[Swift-commit] r6563 - SwiftTutorials/CMTS_2013-06-17/namd_sweep
wilde at ci.uchicago.edu
wilde at ci.uchicago.edu
Sun Jun 16 13:09:49 CDT 2013
Author: wilde
Date: 2013-06-16 13:09:49 -0500 (Sun, 16 Jun 2013)
New Revision: 6563
Added:
SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps
Removed:
SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc
Modified:
SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
Log:
Initial adaptations of rmsd exercise (namd sweep).
Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-16 18:09:49 UTC (rev 6563)
@@ -13,5 +13,11 @@
data in a gnuplot 2D plot data format. This script also prints to screen
the minimum RMSD and the parameter values corresponding to that value.
--Frank X. Vazquez fxv at uchicago.edu
-7-13-2012
+-Frank X. Vazquez fxv at uchicago.edu 7-13-2012
+
+To Run:
+
+ PATH=$PATH:$PWD # Note: must use $PWD, not "." !!!
+
+ swift rmsd.swift -cwd=$PWD -max=0.0 -delta=0.5
+
Copied: SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc)
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps 2013-06-16 18:09:49 UTC (rev 6563)
@@ -0,0 +1,5 @@
+
+localhost gensweep sweep_pd.pl null null null
+localhost analyze analyze_pd.pl null null null
+
+cmtsworkshop rmsd rmsd.sh null null null
Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh 2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh 2013-06-16 18:09:49 UTC (rev 6563)
@@ -1,3 +1,3 @@
#!/bin/bash
-rm -rf *.log *stdout.txt *.rlog *.d *.kml _concurrent *.swiftx PAR/* RMSD/* VMD/* CONF/* OUT/*
+rm -rf *.log *stdout.txt *.rlog *.d *.kml _concurrent *.swiftx PAR/ RMSD/ VMD/ CONF/ OUT/
Deleted: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh 2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh 2013-06-16 18:09:49 UTC (rev 6563)
@@ -1,7 +0,0 @@
-PATH=$PATH:$PWD
-
-# export SBATCH_RESERVATION=swift_test
-
-mkdir -p CONF PAR VMD RMSD OUT
-
-swift -sites.file sites.xml -tc.file tc -config cf rmsd.swift -cwd=$PWD -max=${1:-0.0} -delta=${2:-0.5}
Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml 2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml 2013-06-16 18:09:49 UTC (rev 6563)
@@ -1,11 +1,42 @@
<config>
- <pool handle="local">
+ <pool handle="localhost">
<execution provider="local"/>
<filesystem provider="local"/>
<workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
</pool>
+ <pool handle="cmtsworkshop">
+ <execution provider="coaster" jobmanager="local:slurm"/>
+
+ <!-- Set partition and account here: -->
+ <profile namespace="globus" key="queue">cmtsworkshop</profile>
+ <profile namespace="globus" key="ppn">8</profile>
+ <profile namespace="globus" key="project">cmtsworkshop</profile>
+
+ <!-- Set number of jobs and nodes per job here: -->
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="maxnodes">2</profile>
+ <profile namespace="globus" key="nodegranularity">2</profile>
+ <profile namespace="karajan" key="jobThrottle">.03</profile>
+
+ <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+ <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+ <profile namespace="globus" key="maxtime">1800</profile>
+
+ <!-- Typically leave these constant: -->
+ <profile namespace="globus" key="slurm.exclusive">true</profile>
+ <profile namespace="globus" key="jobtype">single</profile>
+ <profile namespace="globus" key="jobsPerNode">1</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+
+ <!-- Set data staging model and work dir here: -->
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+ </pool>
+
<pool handle="westmere">
<execution provider="coaster" jobmanager="local:slurm"/>
Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl 2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl 2013-06-16 18:09:49 UTC (rev 6563)
@@ -10,6 +10,10 @@
chdir($ARGV[0]);
+# Create dirs
+
+system("mkdir -p CONF PAR VMD RMSD OUT");
+
# Bead names
my $b1name = "PX";
Deleted: SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc 2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc 2013-06-16 18:09:49 UTC (rev 6563)
@@ -1,8 +0,0 @@
-
-local gensweep sweep_pd.pl null null null
-local analyze analyze_pd.pl null null null
-
-#bigmem rmsd rmsd.sh null null null
-#sandyb rmsd rmsd.sh null null null
-#trestles rmsd rmsd.sh null null null
-westmere rmsd rmsd.sh null null null
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