[Swift-commit] r5949 - in SwiftApps/CMTS/trajectory: . conf
davidk at ci.uchicago.edu
davidk at ci.uchicago.edu
Tue Sep 25 15:34:39 CDT 2012
Author: davidk
Date: 2012-09-25 15:34:39 -0500 (Tue, 25 Sep 2012)
New Revision: 5949
Added:
SwiftApps/CMTS/trajectory/namd_wrapper.sh
SwiftApps/CMTS/trajectory/trajectory.swift
Removed:
SwiftApps/CMTS/trajectory/scaling.swift
Modified:
SwiftApps/CMTS/trajectory/conf/local.cf
SwiftApps/CMTS/trajectory/runtrajectory.sh
Log:
Add serial dependencies and wrapper script
Modified: SwiftApps/CMTS/trajectory/conf/local.cf
===================================================================
--- SwiftApps/CMTS/trajectory/conf/local.cf 2012-09-25 20:13:06 UTC (rev 5948)
+++ SwiftApps/CMTS/trajectory/conf/local.cf 2012-09-25 20:34:39 UTC (rev 5949)
@@ -7,4 +7,4 @@
provider.staging.pin.swiftfiles=false
use.wrapper.staging=false
-#app rmsd=$PWD/../rmsd.sh
+#app namd_wrapper=$PWD/../namd_wrapper.sh
Added: SwiftApps/CMTS/trajectory/namd_wrapper.sh
===================================================================
--- SwiftApps/CMTS/trajectory/namd_wrapper.sh (rev 0)
+++ SwiftApps/CMTS/trajectory/namd_wrapper.sh 2012-09-25 20:34:39 UTC (rev 5949)
@@ -0,0 +1,7 @@
+#!/bin/bash -x
+
+namdConf=h0_eq.$numJobs.conf
+
+echo Arguments are: $@
+sed -e "s/_JOB_/$numJobs/g" h0_eq.conf > $namdConf
+mpiexec namd2 $namdConf
Property changes on: SwiftApps/CMTS/trajectory/namd_wrapper.sh
___________________________________________________________________
Added: svn:executable
+ *
Modified: SwiftApps/CMTS/trajectory/runtrajectory.sh
===================================================================
--- SwiftApps/CMTS/trajectory/runtrajectory.sh 2012-09-25 20:13:06 UTC (rev 5948)
+++ SwiftApps/CMTS/trajectory/runtrajectory.sh 2012-09-25 20:34:39 UTC (rev 5949)
@@ -83,7 +83,6 @@
echo "Run dir=$rundir" >> ABOUT
echo "Work dir=$WORK" >> ABOUT
echo "Total jobs=$total_jobs" >> ABOUT
-cp ../tc.data .
if [ "$USE_SCS" == "1" ]; then
runswift "sites.xml"
Deleted: SwiftApps/CMTS/trajectory/scaling.swift
===================================================================
--- SwiftApps/CMTS/trajectory/scaling.swift 2012-09-25 20:13:06 UTC (rev 5948)
+++ SwiftApps/CMTS/trajectory/scaling.swift 2012-09-25 20:34:39 UTC (rev 5949)
@@ -1,47 +0,0 @@
-type file;
-
-// Namd wrapper
-app (file out, file err) namd_wrapper (file psf_file, file pdb_file,
- file coord_restart_file, file velocity_restart_file,
- file system_restart_file, file namd_conf, file charmm_params)
-{
- namd_wrapper @namd_conf stdout=@out stderr=@err;
-}
-
-# Range of nodes to test on
-int jobStart=1;
-int jobStop=5;
-int delta=1;
-
-# Input files
-file psf <"h0_solvion.psf">;
-file pdb <"h0_solvion.pdb">;
-file charmm_parameters <"par_all22_prot.inp">;
-file initial_coords <"h0_eq.0.restart.coor">;
-file initial_velocity <"h0_eq.0.restart.vel">;
-file initial_system <"h0_eq.0.restart.xsc">;
-file initial_config <"h0_eq.conf">;
-
-# File arrays to hold outputs
-file namd_configs[];
-file namd_coordinates[];
-file namd_velocities[];
-file namd_systems[];
-
-# Set initial values
-namd_configs[jobStart - delta] = initial_config;
-namd_coordinates[jobStart - delta] = initial_coords;
-namd_velocities[jobStart - delta] = initial_velocity;
-namd_systems[jobStart - delta] = initial_system;
-
-# Run NAMD
-foreach jobNumber in [jobStart:jobStop:delta] {
- file namd_output <single_file_mapper; file=@strcat("logs/namd.", jobNumber, ".out")>;
- file namd_error <single_file_mapper; file=@strcat("logs/namd.", jobNumber, ".err")>;
- (namd_output, namd_error) = namd_wrapper(psf, pdb, namd_coordinates[jobNumber-delta],
- namd_velocities[jobNumber-delta],
- namd_systems[jobNumber-delta],
- namd_configs[jobNumber-delta],
- charmm_parameters);
-}
-
Copied: SwiftApps/CMTS/trajectory/trajectory.swift (from rev 5948, SwiftApps/CMTS/trajectory/scaling.swift)
===================================================================
--- SwiftApps/CMTS/trajectory/trajectory.swift (rev 0)
+++ SwiftApps/CMTS/trajectory/trajectory.swift 2012-09-25 20:34:39 UTC (rev 5949)
@@ -0,0 +1,57 @@
+type file;
+
+// Namd wrapper
+app (file out, file err, file velocity_file, file system_file, file config_file) namd_wrapper
+ (file psf_file, file pdb_file, file coord_restart_file,
+ file velocity_restart_file, file system_restart_file,
+ file namd_conf, file charmm_params)
+{
+ namd_wrapper @namd_conf stdout=@out stderr=@err;
+}
+
+# Range of nodes to test on
+int jobStart=1;
+int jobStop=5;
+int delta=1;
+
+# Input files
+file psf <"h0_solvion.psf">;
+file pdb <"h0_solvion.pdb">;
+file charmm_parameters <"par_all22_prot.inp">;
+file initial_coords <"h0_eq.0.restart.coor">;
+file initial_velocity <"h0_eq.0.restart.vel">;
+file initial_system <"h0_eq.0.restart.xsc">;
+file initial_config <"h0_eq.conf">;
+
+# File arrays to hold outputs
+file namd_configs[];
+file namd_coordinates[];
+file namd_velocities[];
+file namd_systems[];
+
+# Set initial values
+namd_configs[jobStart - delta] = initial_config;
+namd_coordinates[jobStart - delta] = initial_coords;
+namd_velocities[jobStart - delta] = initial_velocity;
+namd_systems[jobStart - delta] = initial_system;
+
+# Run NAMD
+foreach jobNumber in [jobStart:jobStop:delta] {
+ file namd_output <single_file_mapper; file=@strcat("logs/namd.", jobNumber, ".out")>;
+ file namd_error <single_file_mapper; file=@strcat("logs/namd.", jobNumber, ".err")>;
+ file velocity <single_file_mapper; file=@strcat("h0_eq.", jobNumber, ".restart.vel")>;
+ file system <single_file_mapper; file=@strcat("h0_eq.", jobNumber, ".restart.xsc")>;
+ file config <single_file_mapper; file=@strcat("h0_eq.", jobNumber, ".conf")>;
+ file coords <single_file_mapper; file=@strcat("h0_eq.", jobNumber, "restart.coord")>;
+
+ (namd_output, namd_error, velocity, system, config) = namd_wrapper(psf, pdb, namd_coordinates[jobNumber-delta],
+ namd_velocities[jobNumber-delta],
+ namd_systems[jobNumber-delta],
+ namd_configs[jobNumber-delta],
+ charmm_parameters);
+ namd_velocities[jobNumber] = velocity;
+ namd_systems[jobNumber] = system;
+ namd_configs[jobNumber] = config;
+ namd_coordinates[jobNumber] = coords;
+}
+
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