] <filesys_mapper; location="dock_infiles", suffix=".in">;
+file infiles[] <filesys_mapper; location=".", suffix=".in">;
file logs[];
+file mol2<"zinc_nci_0010.mol2">;
+file defn<"vdw_AMBER_parm99.defn">;
+file flexdefn<"flex.defn">;
+file tbl<"flex_drive.tbl">;
+file nrg<"1VRT.rec.nrg">;
+file sph<"rec.10A.sph">;
+file bmp<"1VRT.rec.bmp">;
+
// Run scaling tests
foreach infile,i in infiles {
- file dock_output <single_file_mapper; file=strcat("logs/dock.", i, ".out")>;
- file dock_error <single_file_mapper; file=strcat("logs/dock.", i, ".err")>;
- file dockoutfile <single_file_mapper; file=strcat("dock.",i, ".sc")>;
- (dockoutfile, dock_output, dock_error) = dock(pdb, 2);
+ 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")>;
+
+ (dockoutfile, dock_output, dock_error) = dock(infile, mol2, defn, flexdefn, tbl, nrg, sph, bmp);
logs[i] = dock_output;
}
Added: SwiftApps/subjobs/dock/rec.10A.sph
===================================================================
--- SwiftApps/subjobs/dock/rec.10A.sph (rev 0)
+++ SwiftApps/subjobs/dock/rec.10A.sph 2014-10-10 18:41:31 UTC (rev 8271)
@@ -0,0 +1,59 @@
+cluster 1 number of spheres in cluster 58
+ 1 4.22300 -36.12100 22.78400 0.700 1
+ 2 3.08000 -36.36800 23.25800 0.700 2
+ 3 2.22500 -37.57000 21.98500 0.700 3
+ 4 2.40900 -38.19300 21.32800 0.700 4
+ 5 5.22700 -35.11900 22.89100 0.700 5
+ 6 2.19200 -38.17200 21.36700 0.700 6
+ 7 5.07700 -34.91600 23.36200 0.700 7
+ 8 1.98300 -38.04700 21.26800 0.700 8
+ 9 1.35800 -37.37500 21.82100 0.700 9
+ 10 2.78200 -35.19800 24.29500 0.700 10
+ 11 6.35400 -38.13000 20.72000 0.700 11
+ 12 1.86600 -38.00700 20.16300 0.700 12
+ 13 3.42600 -34.64500 24.63100 0.700 13
+ 14 1.95000 -39.52600 21.59300 0.700 14
+ 15 2.24600 -37.94100 19.45100 0.700 15
+ 16 1.73100 -35.33700 24.31200 0.700 16
+ 17 2.86700 -40.23100 21.97100 0.700 17
+ 18 0.76400 -35.97900 23.31800 0.700 18
+ 19 0.90200 -35.60200 23.80600 0.700 19
+ 20 6.67000 -38.95100 20.26800 0.700 20
+ 21 2.71900 -38.09700 18.79000 0.700 21
+ 22 2.77600 -34.90300 25.34000 0.700 22
+ 23 3.54100 -34.82100 25.54000 0.700 23
+ 24 2.07600 -40.53100 21.19600 0.700 24
+ 25 3.29000 -34.92600 25.88900 0.700 25
+ 26 2.61200 -34.80200 25.84200 0.700 26
+ 27 -0.33700 -35.77200 22.99600 0.700 27
+ 28 2.15600 -34.72000 25.79800 0.700 28
+ 29 5.21400 -38.26700 17.85800 0.700 29
+ 30 3.76100 -38.12300 17.60800 0.700 30
+ 31 1.88200 -34.66000 25.89800 0.700 31
+ 32 1.75500 -40.73000 20.10000 0.700 32
+ 33 -0.32700 -36.31700 19.25200 0.700 33
+ 34 -0.74300 -35.61200 24.16600 0.700 34
+ 35 -0.59300 -36.21100 19.44600 0.700 35
+ 36 7.89500 -40.62500 20.65000 0.700 36
+ 37 0.04700 -35.30400 18.57400 0.700 37
+ 38 -1.43700 -35.50300 21.59600 0.700 38
+ 39 -1.29300 -36.83600 17.99600 0.700 39
+ 40 -2.83600 -35.85400 22.90100 0.700 40
+ 41 9.75400 -41.11000 23.90500 0.700 41
+ 42 -3.20500 -36.15900 22.46900 0.700 42
+ 43 11.75500 -35.01400 25.70900 0.700 43
+ 44 11.58600 -34.63300 26.00300 0.700 44
+ 45 10.98100 -40.05000 25.25600 0.700 45
+ 46 11.72000 -38.85500 25.12300 0.700 46
+ 47 0.48800 -33.58900 32.74200 0.700 47
+ 48 8.59900 -43.82600 18.54100 0.700 48
+ 49 -7.47000 -40.16500 22.80500 0.700 49
+ 50 -1.56100 -33.95700 31.03400 0.700 50
+ 51 8.10800 -44.69700 18.46400 0.700 51
+ 52 1.82200 -33.81100 33.32600 0.700 52
+ 53 4.28700 -40.85600 13.64200 0.700 53
+ 54 9.92000 -41.90200 24.30400 0.700 54
+ 55 7.56400 -44.63900 19.68900 0.700 55
+ 56 10.72800 -41.39300 24.94700 0.700 56
+ 57 7.05300 -27.88000 24.84000 0.700 57
+ 58 10.01800 -41.78300 24.42400 0.700 58
Added: SwiftApps/subjobs/dock/runswift.sh
===================================================================
--- SwiftApps/subjobs/dock/runswift.sh (rev 0)
+++ SwiftApps/subjobs/dock/runswift.sh 2014-10-10 18:41:31 UTC (rev 8271)
@@ -0,0 +1,10 @@
+#! /bin/sh
+
+#Old method
+#qsub -A ATPESC2014 -n 512 -t 15 --mode script runswift_script.sh -config cf -tc.file apps -sites.file localcoast.xml "$@"
+export COBALT_PROJ=ExM
+#New method
+/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt.xml -config cf -tc.file apps dock.swift
+
+#A testblock run
+#qsub -A ATPESC2013 -n 32 -t 5 -q low --mode c16 --mode script testblock.sh # --disable_preboot
Property changes on: SwiftApps/subjobs/dock/runswift.sh
___________________________________________________________________
Added: svn:executable
+ *
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