[Swift-commit] r5912 - SwiftApps/CMTS/rmsd

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-08-28 14:47:25 -0500 (Tue, 28 Aug 2012)
New Revision: 5912

Modified:
   SwiftApps/CMTS/rmsd/rmsd.sh
   SwiftApps/CMTS/rmsd/rmsd.swift
Log:
Add more debugging info


Modified: SwiftApps/CMTS/rmsd/rmsd.sh
===================================================================
--- SwiftApps/CMTS/rmsd/rmsd.sh	2012-08-27 21:58:26 UTC (rev 5911)
+++ SwiftApps/CMTS/rmsd/rmsd.sh	2012-08-28 19:47:25 UTC (rev 5912)
@@ -8,14 +8,36 @@
 namd_parameters=$6
 vmd_script=$7
 
-sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+echo Command line arguments: $@
+echo
+echo File listing
+echo ------------
+find
+echo
+
+echo Running the following sed commands
+echo sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+echo sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+echo sed -i -e s/HBEPS/-0.01/g -e s/PXEPS/-$b1/g -e s/DTEPS/-$b2/g -e s/AKEPS/-0.01/g -e s/LTEPS/-0.01/g $namd_parameters
+sed -i -e s/BLAB1/$b1name$b1/g -e s/BLAB2/$b2name$b2/g -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
 sed -i -e s/HBEPS/-0.01/g -e s/PXEPS/-$b1/g -e s/DTEPS/-$b2/g -e s/AKEPS/-0.01/g -e s/LTEPS/-0.01/g $namd_parameters
 sed -i -e s/BLAB1/$b1name$b1/g -e s/BLAB2/$b2name$b2/g -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
+echo Done with sed
+echo
 
 namd2=$( which namd2 )
+echo Found namd2 at $namd2
+echo About to run mpiexec -machinefile $PBS_NODEFILE $namd2 $namd_input 
 mpiexec -machinefile $PBS_NODEFILE $namd2 $namd_input 
+
+echo
+echo About to run vmd -dispdev text -e $vmd_script 
 vmd -dispdev text -e $vmd_script 
 
 mv output/cg_clath_cage.dcd output/cg_clath_cage-$b1-$b2.dcd
 mv rmsd.dat output/rmsd.$b1name${b1}_$b2name${b2}.dat
-sleep 5
+
+echo
+echo Files at end of run
+find
+echo

Modified: SwiftApps/CMTS/rmsd/rmsd.swift
===================================================================
--- SwiftApps/CMTS/rmsd/rmsd.swift	2012-08-27 21:58:26 UTC (rev 5911)
+++ SwiftApps/CMTS/rmsd/rmsd.swift	2012-08-28 19:47:25 UTC (rev 5912)
@@ -33,8 +33,8 @@
 
 foreach b1 in [b1min:b1max:delta] {
    foreach b2 in [b2min:b2max:delta] {
-      file output <single_file_mapper; file=@strcat("logs/namd-", b1, "-", b2, ".out.txt")>;
-      file error <single_file_mapper; file=@strcat("logs/namd-", b1, "-", b2, ".err.txt")>;
+      file output <single_file_mapper; file=@strcat("logs/rmsd-", b1, "-", b2, ".out.txt")>;
+      file error <single_file_mapper; file=@strcat("logs/rmsd-", b1, "-", b2, ".err.txt")>;
       file dcd <single_file_mapper; file=@strcat("output/cg_clath_cage-", b1, "-", b2, ".dcd")>;
       file dat <single_file_mapper; file=@strcat("output/rmsd.", b1name, b1, "_", b2name, b2, ".dat")>;
       dats[b1][b2] = dat;